wgEncodeBroadHmm Broad ChromHMM GSE38163 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation  Note: these data have been converted via liftOver from the Mar. 2006 (NCBI36/hg18) version of the track. Description This track displays a chromatin state segmentation for each of nine human cell types. A common set of states across the cell types were learned by computationally integrating ChIP-seq data for nine factors plus input CTCF, H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K9ac, H3K36me3, H4K20me1, H3K27me3, and Input Control --> using a Hidden Markov Model (HMM). In total, fifteen states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements. GM12878 - lymphoblastoid cells H1-ESC - embryonic stem cells HepG2 - hepatocellular carcinoma HUVEC - Human Umbilical Vein Endothelial Cell HMEC - Human Mammary Epithelial Cells HSMM - Normal Human Skeletal Muscle Myoblasts K562 - erythroleukemia cells NHEK - Normal Human Epidermal Keratinocytes NHLF - Normal Human Lung Fibroblasts --> Display Conventions and Configuration This track is a composite track that contains multiple subtracks. Each subtrack represents data for a different cell type and displays individually on the browser. Instructions for configuring tracks with multiple subtracks are here. The fifteen states of the HMM, their associated segment color, and the candidate annotations are as follows: State 1 -  Bright Red  - Active Promoter State 2 -  Light Red  -Weak Promoter State 3 -  Purple  - Inactive/poised Promoter State 4 -  Orange  - Strong enhancer State 5 -  Orange  - Strong enhancer State 6 -  Yellow  - Weak/poised enhancer State 7 -  Yellow  - Weak/poised enhancer State 8 -  Blue  - Insulator State 9 -  Dark Green  - Transcriptional transition State 10 -  Dark Green  - Transcriptional elongation State 11 -  Light Green  - Weak transcribed State 12 -  Gray  - Polycomb-repressed State 13 -  Light Gray  - Heterochromatin; low signal State 14 -  Light Gray  - Repetitive/Copy Number Variation State 15 -  Light Gray  - Repetitive/Copy Number Variation Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods ChIP-seq data from the Broad Histone track was used to generate this track. Data for nine factors plus input and nine cell types was binarized separately at a 200 base pair resolution based on a Poisson background model. The chromatin states were learned from this binarized data using a multivariate Hidden Markov Model (HMM) that explicitly models the combinatorial patterns of observed modifications (Ernst and Kellis, 2010). To learn a common set of states across the nine cell types, first the genomes were concatenated across the cell types. For each of the nine cell types, each 200 base pair interval was then assigned to its most likely state under the model. Detailed information about the model parameters and state enrichments can be found in (Ernst et al, accepted). Release Notes This is release 1 (Jun 2011) of this track. It was lifted over from the NCBI36/hg18 version of the track, and is therefore based on the NCBI36/hg18 release of the Broad Histone track. It is anticipated that the HMM methods will be run on the newer datasets in the GRCh37/hg19 version of the Broad Histone track, and, once that happens, the new data will replace this liftOver. Credits The ChIP-seq data were generated at the Broad Institute and in the Bradley E. Bernstein lab at the Massachusetts General Hospital/Harvard Medical School, and the chromatin state segmentation was produced in Manolis Kellis's Computational Biology group at the Massachusetts Institute of Technology. Contact: Jason Ernst. Data generation and analysis was supported by funds from the NHGRI (ENCODE), the Burroughs Wellcome Fund, Howard Hughes Medical Institute, NSF, Sloan Foundation, Massachusetts General Hospital and the Broad Institute. References Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug;28(8):817-25. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. There is no restriction on the use of segmentation data. 
wgEncodeHistoneSuper ENC Histone ENCODE Histone Modification Regulation Description These tracks display maps of chromatin state of ENCODE cell types. Histones are a group of closely-related proteins that together form the nucleosome. There are six histone families: H1, H2A, H2B, H3, H4, and H5. Each nucleosome core is formed by two H2A-H2B dimers and a H3-H4 tetramer, while H1 and H5 bind the nucleosome and DNA. When histone proteins undergo post-transcriptional modifications at specific amino acids (methylation, acyetylation), these modifications (referred to as marks) perform a role in regulating the winding of the DNA around the nucleosome. This in turn regulates gene expression by controlling the accessibility of the chromatin. Histone marks vary in their effect. Promoters, enhancers, transcribed regions, and silenced regions are each associated with specific histone marks. The ChIP-seq method enables identifying regions of DNA that interact with specific histone marks. This method involves cross-linking histones and other DNA associated proteins to genomic DNA within cells using formaldehyde. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. This has the effect of capturing segments of DNA that are bound to the protein selected by the antibody. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. If the antibody is specific to a given histone mark, then this procedure identifies segments of the genome associated with that mark. Display Conventions These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Geiman TM, Robertson KD. Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together? J Cell Biochem. 2002;87(2):117-25. Segal E, Widom J. What controls nucleosome positions? Trends Genet. 2009 Aug;25(8):335-43. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeBroadHmmNhlfHMM NHLF ChromHMM NHLF Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000792 792 GSM936086 Bernstein Broad hg18 ChromHMM_ENCODEDynamicPaper wgEncodeBroadHmmNhlfHMM HMM lung fibroblasts Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model NHLF Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmNhekHMM NHEK ChromHMM NHEK Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000791 791 GSM936087 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmNhekHMM HMM epidermal keratinocytes Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model NHEK Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHsmmHMM HSMM ChromHMM HSMM Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000787 787 GSM936085 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHsmmHMM HMM skeletal muscle myoblasts Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HSMM Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHmecHMM HMEC ChromHMM HMEC Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000786 786 GSM936084 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHmecHMM HMM mammary epithelial cells Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HMEC Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHuvecHMM HUVEC ChromHMM HUVEC Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000788 788 GSM936089 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHuvecHMM HMM umbilical vein endothelial cells Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HUVEC Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHepg2HMM HepG2 ChromHMM HepG2 Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000789 789 GSM936090 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHepg2HMM HMM hepatocellular carcinoma Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HepG2 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmK562HMM K562 ChromHMM K562 Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000790 790 GSM936088 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmK562HMM HMM leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model K562 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmH1hescHMM H1-hESC ChromHMM H1-hESC Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000785 785 GSM936083 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmH1hescHMM HMM embryonic stem cells Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model H1-hESC Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmGm12878HMM GM12878 ChromHMM GM12878 Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000784 784 GSM936082 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmGm12878HMM HMM B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model GM12878 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHistone Broad Histone 2012-06-30 GSE29611 Histone Modifications by ChIP-seq from ENCODE/Broad Institute Regulation Description This track displays maps of chromatin state generated by the Broad/MGH ENCODE group using ChIP-seq. Chemical modifications (methylation, acetylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. The ChIP-seq method involves first using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA within cells. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. ENCODE tracks typically contain one or more of the following views: Peaks Regions of statistically significant signal enrichment. The score associated with each enriched interval is the mean signal value across the interval. (Note that a broad region with moderate enrichment may deviate from the background more significantly than a short region with high signal.) Signal Density graph (wiggle) of signal enrichment. At each base-pair position, the density is calculated as the number of sequenced tags overlapping a 25 bp window centered at that position. Peaks and signals displayed in this track are the results of pooled replicates. The raw sequence and alignment files for each replicate are available for download. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods ChIP-seq: Cells were grown according to the approved ENCODE cell culture protocols. Cells were fixed in 1% formaldehyde and resuspended in lysis buffer. Chromatin was sheared to 200-700 bp using a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with antibodies against each of the histone antibodies listed above. Antibody-chromatin complexes were pulled down using protein A-sepharose (or anti-IgM-conjugated agarose for RNA polymerase II), washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, treated with RNAse and purified. A quantity of 1-10 ng of DNA was end-repaired, adapter-ligated and sequenced by Illumina Genome Analyzers as recommended by the manufacturer. Alignment: Sequence reads from each IP experiment were aligned to the human reference genome (GRCh37/hg19) using MAQ with default parameters, except '-C 11' and '-H output_file' were added. These options output up to 11 additional best matches for each read (if any are found) to a file. This information was used to filter out any read that had more than 10 best matches on the genome. Note that it is likely that instances where multiple reads align to the same position and with the same orientation are due to enhanced PCR amplification of a single DNA fragment. No attempt has been made, however, to remove such artifacts from the data, following ENCODE practices. Signal: Fragment densities were computed by counting the number of reads overlapping each 25 bp bin along the genome. Densities were computed using igvtools count with default parameters (in particular, '-w 25' to set window size of 25 bp and '-f mean' to report the mean value across the window), except for '-e' which was set to extend the reads to 200 bp, and the .wig output was converted to bigWig using wigToBigWig from the UCSC Kent software package. Peaks: Discrete intervals of ChIP-seq fragment enrichment were identified using Scripture, a scan statistics approach, under the assumption of uniform background signal. All data sets were processed with '-task chip', and with '-windows 100,200,500,1000,5000,10000,100000' (no mask file nor the '-trim' option have been used). The resulting called segments were then further filtered to remove intervals that were significantly enriched only because they contain smaller enriched intervals within them. This post-processing step has been implemented using Matlab. The use of the post-processing step allowed very large enriched intervals (of the order of Mbps for H3K27me3, for instance) to be detected, as well as much smaller intervals, without the need to tailor the parameters of Scripture based on prior expectations. Release Notes This is Release 3 (Aug 2012). It contains 83 new experiments including 6 new cell lines and 25 new antibodies. Please note that an antibody previously labeled "Pol2 (b)" is, in fact, Covance antibody MMS-128P with the target POLR2A. Credits The ChIP-seq data were generated at the Broad Institute and in the Bernstein lab at the Massachusetts General Hospital/Harvard Medical School.    Data generation and analysis were supported by funds from the NHGRI, the Burroughs Wellcome Fund, Massachusetts General Hospital and the Broad Institute. Contact: Noam Shoresh References Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ 3rd, Gingeras TR et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005 Jan 28;120(2):169-81. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006 Apr 21;125(2):315-26. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 2010 May;28(5):503-10. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007 Aug 2;448(7153):553-60. Publications Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23;147(7):1628-39. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until, above. The full data release policy for ENCODE is available here. 
wgEncodeBroadHistoneViewSignal Signal Histone Modifications by ChIP-seq from ENCODE/Broad Institute Regulation 
wgEncodeBroadHistoneOsteoblControlStdSig Osteobl Input Input Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001056 1056 GSM733697 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblControlStdSig None Signal osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoP300kat3bSig Osteobl P300 P300_KAT3B Osteobl std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003113 3113 GSM1003514 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneOsteoP300kat3bSig None Signal Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Osteoblasts P300 KAT3B Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH4k20me1Sig Osteobl H4K20m1 H4K20me1 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002401 2401 GSM1003467 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoH4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k79me2Sig Osteobl H3K79m2 H3K79me2 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002440 2440 GSM1003502 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k36me3StdSig Osteobl H3K36m3 H3K36me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001044 1044 GSM733721 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k27me3Sig Osteobl H3K27m3 H3K27me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002400 2400 GSM1003466 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoH3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k27acStdSig Osteobl H3K27ac H3K27ac Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001043 1043 GSM733739 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k9me3StdSig Osteobl H3K9m3 H3K9me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001047 1047 GSM733681 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k04me3Sig Osteobl H3K4m3 H3K4me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003091 3091 GSM1003506 Bernstein Broad hg19 Illumina_GA2e exp wgEncodeBroadHistoneOsteoH3k04me3Sig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Signal Osteoblasts H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me2StdSig Osteobl H3K4m2 H3K4me2 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001046 1046 GSM733779 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me1StdSig Osteobl H3K4m1 H3K4me1 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001045 1045 GSM733704 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH2azStdSig Osteobl H2A.Z H2A.Z Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001042 1042 GSM733766 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblCtcfStdSig Osteobl CTCF CTCF Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001041 1041 GSM733784 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfControlStdSig NHLF Input Input NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000105 105 GSM733731 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfControlStdSig None Signal lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH4k20me1StdSig NHLF H4K20m1 H4K20me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000104 104 GSM733706 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k79me2Sig NHLF H3K79m2 H3K79me2 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002439 2439 GSM1003549 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k36me3StdSig NHLF H3K36m3 H3K36me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000099 99 GSM733699 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27me3StdSig NHLF H3K27m3 H3K27me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000098 98 GSM733764 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27acStdSig NHLF H3K27ac H3K27ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000097 97 GSM733646 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k09me3Sig NHLF H3K9m3 H3K9me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002424 2424 GSM1003531 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k9acStdSig NHLF H3K9ac H3K9ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000103 103 GSM733652 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me3StdSig NHLF H3K4m3 H3K4me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000102 102 GSM733723 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me2StdSig NHLF H3K4m2 H3K4me2 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000101 101 GSM733781 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me1StdSig NHLF H3K4m1 H3K4me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000100 100 GSM733649 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH2azSig NHLF H2A.Z H2A.Z NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002423 2423 GSM1003530 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfEzh239875Sig NHLF EZH2 EZH2_(39875) NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002422 2422 GSM1003529 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfCtcfStdSig NHLF CTCF CTCF NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000120 120 GSM733695 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekControlStdSig NHEK Input Input NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000072 72 GSM733740 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekControlStdSig None Signal epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekPol2bStdSig NHEK Pol2 Pol2(b) NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000073 73 GSM733671 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekPol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK Pol2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH4k20me1StdSig NHEK H4K20m1 H4K20me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000071 71 GSM733728 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k79me2Sig NHEK H3K79m2 H3K79me2 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002420 2420 GSM1003527 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k36me3StdSig NHEK H3K36m3 H3K36me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000066 66 GSM733726 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27me3StdSig NHEK H3K27m3 H3K27me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000065 65 GSM733701 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27acStdSig NHEK H3K27ac H3K27ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000064 64 GSM733674 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9me1StdSig NHEK H3K9m1 H3K9me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000070 70 GSM733655 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k9me1StdSig None Signal Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K9me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k09me3Sig NHEK H3K9m3 H3K9me3 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002421 2421 GSM1003528 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9acStdSig NHEK H3K9ac H3K9ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000069 69 GSM733665 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me3StdSig NHEK H3K4m3 H3K4me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000068 68 GSM733720 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me2StdSig NHEK H3K4m2 H3K4me2 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000067 67 GSM733686 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me1StdSig NHEK H3K4m1 H3K4me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000062 62 GSM733698 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH2azSig NHEK H2A.Z H2A.Z NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002419 2419 GSM1003488 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekEzh239875Sig NHEK EZH2 EZH2_(39875) NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002418 2418 GSM1003489 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekCtcfStdSig NHEK CTCF CTCF NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000063 63 GSM733636 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadControlStdSig NHDF-Ad Input Input NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001055 1055 GSM733750 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadControlStdSig None Signal adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH4k20me1Sig NHDF-Ad H4K20m1 H4K20me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002417 2417 GSM1003486 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k79me2Sig NHDF-Ad H3K79m2 H3K79me2 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002430 2430 GSM1003554 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k36me3StdSig NHDF-Ad H3K36m3 H3K36me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001051 1051 GSM733733 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27me3StdSig NHDF-Ad H3K27m3 H3K27me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001050 1050 GSM733745 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27acStdSig NHDF-Ad H3K27ac H3K27ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001049 1049 GSM733662 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k09me3Sig NHDF-Ad H3K9m3 H3K9me3 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002431 2431 GSM1003553 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k9acStdSig NHDF-Ad H3K9ac H3K9ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001054 1054 GSM733709 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me3StdSig NHDF-Ad H3K4m3 H3K4me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001053 1053 GSM733650 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me2StdSig NHDF-Ad H3K4m2 H3K4me2 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001052 1052 GSM733753 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k04me1Sig NHDF-Ad H3K4m1 H3K4me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002429 2429 GSM1003526 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k04me1Sig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH2azSig NHDF-Ad H2A.Z H2A.Z NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003090 3090 GSM1003505 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneNhdfadH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal NHDF-Ad H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadEzh239875Sig NHDF-Ad EZH2 EZH2_(39875) NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002438 2438 GSM1003550 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadCtcfStdSig NHDF-Ad CTCF CTCF NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001048 1048 GSM733744 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaControlStdSig NH-A Input Input NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001027 1027 GSM733678 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaControlStdSig None Signal astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH4k20me1Sig NH-A H4K20m1 H4K20me1 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002428 2428 GSM1003525 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k79me2Sig NH-A H3K79m2 H3K79me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002398 2398 GSM1003490 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k36me3StdSig NH-A H3K36m3 H3K36me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001030 1030 GSM733751 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27me3StdSig NH-A H3K27m3 H3K27me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001029 1029 GSM733729 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27acStdSig NH-A H3K27ac H3K27ac NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001028 1028 GSM733763 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09me3Sig NH-A H3K9m3 H3K9me3 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002399 2399 GSM1003491 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09acSig NH-A H3K9ac H3K9ac NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002427 2427 GSM1003534 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k09acSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me3StdSig NH-A H3K4m3 H3K4me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001032 1032 GSM733747 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k04me2Sig NH-A H3K4m2 H3K4me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002426 2426 GSM1003533 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me1StdSig NH-A H3K4m1 H3K4me1 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001031 1031 GSM733710 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH2azSig NH-A H2A.Z H2A.Z NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002397 2397 GSM1003499 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaEzh239875Sig NH-A EZH2 EZH2_(39875) NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002425 2425 GSM1003532 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaCtcfStdSig NH-A CTCF CTCF NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001026 1026 GSM733765 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtControlStdSig HSMMtube Input Input HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001001 1001 GSM733648 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtControlStdSig None Signal skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH4k20me1StdSig HSMMtube H4K20m1 H4K20me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001010 1010 GSM733644 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k79me2StdSig HSMMtube H3K79m2 H3K79me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001008 1008 GSM733727 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k36me3StdSig HSMMtube H3K36m3 H3K36me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001004 1004 GSM733717 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27me3Sig HSMMtube H3K27m3 H3K27me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH003092 3092 GSM1003503 Bernstein Broad hg19 Illumina_GA2e exp wgEncodeBroadHistoneHsmmtH3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Signal HSMMtube H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27acStdSig HSMMtube H3K27ac H3K27ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001003 1003 GSM733666 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k09me3Sig HSMMtube H3K9m3 H3K9me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002394 2394 GSM1003482 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k9acStdSig HSMMtube H3K9ac H3K9ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001009 1009 GSM733639 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me3StdSig HSMMtube H3K4m3 H3K4me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001007 1007 GSM733738 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me2StdSig HSMMtube H3K4m2 H3K4me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001006 1006 GSM733700 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me1StdSig HSMMtube H3K4m1 H3K4me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001005 1005 GSM733661 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH2azStdSig HSMMtube H2A.Z H2A.Z HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001002 1002 GSM733746 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtEzh239875Sig HSMMtube EZH2 EZH2_(39875) HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003083 3083 GSM1003523 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHsmmtEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HSMMtube EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtCtcfStdSig HSMMtube CTCF CTCF HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001000 1000 GSM733783 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmControlStdSig HSMM Input Input HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000119 119 GSM733663 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmControlStdSig None Signal skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH4k20me1StdSig HSMM H4K20m1 H4K20me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000118 118 GSM733676 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k79me2StdSig HSMM H3K79m2 H3K79me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000998 998 GSM733741 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmH3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k36me3StdSig HSMM H3K36m3 H3K36me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000113 113 GSM733702 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27me3StdSig HSMM H3K27m3 H3K27me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000112 112 GSM733667 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27acStdSig HSMM H3K27ac H3K27ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000111 111 GSM733755 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9me3StdSig HSMM H3K9m3 H3K9me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000999 999 GSM733730 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmH3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9acStdSig HSMM H3K9ac H3K9ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000117 117 GSM733775 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me3StdSig HSMM H3K4m3 H3K4me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000116 116 GSM733637 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me2StdSig HSMM H3K4m2 H3K4me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000115 115 GSM733768 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me1StdSig HSMM H3K4m1 H3K4me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000114 114 GSM733761 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH2azStdSig HSMM H2A.Z H2A.Z HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001036 1036 GSM733760 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmEzh239875Sig HSMM EZH2 EZH2_(39875) HSMM std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002415 2415 GSM1003484 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmCtcfStdSig HSMM CTCF CTCF HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000110 110 GSM733762 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecControlStdSig HMEC Input Input HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000093 93 GSM733668 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecControlStdSig None Signal mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH4k20me1StdSig HMEC H4K20m1 H4K20me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000092 92 GSM733647 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k79me2Sig HMEC H3K79m2 H3K79me2 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002435 2435 GSM1003557 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k36me3StdSig HMEC H3K36m3 H3K36me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000078 78 GSM733707 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27me3StdSig HMEC H3K27m3 H3K27me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000077 77 GSM733722 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27acStdSig HMEC H3K27ac H3K27ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000076 76 GSM733660 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k09me3Sig HMEC H3K9m3 H3K9me3 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002414 2414 GSM1003485 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k9acStdSig HMEC H3K9ac H3K9ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000079 79 GSM733713 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me3StdSig HMEC H3K4m3 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000091 91 GSM733712 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me2StdSig HMEC H3K4m2 H3K4me2 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000090 90 GSM733654 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me1StdSig HMEC H3K4m1 H3K4me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000089 89 GSM733705 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH2azSig HMEC H2A.Z H2A.Z HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002413 2413 GSM1003500 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecEzh239875Sig HMEC EZH2 EZH2_(39875) HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002412 2412 GSM1003501 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecCtcfStdSig HMEC CTCF CTCF HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-27 wgEncodeEH000075 75 GSM733724 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41ControlStdSig Dnd41 Input Input Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002434 2434 GSM1003558 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41ControlStdSig None Signal T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H4k20me1Sig Dnd41 H4K20m1 H4K20me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002410 2410 GSM1003481 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k79me2Sig Dnd41 H3K79m2 H3K79me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002409 2409 GSM1003469 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k36me3Sig Dnd41 H3K36m3 H3K36me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002405 2405 GSM1003463 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k36me3Sig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27me3Sig Dnd41 H3K27m3 H3K27me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003081 3081 GSM1003521 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneDnd41H3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal Dnd41 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27acSig Dnd41 H3K27ac H3K27ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002404 2404 GSM1003462 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k27acSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09me3Sig Dnd41 H3K9m3 H3K9me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002433 2433 GSM1003551 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09acSig Dnd41 H3K9ac H3K9ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002432 2432 GSM1003552 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k09acSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me3Sig Dnd41 H3K4m3 H3K4me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002408 2408 GSM1003468 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k04me3Sig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me2Sig Dnd41 H3K4m2 H3K4me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002407 2407 GSM1003461 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me1Sig Dnd41 H3K4m1 H3K4me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002406 2406 GSM1003460 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k04me1Sig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H2azSig Dnd41 H2A.Z H2A.Z Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002403 2403 GSM1003465 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41Ezh239875Sig Dnd41 EZH2 EZH2_(39875) Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003080 3080 GSM1003522 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneDnd41Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal Dnd41 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41CtcfSig Dnd41 CTCF CTCF Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002402 2402 GSM1003464 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746ControlSig CD14+ Control Control Monocytes-CD14+_RO01746 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003130 3130 GSM1003475 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746ControlSig None Signal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ Control Histone Mods by ChIPseq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H4k20me1Sig CD14+ H4K20m1 H4K20me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003074 3074 GSM1003539 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k79me2Sig CD14+ H3K79m2 H3K79me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003072 3072 GSM1003537 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k36me3Sig CD14+ H3K36m3 H3K36me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003069 3069 GSM1003562 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k36me3Sig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27me3Sig CD14+ H3K27m3 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003068 3068 GSM1003564 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27acSig CD14+ H3K27ac H3K27ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003067 3067 GSM1003559 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k27acSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09me3Sig CD14+ H3K9m3 H3K9me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003073 3073 GSM1003538 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09acSig CD14+ H3K9ac H3K9ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003089 3089 GSM1003515 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746H3k09acSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me3Sig CD14+ H3K4m3 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003071 3071 GSM1003536 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k04me3Sig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me2Sig CD14+ H3K4m2 H3K4me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003088 3088 GSM1003516 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746H3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ H3K4me2 Histone Mods by ChIPseq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me1Sig CD14+ H3K4m1 H3K4me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003070 3070 GSM1003535 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k04me1Sig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H2azSig CD14+ H2A.Z H2A.Z Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003066 3066 GSM1003548 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746CtcfSig CD14+ CTCF CTCF Monocytes-CD14+_RO01746 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003097 3097 GSM1003508 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecControlStdSig HUVEC Input Input HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000060 60 GSM733715 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecControlStdSig None Signal umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecPol2bStdSig HUVEC Pol2 Pol2(b) HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000061 61 GSM733749 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecPol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC Pol2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH4k20me1StdSig HUVEC H4K20m1 H4K20me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000059 59 GSM733640 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k79me2Sig HUVEC H3K79m2 H3K79me2 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002437 2437 GSM1003555 Bernstein Broad hg19 exp wgEncodeBroadHistoneHuvecH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k36me3StdSig HUVEC H3K36m3 H3K36me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-26 2009-01-06 2009-10-06 wgEncodeEH000056 56 GSM733757 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27me3StdSig HUVEC H3K27m3 H3K27me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000038 38 GSM733688 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27acStdSig HUVEC H3K27ac H3K27ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000055 55 GSM733691 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9me1StdSig HUVEC H3K9m1 H3K9me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000058 58 GSM733703 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k9me1StdSig None Signal Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K9me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k09me3Sig HUVEC H3K9m3 H3K9me3 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003085 3085 GSM1003517 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHuvecH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HUVEC H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9acStdSig HUVEC H3K9ac H3K9ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000057 57 GSM733735 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me3StdSig HUVEC H3K4m3 H3K4me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000041 41 GSM733673 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me2StdSig HUVEC H3K4m2 H3K4me2 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000040 40 GSM733683 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me1StdSig HUVEC H3K4m1 H3K4me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000039 39 GSM733690 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH2azSig HUVEC H2A.Z H2A.Z HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002436 2436 GSM1003556 Bernstein Broad hg19 exp wgEncodeBroadHistoneHuvecH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecEzh239875Sig HUVEC EZH2 EZH2_(39875) HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003084 3084 GSM1003518 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHuvecEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HUVEC EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecCtcfStdSig HUVEC CTCF CTCF HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000054 54 GSM733716 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2ControlStdSig HepG2 Input Input HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000084 84 GSM733732 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2ControlStdSig None Signal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H4k20me1StdSig HepG2 H4K20m1 H4K20me1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000096 96 GSM733694 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k79me2StdSig HepG2 H3K79m2 H3K79me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001024 1024 GSM733641 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k36me3StdSig HepG2 H3K36m3 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000081 81 GSM733685 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27me3StdSig HepG2 H3K27m3 H3K27me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001023 1023 GSM733754 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27acStdSig HepG2 H3K27ac H3K27ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000094 94 GSM733743 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k09me3Sig HepG2 H3K9m3 H3K9me3 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003087 3087 GSM1003519 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHepg2H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HepG2 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k9acStdSig HepG2 H3K9ac H3K9ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000083 83 GSM733638 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me3StdSig HepG2 H3K4m3 H3K4me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000095 95 GSM733737 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me2StdSig HepG2 H3K4m2 H3K4me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000082 82 GSM733693 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k04me1StdSig HepG2 H3K4m1 H3K4me1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH001749 1749 GSM798321 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2H3k04me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H2azStdSig HepG2 H2A.Z H2A.Z HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001022 1022 GSM733774 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2H2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2Ezh239875Sig HepG2 EZH2 EZH2_(39875) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002416 2416 GSM1003487 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2CtcfStdSig HepG2 CTCF CTCF HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000080 80 GSM733645 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3ControlStdSig HeLa-S3 Input Input HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001013 1013 GSM733659 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3ControlStdSig None Signal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Pol2bStdSig HeLa-S3 Pol2(b) Pol2(b) HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001021 1021 GSM733759 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3Pol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 Pol2(b) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H4k20me1StdSig HeLa-S3 H4K20m1 H4K20me1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001020 1020 GSM733689 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k79me2StdSig HeLa-S3 H3K79m2 H3K79me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001018 1018 GSM733669 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k36me3StdSig HeLa-S3 H3K36m3 H3K36me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001015 1015 GSM733711 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27me3StdSig HeLa-S3 H3K27m3 H3K27me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001037 1037 GSM733696 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27acStdSig HeLa-S3 H3K27ac H3K27ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001014 1014 GSM733684 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k09me3Sig HeLa-S3 H3K9m3 H3K9me3 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002396 2396 GSM1003480 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k9acStdSig HeLa-S3 H3K9ac H3K9ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001019 1019 GSM733756 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me3StdSig HeLa-S3 H3K4m3 H3K4me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001017 1017 GSM733682 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me2StdSig HeLa-S3 H3K4m2 H3K4me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001016 1016 GSM733734 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k04me1StdSig HeLa-S3 H3K4m1 H3K4me1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-14 2012-03-14 wgEncodeEH001750 1750 GSM798322 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k04me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H2azSig HeLa-S3 H2A.Z H2A.Z HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002395 2395 GSM1003483 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Ezh239875Sig HeLa-S3 EZH2 EZH2_(39875) HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003086 3086 GSM1003520 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHelas3Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HeLa-S3 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3CtcfStdSig HeLa-S3 CTCF CTCF HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001012 1012 GSM733785 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H4k20me1Sig CD20+ H4K20m1 H4K20me1 CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003145 3145 GSM1003497 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ro01794H4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ RO01794 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H3k27acSig CD20+ H3K27ac H3K27ac CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003125 3125 GSM1003459 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ro01794H3k27acSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ RO01794 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794Ezh239875Sig CD20+ EZH2 EZH2_(39875) CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003135 3135 GSM1003470 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ro01794Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ RO01794 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ControlSig CD20+ Control Control CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003132 3132 GSM1003477 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ControlSig None Signal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ Control Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H3k04me2Sig CD20+ H3K4m2 H3K4me2 CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003134 3134 GSM1003471 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20H3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H2azSig CD20+ H2A.Z H2A.Z CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003133 3133 GSM1003476 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20CtcfSig CD20+ CTCF CTCF CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003131 3131 GSM1003474 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549ControlEtoh02Sig A549 EtOH Control Control A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003076 3076 GSM1003541 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549ControlEtoh02Sig EtOH_0.02pct Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% Control Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549ControlDex100nmSig A549 DEX Control Control A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003075 3075 GSM1003540 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549ControlDex100nmSig DEX_100nM Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM Control Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H4k20me1Etoh02Sig A549 EtOH H4K20m1 H4K20me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003124 3124 GSM1003458 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H4k20me1Etoh02Sig EtOH_0.02pct Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Etoh02Sig A549 EtOH H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003099 3099 GSM1003512 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k79me2Etoh02Sig EtOH_0.02pct Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Dex100nmSig A549 DEX H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003078 3078 GSM1003543 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k79me2Dex100nmSig DEX_100nM Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Etoh02Sig A549 EtOH H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003121 3121 GSM1003456 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k36me3Etoh02Sig EtOH_0.02pct Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Dex100nmSig A549 DEX H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003142 3142 GSM1003494 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k36me3Dex100nmSig DEX_100nM Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Etoh02Sig A549 EtOH H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003120 3120 GSM1003455 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27me3Etoh02Sig EtOH_0.02pct Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Dex100nmSig A549 DEX H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003119 3119 GSM1003577 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27me3Dex100nmSig DEX_100nM Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acEtoh02Sig A549 EtOH H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003118 3118 GSM1003578 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27acEtoh02Sig EtOH_0.02pct Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acDex100nmSig A549 DEX H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003141 3141 GSM1003493 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27acDex100nmSig DEX_100nM Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09me3Etoh02Sig A549 EtOH H3K9m3 H3K9me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003123 3123 GSM1003454 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k09me3Etoh02Sig EtOH_0.02pct Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09acEtoh02Sig A549 EtOH H3K9ac H3K9ac A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003079 3079 GSM1003544 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k09acEtoh02Sig EtOH_0.02pct Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Etoh02Sig A549 EtOH H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003065 3065 GSM1003561 Bernstein Broad hg19 exp wgEncodeBroadHistoneA549H3k04me3Etoh02Sig EtOH_0.02pct Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Dex100nmSig A549 DEX H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003077 3077 GSM1003542 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me3Dex100nmSig DEX_100nM Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Etoh02Sig A549 EtOH H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003144 3144 GSM1003496 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me2Etoh02Sig EtOH_0.02pct Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Dex100nmSig A549 DEX H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003098 3098 GSM1003511 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me2Dex100nmSig DEX_100nM Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Etoh02Sig A549 EtOH H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003122 3122 GSM1003453 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me1Etoh02Sig EtOH_0.02pct Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Dex100nmSig A549 DEX H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003143 3143 GSM1003495 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me1Dex100nmSig DEX_100nM Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azEtoh02Sig A549 EtOH H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003117 3117 GSM1003546 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H2azEtoh02Sig EtOH_0.02pct Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azDex100nmSig A549 DEX H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003116 3116 GSM1003580 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H2azDex100nmSig DEX_100nM Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfEtoh02Sig A549 EtOH CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003115 3115 GSM1003581 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549CtcfEtoh02Sig EtOH_0.02pct Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfDex100nmSig A549 DEX CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003114 3114 GSM1003582 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549CtcfDex100nmSig DEX_100nM Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562ControlStdSig K562 Input Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000052 52 GSM733780 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562ControlStdSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Suz12051317Sig K562 SUZ12 SUZ12_(05-1317) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003112 3112 GSM1003545 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Suz12051317Sig None Signal SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 SUZ12 (05-1317) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sirt6Sig K562 SIRT6 SIRT6 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003111 3111 GSM1003560 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Sirt6Sig None Signal A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 SIRT6 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Setdb1Sig K562 SETDB1 SETDB1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003129 3129 GSM1003452 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Setdb1Sig None Signal SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 SETDB1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sap3039731StdSig K562 SAP30 SAP30_(39731) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002094 2094 GSM1003445 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Sap3039731StdSig None Signal SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 SAP30 (39731) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rnf2Sig K562 RNF2 RNF2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003110 3110 GSM1003563 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Rnf2Sig None Signal Ring finger protein 2 (RNF2) is a polycomb group (PcG) protein. RNF2 has been shown to interact with, and suppress the activity of, transcription factor CP2 (TFCP2/CP2). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 RNF2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562RestSig K562 REST REST K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003096 3096 GSM1003507 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562RestSig None Signal A transcriptional repressor which represses neuronal genes in non-neuronal tissues. A member of the Kruppel-type zinc finger transcription factor family. Represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element (NRSE) by associating with two corepressors, mSin3 and CoREST, which recruit HDACs to the promoters of REST-regulated genes. Target is GST fusion amino acids 801-1097 of human REST. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 REST Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rbbp5a300109aStdSig K562 RBBP5 RBBP5_(A300-109A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002093 2093 GSM1003449 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Rbbp5a300109aStdSig None Signal Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 RBBP5 (A300-109A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Pol2bStdSig K562 Pol2 Pol2(b) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000053 53 GSM733643 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562Pol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 Pol2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Plu1StdSig K562 PLU1 PLU1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002085 2085 GSM1003586 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Plu1StdSig None Signal JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 PLU1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Phf8a301772aStdSig K562 PHF8 PHF8_(A301-772A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002092 2092 GSM1003450 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Phf8a301772aStdSig None Signal PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 PHF8 (A301-772A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562PcafSig K562 PCAF PCAF K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003109 3109 GSM1003566 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562PcafSig None Signal PCAF (P300/CBP-associated factor) is a histone acetyltransferase (HAT) identified as a factor that associates with P300/CBP, a transcriptional coactivator of nuclear hormone receptors and other transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 PCAF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562P300StdSig K562 P300 p300 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002086 2086 GSM1003583 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562P300StdSig None Signal EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 P300 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Nsd2ab75359Sig K562 NSD2 NSD2_(ab75359) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003140 3140 GSM1003492 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Nsd2ab75359Sig None Signal This is a probable histone methyltransferase, which may act as a transcription regulator that binds DNA and suppresses IL5 transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 NSD2 (ab75359) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562NcorSig K562 NCoR NCoR K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003108 3108 GSM1003565 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562NcorSig None Signal The nuclear receptor corepressor protein (NCoR) mediates gene repression by interacting with nuclear receptors. NCoR mediates repression by associating with SIN3A/B and the histone deacetylases, HDAC1 and HDAC2, and promoting the formation of repressive chromatin structures. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 NCoR Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Lsd1Sig K562 LSD1 LSD1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003107 3107 GSM1003570 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Lsd1Sig None Signal BHC110/LSD1 is a histone demethylase and a component of several histone deacetylase complexes. BHC110/LSD1 is able to specifically catalyze the demethylation of Lys4 of histone H3. As part of histone deacetylase complexes BHC110/LSD1 functions as a corepressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 LSD1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac6a301341aSig K562 HDAC6 HDAC6_(A301-341A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003093 3093 GSM1003504 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Hdac6a301341aSig None Signal Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 HDAC6 (A301-341A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac2a300705aStdSig K562 HDAC2 HDAC2_(A300-705A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002091 2091 GSM1003447 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Hdac2a300705aStdSig None Signal Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 HDAC2 (A300-705A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac1sc6298StdSig K562 HDAC1 HDAC1_(SC-6298) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002090 2090 GSM1003448 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Hdac1sc6298StdSig None Signal Histone deacetylase 1 (HDAC1) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC1 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC1 include RPD3L1, HD1, GON-10, and DKFZp686H12203. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 HDAC1 (SC-6298) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H4k20me1StdSig K562 H4K20m1 H4K20me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000051 51 GSM733675 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k79me2StdSig K562 H3K79m2 H3K79me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001039 1039 GSM733653 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k36me3StdSig K562 H3K36m3 H3K36me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000045 45 GSM733714 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27me3StdSig K562 H3K27m3 H3K27me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000044 44 GSM733658 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27acStdSig K562 H3K27ac H3K27ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000043 43 GSM733656 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me1StdSig K562 H3K9m1 H3K9me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000050 50 GSM733777 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k9me1StdSig None Signal Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K9me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me3StdSig K562 H3K9m3 H3K9me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001040 1040 GSM733776 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562H3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9acStdSig K562 H3K9ac H3K9ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000049 49 GSM733778 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me3StdSig K562 H3K4m3 H3K4me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000048 48 GSM733680 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me2StdSig K562 H3K4m2 H3K4me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000047 47 GSM733651 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me1StdSig K562 H3K4m1 H3K4me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000046 46 GSM733692 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H2azStdSig K562 H2A.Z H2A.Z K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001038 1038 GSM733786 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562H2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Ezh239875StdSig K562 EZH2 EZH2_(39875) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002089 2089 GSM1003576 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Ezh239875StdSig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562CtcfStdSig K562 CTCF CTCF K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000042 42 GSM733719 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd7a301223a1Sig K562 CHD7 CHD7_(A301-223A-1) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003139 3139 GSM1003478 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Chd7a301223a1Sig None Signal CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 CHD7 (A301-223A-1) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd4mi2Sig K562 CHD4 Mi2 CHD4_Mi2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003095 3095 GSM1003510 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Chd4mi2Sig None Signal CHD4/Mi2beta is a helicase component of the nucleosome remodeling and deacetylase (NuRD) complex that functions to remodel chromatin and repress transcription. Outside of the NuRD complex, CHD4/Mi2beta can function as an activator of transcription in association with p300 histone acetyltransferase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 CHD4 Mi2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd1a301218aStdSig K562 CHD1 CHD1_(A301-218A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002088 2088 GSM1003575 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Chd1a301218aStdSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 CHD1 (A301-218A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx8Sig K562 CBX8 CBX8 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003106 3106 GSM1003569 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Cbx8Sig None Signal CBX8 is part of the polycomb group of proteins that are important in embryogenesis and human tumorigenesis and regulates a number of genes involved in cell growth and survival. There are at least 5 CBX proteins in mammals. CBX proteins associate with the core polycomb repressive complex 1 (PRC1) that functions to maintain the transcriptionally repressive state of genes during development. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 CBX8 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx3sc101004Sig K562 CBX3 CBX3_(SC-101004) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003105 3105 GSM1003568 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Cbx3sc101004Sig None Signal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 CBX3 (SC-101004) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx2Sig K562 CBX2 CBX2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003104 3104 GSM1003567 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Cbx2Sig None Signal Chromobox protein homolog 2 is a component of the polycomb group (PcG) multiprotein PRC1 complex, a complex required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. [taken from the Universal Protein Resource (UniProt) www.uniprot.org/uniprot/P19474] leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 CBX2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbpsc369Sig K562 CBP (SC-369) CBP_(sc-369) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003103 3103 GSM1003574 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Cbpsc369Sig None Signal CBP is a histone acetyl transferase that promotes transcription. CBP is recruited by a variety of transcription factors to promoters and enhancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 CBP (sc-369) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescControlStdSig H1-hESC Input Input H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000088 88 GSM733770 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescControlStdSig None Signal embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSuz12051317Sig H1-hESC SUZ12 SUZ12_(05-1317) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003102 3102 GSM1003573 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescSuz12051317Sig None Signal SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC SUZ12 (05-1317) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSirt6Sig H1-hESC SIRT6 SIRT6 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003128 3128 GSM1003451 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescSirt6Sig None Signal A synthetic peptide made to an internal region of the human SIRT6 protein embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC SIRT6 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSap3039731Sig H1-hESC SAP30 SAP30_(39731) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003101 3101 GSM1003572 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescSap3039731Sig None Signal SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC SAP30 (39731) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescRbbp5a300109aStdSig H1-hESC RBBP5 RBBP5_(A300-109A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002087 2087 GSM1003584 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescRbbp5a300109aStdSig None Signal Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC RBBP5 (A300-109A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPlu1Sig H1-hESC PLU1 PLU1 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003127 3127 GSM1003457 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescPlu1Sig None Signal JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC PLU1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPhf8a301772aSig H1-hESC PHF8 PHF8_(A301-772A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003094 3094 GSM1003509 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescPhf8a301772aSig None Signal PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC PHF8 (A301-772A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescP300kat3bSig H1-hESC P300 P300_KAT3B H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003126 3126 GSM1003513 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescP300kat3bSig None Signal Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC P300 KAT3B Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJmjd2aa300861a1Sig H1-hESC JMJD2A JMJD2A_(A300-861A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003138 3138 GSM1003479 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescJmjd2aa300861a1Sig None Signal JMJD2A is a member of the jumonji (jmj) domain containing gene family of histone demethylases that plays a role in chromatin regulation and influences transcriptional activation and suppression. JMJD2A is a trimethylation-specific demethylase and functions as a transcriptional repressor. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC JMJD2A (A300-861A-1) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJarid1aab26049StdSig H1-hESC JARID1A JARID1A_(ab26049) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002096 2096 GSM1003446 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescJarid1aab26049StdSig None Signal Histone demethylase that specifically demethylates embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC JARID1A (ab26049) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac6a301341aSig H1-hESC HDAC6 HDAC6_(A301-341A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003100 3100 GSM1003571 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescHdac6a301341aSig None Signal Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC HDAC6 (A301-341A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac2a300705aSig H1-hESC HDAC2 HDAC2_(A300-705A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003137 3137 GSM1003472 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescHdac2a300705aSig None Signal Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC HDAC2 (A300-705A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH4k20me1StdSig H1-hESC H4K20m1 H4K20me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000087 87 GSM733687 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k79me2StdSig H1-hESC H3K79m2 H3K79me2 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002083 2083 GSM1003547 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k36me3StdSig H1-hESC H3K36m3 H3K36me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000107 107 GSM733725 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27me3StdSig H1-hESC H3K27m3 H3K27me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000074 74 GSM733748 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27acStdSig H1-hESC H3K27ac H3K27ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000997 997 GSM733718 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k09me3StdSig H1-hESC H3K9m3 H3K9me3 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002084 2084 GSM1003585 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH3k09me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k9acStdSig H1-hESC H3K9ac H3K9ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000109 109 GSM733773 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me3StdSig H1-hESC H3K4m3 H3K4me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000086 86 GSM733657 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me2StdSig H1-hESC H3K4m2 H3K4me2 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000108 108 GSM733670 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me1StdSig H1-hESC H3K4m1 H3K4me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-30 2010-06-30 wgEncodeEH000106 106 GSM733782 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH2azStdSig H1-hESC H2A.Z H2A.Z H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-04 2012-05-04 wgEncodeEH002082 2082 GSM1003579 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescEzh239875Sig H1-hESC EZH2 EZH2_(39875) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003082 3082 GSM1003524 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneH1hescEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal H1-hESC EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescCtcfStdSig H1-hESC CTCF CTCF H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000085 85 GSM733672 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd7a301223a1Sig H1-hESC CHD7 CHD7_(A301-223A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003136 3136 GSM1003473 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescChd7a301223a1Sig None Signal CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC CHD7 (A301-223A-1) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd1a301218aStdSig H1-hESC CHD1 CHD1_(A301-218A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002095 2095 GSM1003444 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescChd1a301218aStdSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC CHD1 (A301-218A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878ControlStdSig GM12878 Input Input GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH000037 37 GSM733742 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878ControlStdSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H4k20me1StdSig GM12878 H4K20m1 H4K20me1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000036 36 GSM733642 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k79me2StdSig GM12878 H3K79m2 H3K79me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001034 1034 GSM733736 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k36me3StdSig GM12878 H3K36m3 H3K36me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000032 32 GSM733679 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27me3StdSigV2 GM12878 H3K27m3 H3K27me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2009-10-05 wgEncodeEH000031 31 GSM733758 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k27me3StdSigV2 None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27acStdSig GM12878 H3K27ac H3K27ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000030 30 GSM733771 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9me3StdSig GM12878 H3K9m3 H3K9me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001035 1035 GSM733664 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878H3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9acStdSig GM12878 H3K9ac H3K9ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000035 35 GSM733677 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me3StdSigV2 GM12878 H3K4m3 H3K4me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2009-10-04 wgEncodeEH000028 28 GSM733708 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k04me3StdSigV2 None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k4me2StdSig GM12878 H3K4m2 H3K4me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000034 34 GSM733769 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me1StdSigV2 GM12878 H3K4m1 H3K4me1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2009-10-05 wgEncodeEH000033 33 GSM733772 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k04me1StdSigV2 None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H2azStdSig GM12878 H2A.Z H2A.Z GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001033 1033 GSM733767 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878H2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878Ezh239875Sig GM12878 EZH2 EZH2_(39875) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002411 2411 GSM1003498 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878CtcfStdSig GM12878 CTCF CTCF GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000029 29 GSM733752 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/Broad Institute Regulation 
wgEncodeBroadHistoneOsteoP300kat3bPk Osteobl P300 P300_KAT3B Osteobl std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003113 3113 GSM1003514 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoP300kat3bPk None Peaks Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Osteoblasts P300 KAT3B Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH4k20me1Pk Osteobl H4K20m1 H4K20me1 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002401 2401 GSM1003467 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k79me2Pk Osteobl H3K79m2 H3K79me2 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002440 2440 GSM1003502 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k36me3StdPk Osteobl H3K36m3 H3K36me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001044 1044 GSM733721 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k27me3Pk Osteobl H3K27m3 H3K27me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002400 2400 GSM1003466 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k27acStdPk Osteobl H3K27ac H3K27ac Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001043 1043 GSM733739 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k9me3StdPk Osteobl H3K9m3 H3K9me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001047 1047 GSM733681 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k04me3Pk Osteobl H3K4m3 H3K4me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003091 3091 GSM1003506 Bernstein Broad hg19 Illumina_GA2e exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH3k04me3Pk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Regions of enriched signal in experiment Osteoblasts H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me2StdPk Osteobl H3K4m2 H3K4me2 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001046 1046 GSM733779 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me1StdPk Osteobl H3K4m1 H3K4me1 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001045 1045 GSM733704 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH2azStdPk Osteobl H2A.Z H2A.Z Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001042 1042 GSM733766 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblCtcfStdPk Osteobl CTCF CTCF Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001041 1041 GSM733784 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH4k20me1StdPk NHLF H4K20m1 H4K20me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000104 104 GSM733706 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k79me2Pk NHLF H3K79m2 H3K79me2 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002439 2439 GSM1003549 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k36me3StdPk NHLF H3K36m3 H3K36me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000099 99 GSM733699 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27me3StdPk NHLF H3K27m3 H3K27me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000098 98 GSM733764 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27acStdPk NHLF H3K27ac H3K27ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000097 97 GSM733646 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k09me3Pk NHLF H3K9m3 H3K9me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002424 2424 GSM1003531 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k9acStdPk NHLF H3K9ac H3K9ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000103 103 GSM733652 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me3StdPk NHLF H3K4m3 H3K4me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000102 102 GSM733723 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me2StdPk NHLF H3K4m2 H3K4me2 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000101 101 GSM733781 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me1StdPk NHLF H3K4m1 H3K4me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000100 100 GSM733649 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH2azPk NHLF H2A.Z H2A.Z NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002423 2423 GSM1003530 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfEzh239875Pk NHLF EZH2 EZH2_(39875) NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002422 2422 GSM1003529 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfCtcfStdPk NHLF CTCF CTCF NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000120 120 GSM733695 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekPol2bStdPk NHEK Pol2 Pol2(b) NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000073 73 GSM733671 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekPol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH4k20me1StdPk NHEK H4K20m1 H4K20me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000071 71 GSM733728 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k79me2Pk NHEK H3K79m2 H3K79me2 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002420 2420 GSM1003527 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k36me3StdPk NHEK H3K36m3 H3K36me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000066 66 GSM733726 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27me3StdPk NHEK H3K27m3 H3K27me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000065 65 GSM733701 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27acStdPk NHEK H3K27ac H3K27ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000064 64 GSM733674 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9me1StdPk NHEK H3K9m1 H3K9me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000070 70 GSM733655 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k9me1StdPk None Peaks Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K9me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k09me3Pk NHEK H3K9m3 H3K9me3 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002421 2421 GSM1003528 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9acStdPk NHEK H3K9ac H3K9ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000069 69 GSM733665 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me3StdPk NHEK H3K4m3 H3K4me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000068 68 GSM733720 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me2StdPk NHEK H3K4m2 H3K4me2 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000067 67 GSM733686 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me1StdPk NHEK H3K4m1 H3K4me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000062 62 GSM733698 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH2azPk NHEK H2A.Z H2A.Z NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002419 2419 GSM1003488 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekEzh239875Pk NHEK EZH2 EZH2_(39875) NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002418 2418 GSM1003489 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekCtcfStdPk NHEK CTCF CTCF NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000063 63 GSM733636 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH4k20me1Pk NHDF-Ad H4K20m1 H4K20me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002417 2417 GSM1003486 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k79me2Pk NHDF-Ad H3K79m2 H3K79me2 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002430 2430 GSM1003554 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k36me3StdPk NHDF-Ad H3K36m3 H3K36me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001051 1051 GSM733733 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27me3StdPk NHDF-Ad H3K27m3 H3K27me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001050 1050 GSM733745 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27acStdPk NHDF-Ad H3K27ac H3K27ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001049 1049 GSM733662 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k09me3Pk NHDF-Ad H3K9m3 H3K9me3 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002431 2431 GSM1003553 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k9acStdPk NHDF-Ad H3K9ac H3K9ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001054 1054 GSM733709 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me3StdPk NHDF-Ad H3K4m3 H3K4me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001053 1053 GSM733650 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me2StdPk NHDF-Ad H3K4m2 H3K4me2 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001052 1052 GSM733753 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k04me1Pk NHDF-Ad H3K4m1 H3K4me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002429 2429 GSM1003526 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k04me1Pk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH2azPk NHDF-Ad H2A.Z H2A.Z NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003090 3090 GSM1003505 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment NHDF-Ad H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadEzh239875Pk NHDF-Ad EZH2 EZH2_(39875) NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002438 2438 GSM1003550 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadCtcfStdPk NHDF-Ad CTCF CTCF NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001048 1048 GSM733744 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH4k20me1Pk NH-A H4K20m1 H4K20me1 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002428 2428 GSM1003525 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k79me2Pk NH-A H3K79m2 H3K79me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002398 2398 GSM1003490 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k36me3StdPk NH-A H3K36m3 H3K36me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001030 1030 GSM733751 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27me3StdPk NH-A H3K27m3 H3K27me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001029 1029 GSM733729 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27acStdPk NH-A H3K27ac H3K27ac NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001028 1028 GSM733763 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09me3Pk NH-A H3K9m3 H3K9me3 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002399 2399 GSM1003491 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09acPk NH-A H3K9ac H3K9ac NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002427 2427 GSM1003534 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k09acPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me3StdPk NH-A H3K4m3 H3K4me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001032 1032 GSM733747 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k04me2Pk NH-A H3K4m2 H3K4me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002426 2426 GSM1003533 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me1StdPk NH-A H3K4m1 H3K4me1 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001031 1031 GSM733710 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH2azPk NH-A H2A.Z H2A.Z NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002397 2397 GSM1003499 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaEzh239875Pk NH-A EZH2 EZH2_(39875) NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002425 2425 GSM1003532 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaCtcfStdPk NH-A CTCF CTCF NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001026 1026 GSM733765 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH4k20me1StdPk HSMMtube H4K20m1 H4K20me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001010 1010 GSM733644 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k79me2StdPk HSMMtube H3K79m2 H3K79me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001008 1008 GSM733727 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k36me3StdPk HSMMtube H3K36m3 H3K36me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001004 1004 GSM733717 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27me3Pk HSMMtube H3K27m3 H3K27me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH003092 3092 GSM1003503 Bernstein Broad hg19 Illumina_GA2e exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Regions of enriched signal in experiment HSMMtube H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27acStdPk HSMMtube H3K27ac H3K27ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001003 1003 GSM733666 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k09me3Pk HSMMtube H3K9m3 H3K9me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002394 2394 GSM1003482 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k9acStdPk HSMMtube H3K9ac H3K9ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001009 1009 GSM733639 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me3StdPk HSMMtube H3K4m3 H3K4me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001007 1007 GSM733738 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me2StdPk HSMMtube H3K4m2 H3K4me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001006 1006 GSM733700 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me1StdPk HSMMtube H3K4m1 H3K4me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001005 1005 GSM733661 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH2azStdPk HSMMtube H2A.Z H2A.Z HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001002 1002 GSM733746 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtEzh239875Pk HSMMtube EZH2 EZH2_(39875) HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003083 3083 GSM1003523 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HSMMtube EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtCtcfStdPk HSMMtube CTCF CTCF HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001000 1000 GSM733783 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH4k20me1StdPk HSMM H4K20m1 H4K20me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000118 118 GSM733676 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k79me2StdPk HSMM H3K79m2 H3K79me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000998 998 GSM733741 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k36me3StdPk HSMM H3K36m3 H3K36me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000113 113 GSM733702 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27me3StdPk HSMM H3K27m3 H3K27me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000112 112 GSM733667 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27acStdPk HSMM H3K27ac H3K27ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000111 111 GSM733755 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9me3StdPk HSMM H3K9m3 H3K9me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000999 999 GSM733730 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9acStdPk HSMM H3K9ac H3K9ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000117 117 GSM733775 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me3StdPk HSMM H3K4m3 H3K4me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000116 116 GSM733637 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me2StdPk HSMM H3K4m2 H3K4me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000115 115 GSM733768 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me1StdPk HSMM H3K4m1 H3K4me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000114 114 GSM733761 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH2azStdPk HSMM H2A.Z H2A.Z HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001036 1036 GSM733760 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmEzh239875Pk HSMM EZH2 EZH2_(39875) HSMM std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002415 2415 GSM1003484 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmCtcfStdPk HSMM CTCF CTCF HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000110 110 GSM733762 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH4k20me1StdPk HMEC H4K20m1 H4K20me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000092 92 GSM733647 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k79me2Pk HMEC H3K79m2 H3K79me2 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002435 2435 GSM1003557 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k36me3StdPk HMEC H3K36m3 H3K36me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000078 78 GSM733707 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27me3StdPk HMEC H3K27m3 H3K27me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000077 77 GSM733722 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27acStdPk HMEC H3K27ac H3K27ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000076 76 GSM733660 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k09me3Pk HMEC H3K9m3 H3K9me3 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002414 2414 GSM1003485 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k9acStdPk HMEC H3K9ac H3K9ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000079 79 GSM733713 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me3StdPk HMEC H3K4m3 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000091 91 GSM733712 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me2StdPk HMEC H3K4m2 H3K4me2 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000090 90 GSM733654 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me1StdPk HMEC H3K4m1 H3K4me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000089 89 GSM733705 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH2azPk HMEC H2A.Z H2A.Z HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002413 2413 GSM1003500 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecEzh239875Pk HMEC EZH2 EZH2_(39875) HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002412 2412 GSM1003501 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecCtcfStdPk HMEC CTCF CTCF HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000075 75 GSM733724 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H4k20me1Pk Dnd41 H4K20m1 H4K20me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002410 2410 GSM1003481 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k79me2Pk Dnd41 H3K79m2 H3K79me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002409 2409 GSM1003469 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k36me3Pk Dnd41 H3K36m3 H3K36me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002405 2405 GSM1003463 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k36me3Pk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27me3Pk Dnd41 H3K27m3 H3K27me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003081 3081 GSM1003521 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment Dnd41 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27acPk Dnd41 H3K27ac H3K27ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002404 2404 GSM1003462 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k27acPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09me3Pk Dnd41 H3K9m3 H3K9me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002433 2433 GSM1003551 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09acPk Dnd41 H3K9ac H3K9ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002432 2432 GSM1003552 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k09acPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me3Pk Dnd41 H3K4m3 H3K4me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002408 2408 GSM1003468 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k04me3Pk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me2Pk Dnd41 H3K4m2 H3K4me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002407 2407 GSM1003461 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me1Pk Dnd41 H3K4m1 H3K4me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002406 2406 GSM1003460 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k04me1Pk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H2azPk Dnd41 H2A.Z H2A.Z Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002403 2403 GSM1003465 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41Ezh239875Pk Dnd41 EZH2 EZH2_(39875) Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003080 3080 GSM1003522 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment Dnd41 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41CtcfPk Dnd41 CTCF CTCF Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002402 2402 GSM1003464 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H4k20me1Pk CD14+ H4K20m1 H4K20me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003074 3074 GSM1003539 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k79me2Pk CD14+ H3K79m2 H3K79me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003072 3072 GSM1003537 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k36me3Pk CD14+ H3K36m3 H3K36me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003069 3069 GSM1003562 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k36me3Pk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27me3Pk CD14+ H3K27m3 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003068 3068 GSM1003564 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27acPk CD14+ H3K27ac H3K27ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003067 3067 GSM1003559 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k27acPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09me3Pk CD14+ H3K9m3 H3K9me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003073 3073 GSM1003538 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09acPk CD14+ H3K9ac H3K9ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003089 3089 GSM1003515 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k09acPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Monocytes CD14+ H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me3Pk CD14+ H3K4m3 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003071 3071 GSM1003536 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k04me3Pk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me2Pk CD14+ H3K4m2 H3K4me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003088 3088 GSM1003516 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Monocytes CD14+ H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me1Pk CD14+ H3K4m1 H3K4me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003070 3070 GSM1003535 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k04me1Pk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H2azPk CD14+ H2A.Z H2A.Z Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003066 3066 GSM1003548 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746CtcfPk CD14+ CTCF CTCF Monocytes-CD14+_RO01746 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003097 3097 GSM1003508 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Monocytes CD14+ CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecPol2bStdPk HUVEC Pol2 Pol2(b) HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000061 61 GSM733749 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecPol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH4k20me1StdPk HUVEC H4K20m1 H4K20me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000059 59 GSM733640 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k79me2Pk HUVEC H3K79m2 H3K79me2 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002437 2437 GSM1003555 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k36me3StdPk HUVEC H3K36m3 H3K36me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-12 2011-05-05 wgEncodeEH000056 56 GSM733757 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27me3StdPk HUVEC H3K27m3 H3K27me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000038 38 GSM733688 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27acStdPk HUVEC H3K27ac H3K27ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000055 55 GSM733691 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9me1StdPk HUVEC H3K9m1 H3K9me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000058 58 GSM733703 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k9me1StdPk None Peaks Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K9me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k09me3Pk HUVEC H3K9m3 H3K9me3 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003085 3085 GSM1003517 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HUVEC H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9acStdPk HUVEC H3K9ac H3K9ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000057 57 GSM733735 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me3StdPk HUVEC H3K4m3 H3K4me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000041 41 GSM733673 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me2StdPk HUVEC H3K4m2 H3K4me2 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000040 40 GSM733683 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me1StdPk HUVEC H3K4m1 H3K4me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000039 39 GSM733690 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH2azPk HUVEC H2A.Z H2A.Z HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002436 2436 GSM1003556 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecEzh239875Pk HUVEC EZH2 EZH2_(39875) HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003084 3084 GSM1003518 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HUVEC EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecCtcfStdPk HUVEC CTCF CTCF HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000054 54 GSM733716 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H4k20me1StdPk HepG2 H4K20m1 H4K20me1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000096 96 GSM733694 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k79me2StdPk HepG2 H3K79m2 H3K79me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001024 1024 GSM733641 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k36me3StdPk HepG2 H3K36m3 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000081 81 GSM733685 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27me3StdPk HepG2 H3K27m3 H3K27me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH001023 1023 GSM733754 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27acStdPk HepG2 H3K27ac H3K27ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000094 94 GSM733743 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k09me3Pk HepG2 H3K9m3 H3K9me3 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003087 3087 GSM1003519 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HepG2 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k9acStdPk HepG2 H3K9ac H3K9ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000083 83 GSM733638 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me3StdPk HepG2 H3K4m3 H3K4me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000095 95 GSM733737 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me2StdPk HepG2 H3K4m2 H3K4me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000082 82 GSM733693 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k04me1StdPk HepG2 H3K4m1 H3K4me1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH001749 1749 GSM798321 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k04me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H2azStdPk HepG2 H2A.Z H2A.Z HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH001022 1022 GSM733774 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2Ezh239875Pk HepG2 EZH2 EZH2_(39875) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002416 2416 GSM1003487 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2CtcfStdPk HepG2 CTCF CTCF HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000080 80 GSM733645 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Pol2bStdPk HeLa-S3 Pol2 Pol2(b) HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001021 1021 GSM733759 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3Pol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H4k20me1StdPk HeLa-S3 H4K20m1 H4K20me1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001020 1020 GSM733689 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k79me2StdPk HeLa-S3 H3K79m2 H3K79me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001018 1018 GSM733669 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k36me3StdPk HeLa-S3 H3K36m3 H3K36me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001015 1015 GSM733711 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27me3StdPk HeLa-S3 H3K27m3 H3K27me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001037 1037 GSM733696 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27acStdPk HeLa-S3 H3K27ac H3K27ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001014 1014 GSM733684 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k09me3Pk HeLa-S3 H3K9m3 H3K9me3 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002396 2396 GSM1003480 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k9acStdPk HeLa-S3 H3K9ac H3K9ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001019 1019 GSM733756 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me3StdPk HeLa-S3 H3K4m3 H3K4me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001017 1017 GSM733682 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me2StdPk HeLa-S3 H3K4m2 H3K4me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001016 1016 GSM733734 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k04me1StdPk HeLa-S3 H3K4m1 H3K4me1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-14 2012-03-14 wgEncodeEH001750 1750 GSM798322 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k04me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H2azPk HeLa-S3 H2A.Z H2A.Z HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002395 2395 GSM1003483 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Ezh239875Pk HeLa-S3 EZH2 EZH2_(39875) HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003086 3086 GSM1003520 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HeLa-S3 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3CtcfStdPk HeLa-S3 CTCF CTCF HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001012 1012 GSM733785 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H4k20me1Pk CD20+ H4K20m1 H4K20me1 CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003145 3145 GSM1003497 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20ro01794H4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ RO01794 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H3k27acPk CD20+ H3K27ac H3K27ac CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003125 3125 GSM1003459 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20ro01794H3k27acPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ RO01794 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794Ezh239875Pk CD20+ EZH2 EZH2_(39875) CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003135 3135 GSM1003470 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20ro01794Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ RO01794 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H3k04me2Pk CD20+ H3K4m2 H3K4me2 CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003134 3134 GSM1003471 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20H3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H2azPk CD20+ H2A.Z H2A.Z CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003133 3133 GSM1003476 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20CtcfPk CD20+ CTCF CTCF CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003131 3131 GSM1003474 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H4k20me1Etoh02Pk A549 EtOH H4K20m1 H4K20me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003124 3124 GSM1003458 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H4k20me1Etoh02Pk EtOH_0.02pct Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Etoh02Pk A549 EtOH H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003099 3099 GSM1003512 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k79me2Etoh02Pk EtOH_0.02pct Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Dex100nmPk A549 DEX H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003078 3078 GSM1003543 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k79me2Dex100nmPk DEX_100nM Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Etoh02Pk A549 EtOH H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003121 3121 GSM1003456 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k36me3Etoh02Pk EtOH_0.02pct Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Dex100nmPk A549 DEX H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003142 3142 GSM1003494 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k36me3Dex100nmPk DEX_100nM Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Etoh02Pk A549 EtOH H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003120 3120 GSM1003455 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27me3Etoh02Pk EtOH_0.02pct Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Dex100nmPk A549 DEX H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003119 3119 GSM1003577 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27me3Dex100nmPk DEX_100nM Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acEtoh02Pk A549 EtOH H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003118 3118 GSM1003578 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27acEtoh02Pk EtOH_0.02pct Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acDex100nmPk A549 DEX H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003141 3141 GSM1003493 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27acDex100nmPk DEX_100nM Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09me3Etoh02Pk A549 EtOH H3K9m3 H3K9me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003123 3123 GSM1003454 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k09me3Etoh02Pk EtOH_0.02pct Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09acEtoh02Pk A549 EtOH H3K9ac H3K9ac A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003079 3079 GSM1003544 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k09acEtoh02Pk EtOH_0.02pct Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Etoh02Pk A549 EtOH H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003065 3065 GSM1003561 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me3Etoh02Pk EtOH_0.02pct Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Dex100nmPk A549 DEX H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003077 3077 GSM1003542 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me3Dex100nmPk DEX_100nM Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Etoh02Pk A549 EtOH H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003144 3144 GSM1003496 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me2Etoh02Pk EtOH_0.02pct Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Dex100nmPk A549 DEX H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003098 3098 GSM1003511 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me2Dex100nmPk DEX_100nM Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Etoh02Pk A549 EtOH H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003122 3122 GSM1003453 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me1Etoh02Pk EtOH_0.02pct Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Dex100nmPk A549 DEX H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003143 3143 GSM1003495 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me1Dex100nmPk DEX_100nM Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azEtoh02Pk A549 EtOH H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003117 3117 GSM1003546 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H2azEtoh02Pk EtOH_0.02pct Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azDex100nmPk A549 DEX H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003116 3116 GSM1003580 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H2azDex100nmPk DEX_100nM Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfEtoh02Pk A549 EtOH CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003115 3115 GSM1003581 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549CtcfEtoh02Pk EtOH_0.02pct Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfDex100nmPk A549 DEX CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003114 3114 GSM1003582 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549CtcfDex100nmPk DEX_100nM Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Suz12051317Pk K562 SUZ12 SUZ12_(05-1317) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003112 3112 GSM1003545 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Suz12051317Pk None Peaks SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 SUZ12 (05-1317) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sirt6Pk K562 SIRT6 SIRT6 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003111 3111 GSM1003560 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Sirt6Pk None Peaks A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 SIRT6 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Setdb1Pk K562 SETDB1 SETDB1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003129 3129 GSM1003452 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Setdb1Pk None Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 SETDB1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sap3039731StdPk K562 SAP30 SAP30_(39731) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002094 2094 GSM1003445 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Sap3039731StdPk None Peaks SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 SAP30 (39731) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rnf2Pk K562 RNF2 RNF2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003110 3110 GSM1003563 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Rnf2Pk None Peaks Ring finger protein 2 (RNF2) is a polycomb group (PcG) protein. RNF2 has been shown to interact with, and suppress the activity of, transcription factor CP2 (TFCP2/CP2). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 RNF2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562RestPk K562 REST REST K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003096 3096 GSM1003507 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562RestPk None Peaks A transcriptional repressor which represses neuronal genes in non-neuronal tissues. A member of the Kruppel-type zinc finger transcription factor family. Represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element (NRSE) by associating with two corepressors, mSin3 and CoREST, which recruit HDACs to the promoters of REST-regulated genes. Target is GST fusion amino acids 801-1097 of human REST. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 REST Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rbbp5a300109aStdPk K562 RBBP5 RBBP5_(A300-109A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002093 2093 GSM1003449 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Rbbp5a300109aStdPk None Peaks Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 RBBP5 (A300-109A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Pol2bStdPk K562 Pol2 Pol2(b) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000053 53 GSM733643 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Pol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Plu1StdPk K562 PLU1 PLU1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002085 2085 GSM1003586 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Plu1StdPk None Peaks JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 PLU1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Phf8a301772aStdPk K562 PHF8 PHF8_(A301-772A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002092 2092 GSM1003450 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Phf8a301772aStdPk None Peaks PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 PHF8 (A301-772A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562PcafPk K562 PCAF PCAF K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003109 3109 GSM1003566 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562PcafPk None Peaks PCAF (P300/CBP-associated factor) is a histone acetyltransferase (HAT) identified as a factor that associates with P300/CBP, a transcriptional coactivator of nuclear hormone receptors and other transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 PCAF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562P300StdPk K562 P300 p300 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002086 2086 GSM1003583 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562P300StdPk None Peaks EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 P300 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Nsd2ab75359Pk K562 NSD2 NSD2_(ab75359) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003140 3140 GSM1003492 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Nsd2ab75359Pk None Peaks This is a probable histone methyltransferase, which may act as a transcription regulator that binds DNA and suppresses IL5 transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 NSD2 (ab75359) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562NcorPk K562 NCoR NCoR K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003108 3108 GSM1003565 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562NcorPk None Peaks The nuclear receptor corepressor protein (NCoR) mediates gene repression by interacting with nuclear receptors. NCoR mediates repression by associating with SIN3A/B and the histone deacetylases, HDAC1 and HDAC2, and promoting the formation of repressive chromatin structures. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 NCoR Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Lsd1Pk K562 LSD1 LSD1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003107 3107 GSM1003570 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Lsd1Pk None Peaks BHC110/LSD1 is a histone demethylase and a component of several histone deacetylase complexes. BHC110/LSD1 is able to specifically catalyze the demethylation of Lys4 of histone H3. As part of histone deacetylase complexes BHC110/LSD1 functions as a corepressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 LSD1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac6a301341aPk K562 HDAC6 HDAC6_(A301-341A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003093 3093 GSM1003504 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Hdac6a301341aPk None Peaks Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 HDAC6 (A301-341A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac2a300705aStdPk K562 HDAC2 HDAC2_(A300-705A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002091 2091 GSM1003447 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Hdac2a300705aStdPk None Peaks Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 HDAC2 (A300-705A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac1sc6298StdPk K562 HDAC1 HDAC1_(SC-6298) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002090 2090 GSM1003448 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Hdac1sc6298StdPk None Peaks Histone deacetylase 1 (HDAC1) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC1 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC1 include RPD3L1, HD1, GON-10, and DKFZp686H12203. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 HDAC1 (SC-6298) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H4k20me1StdPk K562 H4K20m1 H4K20me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000051 51 GSM733675 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k79me2StdPk K562 H3K79m2 H3K79me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001039 1039 GSM733653 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k36me3StdPk K562 H3K36m3 H3K36me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000045 45 GSM733714 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27me3StdPk K562 H3K27m3 H3K27me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000044 44 GSM733658 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27acStdPk K562 H3K27ac H3K27ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000043 43 GSM733656 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me1StdPk K562 H3K9m1 H3K9me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000050 50 GSM733777 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k9me1StdPk None Peaks Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K9me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me3StdPk K562 H3K9m3 H3K9me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001040 1040 GSM733776 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9acStdPk K562 H3K9ac H3K9ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000049 49 GSM733778 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me3StdPk K562 H3K4m3 H3K4me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000048 48 GSM733680 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me2StdPk K562 H3K4m2 H3K4me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000047 47 GSM733651 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me1StdPk K562 H3K4m1 H3K4me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000046 46 GSM733692 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H2azStdPk K562 H2A.Z H2A.Z K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001038 1038 GSM733786 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Ezh239875StdPk K562 EZH2 EZH2_(39875) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002089 2089 GSM1003576 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Ezh239875StdPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562CtcfStdPk K562 CTCF CTCF K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000042 42 GSM733719 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd7a301223a1Pk K562 CHD7 CHD7_(A301-223A-1) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003139 3139 GSM1003478 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Chd7a301223a1Pk None Peaks CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 CHD7 (A301-223A-1) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd4mi2Pk K562 CHD4 Mi2 CHD4_Mi2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003095 3095 GSM1003510 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Chd4mi2Pk None Peaks CHD4/Mi2beta is a helicase component of the nucleosome remodeling and deacetylase (NuRD) complex that functions to remodel chromatin and repress transcription. Outside of the NuRD complex, CHD4/Mi2beta can function as an activator of transcription in association with p300 histone acetyltransferase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 CHD4 Mi2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd1a301218aStdPk K562 CHD1 CHD1_(A301-218A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002088 2088 GSM1003575 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Chd1a301218aStdPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 CHD1 (A301-218A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx8Pk K562 CBX8 CBX8 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003106 3106 GSM1003569 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbx8Pk None Peaks CBX8 is part of the polycomb group of proteins that are important in embryogenesis and human tumorigenesis and regulates a number of genes involved in cell growth and survival. There are at least 5 CBX proteins in mammals. CBX proteins associate with the core polycomb repressive complex 1 (PRC1) that functions to maintain the transcriptionally repressive state of genes during development. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 CBX8 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx3sc101004Pk K562 CBX3 CBX3_(SC-101004) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003105 3105 GSM1003568 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbx3sc101004Pk None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 CBX3 (SC-101004) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx2Pk K562 CBX2 CBX2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003104 3104 GSM1003567 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbx2Pk None Peaks Chromobox protein homolog 2 is a component of the polycomb group (PcG) multiprotein PRC1 complex, a complex required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. [taken from the Universal Protein Resource (UniProt) www.uniprot.org/uniprot/P19474] leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 CBX2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbpsc369Pk K562 CBP (SC-369) CBP_(sc-369) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003103 3103 GSM1003574 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbpsc369Pk None Peaks CBP is a histone acetyl transferase that promotes transcription. CBP is recruited by a variety of transcription factors to promoters and enhancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 CBP (sc-369) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSuz12051317Pk H1-hESC SUZ12 SUZ12_(05-1317) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003102 3102 GSM1003573 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescSuz12051317Pk None Peaks SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC SUZ12 (05-1317) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSirt6Pk H1-hESC SIRT6 SIRT6 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003128 3128 GSM1003451 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescSirt6Pk None Peaks A synthetic peptide made to an internal region of the human SIRT6 protein embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC SIRT6 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSap3039731Pk H1-hESC SAP30 SAP30_(39731) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003101 3101 GSM1003572 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescSap3039731Pk None Peaks SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC SAP30 (39731) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescRbbp5a300109aStdPk H1-hESC RBBP5 RBBP5_(A300-109A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002087 2087 GSM1003584 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescRbbp5a300109aStdPk None Peaks Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC RBBP5 (A300-109A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPlu1Pk H1-hESC PLU1 PLU1 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003127 3127 GSM1003457 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescPlu1Pk None Peaks JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC PLU1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPhf8a301772aPk H1-hESC PHF8 PHF8_(A301-772A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003094 3094 GSM1003509 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescPhf8a301772aPk None Peaks PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC PHF8 (A301-772A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescP300kat3bPk H1-hESC P300 P300_KAT3B H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003126 3126 GSM1003513 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescP300kat3bPk None Peaks Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC P300 KAT3B Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJmjd2aa300861a1Pk H1-hESC JMJD2A JMJD2A_(A300-861A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003138 3138 GSM1003479 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescJmjd2aa300861a1Pk None Peaks JMJD2A is a member of the jumonji (jmj) domain containing gene family of histone demethylases that plays a role in chromatin regulation and influences transcriptional activation and suppression. JMJD2A is a trimethylation-specific demethylase and functions as a transcriptional repressor. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC JMJD2A (A300-861A-1) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJarid1aab26049StdPk H1-hESC JARID1A JARID1A_(ab26049) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002096 2096 GSM1003446 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescJarid1aab26049StdPk None Peaks Histone demethylase that specifically demethylates embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC JARID1A (ab26049) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac6a301341aPk H1-hESC HDAC6 HDAC6_(A301-341A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003100 3100 GSM1003571 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescHdac6a301341aPk None Peaks Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC HDAC6 (A301-341A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac2a300705aPk H1-hESC HDAC2 HDAC2_(A300-705A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003137 3137 GSM1003472 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescHdac2a300705aPk None Peaks Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC HDAC2 (A300-705A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH4k20me1StdPk H1-hESC H4K20m1 H4K20me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000087 87 GSM733687 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k79me2StdPk H1-hESC H3K79m2 H3K79me2 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002083 2083 GSM1003547 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k36me3StdPk H1-hESC H3K36m3 H3K36me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000107 107 GSM733725 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27me3StdPk H1-hESC H3K27m3 H3K27me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000074 74 GSM733748 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27acStdPk H1-hESC H3K27ac H3K27ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000997 997 GSM733718 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k09me3StdPk H1-hESC H3K9m3 H3K9me3 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002084 2084 GSM1003585 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k09me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k9acStdPk H1-hESC H3K9ac H3K9ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000109 109 GSM733773 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me3StdPk H1-hESC H3K4m3 H3K4me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000086 86 GSM733657 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me2StdPk H1-hESC H3K4m2 H3K4me2 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000108 108 GSM733670 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me1StdPk H1-hESC H3K4m1 H3K4me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000106 106 GSM733782 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH2azStdPk H1-hESC H2A.Z H2A.Z H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-04 2012-05-04 wgEncodeEH002082 2082 GSM1003579 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescEzh239875Pk H1-hESC EZH2 EZH2_(39875) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003082 3082 GSM1003524 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment H1-hESC EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescCtcfStdPk H1-hESC CTCF CTCF H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000085 85 GSM733672 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd7a301223a1Pk H1-hESC CHD7 CHD7_(A301-223A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003136 3136 GSM1003473 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescChd7a301223a1Pk None Peaks CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC CHD7 (A301-223A-1) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd1a301218aStdPk H1-hESC CHD1 CHD1_(A301-218A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002095 2095 GSM1003444 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescChd1a301218aStdPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC CHD1 (A301-218A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H4k20me1StdPk GM12878 H4K20m1 H4K20me1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000036 36 GSM733642 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k79me2StdPk GM12878 H3K79m2 H3K79me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001034 1034 GSM733736 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k36me3StdPk GM12878 H3K36m3 H3K36me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000032 32 GSM733679 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27me3StdPkV2 GM12878 H3K27m3 H3K27me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2011-08-05 wgEncodeEH000031 31 GSM733758 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k27me3StdPkV2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27acStdPk GM12878 H3K27ac H3K27ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000030 30 GSM733771 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9me3StdPk GM12878 H3K9m3 H3K9me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001035 1035 GSM733664 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9acStdPk GM12878 H3K9ac H3K9ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000035 35 GSM733677 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me3StdPkV2 GM12878 H3K4m3 H3K4me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2011-08-05 wgEncodeEH000028 28 GSM733708 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k04me3StdPkV2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k4me2StdPk GM12878 H3K4m2 H3K4me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000034 34 GSM733769 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 GM12878 H3K4m1 H3K4me1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2011-08-05 wgEncodeEH000033 33 GSM733772 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H2azStdPk GM12878 H2A.Z H2A.Z GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001033 1033 GSM733767 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878Ezh239875Pk GM12878 EZH2 EZH2_(39875) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002411 2411 GSM1003498 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878CtcfStdPk GM12878 CTCF CTCF GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000029 29 GSM733752 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeCaltechRnaSeq Caltech RNA-seq GSE33480 RNA-seq from ENCODE/Caltech Expression Description This track was produced as part of the ENCODE Project. RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly. RNA-seq was performed by reverse-transcribing an RNA sample into cDNA, followed by high-throughput DNA sequencing, which was done on an Illumina Genome Analyzer (GAI or GAIIx) (Mortazavi et al., 2008). The transcriptome measurements shown on these tracks were performed on polyA selected RNA from total cellular RNA using two different protocols: one that preserves information about which strand the read is coming from and one that does not. Due to the specifics of the enzymology of library construction, gene and transcript quantification is more accurate based on the non-strand-specific protocol, while the strand-specific protocol is useful for assigning strandedness, but in general less reliable for quantification. Non-strand-specific Protocol (deep "reference" transcriptome measurements, 2x75 bp reads) PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis, converted into cDNA by random priming and then amplified. Data were produced in two formats: single reads, each of which came from one end of a cDNA molecule, and paired-end reads, which were obtained as pairs from both ends of cDNAs. This RNA-seq protocol does not specify the coding strand. As a result, there is ambiguity at loci where both strands are transcribed. The "randomly primed" reverse transcription is, apparently, not fully random. This is inferred from a sequence bias in the first residues of the read population, and this likely contributes to observed unevenness in sequence coverage across transcripts. Strand-specific Protocol (1x75 bp reads) PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis. A set of 3' and 5' adapters were ligated to the 3' and 5' ends of the fragments, respectively. The resulting RNA molecules were converted to cDNA and amplified. This RNA-seq protocol does specify the coding strand as each read is in the same 5'-3' orientation as the original RNA strand. As a result, loci where both strands are transcribed can be disambiguated. However, RNA ligation is an inherently biased process and as a result, greater unevenness in sequence coverage across transcripts is observed compared to the non-strand-specific data, and quantification is less accurate. Data Analysis Reads were aligned to the hg19 human reference genome using TopHat (Trapnell et al., 2009), a program specifically designed to align RNA-seq reads and discover splice junctions de novo. Cufflinks (Trapnell et al., 2010), a de novo transcript assembly and quantification software package, was run on the TopHat alignments to discover and quantify novel transcripts and to obtain transcript expression estimates based on the GENCODE annotation. All sequence files, alignments, gene and transcript models and expression estimates files are available for download. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. The following views are in this track: Alignments The Alignments view shows reads aligned to the genome. Alignments are colored by cell type. The tags used in this file are: NH XS CP NM CC. The 'XS' custom tag indicates the sense/anti-sense of the strand. See the Bowtie Manual (Langmead et al., 2009) for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format. For Stranded Data (1x75) Plus Raw Signal (only for stranded data) Density graph (wiggle) of signal enrichment based on a normalized aligned read density (Read Per Million, RPM) for reads aligning to the forward strand. Minus Raw Signal (only for stranded data) Density graph (wiggle) of signal enrichment based on a normalized aligned read density (Read Per Million, RPM) for reads aligning to the reverse strand. Minus strand score is multiplied by -1 for display purposes so that data can be viewed around an axis. For Paired-End Non-Stranded Data (2x75) Raw Signal (only for paired-end data) Density graph (wiggle) of signal enrichment based on a normalized aligned read density (Read Per Million, RPM). The RPM measure assists in visualizing the relative amount of a given transcript across multiple samples. A separate track for the forward (plus) and reverse (minus) strands are provided for strand-specific data. Splice Sites Subset of aligned reads that crosses splice junctions. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Experimental Procedures Cells were grown according to the approved ENCODE cell culture protocols except for H1-hESC for which frozen cell pellets were purchased from Cellular Dynamics. Cells were lysed in RLT buffer (Qiagen RNeasy kit) and processed on RNeasy midi columns according to the manufacturer's protocol, with the inclusion of the "on-column" DNase digestion step to remove residual genomic DNA. A quantity of 75 µg of total RNA was selected twice with oligo-dT beads (Dynal) according to the manufacturer's protocol to isolate mRNA from each of the preparations. For 2x75 bp non-stranded RNA-seq, 100 ng of mRNA was then processed according to the protocol in Mortazavi et al. (2008), and prepared for sequencing on the Genome Analyzer flow cell according to the protocol for the ChIP-seq DNA genomic DNA kit (Illumina). The majority of paired-end libraries were size-selected around 200 bp (fragment length) with the exception of a few additional replicates that were size-selected at 400 bp with the specific intent to investigate the effect of fragment length on results. Strand-specific RNA-seq libraries were prepared from 100 ng of mRNA from the same preparation following Illumina's Strand-Specific RNA-seq protocol. Libraries were sequenced with an Illumina Genome Analyzer I or an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. Reads of 75 bp length were obtained, single-end for directional, strand-specific libraries (1x75D) and paired-end for non-strand-specific libraries (2x75). Data Processing and Analysis Reads were mapped to the reference human genome (version hg19), with or without the Y chromosome, depending on the sex of the cell line, and without the random chromosomes and haplotypes in all cases, using TopHat (version 1.0.14). TopHat was used with default settings with the exception of specifying an empirically determined mean inner-mate distance. After mapping reads to the genome and identifying splice junctions, the data were further analyzed using the transcript assembly and quantification software Cufflinks (version 0.9.3) using the sequence bias detection and correction option. Cufflinks was used in two modes: 1) expression for genes and individual transcripts was quantified based on the GENCODE annotation, for both versions v3c and v4 of GENCODE GRCh37; 2) Cufflinks was run in de novo transcript assembly and quantification mode to obtain candidate novel transcript and gene models and expression estimates for them. Downloadable Files The following files can be found on the downloads page: .fastq - Raw sequence files in fastq format with phred33 quality scores. Junctions.bedRnaElements - A BED file containing TopHat-defined splice junctions. TranscriptDeNovo.gtf - A GTF file containing transcript models and expression estimates in FPKM (Fragments Per Kilobase per Million reads) produced by Cufflinks in de novo mode. TranscriptGencV3c.gtf - Expression level estimates at the transcript level for the GENCODE GRCh37.v3c annotation in GTF format. GenesDeNovo.gtf - Expression estimates for genes defined by Cufflinks in de novo mode in GTF format. GeneGencV3c.gtf - Expression level estimates at the gene level for the GENCODE GRCh37.v3c annotation in GTF format. ExonGencV3c.gtf - Expression level estimates for GENCODE GRCh37.v3c exons in GTF format derived by summing the expression levels in FPKM for all transcripts containing a given exon. TSS.gtf - Expression level estimates for GENCODE GRCh37.v3c transcription start sites (TSS) in GTF format derived by summing the expression levels in FPKM for all transcripts originating from a given TSS. Verification Known exon maps as displayed on the genome browser are confirmed by the alignment of sequence reads. Known spliced exons are detected at the expected frequency for transcripts of given abundance. Linear range detection of spiked-in RNA transcripts from Arabidopsis and phage lambda over 5 orders of magnitude. Endpoint RT-PCR confirms presence of selected 3' UTR extensions. Correlation to published microarray data r = 0.62. Release Notes This is release 4 (August 2012). Fastq files for GM12892, GM12891 and K562 (R1x75) were replaced after errors were found in the GEO submission process. Credits Wold Group: Ali Mortazavi, Brian Williams, Georgi Marinov, Diane Trout, Brandon King, Ken McCue, Lorian Schaeffer. Myers Group: Norma Neff, Florencia Pauli, Fan Zhang, Tim Reddy, Rami Rauch, Chris Partridge. Illumina gene expression group: Gary Schroth, Shujun Luo, Eric Vermaas. TopHat/Cufflinks development: Cole Trapnell, Lior Pachter, Steven Salzberg. Contacts: Georgi Marinov (data coordination/informatics/experimental), Diane Trout (informatics) and Brian Williams (experimental). References Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeRnaSeqSuper ENC RNA-seq ENCODE RNA-seq Expression Description RNA sequencing, or RNA-seq, is a method for mapping and quantifying the total amount of RNA transcripts in a cell at any given time, otherwise known as the transcriptome, for any organism that has a genomic DNA sequence assembly. Compared to microarrays that detect and quantify transcripts by hybridization against known sequences, RNA-seq directly sequences transcripts and is especially well-suited for de novo discovery of RNA splicing patterns and for determining unequivocally the presence or absence of lower abundance class RNAs. RNA-seq is performed by reverse-transcribing an RNA sample into cDNA followed by high throughput DNA sequencing. Most data is produced in the format of either single reads or paired-end reads. In the format of single reads each sequence read comes from one end of a randomly primed cDNA molecule (and represent one end of one cDNA segment), while paired-end reads are obtained as pairs from both ends of a randomly primed cDNA (and represent two opposite ends of one cDNA segment). The resulting sequence reads are then informatically mapped onto the genome sequence (Alignments). The current mappers (TopHat and STAR) have the ability to map reads to annotated and unannotated genomic regions. Reads mapped to annotated or novel RNA splice junctions are (Splice Sites). Earlier versions of this software did not map reads to unannotated genomic regions. Some RNA-seq protocols do not specify the coding strand. As a result, there can be ambiguity at loci where both strands are transcribed. Display Conventions These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics. 2009;10:135-51. Metzker ML. Sequencing technologies - the next generation. Nature Reviews: Genetics. 2010 Jan;11(1):31-46 Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeCaltechRnaSeqViewSplices Splice Juctions RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep2V2 NHLF 2x75 Sp 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11588 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep2V2 Splices lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHLF 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep1V2 NHLF 2x75 Sp 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11587 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep1V2 Splices lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHLF 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dSplicesRep1V2 NHEK 1x75D Sp 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000136 136 GSM958741 Myers Caltech 11204 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqNhekR1x75dSplicesRep1V2 Splices epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHEK single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep2V2 NHEK 2x75 Sp 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000131 131 GSM958736 Myers Caltech 11586 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep2V2 Splices epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHEK 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep1V2 NHEK 2x75 Sp 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000131 131 GSM958736 Myers Caltech 10884 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep1V2 Splices epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHEK 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep2V2 HSMM 2x75 Sp 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11585 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep2V2 Splices skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HSMM 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep1V2 HSMM 2x75 Sp 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11584 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep1V2 Splices skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HSMM 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep2V2 HCT6 2x75 Sp 2 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2011-02-12 2011-11-11 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12097 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep2V2 Splices colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HCT-116 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep1V2 HCT6 2x75 Sp 1 HCT-116 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12096 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep1V2 Splices colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HCT-116 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep3V2 GM92 2x75 Sp 3 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2973 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep3V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12892 200 bp paired read RNA-seq Splices Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep2V2 GM92 2x75 Sp 2 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2970 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12892 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep1V2 GM92 2x75 Sp 1 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 GSM958748 Myers Caltech 11039 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12892 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep2V2 GM91 2x75 Sp 2 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2011-03-14 2011-12-14 wgEncodeEH001423 1423 GSM958747 Myers Caltech SL2971 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12891 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep1V2 GM91 2x75 Sp 1 GM12891 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001423 1423 GSM958747 Myers Caltech 11038 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12891 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep3V2 MCF7 2x75 Sp 3 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-04-20 2012-01-20 wgEncodeEH001421 1421 GSM958745 Myers Caltech 12098 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep3V2 Splices mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions MCF-7 200 bp paired read RNA-seq Splices Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep2V2 MCF7 2x75 Sp 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11582 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep2V2 Splices mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions MCF-7 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep1V2 MCF7 2x75 Sp 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11581 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep1V2 Splices mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions MCF-7 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dSplicesRep1 LHCND 2x75 Sp 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-05 2012-02-05 wgEncodeEH001670 1670 GSM958751 Myers Caltech 11622 myocyte cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dSplicesRep1 DIFF_7d Splices skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) Subset of aligned reads that cross splice junctions LHCN-M2 Myocyte 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200SplicesRep1V2 LHCN 2x75 Sp 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEH001669 1669 GSM958750 Myers Caltech 11621 myoblast cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200SplicesRep1V2 Splices skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions LHCN-M2 Myoblast 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep2V2 HUVEC 1x75D Sp 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 GSM958738 Myers Caltech 11205 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep2V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep1V2 HUVEC 1x75D Sp 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 GSM958738 Myers Caltech 11206 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep1V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep2V2 HUVEC 2x75 Sp 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 GSM958734 Myers Caltech 10885 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep2V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep1V2 HUVEC 2x75 Sp 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 GSM958734 Myers Caltech 10883 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep1V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep2V2 HepG 1x75D Sp 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000135 135 GSM958740 Myers Caltech 11209 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep2V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep1V2 HepG 1x75D Sp 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000135 135 GSM958740 Myers Caltech 11210 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep1V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep2V2 HepG 2x75 Sp 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-22 2010-10-22 wgEncodeEH000127 127 GSM958732 Myers Caltech 10879 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep2V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep1V2 HepG 2x75 Sp 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-12 2010-10-11 wgEncodeEH000127 127 GSM958732 Myers Caltech 10878 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep1V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep2V2 HeLa 1x75D Sp 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 GSM958739 Myers Caltech 11207 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep2V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep1V2 HeLa 1x75D Sp 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 GSM958739 Myers Caltech 11208 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep1V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep2V2 HeLa 2x75 Sp 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 GSM958735 Myers Caltech 10882 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep2V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep1V2 HeLa 2x75 Sp 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 GSM958735 Myers Caltech 10881 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep1V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dSplicesRep2V2 K562 1x75D Sp 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000126 126 GSM958731 Myers Caltech 11007 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqK562R1x75dSplicesRep2V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dSplicesRep1V2 K562 1x75D Sp 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-06 2010-10-06 wgEncodeEH000126 126 GSM958731 Myers Caltech 11008 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqK562R1x75dSplicesRep1V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep2V2 K562 2x75 Sp 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 GSM958729 Myers Caltech 10567 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep2V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep1V2 K562 2x75 Sp 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 GSM958729 Myers Caltech 10517 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep1V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep2V2 H1ES 1x75D Sp 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000132 132 GSM958737 Myers Caltech 11009 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep2V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep1V2 H1ES 1x75D Sp 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000132 132 GSM958737 Myers Caltech 10947 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep1V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il400SplicesRep1V2 H1ES 400 Sp 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000138 138 GSM958743 Myers Caltech 10876 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il400SplicesRep1V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 400 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep4V2 H1ES 2x75 Sp 4 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000128 128 GSM958733 Myers Caltech 10874 cell TH1014 hg18 2x75 4 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep4V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 4 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep3V2 H1ES 2x75 Sp 3 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 GSM958733 Myers Caltech 11289 cell TH1014 hg18 2x75 3 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep3V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep2V2 H1ES 2x75 Sp 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 GSM958733 Myers Caltech 11288 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep2V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep1V2 H1ES 2x75 Sp 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-13 wgEncodeEH000128 128 GSM958733 Myers Caltech 11286 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep1V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep2V2 GM78 1x75D Sp 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000125 125 GSM958730 Myers Caltech 11010 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep1V2 GM78 1x75D Sp 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-04 2010-10-04 wgEncodeEH000125 125 GSM958730 Myers Caltech 11011 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il400SplicesRep2V2 GM78 400 Sp 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000137 137 GSM958742 Myers Caltech 10516 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il400SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 400 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep2V2 GM78 2x75 Sp 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 GSM958728 Myers Caltech 10515 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep1V2 GM78 2x75 Sp 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 GSM958728 Myers Caltech 10565 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewSignal Signal RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep2V4 NHLF 2x75 Sg 2 NHLF RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11588 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep2V4 Signal lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal NHLF 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep1V4 NHLF 2x75 Sg 1 NHLF RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11587 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep1V4 Signal lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal NHLF 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep2V4 NHEK 2x75 Sg 2 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH000131 131 GSM958736 Myers Caltech 11586 cell TH1014 2x75 2 longPolyA U wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep2V4 Signal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal NHEK 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep1V4 NHEK 2x75 Sg 1 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH000131 131 GSM958736 Myers Caltech 10884 cell TH1014 2x75 1 longPolyA U wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep1V4 Signal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal NHEK 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep2V4 HSMM 2x75 Sg 2 HSMM RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11585 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep2V4 Signal skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HSMM 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep1V4 HSMM 2x75 Sg 1 HSMM RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11584 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep1V4 Signal skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HSMM 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep2V4 HCT6 2x75 Sg 2 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12097 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep2V4 Signal colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HCT-116 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep1V4 HCT6 2x75 Sg 1 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12096 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep1V4 Signal colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HCT-116 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep3V4 GM92 2x75 Sg 3 GM12892 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2973 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep3V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12892 200 bp paired read RNA-seq Signal Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep2V4 GM92 2x75 Sg 2 GM12892 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2970 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12892 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep1V4 GM92 2x75 Sg 1 GM12892 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001424 1424 GSM958748 Myers Caltech 11039 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep1V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12892 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep2V4 GM91 2x75 Sg 2 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001423 1423 GSM958747 Myers Caltech SL2971 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12891 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep1V4 GM91 2x75 Sg 1 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001423 1423 GSM958747 Myers Caltech 11038 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep1V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12891 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep3V4 MCF7 2x75 Sg 3 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001421 1421 GSM958745 Myers Caltech 12098 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep3V4 Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal MCF-7 200 bp paired read RNA-seq Signal Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep2V4 MCF7 2x75 Sg 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11582 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep2V4 Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal MCF-7 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep1V4 MCF7 2x75 Sg 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11581 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep1V4 Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal MCF-7 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200Diff7dSigRep1V4 LHCND 2x75 Sg 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH001670 1670 GSM958751 Myers Caltech 11622 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200Diff7dSigRep1V4 DIFF_7d Signal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) Signal LHCN-M2 Myocyte 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200USigRep1V4 LHCN 2x75 Sg 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH001669 1669 GSM958750 Myers Caltech 11621 cell TH1014 2x75 1 longPolyA U wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200USigRep1V4 Signal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal LHCN-M2 Myoblast 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep2V4 HUVEC 2x75 Sg 2 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000129 129 GSM958734 Myers Caltech 10885 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep2V4 Signal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HUVEC 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep1V4 HUVEC 2x75 Sg 1 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000129 129 GSM958734 Myers Caltech 10883 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep1V4 Signal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HUVEC 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep2V4 HepG 2x75 Sg 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000127 127 GSM958732 Myers Caltech 10879 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep2V4 Signal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HepG2 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep1V4 HepG 2x75 Sg 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000127 127 GSM958732 Myers Caltech 10878 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep1V4 Signal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HepG2 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep2V4 HeLa 2x75 Sg 2 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000130 130 GSM958735 Myers Caltech 10882 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep2V4 Signal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HeLa-S3 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep1V4 HeLa 2x75 Sg 1 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000130 130 GSM958735 Myers Caltech 10881 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep1V4 Signal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HeLa-S3 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep2V4 K562 2x75 Sg 2 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000124 124 GSM958729 Myers Caltech 10567 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep2V4 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal K562 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep1V4 K562 2x75 Sg 1 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000124 124 GSM958729 Myers Caltech 10517 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep1V4 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal K562 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il400SigRep1V4 H1ES 400 Sg 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000138 138 GSM958743 Myers Caltech 10876 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il400SigRep1V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 400 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep4V4 H1ES 2x75 Sg 4 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 10874 cell TH1014 2x75 4 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep4V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 4 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep3V4 H1ES 2x75 Sg 3 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 11289 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep3V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep2V4 H1ES 2x75 Sg 2 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 11288 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep2V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep1V4 H1ES 2x75 Sg 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 11286 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep1V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il400USigRep2V4 GM78 400 Sg 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000137 137 GSM958742 Myers Caltech 10516 cell TH1014 2x75 2 longPolyA U wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il400USigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal GM12878 400 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep2V4 GM78 2x75 Sg 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000122 122 GSM958728 Myers Caltech 10515 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12878 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep1V4 GM78 2x75 Sg 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000122 122 GSM958728 Myers Caltech 10565 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep1V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12878 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewPlusSignal Plus Raw Signal RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dTh1014UPlusRawRep1V4 NHEK 1x75D + 1 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000136 136 GSM958741 Myers Caltech 11204 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqNhekR1x75dTh1014UPlusRawRep1V4 PlusRawSignal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand NHEK single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep2V4 HUVEC 1x75D + 2 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11205 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep2V4 PlusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HUVEC single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep1V4 HUVEC 1x75D + 1 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11206 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep1V4 PlusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HUVEC single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep2V4 HepG 1x75D + 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11209 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep2V4 PlusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HepG2 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep1V4 HepG 1x75D + 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11210 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep1V4 PlusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HepG2 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep2V4 HeLa 1x75D + 2 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11207 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep2V4 PlusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HeLa-S3 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep1V4 HeLa 1x75D + 1 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11208 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep1V4 PlusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HeLa-S3 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep2V4 K562 1x75D + 2 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11007 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep2V4 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand K562 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep1V4 K562 1x75D + 1 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11008 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep1V4 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand K562 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep2V4 H1ES 1x75D + 2 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 11009 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep2V4 PlusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand H1-hESC single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep1V4 H1ES 1x75D + 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 10947 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep1V4 PlusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand H1-hESC single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep2V4 GM78 1x75D + 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11010 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep2V4 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand GM12878 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep1V4 GM78 1x75D + 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11011 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep1V4 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand GM12878 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewMinusSignal Minus Raw Signal RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dTh1014UMinusRawRep1V4 NHEK 1x75D - 1 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000136 136 GSM958741 Myers Caltech 11204 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqNhekR1x75dTh1014UMinusRawRep1V4 MinusRawSignal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand NHEK single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep2V4 HUVEC 1x75D - 2 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11205 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep2V4 MinusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HUVEC single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep1V4 HUVEC 1x75D - 1 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11206 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep1V4 MinusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HUVEC single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep2V4 HepG 1x75D - 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11209 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep2V4 MinusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HepG2 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep1V4 HepG 1x75D - 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11210 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep1V4 MinusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HepG2 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep2V4 HeLa 1x75D - 2 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11207 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep2V4 MinusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HeLa-S3 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep1V4 HeLa 1x75D - 1 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11208 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep1V4 MinusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HeLa-S3 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep2V4 K562 1x75D - 2 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11007 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep2V4 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand K562 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep1V4 K562 1x75D - 1 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11008 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep1V4 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand K562 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep2V4 H1ES 1x75D - 2 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 11009 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep2V4 MinusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand H1-hESC single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep1V4 H1ES 1x75D - 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 10947 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep1V4 MinusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand H1-hESC single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep2V4 GM78 1x75D - 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11010 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep2V4 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand GM12878 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep1V4 GM78 1x75D - 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11011 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep1V4 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand GM12878 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewAligns Alignments RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep2V2 NHLF 2x75 A 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 Myers Caltech 11588 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep2V2 Alignments lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep1V2 NHLF 2x75 A 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 Myers Caltech 11587 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep1V2 Alignments lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dAlignsRep1V2 NHEK 1x75D A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000136 136 Myers Caltech 11204 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqNhekR1x75dAlignsRep1V2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep2V2 NHEK 2x75 A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000131 131 Myers Caltech 11586 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep2V2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep1V2 NHEK 2x75 A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000131 131 Myers Caltech 10884 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep1V2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep2V2 HSMM 2x75 A 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 Myers Caltech 11585 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep2V2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep1V2 HSMM 2x75 A 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 Myers Caltech 11584 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep1V2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep2V2 HCT6 2x75 A 2 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2011-02-12 2011-11-11 wgEncodeEH001425 1425 Myers Caltech 12097 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep2V2 Alignments colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HCT-116 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep1V2 HCT6 2x75 A 1 HCT-116 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001425 1425 Myers Caltech 12096 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep1V2 Alignments colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HCT-116 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep3V2 GM92 2x75 A 3 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 Myers Caltech SL2973 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep3V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12892 200 bp paired read RNA-seq Alignments Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep2V2 GM92 2x75 A 2 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 Myers Caltech SL2970 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12892 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep1V2 GM92 2x75 A 1 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 Myers Caltech 11039 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12892 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep2V2 GM91 2x75 A 2 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2011-03-14 2011-12-14 wgEncodeEH001423 1423 Myers Caltech SL2971 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12891 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep1V2 GM91 2x75 A 1 GM12891 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001423 1423 Myers Caltech 11038 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12891 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep3V2 MCF7 2x75 A 3 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-02-12 2011-11-11 wgEncodeEH001421 1421 Myers Caltech 12098 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep3V2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 200 bp paired read RNA-seq Alignments Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep2V2 MCF7 2x75 A 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 Myers Caltech 11582 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep2V2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep1V2 MCF7 2x75 A 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 Myers Caltech 11581 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep1V2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dAlignsRep1 LHCND 2x75 A 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-05 2012-02-05 wgEncodeEH001670 1670 Myers Caltech 11622 myocyte cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dAlignsRep1 DIFF_7d Alignments skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) Shows individual reads mapped to the genome and indicates where bases may mismatch LHCN-M2 Myocyte 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200AlignsRep1V2 LHCN 2x75 A 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEH001669 1669 Myers Caltech 11621 myoblast cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200AlignsRep1V2 Alignments skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch LHCN-M2 Myoblast 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep2V2 HUVEC 1x75D A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 Myers Caltech 11205 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep2V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep1V2 HUVEC 1x75D A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 Myers Caltech 11206 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep1V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep2V2 HUVEC 2x75 A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 Myers Caltech 10885 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep2V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep1V2 HUVEC 2x75 A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 Myers Caltech 10883 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep1V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep2V3 HepG 1x75D A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-09-08 2010-01-14 2010-10-14 wgEncodeEH000135 135 Myers Caltech 11209 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep2V3 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep1V3 HepG 1x75D A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-09-08 2010-01-14 2010-10-14 wgEncodeEH000135 135 Myers Caltech 11210 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep1V3 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep2V2 HepG 2x75 A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-22 2010-10-22 wgEncodeEH000127 127 Myers Caltech 10879 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep2V2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep1V2 HepG 2x75 A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-12 2010-10-11 wgEncodeEH000127 127 Myers Caltech 10878 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep1V2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep2V2 HeLa 1x75D A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 Myers Caltech 11207 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep2V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep1V2 HeLa 1x75D A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 Myers Caltech 11208 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep1V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep2V2 HeLa 2x75 A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 Myers Caltech 10882 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep2V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep1V2 HeLa 2x75 A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 Myers Caltech 10881 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep1V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dAlignsRep2V2 K562 1x75D A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000126 126 Myers Caltech 11007 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqK562R1x75dAlignsRep2V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dAlignsRep1V2 K562 1x75D A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-06 2010-10-06 wgEncodeEH000126 126 Myers Caltech 11008 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqK562R1x75dAlignsRep1V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep2V2 K562 2x75 A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 Myers Caltech 10567 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep2V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep1V2 K562 2x75 A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 Myers Caltech 10517 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep1V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep2V2 H1ES 1x75D A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000132 132 Myers Caltech 11009 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep2V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep1V2 H1ES 1x75D A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000132 132 Myers Caltech 10947 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep1V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il400AlignsRep1V2 H1ES 400 A 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000138 138 Myers Caltech 10876 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il400AlignsRep1V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 400 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep4V2 H1ES 2x75 A 4 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000128 128 Myers Caltech 10874 cell TH1014 hg18 2x75 4 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep4V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 4 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep3V2 H1ES 2x75 A 3 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 Myers Caltech 11289 cell TH1014 hg18 2x75 3 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep3V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep2V2 H1ES 2x75 A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 Myers Caltech 11288 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep2V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep1V2 H1ES 2x75 A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-13 wgEncodeEH000128 128 Myers Caltech 11286 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep1V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2 GM78 1x75D A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000125 125 Myers Caltech 11010 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep1V2 GM78 1x75D A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-04 2010-10-04 wgEncodeEH000125 125 Myers Caltech 11011 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il400AlignsRep2V2 GM78 400 A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000137 137 Myers Caltech 10516 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il400AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 400 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep2V2 GM78 2x75 A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 Myers Caltech 10515 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep1V2 GM78 2x75 A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 Myers Caltech 10565 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCshlLongRnaSeq CSHL Long RNA-seq GSE30567 Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression Description These tracks were generated by the ENCODE Consortium. They contain information about human RNAs greater than 200 nucleotides in length that were obtained as short reads from the Illumina GAIIx platform. Data are available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, there are also data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, see the RIKEN CAGE Loc track), Small RNA-seq (less than 200 nucleotides, see the CSHL Sm RNA-seq track) and Pair-End di-TAG-RNA (PET-RNA, see the GIS RNA PET track) datasets available from the same biological replicates. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types and compartments. Contigs The Contigs represent blocks of overlapping mapped reads from the pooled biological replicates. Specific column specifications can be found in the supplemental directory. Signals The Plus Signal and Minus Signal views show the density of mapped reads on the plus and minus strands (wiggle format), respectively. Alignments The Alignments view shows individual reads mapped from biological replicates to the genome and indicates where bases may mismatch. Every mapped read is displayed, i.e. uncollapsed. The alignment file follows the standard SAM format. See the SAM Format Specification for more information on the SAM/BAM file format. Splice Junctions Subset of aligned reads that cross splice junctions. Specific column specifications can be found in the supplemental directory. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Additional views are available on the downloads page. Methods Cell Culture Cells were grown according to the approved ENCODE cell culture protocols. Library Preparation The published cDNA sequencing protocol was used. This protocol generates directional libraries and reports the transcripts' strand of origin. Exogenous RNA spike-ins were added to each endogenous RNA isolate and carried through library construction and sequencing. The Illumina PhiX control library was also spiked-in at 1% to each completed human library just prior to cluster formation. Accompanying each RNA-seq dataset is a Protocol document available for download as a PDF. This document contains details about the RNA isolations and treatments, library construction, spike-ins as well as quality control figures for individual libraries. The spike-in sequence and the concentrations are available for download in the supplemental directory. Sequencing and Mapping The libraries were sequenced on the Illumina GAIIx platform as paired-ends for 76 or 101 cycles for each read. The average depth of sequencing was ~200 million reads (100 million paired-ends). The data were mapped against hg19 using Spliced Transcript Alignment and Reconstruction (STAR) written by Alex Dobin (CSHL). More information about STAR, including the parameters used for these data, is available from the Gingeras lab. For each experiment there are additional element data views data files available for download. These elements were assessed for reproducibility using a nonparametric irreproducible detection (IDR) rate script. The IDR values for each element are included in the files for end-users to use as a threshold. An IDR value of 0.1 means that the probability of detecting that element in a third experiment equivalent in depth to the sum of the bioreplicates is 90%. In addition, expression values for annotated genes, transcripts and exons were computed. Further explanation of these files is available for download in the supplemental directory. Verification FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated for annotated Gencode exons and Spearman values were compared. In general, Rho values are greater than .90 between biological replicates. Release Notes This is release 3 (Sept 2012) of this track for hg19. It has no new experiments, but has additional files for many experiments. The hMNC-CB experiment has been revoked. The doubly compressed spike-ins files have been uncompressed. The hMNC-PB experiment has been replaced with improved depth. The current downloadable elements files (Transcripts, Genes and Exons) were generated using GENCODE V10, while the older datasets were generated using GENCODE V7. The "view" metadata will specify V7 or V10 for these files. Errata 6/6/2013 - CSHL reports that one lane of reads is missing from the SK-N-SH-RA fastq read2 file (wgEncodeCshlLongRnaSeqSknshraCellPapFastqRd2Rep1.fastq.gz). Credits These data were generated and analyzed by the transcriptome group led by Tom Gingeras at Cold Spring Harbor Laboratories and the laboratory of Roderic Guigo at the Center for Genomic Regulation (CRG) in Barcelona. Contact: Carrie Davis References Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Oct;37(18):e123. Publications Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012 Sep;22(9):1658-67. Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR et al. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 2011 Oct 23;43(12):1179-85. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res. 2012 Sep;22(9):1775-89. Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E et al. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012 Sep 5;13(9):R53. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 2011 Sep;21(9):1543-51. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeCshlLongRnaSeqViewJunctions Splice Junctions Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapJunctions SKRA cel pA+ J SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967,LID8968 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapJunctions Junctions neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH RA whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPamJunctions SKRA cel pA- J SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003,LID9011 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPamJunctions Junctions neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH RA whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmcCellTotalJunctions SkMC cel tot J SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245,LID47246 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmcCellTotalJunctions Junctions Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SkMC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapJunctions NHLF cel pA+ J NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692,LID8701 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapJunctions Junctions lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHLF whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPamJunctions NHLF cel pA- J NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828,LID8829 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPamJunctions Junctions lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHLF whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm2CellTotalJunctions NHMM2 cel tot J NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258,LID47259 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm2CellTotalJunctions Junctions Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEM M2 whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm2CellTotalJunctions NHMf cel tot J NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256,LID47257 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm2CellTotalJunctions Junctions Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEM.f M2 whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapJunctions NHEK nuc pA+ J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797,LID8798 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPamJunctions NHEK nuc pA- J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204,LID9205 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPamJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapJunctions NHEK cyt pA+ J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795,LID8796 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPamJunctions NHEK cyt pA- J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPamJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapJunctions NHEK cel pA+ J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID8694 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPamJunctions NHEK cel pA- J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8830 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPamJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdfCellTotalJunctions NHDF cel tot J NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247,LID47248 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdfCellTotalJunctions Junctions Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHDF whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwpCellTotalJunctions HWP cel tot J HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254,LID47255 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwpCellTotalJunctions Junctions Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HWP whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmfCellTotalJunctions HVMF cel tot J HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249,LID47250 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmfCellTotalJunctions Junctions villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HVMF whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapJunctions HSMM cel pA+ J HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710,LID8711 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapJunctions Junctions skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HSMM whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPamJunctions HSMM cel pA- J HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826,LID8827 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPamJunctions Junctions skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HSMM whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalJunctions HSVEC cel tot J HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261,LID47260 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalJunctions Junctions Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HSaVEC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalJunctions HPIEC cel tot J HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105,LID47253 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalJunctions Junctions Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HPIEpC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalJunctions HPCPL cel tot J HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301,LID47104 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalJunctions Junctions Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HPC-PL whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHobCellTotalJunctions HOB cel tot J HOB RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251,LID47252 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHobCellTotalJunctions Junctions Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HOB whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscucCellTotalJunctions hMSUC cel tot J hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299,LID47300 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscucCellTotalJunctions Junctions Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMSC-UC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbmCellTotalJunctions hMSBM cel tot J hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099,LID47100 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbmCellTotalJunctions Junctions Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMSC-BM whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscatCellTotalJunctions hMSAT cel tot J hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097,LID47098 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscatCellTotalJunctions Junctions Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMSC-AT whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalJunctionsV2 hMNPB cel tot J hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-07-04 2013-04-04 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalJunctionsV2 Junctions Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMNC-PB whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalJunctions HMEpC cel tot J HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalJunctions Junctions Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HMEpC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapJunctions HMEC cel pA+ J HMEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapJunctions Junctions mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HMEC whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPamJunctions HMEC cel pA- J HMEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPamJunctions Junctions mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HMEC whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpcCellTotalJunctions HFDPC cel tot J HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094,LID47095 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpcCellTotalJunctions Junctions Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HFDPC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHchCellTotalJunctions HCH cel tot J HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024,LID47025 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHchCellTotalJunctions Junctions Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HCH whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalJunctions HAoEC cel tot J HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022,LID47023 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalJunctions Junctions Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HAoEC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalJunctions HAoAF cel tot J HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021,LID47020 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalJunctions Junctions Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HAoAF whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalJunctions CD34 cel tot J CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalJunctions Junctions hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CD34+ Mobilized whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapJunctions BJ cel pA+ J BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969,LID8970 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapJunctions Junctions skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions BJ whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPamJunctions BJ cel pA- J BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007,LID9008 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPamJunctions Junctions skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions BJ whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapJunctions AG50 cel pA+ J AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965,LID8966 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapJunctions Junctions fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions AG04450 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPamJunctions AG50 cel pA- J AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001,LID9002 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPamJunctions Junctions fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions AG04450 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapJunctions SKNSH nuc pA+ J SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596,LID46597 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapJunctions Junctions neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapJunctions SKNSH cyt pA+ J SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594,LID46595 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapJunctions Junctions neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapJunctions SKNSH cel pA+ J SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598,LID46599 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapJunctions Junctions neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapJunctions CD14 cel pA+ J Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594,LID44497 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapJunctions Junctions Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MonocytesCD14+ whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamJunctions CD14 cel pA- J Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657,LID44658 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamJunctions Junctions Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MonocytesCD14+ whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapJunctions MCF7 nuc pA+ J MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859,LID46860 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapJunctions MCF7 cyt pA+ J MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857,LID46858 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapJunctions MCF7 cel pA+ J MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686,LID8687 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPamJunctions MCF7 cel pA- J MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824,LID8825 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPamJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapJunctions IMR90 nuc pA+ J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635,LID45613 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapJunctions IMR90 cyt pA+ J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611,LID45612 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalJunctions IMR90 cel tot J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238,LID45239 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapJunctions IMR90 cel pA+ J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016,LID45017 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapJunctions HUVEC nuc pA+ J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690,LID8691 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPamJunctions HUVEC nuc pA- J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206,LID9207 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPamJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapJunctions HUVEC cyt pA+ J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688,LID8689 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPamJunctions HUVEC cyt pA- J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPamJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapJunctions HUVEC cel pA+ J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463,LID8464 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPamJunctions HUVEC cel pA- J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788,LID8789 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPamJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapJunctions HeG2 nuc pA+ J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534,LID8535 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPamJunctions HeG2 nuc pA- J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202,LID9203 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPamJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapJunctions HeG2 cyt pA+ J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471,LID8472 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPamJunctions HeG2 cyt pA- J HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552,LID18553 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPamJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapJunctions HeG2 cel pA+ J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635,LID16636 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPamJunctions HeG2 cel pA- J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792,LID8793 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPamJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapJunctions HeS3 nuc pA+ J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559,LID8560 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPamJunctions HeS3 nuc pA- J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200,LID9201 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPamJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapJunctions HeS3 cyt pA+ J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469,LID8470 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPamJunctions HeS3 cyt pA- J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPamJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapJunctions HeS3 cel pA+ J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633,LID16634 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPamJunctions HeS3 cel pA- J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790,LID8791 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPamJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapJunctions CD20 cel pA+ J CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498,LID44499 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapJunctions Junctions B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CD20+ whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamJunctions CD20 cel pA- J CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659,LID44660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamJunctions Junctions B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CD20+ whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapJunctions A549 nuc pA+ J A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899,LID45900 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapJunctions A549 cyt pA+ J A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897,LID45898 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapJunctions A549 cel pA+ J A549 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963,LID8964 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPamJunctions A549 cel pA- J A549 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005,LID9006 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPamJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapJunctions K562 nuc pA+ J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556,LID8557 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPamJunctions K562 nuc pA- J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195,LID9196 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPamJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalJunctions K562 ncpm tot J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189,LID9190 iIDR nucleoplasm 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 nucleoplasm total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapJunctions K562 cyt pA+ J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465,LID8466 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPamJunctions K562 cyt pA- J K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545,LID18546 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPamJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalJunctions K562 chrm tot J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185,LID9186 iIDR chromatin 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 chromatin total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapJunctions K562 cel pA+ J K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627,LID16628 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPamJunctions K562 cel pA- J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659,LID8660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPamJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapJunctions H1hSC nuc pA+ J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPamJunctions H1hSC nuc pA- J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPamJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapJunctions H1hSC cyt pA+ J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPamJunctions H1hSC cyt pA- J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPamJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapJunctions H1hSC cel pA+ J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461,LID8462 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPamJunctions H1hSC cel pA- J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663,LID8664 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPamJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapJunctions GM78 nuc pA+ J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532,LID8533 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPamJunctions GM78 nuc pA- J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197,LID9198 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPamJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalJunctions GM78 nlus tot J GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963,LID47964 iIDR nucleolus 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 nucleolus total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapJunctions GM78 cyt pA+ J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467,LID8468 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPamJunctions GM78 cyt pA- J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547,LID18548 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPamJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapJunctions GM78 cel pA+ J GM12878 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629,LID16630 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPamJunctions GM78 cel pA- J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661,LID8662 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPamJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewPlusSig Plus Signal Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep2 SKRA cel pA+ + 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8968 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep2 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep1 SKRA cel pA+ + 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep1 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep2 SKRA cel pA- + 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9011 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep2 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep1 SKRA cel pA- + 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep1 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc812190217CellTotalPlusRep2 SkMC cel tot + 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47246 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc812190217CellTotalPlusRep2 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc9011302CellTotalPlusRep1 SkMC cel tot + 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc9011302CellTotalPlusRep1 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep2 NHLF cel pA+ + 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8701 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep2 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep1 NHLF cel pA+ + 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep1 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep2 NHLF cel pA- + 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8829 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep2 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep1 NHLF cel pA- + 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep1 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm270110012CellTotalPlusRep2 NHMM2 cel tot + 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47259 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm270110012CellTotalPlusRep2 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM M2 whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm27012303CellTotalPlusRep1 NHMM2 cel tot + 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm27012303CellTotalPlusRep1 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM M2 whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalPlusRep2 NHMf cel tot + 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47257 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalPlusRep2 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f M2 whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalPlusRep1 NHMf cel tot + 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalPlusRep1 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f M2 whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep4 NHEK nuc pA+ + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8798 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep3 NHEK nuc pA+ + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep4 NHEK nuc pA- + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9205 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep3 NHEK nuc pA- + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep4 NHEK cyt pA+ + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8796 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep3 NHEK cyt pA+ + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaPlusRawSigRep3 NHEK cyt pA- + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep2 NHEK cel pA+ + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16632 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep2 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep1 NHEK cel pA+ + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16631 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep1 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep2 NHEK cel pA- + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8666 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep2 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep1 NHEK cel pA- + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8665 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep1 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf00608013CellTotalPlusRep2 NHDF cel tot + 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47248 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf00608013CellTotalPlusRep2 PlusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf70717012CellTotalPlusRep1 NHDF cel tot + 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf70717012CellTotalPlusRep1 PlusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp0092205CellTotalPlusRep2 HWP cel tot + 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47255 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp0092205CellTotalPlusRep2 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp81202015CellTotalPlusRep1 HWP cel tot + 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp81202015CellTotalPlusRep1 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf61004013CellTotalPlusRep2 HVMF cel tot + 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47250 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf61004013CellTotalPlusRep2 PlusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf60912033CellTotalPlusRep1 HVMF cel tot + 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf60912033CellTotalPlusRep1 PlusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep2 HSMM cel pA+ + 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8711 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep2 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep1 HSMM cel pA+ + 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep1 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep2 HSMM cel pA- + 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8827 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep2 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep1 HSMM cel pA- + 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep1 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep2 HSVEC cel tot + 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep2 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep1 HSVEC cel tot + 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47260 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep1 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep2 HPIEC cel tot + 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47253 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep2 PlusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep1 HPIEC cel tot + 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep1 PlusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep2 HPCPL cel tot + 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47104 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep2 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep1 HPCPL cel tot + 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep1 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob00902021CellTotalPlusRep2 HOB cel tot + 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47252 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob00902021CellTotalPlusRep2 PlusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob0091301CellTotalPlusRep1 HOB cel tot + 1 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob0091301CellTotalPlusRep1 PlusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalPlusRep2 hMSUC cel tot + 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47300 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalPlusRep1 hMSUC cel tot + 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalPlusRep2 hMSBM cel tot + 2 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47100 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalPlusRep1 hMSBM cel tot + 1 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat906160112CellTotalPlusRep2 hMSAT cel tot + 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47098 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat906160112CellTotalPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat010260412CellTotalPlusRep1 hMSAT cel tot + 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat010260412CellTotalPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalPlusSignalRep1V2 hMNPB cel tot + 1 hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalPlusSignalRep1V2 PlusSignal Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMNC-PB whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalPlusRep1 HMEpC cel tot + 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalPlusRep1 PlusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HMEpC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapPlusRawSigRep1 HMEC cel pA+ + 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapPlusRawSigRep1 PlusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HMEC whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaPlusRawSigRep1 HMEC cel pA- + 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaPlusRawSigRep1 PlusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HMEC whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalPlusRep2 HFDPC cel tot + 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47095 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalPlusRep2 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalPlusRep1 HFDPC cel tot + 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalPlusRep1 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch81008082CellTotalPlusRep2 HCH cel tot + 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47025 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch81008082CellTotalPlusRep2 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch00113082pCellTotalPlusRep1 HCH cel tot + 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch00113082pCellTotalPlusRep1 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalPlusRep2 HAoEC cel tot + 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47023 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalPlusRep2 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoec70717061CellTotalPlusRep1 HAoEC cel tot + 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoec70717061CellTotalPlusRep1 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalPlusRep2 HAoAF cel tot + 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalPlusRep2 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalPlusSignalRep1 HAoAF cel tot + 1 HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47020 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalPlusSignalRep1 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalPlusRep1 CD34 cel tot + 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalPlusRep1 PlusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand CD34+ Mobilized whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep2 BJ cel pA+ + 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8970 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep2 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep1 BJ cel pA+ + 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep1 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep2 BJ cel pA- + 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9008 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep2 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep1 BJ cel pA- + 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep1 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep2 AG50 cel pA+ + 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8966 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep2 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep1 AG50 cel pA+ + 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep1 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep2 AG50 cel pA- + 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9002 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep2 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep1 AG50 cel pA- + 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep1 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep4 SKNSH nuc pA+ + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46597 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep3 SKNSH nuc pA+ + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep4 SKNSH cyt pA+ + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46595 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep3 SKNSH cyt pA+ + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapPlusRep4 SKNSH cel pA+ + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46599 cell 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapPlusRep3 SKNSH cel pA+ + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598 cell 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep2 CD14 cel pA+ + 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44497 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep2 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep1 CD14 cel pA+ + 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep1 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep2 CD14 cel pA- + 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44658 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep2 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep1 CD14 cel pA- + 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep1 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep4 MCF7 nuc pA+ + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46860 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep3 MCF7 nuc pA+ + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep4 MCF7 cyt pA+ + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46858 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep3 MCF7 cyt pA+ + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep2 MCF7 cel pA+ + 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8687 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep2 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep1 MCF7 cel pA+ + 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep1 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep2 MCF7 cel pA- + 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8825 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep2 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep1 MCF7 cel pA- + 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep1 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep2 IMR90 nuc pA+ + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635 nucleus 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep1 IMR90 nuc pA+ + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45613 nucleus 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep2 IMR90 cyt pA+ + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45612 cytosol 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep1 IMR90 cyt pA+ + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611 cytosol 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep2 IMR90 cel tot + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45239 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep1 IMR90 cel tot + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapPlusRep2 IMR90 cel pA+ + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45017 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapPlusRep1 IMR90 cel pA+ + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep4 HUVEC nuc pA+ + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8691 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep3 HUVEC nuc pA+ + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep4 HUVEC nuc pA- + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9207 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep3 HUVEC nuc pA- + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep4 HUVEC cyt pA+ + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8689 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep3 HUVEC cyt pA+ + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaPlusRawSigRep3 HUVEC cyt pA- + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep2 HUVEC cel pA+ + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8464 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep2 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep1 HUVEC cel pA+ + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep1 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep2 HUVEC cel pA- + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8789 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep2 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep1 HUVEC cel pA- + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep1 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep2 HeG2 nuc pA+ + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8535 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep1 HeG2 nuc pA+ + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep2 HeG2 nuc pA- + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9203 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep1 HeG2 nuc pA- + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep2 HeG2 cyt pA+ + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8472 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep1 HeG2 cyt pA+ + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep2 HeG2 cyt pA- + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18553 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep1 HeG2 cyt pA- + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep2 HeG2 cel pA+ + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16636 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep1 HeG2 cel pA+ + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep2 HeG2 cel pA- + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8793 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep1 HeG2 cel pA- + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep2 HeS3 nuc pA+ + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8560 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep1 HeS3 nuc pA+ + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep2 HeS3 nuc pA- + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9201 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep1 HeS3 nuc pA- + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep2 HeS3 cyt pA+ + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8470 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep1 HeS3 cyt pA+ + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaPlusRawSigRep2 HeS3 cyt pA- + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep2 HeS3 cel pA+ + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16634 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep1 HeS3 cel pA+ + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep2 HeS3 cel pA- + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8791 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep1 HeS3 cel pA- + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapPlusRep2 CD20 cel pA+ + 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44499 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapPlusRep2 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapPlusRep1 CD20 cel pA+ + 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapPlusRep1 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamPlusRep2 CD20 cel pA- + 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamPlusRep2 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamPlusRep1 CD20 cel pA- + 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamPlusRep1 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep4 A549 nuc pA+ + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45900 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep3 A549 nuc pA+ + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep4 A549 cyt pA+ + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45898 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep3 A549 cyt pA+ + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep2 A549 cel pA+ + 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8964 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep2 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep1 A549 cel pA+ + 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep1 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2 A549 cel pA- + 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9006 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1 A549 cel pA- + 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep2 K562 nuc pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8557 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep1 K562 nuc pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep2 K562 nuc pA- + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9196 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep1 K562 nuc pA- + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep4 K562 ncpm tot + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9190 nucleoplasm 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleoplasm total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep3 K562 ncpm tot + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189 nucleoplasm 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep3 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleoplasm total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleolusTotalPlusRawSigRep4 K562 nlus tot + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000181 181 GSM765393 Gingeras CSHL LID9188 nucleolus 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleolusTotalPlusRawSigRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleolus total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep2 K562 cyt pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8466 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep1 K562 cyt pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2009-07-06 2010-04-06 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep2 K562 cyt pA- + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18546 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep1 K562 cyt pA- + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep4 K562 chrm tot + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9186 chromatin 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 chromatin total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep3 K562 chrm tot + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185 chromatin 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep3 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 chromatin total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep2 K562 cel pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16628 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep1 K562 cel pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep2 K562 cel pA- + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep1 K562 cel pA- + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapPlusRawSigRep2 H1hSC nuc pA+ + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaPlusRawSigRep2 H1hSC nuc pA- + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapPlusRawSigRep2 H1hSC cyt pA+ + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaPlusRawSigRep2 H1hSC cyt pA- + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep2 H1hSC cel pA+ + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8462 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep1 H1hSC cel pA+ + 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep1 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep2 H1hSC cel pA- + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8664 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep1 H1hSC cel pA- + 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep1 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep2 GM78 nuc pA+ + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8533 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep1 GM78 nuc pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep2 GM78 nuc pA- + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9198 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep1 GM78 nuc pA- + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep4 GM78 nlus tot + 4 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-28 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47964 nucleolus 2x101D 4 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep4 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 nucleolus total RNA-seq Plus signal Rep 4 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep3 GM78 nlus tot + 3 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963 nucleolus 2x101D 3 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep3 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 nucleolus total RNA-seq Plus signal Rep 3 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep2 GM78 cyt pA+ + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8468 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep1 GM78 cyt pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep2 GM78 cyt pA- + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18548 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep1 GM78 cyt pA- + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep2 GM78 cel pA+ + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16630 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep1 GM78 cel pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep2 GM78 cel pA- + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8662 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep1 GM78 cel pA- + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewMinusSig Minus Signal Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep2 SKRA cel pA+ - 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8968 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep2 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep1 SKRA cel pA+ - 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep1 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep2 SKRA cel pA- - 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9011 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep2 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep1 SKRA cel pA- - 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep1 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc812190217CellTotalMinusRep2 SkMC cel tot - 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47246 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc812190217CellTotalMinusRep2 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc9011302CellTotalMinusRep1 SkMC cel tot - 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc9011302CellTotalMinusRep1 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep2 NHLF cel pA+ - 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8701 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep2 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep1 NHLF cel pA+ - 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep1 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep2 NHLF cel pA- - 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8829 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep2 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep1 NHLF cel pA- - 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep1 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm270110012CellTotalMinusRep2 NHMM2 cel tot - 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47259 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm270110012CellTotalMinusRep2 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM M2 whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm27012303CellTotalMinusRep1 NHMM2 cel tot - 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm27012303CellTotalMinusRep1 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM M2 whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalMinusRep2 NHMf cel tot - 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47257 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalMinusRep2 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f M2 whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalMinusRep1 NHMf cel tot - 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalMinusRep1 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f M2 whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep4 NHEK nuc pA+ - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8798 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep3 NHEK nuc pA+ - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep4 NHEK nuc pA- - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9205 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep3 NHEK nuc pA- - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep4 NHEK cyt pA+ - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8796 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep3 NHEK cyt pA+ - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaMinusRawSigRep3 NHEK cyt pA- - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep2 NHEK cel pA+ - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16632 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep2 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep1 NHEK cel pA+ - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16631 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep1 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep2 NHEK cel pA- - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8666 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep2 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep1 NHEK cel pA- - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8665 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep1 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf00608013CellTotalMinusRep2 NHDF cel tot - 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47248 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf00608013CellTotalMinusRep2 MinusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf70717012CellTotalMinusRep1 NHDF cel tot - 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf70717012CellTotalMinusRep1 MinusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp0092205CellTotalMinusRep2 HWP cel tot - 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47255 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp0092205CellTotalMinusRep2 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp81202015CellTotalMinusRep1 HWP cel tot - 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp81202015CellTotalMinusRep1 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf61004013CellTotalMinusRep2 HVMF cel tot - 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47250 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf61004013CellTotalMinusRep2 MinusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf60912033CellTotalMinusRep1 HVMF cel tot - 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf60912033CellTotalMinusRep1 MinusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep2 HSMM cel pA+ - 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8711 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep2 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep1 HSMM cel pA+ - 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep1 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep2 HSMM cel pA- - 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8827 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep2 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep1 HSMM cel pA- - 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep1 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep2 HSVEC cel tot - 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep2 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep1 HSVEC cel tot - 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47260 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep1 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep2 HPIEC cel tot - 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47253 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep2 MinusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep1 HPIEC cel tot - 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep1 MinusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep2 HPCPL cel tot - 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47104 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep2 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep1 HPCPL cel tot - 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep1 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob00902021CellTotalMinusRep2 HOB cel tot - 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47252 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob00902021CellTotalMinusRep2 MinusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob0091301CellTotalMinusRep1 HOB cel tot - 1 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob0091301CellTotalMinusRep1 MinusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalMinusRep2 hMSUC cel tot - 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47300 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalMinusRep1 hMSUC cel tot - 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalMinusRep2 hMSBM cel tot - 2 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47100 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalMinusRep1 hMSBM cel tot - 1 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat906160112CellTotalMinusRep2 hMSAT cel tot - 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47098 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat906160112CellTotalMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat010260412CellTotalMinusRep1 hMSAT cel tot - 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat010260412CellTotalMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalMinusSignalRep1V2 hMNPB cel tot - 1 hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalMinusSignalRep1V2 MinusSignal Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMNC-PB whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalMinusRep1 HMEpC cel tot - 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalMinusRep1 MinusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HMEpC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapMinusRawSigRep1 HMEC cel pA+ - 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapMinusRawSigRep1 MinusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HMEC whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaMinusRawSigRep1 HMEC cel pA- - 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaMinusRawSigRep1 MinusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HMEC whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalMinusRep2 HFDPC cel tot - 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47095 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalMinusRep2 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalMinusRep1 HFDPC cel tot - 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalMinusRep1 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch81008082CellTotalMinusRep2 HCH cel tot - 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47025 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch81008082CellTotalMinusRep2 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch00113082pCellTotalMinusRep1 HCH cel tot - 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch00113082pCellTotalMinusRep1 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalMinusRep2 HAoEC cel tot - 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47023 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalMinusRep2 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoec70717061CellTotalMinusRep1 HAoEC cel tot - 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoec70717061CellTotalMinusRep1 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalMinusRep2 HAoAF cel tot - 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalMinusRep2 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalMinusSignalRep1 HAoAF cel tot - 1 HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47020 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalMinusSignalRep1 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalMinusRep1 CD34 cel tot - 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalMinusRep1 MinusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand CD34+ Mobilized whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep2 BJ cel pA+ - 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8970 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep2 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep1 BJ cel pA+ - 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep1 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep2 BJ cel pA- - 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9008 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep2 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep1 BJ cel pA- - 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep1 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep2 AG50 cel pA+ - 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8966 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep2 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep1 AG50 cel pA+ - 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep1 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep2 AG50 cel pA- - 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9002 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep2 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep1 AG50 cel pA- - 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep1 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep4 SKNSH nuc pA+ - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46597 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep3 SKNSH nuc pA+ - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep4 SKNSH cyt pA+ - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46595 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep3 SKNSH cyt pA+ - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapMinusRep4 SKNSH cel pA+ - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46599 cell 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapMinusRep3 SKNSH cel pA+ - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598 cell 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep2 CD14 cel pA+ - 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44497 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep2 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep1 CD14 cel pA+ - 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep1 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep2 CD14 cel pA- - 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44658 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep2 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep1 CD14 cel pA- - 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep1 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep4 MCF7 nuc pA+ - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46860 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep3 MCF7 nuc pA+ - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep4 MCF7 cyt pA+ - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46858 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep3 MCF7 cyt pA+ - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep2 MCF7 cel pA+ - 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8687 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep2 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep1 MCF7 cel pA+ - 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep1 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep2 MCF7 cel pA- - 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8825 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep2 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep1 MCF7 cel pA- - 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep1 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep2 IMR90 nuc pA+ - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635 nucleus 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep1 IMR90 nuc pA+ - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45613 nucleus 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep2 IMR90 cyt pA+ - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45612 cytosol 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep1 IMR90 cyt pA+ - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611 cytosol 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep2 IMR90 cel tot - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45239 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep1 IMR90 cel tot - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapMinusRep2 IMR90 cel pA+ - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45017 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapMinusRep1 IMR90 cel pA+ - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep4 HUVEC nuc pA+ - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8691 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep3 HUVEC nuc pA+ - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep4 HUVEC nuc pA- - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9207 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep3 HUVEC nuc pA- - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep4 HUVEC cyt pA+ - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8689 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep3 HUVEC cyt pA+ - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaMinusRawSigRep3 HUVEC cyt pA- - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep2 HUVEC cel pA+ - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8464 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep2 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep1 HUVEC cel pA+ - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep1 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep2 HUVEC cel pA- - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8789 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep2 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep1 HUVEC cel pA- - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep1 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep2 HeG2 nuc pA+ - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8535 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep1 HeG2 nuc pA+ - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep2 HeG2 nuc pA- - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9203 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep1 HeG2 nuc pA- - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep2 HeG2 cyt pA+ - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8472 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep1 HeG2 cyt pA+ - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep2 HeG2 cyt pA- - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18553 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep1 HeG2 cyt pA- - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep2 HeG2 cel pA+ - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16636 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep1 HeG2 cel pA+ - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep2 HeG2 cel pA- - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8793 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep1 HeG2 cel pA- - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep2 HeS3 nuc pA+ - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8560 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep1 HeS3 nuc pA+ - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep2 HeS3 nuc pA- - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9201 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep1 HeS3 nuc pA- - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep2 HeS3 cyt pA+ - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8470 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep1 HeS3 cyt pA+ - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaMinusRawSigRep2 HeS3 cyt pA- - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep2 HeS3 cel pA+ - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16634 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep1 HeS3 cel pA+ - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep2 HeS3 cel pA- - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8791 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep1 HeS3 cel pA- - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapMinusRep2 CD20 cel pA+ - 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44499 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapMinusRep2 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapMinusRep1 CD20 cel pA+ - 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapMinusRep1 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamMinusRep2 CD20 cel pA- - 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamMinusRep2 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamMinusRep1 CD20 cel pA- - 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamMinusRep1 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep4 A549 nuc pA+ - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45900 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep3 A549 nuc pA+ - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep4 A549 cyt pA+ - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45898 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep3 A549 cyt pA+ - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep2 A549 cel pA+ - 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8964 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep2 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep1 A549 cel pA+ - 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep1 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2 A549 cel pA- - 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9006 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1 A549 cel pA- - 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep2 K562 nuc pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8557 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep1 K562 nuc pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep2 K562 nuc pA- - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9196 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep1 K562 nuc pA- - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep4 K562 ncpm tot - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9190 nucleoplasm 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleoplasm total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep3 K562 ncpm tot - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189 nucleoplasm 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep3 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleoplasm total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleolusTotalMinusRawSigRep4 K562 nlus tot - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000181 181 GSM765393 Gingeras CSHL LID9188 nucleolus 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleolusTotalMinusRawSigRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleolus total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep2 K562 cyt pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8466 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep1 K562 cyt pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2009-07-06 2010-04-06 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep2 K562 cyt pA- - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18546 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep1 K562 cyt pA- - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep4 K562 chrm tot - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9186 chromatin 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 chromatin total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep3 K562 chrm tot - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185 chromatin 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep3 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 chromatin total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep2 K562 cel pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16628 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep1 K562 cel pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep2 K562 cel pA- - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep1 K562 cel pA- - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapMinusRawSigRep2 H1hSC nuc pA+ - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaMinusRawSigRep2 H1hSC nuc pA- - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapMinusRawSigRep2 H1hSC cyt pA+ - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaMinusRawSigRep2 H1hSC cyt pA- - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep2 H1hSC cel pA+ - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8462 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep1 H1hSC cel pA+ - 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep1 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep2 H1hSC cel pA- - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8664 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep1 H1hSC cel pA- - 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep1 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep2 GM78 nuc pA+ - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8533 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep1 GM78 nuc pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep2 GM78 nuc pA- - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9198 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep1 GM78 nuc pA- - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep4 GM78 nlus tot - 4 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-28 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47964 nucleolus 2x101D 4 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep4 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 nucleolus total RNA-seq Minus signal Rep 4 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep3 GM78 nlus tot - 3 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963 nucleolus 2x101D 3 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep3 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 nucleolus total RNA-seq Minus signal Rep 3 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep2 GM78 cyt pA+ - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8468 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep1 GM78 cyt pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep2 GM78 cyt pA- - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18548 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep1 GM78 cyt pA- - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep2 GM78 cel pA+ - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16630 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep1 GM78 cel pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep2 GM78 cel pA- - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8662 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep1 GM78 cel pA- - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewContigs Contigs Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapContigs SKRA cel pA+ C SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967,LID8968 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapContigs Contigs neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH RA whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPamContigs SKRA cel pA- C SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003,LID9011 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPamContigs Contigs neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH RA whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmcCellTotalContigs SkMC cel tot C SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245,LID47246 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmcCellTotalContigs Contigs Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SkMC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapContigs NHLF cel pA+ C NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692,LID8701 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapContigs Contigs lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHLF whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPamContigs NHLF cel pA- C NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828,LID8829 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPamContigs Contigs lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHLF whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm2CellTotalContigs NHMM2 cel tot C NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258,LID47259 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm2CellTotalContigs Contigs Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEM M2 whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm2CellTotalContigs NHMf cel tot C NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256,LID47257 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm2CellTotalContigs Contigs Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEM.f M2 whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapContigs NHEK nuc pA+ C NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797,LID8798 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPamContigs NHEK nuc pA- C NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204,LID9205 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPamContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapContigs NHEK cyt pA+ C NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795,LID8796 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPamContigsV2 NHEK cyt pA- C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPamContigsV2 Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapContigsV2 NHEK cel pA+ C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID8694 cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapContigsV2 Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPamContigsV2 NHEK cel pA- C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8830 cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPamContigsV2 Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdfCellTotalContigs NHDF cel tot C NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247,LID47248 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdfCellTotalContigs Contigs Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHDF whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwpCellTotalContigs HWP cel tot C HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254,LID47255 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwpCellTotalContigs Contigs Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HWP whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmfCellTotalContigs HVMF cel tot C HVMF RnaSeq ENCODE Jul 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249,LID47250 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmfCellTotalContigs Contigs villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HVMF whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapContigs HSMM cel pA+ C HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710,LID8711 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapContigs Contigs skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSMM whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPamContigs HSMM cel pA- C HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826,LID8827 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPamContigs Contigs skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSMM whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalContigs HSVEC cel tot C HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261,LID47260 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalContigs Contigs Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSaVEC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalContigs HPIEC cel tot C HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105,LID47253 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalContigs Contigs Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HPIEpC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalContigs HPCPL cel tot C HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301,LID47104 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalContigs Contigs Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HPC-PL whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHobCellTotalContigs HOB cel tot C HOB RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251,LID47252 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHobCellTotalContigs Contigs Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HOB whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscucCellTotalContigs hMSUC cel tot C hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299,LID47300 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscucCellTotalContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-UC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbmCellTotalContigs hMSBM cel tot C hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099,LID47100 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbmCellTotalContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-BM whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscatCellTotalContigs hMSAT cel tot C hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097,LID47098 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscatCellTotalContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-AT whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalContigsV2 hMNPB cel tot C hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-07-04 2013-04-04 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalContigsV2 Contigs Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMNC-PB whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalContigs HMEpC cel tot C HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalContigs Contigs Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEpC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapContigsV2 HMEC cel pA+ C HMEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapContigsV2 Contigs mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEC whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPamContigsV2 HMEC cel pA- C HMEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPamContigsV2 Contigs mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEC whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpcCellTotalContigs HFDPC cel tot C HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094,LID47095 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpcCellTotalContigs Contigs Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HFDPC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHchCellTotalContigs HCH cel tot C HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024,LID47025 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHchCellTotalContigs Contigs Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HCH whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalContigs HAoEC cel tot C HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022,LID47023 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalContigs Contigs Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HAoEC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalContigs HAoAF cel tot C HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021,LID47020 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalContigs Contigs Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HAoAF whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalContigs CD34 cel tot C CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalContigs Contigs hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD34+ Mobilized whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapContigs BJ cel pA+ C BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969,LID8970 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapContigs Contigs skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). BJ whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPamContigs BJ cel pA- C BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007,LID9008 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPamContigs Contigs skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). BJ whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapContigs AG50 cel pA+ C AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965,LID8966 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapContigs Contigs fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). AG04450 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPamContigs AG50 cel pA- C AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001,LID9002 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPamContigs Contigs fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). AG04450 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapContigs SKNSH nuc pA+ C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596,LID46597 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapContigs SKNSH cyt pA+ C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594,LID46595 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapContigs SKNSH cel pA+ C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598,LID46599 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapContigs CD14 cel pA+ C Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594,LID44497 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapContigs Contigs Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MonocytesCD14+ whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamContigs CD14 cel pA- C Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657,LID44658 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamContigs Contigs Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MonocytesCD14+ whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapContigs MCF7 nuc pA+ C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859,LID46860 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapContigs MCF7 cyt pA+ C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857,LID46858 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapContigs MCF7 cel pA+ C MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686,LID8687 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPamContigs MCF7 cel pA- C MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824,LID8825 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPamContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapContigs IMR90 nuc pA+ C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635,LID45613 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapContigs IMR90 cyt pA+ C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611,LID45612 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalContigs IMR90 cel tot C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238,LID45239 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapContigs IMR90 cel pA+ C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016,LID45017 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapContigs HUVEC nuc pA+ C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690,LID8691 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPamContigs HUVEC nuc pA- C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206,LID9207 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPamContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapContigs HUVEC cyt pA+ C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688,LID8689 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPamContigsV2 HUVEC cyt pA- C HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPamContigsV2 Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapContigs HUVEC cel pA+ C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463,LID8464 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPamContigs HUVEC cel pA- C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788,LID8789 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPamContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapContigs HeG2 nuc pA+ C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534,LID8535 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPamContigs HeG2 nuc pA- C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202,LID9203 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPamContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapContigs HeG2 cyt pA+ C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471,LID8472 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPamContigs HeG2 cyt pA- C HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552,LID18553 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPamContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapContigs HeG2 cel pA+ C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635,LID16636 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPamContigs HeG2 cel pA- C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792,LID8793 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPamContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapContigs HeS3 nuc pA+ C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559,LID8560 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPamContigs HeS3 nuc pA- C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200,LID9201 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPamContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapContigs HeS3 cyt pA+ C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469,LID8470 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPamContigsV2 HeS3 cyt pA- C HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPamContigsV2 Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapContigs HeS3 cel pA+ C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633,LID16634 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPamContigs HeS3 cel pA- C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790,LID8791 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPamContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapContigs CD20 cel pA+ C CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498,LID44499 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapContigs Contigs B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD20+ whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamContigs CD20 cel pA- C CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659,LID44660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamContigs Contigs B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD20+ whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapContigs A549 nuc pA+ C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899,LID45900 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapContigs A549 cyt pA+ C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897,LID45898 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapContigs A549 cel pA+ C A549 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963,LID8964 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPamContigs A549 cel pA- C A549 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005,LID9006 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPamContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapContigs K562 nuc pA+ C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556,LID8557 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPamContigs K562 nuc pA- C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195,LID9196 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPamContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalContigs K562 ncpm tot C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189,LID9190 iIDR nucleoplasm 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 nucleoplasm total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapContigs K562 cyt pA+ C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465,LID8466 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPamContigs K562 cyt pA- C K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545,LID18546 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPamContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalContigs K562 chrm tot C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185,LID9186 iIDR chromatin 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 chromatin total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapContigs K562 cel pA+ C K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627,LID16628 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPamContigs K562 cel pA- C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659,LID8660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPamContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapContigsV2 H1hSC nuc pA+ C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPamContigsV2 H1hSC nuc pA- C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPamContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapContigsV2 H1hSC cyt pA+ C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPamContigsV2 H1hSC cyt pA- C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPamContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapContigs H1hSC cel pA+ C H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461,LID8462 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapContigs Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPamContigs H1hSC cel pA- C H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663,LID8664 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPamContigs Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapContigs GM78 nuc pA+ C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532,LID8533 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPamContigs GM78 nuc pA- C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197,LID9198 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPamContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalContigs GM78 nlus tot C GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963,LID47964 iIDR nucleolus 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 nucleolus total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapContigs GM78 cyt pA+ C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467,LID8468 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPamContigs GM78 cyt pA- C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547,LID18548 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPamContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapContigs GM78 cel pA+ C GM12878 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629,LID16630 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPamContigs GM78 cel pA- C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661,LID8662 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPamContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewAlignments Alignments Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep2 SKRA cel pA+ A 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8968 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep2 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep1 SKRA cel pA+ A 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep1 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep2 SKRA cel pA- A 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9011 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep2 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep1 SKRA cel pA- A 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep1 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc812190217CellTotalAlnRep2 SkMC cel tot A 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002678 2678 Gingeras CSHL LID47246 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc812190217CellTotalAlnRep2 Alignments Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SkMC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc9011302CellTotalAlnRep1 SkMC cel tot A 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002678 2678 Gingeras CSHL LID47245 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc9011302CellTotalAlnRep1 Alignments Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SkMC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep2 NHLF cel pA+ A 2 NHLF RnaSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8701 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep2 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep1 NHLF cel pA+ A 1 NHLF RnaSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep1 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep2 NHLF cel pA- A 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8829 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep2 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep1 NHLF cel pA- A 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep1 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm270110012CellTotalAlnRep2 NHMM2 cel tot A 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 Gingeras CSHL LID47259 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm270110012CellTotalAlnRep2 Alignments Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM M2 whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm27012303CellTotalAlnRep1 NHMM2 cel tot A 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 Gingeras CSHL LID47258 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm27012303CellTotalAlnRep1 Alignments Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM M2 whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalAlnRep2 NHMf cel tot A 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 Gingeras CSHL LID47257 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalAlnRep2 Alignments Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM.f M2 whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalAlnRep1 NHMf cel tot A 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 Gingeras CSHL LID47256 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalAlnRep1 Alignments Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM.f M2 whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep4 NHEK nuc pA+ A 2 NHEK RnaSeq ENCODE Mar 2012 Freeze 2011-06-08 2012-03-08 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8798 nucleus 2x76D 4 longPolyA Illumina_GA2x U wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep4 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep3 NHEK nuc pA+ A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep4 NHEK nuc pA- A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9205 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep4 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep3 NHEK nuc pA- A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep4 NHEK cyt pA+ A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8796 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep4 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep3 NHEK cyt pA+ A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaAlnRep3 NHEK cyt pA- A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapAlnRep2 NHEK cel pA+ A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16632 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapAlnRep2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapAlnRep1 NHEK cel pA+ A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16631 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapAlnRep1 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep2 NHEK cel pA- A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8666 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep1 NHEK cel pA- A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8665 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep1 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf00608013CellTotalAlnRep2 NHDF cel tot A 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002677 2677 Gingeras CSHL LID47248 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf00608013CellTotalAlnRep2 Alignments Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHDF whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf70717012CellTotalAlnRep1 NHDF cel tot A 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002677 2677 Gingeras CSHL LID47247 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf70717012CellTotalAlnRep1 Alignments Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHDF whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp0092205CellTotalAlnRep2 HWP cel tot A 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002682 2682 Gingeras CSHL LID47255 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp0092205CellTotalAlnRep2 Alignments Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HWP whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp81202015CellTotalAlnRep1 HWP cel tot A 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002682 2682 Gingeras CSHL LID47254 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp81202015CellTotalAlnRep1 Alignments Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HWP whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf61004013CellTotalAlnRep2 HVMF cel tot A 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002681 2681 Gingeras CSHL LID47250 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf61004013CellTotalAlnRep2 Alignments villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HVMF whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf60912033CellTotalAlnRep1 HVMF cel tot A 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002681 2681 Gingeras CSHL LID47249 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf60912033CellTotalAlnRep1 Alignments villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HVMF whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep2 HSMM cel pA+ A 2 HSMM RnaSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8711 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep1 HSMM cel pA+ A 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep1 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep2 HSMM cel pA- A 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8827 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep1 HSMM cel pA- A 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep1 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep2 HSVEC cel tot A 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002676 2676 Gingeras CSHL LID47261 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep2 Alignments Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HSaVEC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep1 HSVEC cel tot A 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002676 2676 Gingeras CSHL LID47260 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep1 Alignments Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HSaVEC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep2 HPIEC cel tot A 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002685 2685 Gingeras CSHL LID47253 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep2 Alignments Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPIEpC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep1 HPIEC cel tot A 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002685 2685 Gingeras CSHL LID47105 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep1 Alignments Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPIEpC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep2 HPCPL cel tot A 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002667 2667 Gingeras CSHL LID47104 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep2 Alignments Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPC-PL whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep1 HPCPL cel tot A 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002667 2667 Gingeras CSHL LID47301 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep1 Alignments Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPC-PL whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob00902021CellTotalAlnRep2 HOB cel tot A 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002675 2675 Gingeras CSHL LID47252 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob00902021CellTotalAlnRep2 Alignments Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HOB whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob0091301CellTotalAlnRep1 HOB cel tot A 1 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002675 2675 Gingeras CSHL LID47251 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob0091301CellTotalAlnRep1 Alignments Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HOB whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalAlnRep2 hMSUC cel tot A 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002684 2684 Gingeras CSHL LID47300 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-UC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalAlnRep1 hMSUC cel tot A 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002684 2684 Gingeras CSHL LID47299 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-UC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalAlnRep2 hMSBM cel tot A 2 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002673 2673 Gingeras CSHL LID47100 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-BM whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalAlnRep1 hMSBM cel tot A 1 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002673 2673 Gingeras CSHL LID47099 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-BM whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat906160112CellTotalAlnRep2 hMSAT cel tot A 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002669 2669 Gingeras CSHL LID47098 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat906160112CellTotalAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-AT whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat010260412CellTotalAlnRep1 hMSAT cel tot A 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002669 2669 Gingeras CSHL LID47097 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat010260412CellTotalAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-AT whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalAlnRep1V2 hMNPB cel tot A 1 hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002878 2878 Gingeras CSHL LID47807 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalAlnRep1V2 Alignments Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMNC-PB whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalAlnRep1 HMEpC cel tot A 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002683 2683 Gingeras CSHL LID47096 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalAlnRep1 Alignments Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HMEpC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapAlnRep1 HMEC cel pA+ A 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapAlnRep1 Alignments mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HMEC whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaAlnRep1 HMEC cel pA- A 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaAlnRep1 Alignments mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HMEC whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalAlnRep2 HFDPC cel tot A 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002671 2671 Gingeras CSHL LID47095 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalAlnRep2 Alignments Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HFDPC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalAlnRep1 HFDPC cel tot A 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002671 2671 Gingeras CSHL LID47094 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalAlnRep1 Alignments Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HFDPC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch81008082CellTotalAlnRep2 HCH cel tot A 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 Gingeras CSHL LID47025 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch81008082CellTotalAlnRep2 Alignments Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HCH whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch00113082pCellTotalAlnRep1 HCH cel tot A 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 Gingeras CSHL LID47024 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch00113082pCellTotalAlnRep1 Alignments Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HCH whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalAlnRep2 HAoEC cel tot A 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002680 2680 Gingeras CSHL LID47023 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalAlnRep2 Alignments Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoEC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoec70717061CellTotalAlnRep1 HAoEC cel tot A 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002680 2680 Gingeras CSHL LID47022 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoec70717061CellTotalAlnRep1 Alignments Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoEC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalAlnRep2 HAoAF cel tot A 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002679 2679 Gingeras CSHL LID47021 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalAlnRep2 Alignments Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoAF whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalAlnRep1 HAoAF cel tot A 1 HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 Gingeras CSHL LID47020 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalAlnRep1 Alignments Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoAF whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalAlnRep1 CD34 cel tot A 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002670 2670 Gingeras CSHL LID45901 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalAlnRep1 Alignments hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch CD34+ Mobilized whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapAlnRep2 BJ cel pA+ A 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8970 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapAlnRep2 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapAlnRep1 BJ cel pA+ A 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapAlnRep1 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaAlnRep2 BJ cel pA- A 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9008 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaAlnRep2 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaAlnRep1 BJ cel pA- A 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaAlnRep1 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapAlnRep2 AG50 cel pA+ A 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8966 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapAlnRep2 Alignments fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapAlnRep1 AG50 cel pA+ A 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapAlnRep1 Alignments fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaAlnRep2 AG50 cel pA- A 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9002 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaAlnRep2 Alignments fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaAlnRep1 AG50 cel pA- A 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaAlnRep1 Alignments fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapAlnRep4 SKNSH nuc pA+ A 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002631 2631 Gingeras CSHL LID46597 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapAlnRep3 SKNSH nuc pA+ A 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002631 2631 Gingeras CSHL LID46596 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapAlnRep4 SKNSH cyt pA+ A 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 Gingeras CSHL LID46595 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapAlnRep3 SKNSH cyt pA+ A 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 Gingeras CSHL LID46594 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapAlnRep4 SKNSH cel pA+ A 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002632 2632 Gingeras CSHL LID46599 cell 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapAlnRep3 SKNSH cel pA+ A 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002632 2632 Gingeras CSHL LID46598 cell 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapAlnRep2 CD14 cel pA+ A 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 Gingeras CSHL LID44497 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapAlnRep2 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MonocytesCD14+ whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapAlnRep1 CD14 cel pA+ A 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 Gingeras CSHL LID44594 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapAlnRep1 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MonocytesCD14+ whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep2 CD14 cel pA- A 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002668 2668 Gingeras CSHL LID44658 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep2 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MonocytesCD14+ whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep1 CD14 cel pA- A 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002668 2668 Gingeras CSHL LID44657 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep1 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MonocytesCD14+ whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapAlnRep4 MCF7 nuc pA+ A 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002627 2627 Gingeras CSHL LID46860 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapAlnRep4 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapAlnRep3 MCF7 nuc pA+ A 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002627 2627 Gingeras CSHL LID46859 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapAlnRep3 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapAlnRep4 MCF7 cyt pA+ A 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-05-14 wgEncodeEH002633 2633 Gingeras CSHL LID46858 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapAlnRep4 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapAlnRep3 MCF7 cyt pA+ A 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002633 2633 Gingeras CSHL LID46857 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapAlnRep3 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapAlnRep2 MCF7 cel pA+ A 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8687 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapAlnRep2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapAlnRep1 MCF7 cel pA+ A 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapAlnRep1 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaAlnRep2 MCF7 cel pA- A 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8825 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaAlnRep2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaAlnRep1 MCF7 cel pA- A 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaAlnRep1 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapAlnRep2 IMR90 nuc pA+ A 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 Gingeras CSHL LID45635 nucleus 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapAlnRep1 IMR90 nuc pA+ A 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 Gingeras CSHL LID45613 nucleus 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapAlnRep2 IMR90 cyt pA+ A 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002626 2626 Gingeras CSHL LID45612 cytosol 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapAlnRep1 IMR90 cyt pA+ A 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002626 2626 Gingeras CSHL LID45611 cytosol 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalAlnRep2 IMR90 cel tot A 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002623 2623 Gingeras CSHL LID45239 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalAlnRep1 IMR90 cel tot A 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002623 2623 Gingeras CSHL LID45238 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapAlnRep2 IMR90 cel pA+ A 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 Gingeras CSHL LID45017 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapAlnRep1 IMR90 cel pA+ A 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 Gingeras CSHL LID45016 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapAlnRep4 HUVEC nuc pA+ A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8691 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapAlnRep4 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapAlnRep3 HUVEC nuc pA+ A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapAlnRep3 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaAlnRep4 HUVEC nuc pA- A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9207 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaAlnRep4 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaAlnRep3 HUVEC nuc pA- A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaAlnRep3 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapAlnRep4 HUVEC cyt pA+ A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8689 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapAlnRep4 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapAlnRep3 HUVEC cyt pA+ A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapAlnRep3 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaAlnRep3 HUVEC cyt pA- A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaAlnRep3 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapAlnRep2 HUVEC cel pA+ A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8464 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapAlnRep2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapAlnRep1 HUVEC cel pA+ A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapAlnRep1 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaAlnRep2 HUVEC cel pA- A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8789 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaAlnRep2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaAlnRep1 HUVEC cel pA- A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaAlnRep1 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapAlnRep2 HeG2 nuc pA+ A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8535 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapAlnRep1 HeG2 nuc pA+ A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaAlnRep2 HeG2 nuc pA- A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9203 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaAlnRep1 HeG2 nuc pA- A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapAlnRep2 HeG2 cyt pA+ A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8472 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapAlnRep1 HeG2 cyt pA+ A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaAlnRep2 HeG2 cyt pA- A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18553 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaAlnRep1 HeG2 cyt pA- A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapAlnRep2 HeG2 cel pA+ A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16636 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapAlnRep1 HeG2 cel pA+ A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaAlnRep2 HeG2 cel pA- A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8793 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaAlnRep1 HeG2 cel pA- A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapAlnRep2 HeS3 nuc pA+ A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8560 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapAlnRep1 HeS3 nuc pA+ A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaAlnRep2 HeS3 nuc pA- A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9201 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaAlnRep1 HeS3 nuc pA- A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapAlnRep2 HeS3 cyt pA+ A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8470 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapAlnRep1 HeS3 cyt pA+ A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaAlnRep2 HeS3 cyt pA- A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapAlnRep2 HeS3 cel pA+ A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16634 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapAlnRep1 HeS3 cel pA+ A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaAlnRep2 HeS3 cel pA- A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8791 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaAlnRep1 HeS3 cel pA- A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapAlnRep2 CD20 cel pA+ A 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002665 2665 Gingeras CSHL LID44499 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapAlnRep2 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapAlnRep1 CD20 cel pA+ A 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002665 2665 Gingeras CSHL LID44498 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapAlnRep1 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamAlnRep2 CD20 cel pA- A 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002666 2666 Gingeras CSHL LID44660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamAlnRep2 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamAlnRep1 CD20 cel pA- A 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002666 2666 Gingeras CSHL LID44659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamAlnRep1 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapAlnRep4 A549 nuc pA+ A 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002625 2625 Gingeras CSHL LID45900 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapAlnRep4 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapAlnRep3 A549 nuc pA+ A 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002625 2625 Gingeras CSHL LID45899 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapAlnRep3 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapAlnRep4 A549 cyt pA+ A 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002624 2624 Gingeras CSHL LID45898 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapAlnRep4 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapAlnRep3 A549 cyt pA+ A 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002624 2624 Gingeras CSHL LID45897 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapAlnRep3 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapAlnRep2 A549 cel pA+ A 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8964 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapAlnRep2 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapAlnRep1 A549 cel pA+ A 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapAlnRep1 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaAlnRep2 A549 cel pA- A 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9006 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaAlnRep2 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaAlnRep1 A549 cel pA- A 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaAlnRep1 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapAlnRep2 K562 nuc pA+ A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8557 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapAlnRep1 K562 nuc pA+ A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaAlnRep2 K562 nuc pA- A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9196 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaAlnRep1 K562 nuc pA- A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalAlnRep4 K562 ncpm tot A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9190 nucleoplasm 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalAlnRep4 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleoplasm total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalAlnRep3 K562 ncpm tot A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189 nucleoplasm 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalAlnRep3 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleoplasm total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleolusTotalAlnRep4 K562 nlus tot A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000181 181 GSM765393 Gingeras CSHL LID9188 nucleolus 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleolusTotalAlnRep4 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleolus total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapAlnRep2 K562 cyt pA+ A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000140 140 Gingeras CSHL LID8466 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapAlnRep1 K562 cyt pA+ A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2009-07-06 2010-04-06 wgEncodeEH000140 140 Gingeras CSHL LID8465 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaAlnRep2 K562 cyt pA- A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18546 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaAlnRep1 K562 cyt pA- A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalAlnRep4 K562 chrm tot A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9186 chromatin 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalAlnRep4 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 chromatin total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalAlnRep3 K562 chrm tot A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185 chromatin 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalAlnRep3 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 chromatin total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapAlnRep2 K562 cel pA+ A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16628 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapAlnRep1 K562 cel pA+ A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaAlnRep2 K562 cel pA- A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaAlnRep1 K562 cel pA- A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapAlnRep2 H1hSC nuc pA+ A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaAlnRep2 H1hSC nuc pA- A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapAlnRep2 H1hSC cyt pA+ A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaAlnRep2 H1hSC cyt pA- A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapAlnRep2 H1hSC cel pA+ A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8462 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapAlnRep1 H1hSC cel pA+ A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapAlnRep1 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaAlnRep2 H1hSC cel pA- A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8664 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaAlnRep1 H1hSC cel pA- A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaAlnRep1 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapAlnRep2 GM78 nuc pA+ A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8533 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapAlnRep1 GM78 nuc pA+ A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaAlnRep2 GM78 nuc pA- A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9198 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaAlnRep1 GM78 nuc pA- A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalAlnRep4 GM78 nlus tot A 4 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-28 2013-03-28 wgEncodeEH003034 3034 Gingeras CSHL LID47964 nucleolus 2x101D 4 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalAlnRep4 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleolus total RNA-seq Alignments Rep 4 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalAlnRep3 GM78 nlus tot A 3 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH003034 3034 Gingeras CSHL LID47963 nucleolus 2x101D 3 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalAlnRep3 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleolus total RNA-seq Alignments Rep 3 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapAlnRep2 GM78 cyt pA+ A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8468 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapAlnRep1 GM78 cyt pA+ A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaAlnRep2 GM78 cyt pA- A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18548 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaAlnRep1 GM78 cyt pA- A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapAlnRep2 GM78 cel pA+ A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16630 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapAlnRep1 GM78 cel pA+ A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaAlnRep2 GM78 cel pA- A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8662 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaAlnRep1 GM78 cel pA- A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeDukeAffyExon Duke Affy Exon GSE15805 Affymetrix Exon Array from ENCODE/Duke Expression Description This track displays human tissue microarray data using Affymetrix Human Exon 1.0 ST expression arrays. This RNA expression track was produced as part of the ENCODE Project. The RNA was extracted from cells that were also analyzed by DNaseI hypersensitivity (Duke DNaseI HS), FAIRE (UNC FAIRE), and ChIP (UTA TFBS). Display Conventions and Configuration In contrast to the hg18 annotation, this track now displays exon array data that has been aggregated to the gene level for those probes that have been linked to genes. Probes not linked to genes are not included. The display for this track shows gene probe location and signal value as grayscale-colored items where higher signal values correspond to darker-colored blocks. Items with scores between 900-1000 have signal values greater than 9 that have been linearly scaled for that particular cell type. Items scoring 400-900 have signal values between 4 and 9, and the signal is simply multiplied by 100 to get the score. Items with scores between 200-400 have signal values below 4 that have been linearly scaled to fit that score range. The subtracks within this composite annotation track correspond to data from different cell types and tissues. The configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For information regarding specific microarray probes, turn on the Affy Exon Probes track, which can be found in the Expression track group. See Methods for a description as to how probe level data was processed to produce gene level annotations. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Data from these tracks are stored as bed files whose first six fields follow the bed file standard. The three additional fields are as follows: signalValue: The normalized expression value for a gene, calculated as described below. exonCount: The number of exons used in the calculation of the expression value. constitutiveExons: The number of constitutive exons used in the calculation of the expression value. Methods Cells were grown according to the approved ENCODE cell culture protocols. Total RNA was isolated from these cells using trizol extraction followed by cleanup on RNEasy column (Qiagen) that included a DNaseI step. The RNA was checked for quality using a nanodrop and an Agilent Bioanalyzer. RNA (1 µg) deemed to be of good quality was then processed either by 1) the standard Affymetrix Whole transcript Sense Target labeling protocol that included a riboreduction step, or 2) the NuGEN labeling system. The fragmented biotin-labeled cDNA was hybridized over 16 h to Affymetrix Exon 1.0 ST arrays and scanned on an Affymetrix Scanner 3000 7G using AGCC software. Data from all replicates were then normalized together. Probesets flagged as cross-hybridizing were removed from the analysis (Salomonis et al. 2010). Though these arrays provide exon-level resolution, gene-level expression was estimated by grouping probesets by gene for normalization (Bemmo et al. 2008). Probesets were assigned to genes based on the GENCODE v10 annotation (July 2011). An exon was classified as constitutive or non-constitutive based on whether it was present in all protein-coding transcripts. For genes with at least 4 constitutive probes, only constitutive probesets were used to estimate gene expression. For all other genes, including all non-protein-coding genes, all (non-cross-hybridizing) probesets that mapped to an expressed exon in any transcript of the gene were used. Gene-level expression estimates were normalized using Affymetrix Power Tools (APT) (Lockstone 2011) with the chipstream command "rma-bg, med-norm, pm-gcbg, med-polish". This chipstream calls for an RMA normalization with gc-background correction using antigenomic background probes. While the data was generated using the same microarray platform, two different experimental backgrounds were present due to a change in labeling reagents (Affymetrix vs. NuGEN; see Methods above). It was found that batch effects related to this change were causing array data to group by experimental protocol rather than cell type relatedness. We used an R script (ComBat) to correct for this batch effect (Johnson et al. 2007). Verification When biological replicates were available, data were verified by analyzing replicates displaying a Pearson correlation coefficient > 0.9. Release Notes This is release 3 of this track (April 2012). Several new cell types have been added. The name of cell line Astrocy was changed to NH-A. Credits RNA was extracted from each cell type by Greg Crawford's group at Duke University. RNA was purified and hybridized to Affymetrix Exon arrays by Sridar Chittur and Scott Tenenbaum at the University of Albany-SUNY. Data analyses were primarily performed by Nathan Sheffield (Duke University) with assistance from Melissa Cline (UCSC), Zhancheng Zhang (UNC Chapel Hill), and Darin London (Duke University). Contact: Terry Furey References Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J. Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics. 2008 Nov 7;9:529. Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007 Jan;8(1):118-27. Lockstone HE. Exon array data analysis using Affymetrix power tools and R statistical software. Brief Bioinform. 2011 Nov;12(6):634-44. Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS et al. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10514-9. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeExonArraySuper ENC Exon Array ENCODE Exon Array Expression Description These tracks display microarray data. Samples are hybridized to the Affymetrix Human Exon 1.0 GeneChip. In contrast to traditional microarrays, which are designed to measure overall gene expression, the Affymetrix exon arrays contain separate probesets for each exon. This allows large-scale measurement of alternative splicing, alternative polyadenylation, and alternative promoter usage. Additionally, analysis of the constitutive exons (those included in all transcripts) offer accurate measurement of overall gene expression levels. Further information on the design and content of exon arrays can be found here. Display Conventions Items on these tracks pertain to Affymetrix exon array probesets. For information regarding specific microarray probesets, turn on the Affy Exon Array track, which can be found in the "Expression" track group. These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J. Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics. 2008 Nov 7;9:529. Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, Davies C, Williams A, Turpaz Y. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics. 2006 Dec 27;7:325. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeDukeAffyExonUrothelSimpleSignalRep2 Urothelia 2 Urothelia AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001076 1076 GSM993598 Crawford Duke 2.0 2 wgEncodeDukeAffyExonUrothelSimpleSignalRep2 None SimpleSignal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Urothelia Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUrothelSimpleSignalRep1V2 Urothelia 1 Urothelia AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001076 1076 GSM993597 Crawford Duke 2.0 1 wgEncodeDukeAffyExonUrothelSimpleSignalRep1V2 None SimpleSignal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Urothelia Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUrothelUt189SimpleSignalRep2 Uro UT189 2 Urothelia AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001077 1077 GSM993600 Crawford Duke 2.0 2 wgEncodeDukeAffyExonUrothelUt189SimpleSignalRep2 UT189 SimpleSignal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene Affymetrix Exon Microarray Crawford Crawford - Duke University UT189 E.Coli treatment 1 hour, followed by 24 hour incubation Simple Signal Urothelia UT189 E. coli Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUrothelUt189SimpleSignalRep1V2 Uro UT189 1 Urothelia AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001077 1077 GSM993599 Crawford Duke 2.0 1 wgEncodeDukeAffyExonUrothelUt189SimpleSignalRep1V2 UT189 SimpleSignal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene Affymetrix Exon Microarray Crawford Crawford - Duke University UT189 E.Coli treatment 1 hour, followed by 24 hour incubation Simple Signal Urothelia UT189 E. coli Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUch1SimpleSignalRep2 UCH-1 2 UCH-1 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002700 2700 GSM993603 Crawford Duke 2.0 2 wgEncodeDukeAffyExonUch1SimpleSignalRep2 None SimpleSignal chordoma cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal UCH-1 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUch1SimpleSignalRep1 UCH-1 1 UCH-1 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002700 2700 GSM993602 Crawford Duke 2.0 1 wgEncodeDukeAffyExonUch1SimpleSignalRep1 None SimpleSignal chordoma cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal UCH-1 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonStellateSimpleSignalRep2 Stellate 2 Stellate AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001075 1075 GSM993596 Crawford Duke 2.0 2 wgEncodeDukeAffyExonStellateSimpleSignalRep2 None SimpleSignal hepatic stellate cells, liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Stellate Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonStellateSimpleSignalRep1V2 Stellate 1 Stellate AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001075 1075 GSM993595 Crawford Duke 2.0 1 wgEncodeDukeAffyExonStellateSimpleSignalRep1V2 None SimpleSignal hepatic stellate cells, liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Stellate Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonProgfibSimpleSignalRep2V2 ProgFib 2 ProgFib AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000241 241 GSM993594 Crawford Duke 2.0 2 wgEncodeDukeAffyExonProgfibSimpleSignalRep2V2 None SimpleSignal fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal ProgFib Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonProgfibSimpleSignalRep1V2 ProgFib 1 ProgFib AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000241 241 GSM993593 Crawford Duke 2.0 1 wgEncodeDukeAffyExonProgfibSimpleSignalRep1V2 None SimpleSignal fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal ProgFib Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonOsteoSimpleSignalRep3V2 Osteobl 3 Osteobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000240 240 GSM993592 Crawford Duke 2.0 3 wgEncodeDukeAffyExonOsteoSimpleSignalRep3V2 None SimpleSignal osteoblasts (NHOst) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Osteobl Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonOsteoSimpleSignalRep2V2 Osteobl 2 Osteobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000240 240 GSM993591 Crawford Duke 2.0 2 wgEncodeDukeAffyExonOsteoSimpleSignalRep2V2 None SimpleSignal osteoblasts (NHOst) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Osteobl Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonOsteoSimpleSignalRep1V2 Osteobl 1 Osteobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000240 240 GSM993590 Crawford Duke 2.0 1 wgEncodeDukeAffyExonOsteoSimpleSignalRep1V2 None SimpleSignal osteoblasts (NHOst) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Osteobl Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonNhekSimpleSignalRep2V2 NHEK 2 NHEK AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000239 239 GSM993589 Crawford Duke 2.0 2 F wgEncodeDukeAffyExonNhekSimpleSignalRep2V2 None SimpleSignal epidermal keratinocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Female Simple Signal NHEK Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonNhekSimpleSignalRep1V2 NHEK 1 NHEK AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000239 239 GSM993588 Crawford Duke 2.0 1 F wgEncodeDukeAffyExonNhekSimpleSignalRep1V2 None SimpleSignal epidermal keratinocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Female Simple Signal NHEK Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonNhaSimpleSignalRep2V2 NH-A 2 NH-A AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000214 214 GSM993460 Crawford Duke 2.0 2 wgEncodeDukeAffyExonNhaSimpleSignalRep2V2 None SimpleSignal astrocytes (also called Astrocy) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal NH-A Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonNhaSimpleSignalRep1V2 NH-A 1 NH-A AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000214 214 GSM993459 Crawford Duke 2.0 1 wgEncodeDukeAffyExonNhaSimpleSignalRep1V2 None SimpleSignal astrocytes (also called Astrocy) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal NH-A Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMyometrSimpleSignalRep2V2 Myometr 2 Myometr AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001074 1074 GSM993587 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMyometrSimpleSignalRep2V2 None SimpleSignal myometrial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Myometr Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMyometrSimpleSignalRep1V2 Myometr 1 Myometr AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001074 1074 GSM993586 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMyometrSimpleSignalRep1V2 None SimpleSignal myometrial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Myometr Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMelanoSimpleSignalRep4V2 Melano 4 Melano AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001073 1073 GSM993585 Crawford Duke 2.0 4 wgEncodeDukeAffyExonMelanoSimpleSignalRep4V2 None SimpleSignal epidermal melanocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Melano Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMelanoSimpleSignalRep3V2 Melano 3 Melano AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001073 1073 GSM993584 Crawford Duke 2.0 3 wgEncodeDukeAffyExonMelanoSimpleSignalRep3V2 None SimpleSignal epidermal melanocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Melano Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMelanoSimpleSignalRep2V2 Melano 2 Melano AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001073 1073 GSM993583 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMelanoSimpleSignalRep2V2 None SimpleSignal epidermal melanocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Melano Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMelanoSimpleSignalRep1V2 Melano 1 Melano AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001073 1073 GSM993582 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMelanoSimpleSignalRep1V2 None SimpleSignal epidermal melanocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Melano Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMel2183SimpleSignalRep2 Mel_2183 2 Mel_2183 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002699 2699 GSM993581 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMel2183SimpleSignalRep2 None SimpleSignal Melanoma Cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Mel 2183 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMel2183SimpleSignalRep1 Mel_2183 1 Mel_2183 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002699 2699 GSM993580 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMel2183SimpleSignalRep1 None SimpleSignal Melanoma Cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Mel 2183 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMedulloSimpleSignalRep3V2 Medullo 3 Medullo AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000238 238 GSM993579 Crawford Duke 2.0 3 wgEncodeDukeAffyExonMedulloSimpleSignalRep3V2 None SimpleSignal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Medullo Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMedulloSimpleSignalRep2V2 Medullo 2 Medullo AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000238 238 GSM993578 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMedulloSimpleSignalRep2V2 None SimpleSignal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Medullo Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMedulloSimpleSignalRep1V2 Medullo 1 Medullo AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000238 238 GSM993577 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMedulloSimpleSignalRep1V2 None SimpleSignal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Medullo Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonLncapSimpleSignalRep2V2 LNCaP 2 LNCaP AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000233 233 GSM993565 Crawford Duke 2.0 2 wgEncodeDukeAffyExonLncapSimpleSignalRep2V2 None SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal LNCaP Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonLncapSimpleSignalRep1V2 LNCaP 1 LNCaP AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000233 233 GSM993564 Crawford Duke 2.0 1 wgEncodeDukeAffyExonLncapSimpleSignalRep1V2 None SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal LNCaP Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonLncapAndroSimpleSignalRep2V2 LNCaP ANDRO 2 LNCaP AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000234 234 GSM993563 Crawford Duke 2.0 2 wgEncodeDukeAffyExonLncapAndroSimpleSignalRep2V2 androgen SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Crawford Crawford - Duke University 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Simple Signal LNCaP Methyltrienolone Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonLncapAndroSimpleSignalRep1V2 LNCaP ANDRO 1 LNCaP AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000234 234 GSM993562 Crawford Duke 2.0 1 wgEncodeDukeAffyExonLncapAndroSimpleSignalRep1V2 androgen SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Crawford Crawford - Duke University 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Simple Signal LNCaP Methyltrienolone Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpsnihi7SimpleSignalRep2 iPS_NIHi7 2 iPS_NIHi7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002703 2703 GSM993550 Crawford Duke 2.0 2 wgEncodeDukeAffyExonIpsnihi7SimpleSignalRep2 None SimpleSignal iPS cells derived from AG08395 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (NIHi7) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpsnihi7SimpleSignalRep1 iPS_NIHi7 1 iPS_NIHi7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002703 2703 GSM993549 Crawford Duke 2.0 1 wgEncodeDukeAffyExonIpsnihi7SimpleSignalRep1 None SimpleSignal iPS cells derived from AG08395 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (NIHi7) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpsnihi11SimpleSignalRep2 iPS_NIHi11 2 iPS_NIHi11 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002702 2702 GSM993548 Crawford Duke 2.0 2 wgEncodeDukeAffyExonIpsnihi11SimpleSignalRep2 None SimpleSignal iPS cells derived from AG20443 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (NIHi11) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpsnihi11SimpleSignalRep1 iPS_NIHi11 1 iPS_NIHi11 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002702 2702 GSM993547 Crawford Duke 2.0 1 wgEncodeDukeAffyExonIpsnihi11SimpleSignalRep1 None SimpleSignal iPS cells derived from AG20443 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (NIHi11) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpscwru1SimpleSignalRep2 iPS_CWRU1 2 iPS_CWRU1 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002701 2701 GSM993546 Crawford Duke 2.0 2 wgEncodeDukeAffyExonIpscwru1SimpleSignalRep2 None SimpleSignal iPS cells derived from MSC658 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (CWRU1) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpscwru1SimpleSignalRep1 iPS_CWRU1 1 iPS_CWRU1 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002701 2701 GSM993545 Crawford Duke 2.0 1 wgEncodeDukeAffyExonIpscwru1SimpleSignalRep1 None SimpleSignal iPS cells derived from MSC658 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (CWRU1) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuh75SimpleSignalRep2 Huh-7.5 2 Huh-7.5 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001071 1071 GSM993542 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHuh75SimpleSignalRep2 None SimpleSignal hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Huh-7.5 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuh75SimpleSignalRep1V2 Huh-7.5 1 Huh-7.5 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001071 1071 GSM993541 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHuh75SimpleSignalRep1V2 None SimpleSignal hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Huh-7.5 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuh7SimpleSignalRep2 Huh-7 2 Huh-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001070 1070 GSM993540 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHuh7SimpleSignalRep2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Huh-7 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuh7SimpleSignalRep1V2 Huh-7 1 Huh-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001070 1070 GSM993539 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHuh7SimpleSignalRep1V2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Huh-7 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHtr8SimpleSignalRep2V2 HTR8svn 2 HTR8svn AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001068 1068 GSM993538 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHtr8SimpleSignalRep2V2 None SimpleSignal trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HTR8svn Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHtr8SimpleSignalRep1V2 HTR8svn 1 HTR8svn AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001068 1068 GSM993537 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHtr8SimpleSignalRep1V2 None SimpleSignal trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HTR8svn Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep3 HSMMtube_FSHD 3 HSMMtube_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002694 2694 GSM993536 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep3 None SimpleSignal myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube_FSHD Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep2 HSMMtube_FSHD 2 HSMMtube_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002694 2694 GSM993535 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep2 None SimpleSignal myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube_FSHD Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep1 HSMMtube_FSHD 1 HSMMtube_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002694 2694 GSM993534 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep1 None SimpleSignal myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube_FSHD Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtSimpleSignalRep3V2 HSMMtube 3 HSMMtube AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001067 1067 GSM993533 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHsmmtSimpleSignalRep3V2 None SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtSimpleSignalRep2V2 HSMMtube 2 HSMMtube AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001067 1067 GSM993532 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHsmmtSimpleSignalRep2V2 None SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtSimpleSignalRep1V2 HSMMtube 1 HSMMtube AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001067 1067 GSM993531 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHsmmtSimpleSignalRep1V2 None SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep3 HSMM_FSHD 3 HSMM_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002693 2693 GSM993530 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep3 None SimpleSignal primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM_FSHD Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep2 HSMM_FSHD 2 HSMM_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002693 2693 GSM993529 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep2 None SimpleSignal primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM_FSHD Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep1 HSMM_FSHD 1 HSMM_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002693 2693 GSM993528 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep1 None SimpleSignal primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM_FSHD Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmSimpleSignalRep3V2 HSMM 3 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001066 1066 GSM993527 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHsmmSimpleSignalRep3V2 None SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmSimpleSignalRep2V2 HSMM 2 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001066 1066 GSM993526 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHsmmSimpleSignalRep2V2 None SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmSimpleSignalRep1V2 HSMM 1 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001066 1066 GSM993525 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHsmmSimpleSignalRep1V2 None SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHpde6e6e7SimpleSignalRep2V2 HPDE6-E6E7 2 HPDE6-E6E7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001065 1065 GSM993524 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHpde6e6e7SimpleSignalRep2V2 None SimpleSignal pancreatic duct cells immortalized with E6E7 gene of HPV Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HPDE6-E6E7 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHpde6e6e7SimpleSignalRep1V2 HPDE6-E6E7 1 HPDE6-E6E7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001065 1065 GSM993523 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHpde6e6e7SimpleSignalRep1V2 None SimpleSignal pancreatic duct cells immortalized with E6E7 gene of HPV Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HPDE6-E6E7 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHmecSimpleSignalRep2V2 HMEC 2 HMEC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000225 225 GSM993522 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHmecSimpleSignalRep2V2 None SimpleSignal mammary epithelial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HMEC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHmecSimpleSignalRep1V2 HMEC 1 HMEC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000225 225 GSM993521 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHmecSimpleSignalRep1V2 None SimpleSignal mammary epithelial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HMEC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepatoSimpleSignalRep2V2 Hepatocytes 2 Hepatocytes AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001069 1069 GSM993517 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHepatoSimpleSignalRep2V2 None SimpleSignal primary hepatocytes, liver perfused by enzymes to generate single cell suspension Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Hepatocytes Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepatoSimpleSignalRep1V2 Hepatocytes 1 Hepatocytes AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001069 1069 GSM993516 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHepatoSimpleSignalRep1V2 None SimpleSignal primary hepatocytes, liver perfused by enzymes to generate single cell suspension Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Hepatocytes Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHek293tSimpleSignalRep2 HEK293T 2 HEK293T AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002692 2692 GSM993508 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHek293tSimpleSignalRep2 None SimpleSignal embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HEK293T Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHek293tSimpleSignalRep1 HEK293T 1 HEK293T AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002692 2692 GSM993507 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHek293tSimpleSignalRep1 None SimpleSignal embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HEK293T Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH9esSimpleSignalRep3 H9ES 3 H9ES AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001064 1064 GSM993506 Crawford Duke 2.0 3 wgEncodeDukeAffyExonH9esSimpleSignalRep3 None SimpleSignal embryonic stem cell (hESC) H9 Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H9ES Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH9esSimpleSignalRep2 H9ES 2 H9ES AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001064 1064 GSM993505 Crawford Duke 2.0 2 wgEncodeDukeAffyExonH9esSimpleSignalRep2 None SimpleSignal embryonic stem cell (hESC) H9 Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H9ES Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH9esSimpleSignalRep1V2 H9ES 1 H9ES AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001064 1064 GSM993504 Crawford Duke 2.0 1 wgEncodeDukeAffyExonH9esSimpleSignalRep1V2 None SimpleSignal embryonic stem cell (hESC) H9 Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H9ES Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH7esSimpleSignalRep3 H7-hESC 3 H7-hESC AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002691 2691 GSM993503 Crawford Duke 2.0 3 wgEncodeDukeAffyExonH7esSimpleSignalRep3 None SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H7-hESC Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH7esSimpleSignalRep2 H7-hESC 2 H7-hESC AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002691 2691 GSM993502 Crawford Duke 2.0 2 wgEncodeDukeAffyExonH7esSimpleSignalRep2 None SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H7-hESC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH7esSimpleSignalRep1 H7-hESC 1 H7-hESC AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002691 2691 GSM993501 Crawford Duke 2.0 1 wgEncodeDukeAffyExonH7esSimpleSignalRep1 None SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H7-hESC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19240SimpleSignalRep2V2 GM19240 2 GM19240 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000223 223 GSM993496 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm19240SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19240 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19240SimpleSignalRep1V2 GM19240 1 GM19240 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000223 223 GSM993495 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm19240SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19240 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19239SimpleSignalRep2V2 GM19239 2 GM19239 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000222 222 GSM993494 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm19239SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19239 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19239SimpleSignalRep1V2 GM19239 1 GM19239 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000222 222 GSM993493 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm19239SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19239 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19238SimpleSignalRep2V2 GM19238 2 GM19238 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000221 221 GSM993492 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm19238SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19238 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19238SimpleSignalRep1V2 GM19238 1 GM19238 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000221 221 GSM993491 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm19238SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19238 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm18507SimpleSignalRep3V2 GM18507 3 GM18507 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000220 220 GSM993490 Crawford Duke 2.0 3 wgEncodeDukeAffyExonGm18507SimpleSignalRep3V2 None SimpleSignal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM18507 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm18507SimpleSignalRep2V2 GM18507 2 GM18507 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000220 220 GSM993489 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm18507SimpleSignalRep2V2 None SimpleSignal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM18507 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm18507SimpleSignalRep1V2 GM18507 1 GM18507 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000220 220 GSM993488 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm18507SimpleSignalRep1V2 None SimpleSignal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM18507 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12892SimpleSignalRep2V2 GM12892 2 GM12892 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000219 219 GSM993487 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm12892SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12892 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12892SimpleSignalRep1V2 GM12892 1 GM12892 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000219 219 GSM993486 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm12892SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12892 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12891SimpleSignalRep2V2 GM12891 2 GM12891 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000218 218 GSM993485 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm12891SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12891 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12891SimpleSignalRep1V2 GM12891 1 GM12891 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000218 218 GSM993484 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm12891SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12891 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGlioblaSimpleSignalRep4V2 Gliobla 4 Gliobla AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000224 224 GSM993480 Crawford Duke 2.0 4 wgEncodeDukeAffyExonGlioblaSimpleSignalRep4V2 None SimpleSignal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Gliobla Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGlioblaSimpleSignalRep3V2 Gliobla 3 Gliobla AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000224 224 GSM993479 Crawford Duke 2.0 3 wgEncodeDukeAffyExonGlioblaSimpleSignalRep3V2 None SimpleSignal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Gliobla Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGlioblaSimpleSignalRep2V2 Gliobla 2 Gliobla AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000224 224 GSM993478 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGlioblaSimpleSignalRep2V2 None SimpleSignal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Gliobla Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGlioblaSimpleSignalRep1V2 Gliobla 1 Gliobla AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000224 224 GSM993477 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGlioblaSimpleSignalRep1V2 None SimpleSignal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Gliobla Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag20443SimpleSignalRep3 FibroP_AG20443 3 FibroP_AG20443 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002706 2706 GSM993476 Crawford Duke 2.0 3 wgEncodeDukeAffyExonFibropag20443SimpleSignalRep3 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG20443) Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag20443SimpleSignalRep2 FibroP_AG20443 2 FibroP_AG20443 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002706 2706 GSM993475 Crawford Duke 2.0 2 wgEncodeDukeAffyExonFibropag20443SimpleSignalRep2 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG20443) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag20443SimpleSignalRep1 FibroP_AG20443 1 FibroP_AG20443 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002706 2706 GSM993474 Crawford Duke 2.0 1 wgEncodeDukeAffyExonFibropag20443SimpleSignalRep1 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG20443) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08396SimpleSignalRep3 FibroP_AG08396 3 FibroP_AG08396 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002705 2705 GSM993473 Crawford Duke 2.0 3 wgEncodeDukeAffyExonFibropag08396SimpleSignalRep3 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08396) Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08396SimpleSignalRep2 FibroP_AG08396 2 FibroP_AG08396 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002705 2705 GSM993472 Crawford Duke 2.0 2 wgEncodeDukeAffyExonFibropag08396SimpleSignalRep2 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08396) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08396SimpleSignalRep1 FibroP_AG08396 1 FibroP_AG08396 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002705 2705 GSM993471 Crawford Duke 2.0 1 wgEncodeDukeAffyExonFibropag08396SimpleSignalRep1 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08396) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08395SimpleSignalRep3 FibroP_AG08395 3 FibroP_AG08395 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002704 2704 GSM993470 Crawford Duke 2.0 3 wgEncodeDukeAffyExonFibropag08395SimpleSignalRep3 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08395) Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08395SimpleSignalRep2 FibroP_AG08395 2 FibroP_AG08395 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002704 2704 GSM993469 Crawford Duke 2.0 2 wgEncodeDukeAffyExonFibropag08395SimpleSignalRep2 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08395) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08395SimpleSignalRep1 FibroP_AG08395 1 FibroP_AG08395 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002704 2704 GSM993468 Crawford Duke 2.0 1 wgEncodeDukeAffyExonFibropag08395SimpleSignalRep1 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08395) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibroblSimpleSignalRep2V2 Fibrobl 2 Fibrobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000216 216 GSM993467 Crawford Duke 2.0 2 wgEncodeDukeAffyExonFibroblSimpleSignalRep2V2 None SimpleSignal child fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Fibrobl Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibroblSimpleSignalRep1V2 Fibrobl 1 Fibrobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000216 216 GSM993466 Crawford Duke 2.0 1 wgEncodeDukeAffyExonFibroblSimpleSignalRep1V2 None SimpleSignal child fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Fibrobl Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonColo829SimpleSignalRep2 Colo829 2 Colo829 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002690 2690 GSM993465 Crawford Duke 2.0 2 wgEncodeDukeAffyExonColo829SimpleSignalRep2 None SimpleSignal malignant melanoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Colo829 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonColo829SimpleSignalRep1 Colo829 1 Colo829 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002690 2690 GSM993464 Crawford Duke 2.0 1 wgEncodeDukeAffyExonColo829SimpleSignalRep1 None SimpleSignal malignant melanoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Colo829 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonCllSimpleSignalRep2V2 CLL 2 CLL AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001061 1061 GSM993463 Crawford Duke 2.0 2 wgEncodeDukeAffyExonCllSimpleSignalRep2V2 None SimpleSignal chronic lymphocytic leukemia cell, T-cell lymphocyte Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal CLL Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonCllSimpleSignalRep1V2 CLL 1 CLL AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001061 1061 GSM993462 Crawford Duke 2.0 1 wgEncodeDukeAffyExonCllSimpleSignalRep1V2 None SimpleSignal chronic lymphocytic leukemia cell, T-cell lymphocyte Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal CLL Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonChorionSimpleSignalRep1V2 Chorion 1 Chorion AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000215 215 GSM993461 Crawford Duke 2.0 1 wgEncodeDukeAffyExonChorionSimpleSignalRep1V2 None SimpleSignal chorion cells (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes. Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Chorion Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcSimpleSignalRep2V2 AoSMC 2 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001059 1059 GSM993454 Crawford Duke 2.0 2 wgEncodeDukeAffyExonAosmcSimpleSignalRep2V2 None SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal AoSMC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcSimpleSignalRep1V2 AoSMC 1 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001059 1059 GSM993453 Crawford Duke 2.0 1 wgEncodeDukeAffyExonAosmcSimpleSignalRep1V2 None SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal AoSMC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcTgfbSimpleSignalRep2V2 AoSMC TGFb 2 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001060 1060 GSM993458 Crawford Duke 2.0 2 wgEncodeDukeAffyExonAosmcTgfbSimpleSignalRep2V2 TGFb SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University 1 ng/mL transforming growth factor beta for 24 hours (Crawford) Simple Signal AoSMC TGFb Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcTgfbSimpleSignalRep1V2 AoSMC TGFb 1 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001060 1060 GSM993457 Crawford Duke 2.0 1 wgEncodeDukeAffyExonAosmcTgfbSimpleSignalRep1V2 TGFb SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University 1 ng/mL transforming growth factor beta for 24 hours (Crawford) Simple Signal AoSMC TGFb Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcSerumfreeSimpleSignalRep2V2 AoSMC 2 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001058 1058 GSM993456 Crawford Duke 2.0 2 wgEncodeDukeAffyExonAosmcSerumfreeSimpleSignalRep2V2 serum_free_media SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford) Simple Signal AoSMC Serum-free media Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcSerumfreeSimpleSignalRep1V2 AoSMC 1 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001058 1058 GSM993455 Crawford Duke 2.0 1 wgEncodeDukeAffyExonAosmcSerumfreeSimpleSignalRep1V2 serum_free_media SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford) Simple Signal AoSMC Serum-free media Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExon8988tSimpleSignalRep2V2 8988T 2 8988T AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001057 1057 GSM993450 Crawford Duke 2.0 2 wgEncodeDukeAffyExon8988tSimpleSignalRep2V2 None SimpleSignal pancreas adenocarcinoma (PA-TU-8988T), "established in 1985 from the liver metastasis of a primary pancreatic adenocarcinoma from a 64-year-old woman" - DSMZ Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal 8988T Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExon8988tSimpleSignalRep1V2 8988T 1 8988T AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001057 1057 GSM993449 Crawford Duke 2.0 1 wgEncodeDukeAffyExon8988tSimpleSignalRep1V2 None SimpleSignal pancreas adenocarcinoma (PA-TU-8988T), "established in 1985 from the liver metastasis of a primary pancreatic adenocarcinoma from a 64-year-old woman" - DSMZ Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal 8988T Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7SimpleSignalRep1V2 MCF-7 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000235 235 GSM993601 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7SimpleSignalRep1V2 None SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal MCF-7 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7VehSimpleSignalRep2V2 MCF-7 Veh 2 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000237 237 GSM993576 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMcf7VehSimpleSignalRep2V2 vehicle SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Charcoal stripped hormone-free FBS for 72 hours (Crawford) Simple Signal MCF-7 Vehicle Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7VehSimpleSignalRep1V2 MCF-7 Veh 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000237 237 GSM993575 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7VehSimpleSignalRep1V2 vehicle SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Charcoal stripped hormone-free FBS for 72 hours (Crawford) Simple Signal MCF-7 Vehicle Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep3 MCF-7 RANDsh 3 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002698 2698 GSM993574 Crawford Duke 2.0 3 wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep3 Randomized_shRNA_control SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Simple Signal MCF-7 Randomized shRNA control Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep2 MCF-7 RANDsh 2 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002698 2698 GSM993573 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep2 Randomized_shRNA_control SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Simple Signal MCF-7 Randomized shRNA control Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep1 MCF-7 RANDsh 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002698 2698 GSM993572 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep1 Randomized_shRNA_control SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Simple Signal MCF-7 Randomized shRNA control Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7HypoxlacSimpleSignalRep1 MCF-7 Hypox 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002697 2697 GSM993571 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7HypoxlacSimpleSignalRep1 Hypoxia_LacAcid SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) Simple Signal MCF-7 Hypoxia, Lactic acidosis Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7EstroSimpleSignalRep2V2 MCF-7 ESTRO 2 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000236 236 GSM993570 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMcf7EstroSimpleSignalRep2V2 estrogen SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University 45 min with 100 nM Estradiol (Crawford) Simple Signal MCF-7 Estradiol 100 nM Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7EstroSimpleSignalRep1V2 MCF-7 ESTRO 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000236 236 GSM993569 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7EstroSimpleSignalRep1V2 estrogen SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University 45 min with 100 nM Estradiol (Crawford) Simple Signal MCF-7 Estradiol 100 nM Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep3 MCF-7 CTCFsh 3 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002696 2696 GSM993568 Crawford Duke 2.0 3 wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep3 CTCF_shRNA_knockdown SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Simple Signal MCF-7 CTCF shRNA knockdown Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep2 MCF-7 CTCFsh 2 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002696 2696 GSM993567 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep2 CTCF_shRNA_knockdown SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Simple Signal MCF-7 CTCF shRNA knockdown Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep1 MCF-7 CTCFsh 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002696 2696 GSM993566 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep1 CTCF_shRNA_knockdown SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Simple Signal MCF-7 CTCF shRNA knockdown Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuvecSimpleSignalRep2V2 HUVEC 2 HUVEC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000226 226 GSM993544 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHuvecSimpleSignalRep2V2 None SimpleSignal umbilical vein endothelial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HUVEC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuvecSimpleSignalRep1V2 HUVEC 1 HUVEC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000226 226 GSM993543 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHuvecSimpleSignalRep1V2 None SimpleSignal umbilical vein endothelial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HUVEC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepg2SimpleSignalRep3V2 HepG2 3 HepG2 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000230 230 GSM993520 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHepg2SimpleSignalRep3V2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HepG2 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepg2SimpleSignalRep2V2 HepG2 2 HepG2 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000230 230 GSM993519 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHepg2SimpleSignalRep2V2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HepG2 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepg2SimpleSignalRep1V2 HepG2 1 HepG2 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000230 230 GSM993518 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHepg2SimpleSignalRep1V2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HepG2 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3SimpleSignalRep3V2 HeLa-S3 3 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000227 227 GSM993511 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHelas3SimpleSignalRep3V2 None SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HeLa-S3 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3SimpleSignalRep2V2 HeLa-S3 2 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000227 227 GSM993510 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHelas3SimpleSignalRep2V2 None SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HeLa-S3 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3SimpleSignalRep1V2 HeLa-S3 1 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000227 227 GSM993509 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHelas3SimpleSignalRep1V2 None SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HeLa-S3 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3Ifng4hSimpleSignalRep2V2 HeLa-S3 2 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000229 229 GSM993515 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHelas3Ifng4hSimpleSignalRep2V2 IFNg4h SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Interferon gamma treatment - 4 hours with 5 ng/ml (Crawford) Simple Signal HeLa-S3 IFN-g 4 h Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3Ifng4hSimpleSignalRep1V2 HeLa-S3 1 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000229 229 GSM993514 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHelas3Ifng4hSimpleSignalRep1V2 IFNg4h SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Interferon gamma treatment - 4 hours with 5 ng/ml (Crawford) Simple Signal HeLa-S3 IFN-g 4 h Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3Ifna4hSimpleSignalRep2V2 HeLa-S3 2 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000228 228 GSM993513 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHelas3Ifna4hSimpleSignalRep2V2 IFNa4h SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University 4 hours of 500 U/ml Interferon alpha (Crawford) Simple Signal HeLa-S3 IFN-a 4 h Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3Ifna4hSimpleSignalRep1V2 HeLa-S3 1 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000228 228 GSM993512 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHelas3Ifna4hSimpleSignalRep1V2 IFNa4h SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University 4 hours of 500 U/ml Interferon alpha (Crawford) Simple Signal HeLa-S3 IFN-a 4 h Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonA549SimpleSignalRep2 A549 2 A549 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002689 2689 GSM993452 Crawford Duke 2.0 2 wgEncodeDukeAffyExonA549SimpleSignalRep2 None SimpleSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal A549 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonA549SimpleSignalRep1 A549 1 A549 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002689 2689 GSM993451 Crawford Duke 2.0 1 wgEncodeDukeAffyExonA549SimpleSignalRep1 None SimpleSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal A549 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562SimpleSignalRep4 K562 4 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001072 1072 GSM993557 Crawford Duke 2.0 4 wgEncodeDukeAffyExonK562SimpleSignalRep4 None SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal K562 Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562SimpleSignalRep3V2 K562 3 K562 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001072 1072 GSM993556 Crawford Duke 2.0 3 wgEncodeDukeAffyExonK562SimpleSignalRep3V2 None SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal K562 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562SimpleSignalRep2V2 K562 2 K562 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001072 1072 GSM993554 Crawford Duke 2.0 2 wgEncodeDukeAffyExonK562SimpleSignalRep2V2 None SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal K562 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562SimpleSignalRep1V2 K562 1 K562 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001072 1072 GSM993552 Crawford Duke 2.0 1 wgEncodeDukeAffyExonK562SimpleSignalRep1V2 None SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal K562 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562NabutSimpleSignalRep4 K562 Nabut 4 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002695 2695 GSM993561 Crawford Duke 2.0 4 wgEncodeDukeAffyExonK562NabutSimpleSignalRep4 NaBut SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Simple Signal K562 NaBut Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562NabutSimpleSignalRep3 K562 Nabut 3 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002695 2695 GSM993560 Crawford Duke 2.0 3 wgEncodeDukeAffyExonK562NabutSimpleSignalRep3 NaBut SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Simple Signal K562 NaBut Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562NabutSimpleSignalRep2 K562 Nabut 2 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002695 2695 GSM993559 Crawford Duke 2.0 2 wgEncodeDukeAffyExonK562NabutSimpleSignalRep2 NaBut SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Simple Signal K562 NaBut Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562NabutSimpleSignalRep1 K562 NaBut 1 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002695 2695 GSM993558 Crawford Duke 2.0 1 wgEncodeDukeAffyExonK562NabutSimpleSignalRep1 NaBut SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Simple Signal K562 NaBut Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH1hescSimpleSignalRep4V2 H1-hESC 4 H1-hESC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001063 1063 GSM993500 Crawford Duke 2.0 4 wgEncodeDukeAffyExonH1hescSimpleSignalRep4V2 None SimpleSignal embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H1-hESC Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH1hescSimpleSignalRep3V2 H1-hESC 3 H1-hESC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001063 1063 GSM993499 Crawford Duke 2.0 3 wgEncodeDukeAffyExonH1hescSimpleSignalRep3V2 None SimpleSignal embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H1-hESC Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH1hescSimpleSignalRep2V2 H1-hESC 2 H1-hESC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001063 1063 GSM993498 Crawford Duke 2.0 2 wgEncodeDukeAffyExonH1hescSimpleSignalRep2V2 None SimpleSignal embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H1-hESC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH1hescSimpleSignalRep1V2 H1-hESC 1 H1-hESC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001063 1063 GSM993497 Crawford Duke 2.0 1 wgEncodeDukeAffyExonH1hescSimpleSignalRep1V2 None SimpleSignal embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H1-hESC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12878SimpleSignalRep3V2 GM12878 3 GM12878 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000217 217 GSM993483 Crawford Duke 2.0 3 wgEncodeDukeAffyExonGm12878SimpleSignalRep3V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12878 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12878SimpleSignalRep2V2 GM12878 2 GM12878 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000217 217 GSM993482 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm12878SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12878 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12878SimpleSignalRep1V2 GM12878 1 GM12878 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000217 217 GSM993481 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm12878SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12878 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeGisChiaPet GIS ChIA-PET GSE39495 Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan Regulation Description This track was produced as part of the ENCODE Project. It shows the locations of protein factor mediated chromatin interactions determined by Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) data (Fullwood et al., 2010) extracted from five different human cancer cell lines (K562 (chronic myeloid leukemia), HCT116 (colorectal cancer), HeLa-S3 (cervical cancer), MCF-7 (breast cancer), and NB4 (promyelocytic)). A chromatin interaction is defined as the association of two regions of the genome that are far apart in terms of genomic distance, but are spatially proximate to each other in the 3-dimensional cellular nucleus. Additionally, ChIA-PET experiments generate transcription factor binding sites. A binding site is defined as a region of the genome that is highly enriched by specific Chromatin ImmunoPrecipitation (ChIP) against a transcription factor, which indicates that the transcription factor binds specifically to this region. The protein factors displayed in the track include estrogen receptor alpha (ER&#945;), RNA polymerase II (RNAPII), and CCCTC binding factor (CTCF). Display Conventions and Configuration In the graphical display, the PETs are represented by two blocks one for each end. These blocks are connected by a horizontal line if both ends are in the same chromosome. If the two ends are on different chromosomes, only one block will display. PET sequences that overlap at both ends form PET clusters. The number of PETs in a cluster reflects the strength of a chromatin interaction. Singleton PETs (PETs without a cluster) are potentially false positives, whereas PET clusters of more than 3 PETs could indicate genuine chromatin interactions. The density graph of the tags shows the ChIP enrichment at different points of genome, and high peaks indicate transcription factor binding sites. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Interactions ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. Signal Density graph (wiggle) of signal enrichment based on aligned read density. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a global de novo high-throughput method for characterizing the 3-dimensional structure of chromatin in the nucleus. In the ChIA-PET protocol, samples were cross-linked and fragmented, then subjected to chromatin immunoprecipitation. The DNA fragments that were brought together by the chromatin interactions were then proximity-ligated. During this proximity-ligation step, the half-linkers (created by the fragmentation) containing flanking MmeI sites (type IIS restriction enzymes) were first ligated to the DNA fragments and then ligated to each other to form full linkers. Full linkers bridge either two ends of a self-circularized fragment, or two ends of two different chromatin fragments. The material was then reverse cross-linked, purified and digested with MmeI. MmeI cuts 20 base pairs away from its recognition site. Tag-linker-tag (paired-end tag, PET) constructs were sequenced by ultra-high-throughput methods (Illumina or SOLiD paired-end sequencing). ChIA-PET reads were processed with the ChIA-PET Tool (Li et al., 2010) by the following steps: linker filtering, short reads mapping, PET classification, binding site identification, and interaction cluster identification. The high-confidence binding sites and chromatin interaction clusters were reported. Verification Chromatin interactions identified by ChIA-PET have been validated by 3C, ChIP-3C, 4C and DNA-FISH (Fullwood et al., 2009). Credits Genome Institute of Singapore: Guoliang Li, Xiaoan Ruan, Kuljeet Singh Sandhu, Fabianus Hendriyan Mulawadi, Huay Mei Poh, Yufen Goh, Su Qin Peh, Wing-Kin Sung, Yijun Ruan Stanford University: Raymond Auerbach, Michael Snyder Contact: Yijun Ruan References Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009 Nov 5;462(7269):58-64. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22. Publications Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012 Jan 20;148(1-2):84-98. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeChromSuper ENC Chromatin ENCODE Chromatin Interactions Expression Description These tracks display evidence of chromatin interactions in ENCODE cell types. A chromatin interaction is defined as two regions of the genome that are far apart in terms of genomic distance, but are spatially proximate to each other in the 3-dimensional cellular nucleus. Binding sites are also displayed when a transcription factor is used in the assay. A binding site is defined as a region of the genome that is highly enriched by specific Chromatin Immunoprecipitation (ChIP) against a transcription factor, which indicates that the transcription factor binds specifically to this region. ChIA-PET: The Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) (Li 2010, Fullwood 2010) track shows the locations of RNA polymerase II-bound (RNAPII-bound) chromatin interactions determined by Paired-End Tag (PET) sequencing using proximity-ligated chromatin extracts from human cell lines. The RNAPII ChIA-PET experiment generates RNAPII binding sites. Generally, a chromatin interaction is more likely to connect two RNAPII binding sites together. 5C: Chromosome Conformation Capture Carbon Copy (5C) (Dostie 2006) maps genomic interactions of a focused set of restriction enzymes. The three-dimensional organization of chromosomes and chromatin domains is obtained by cross-linking, digestion, ligation and then detection (Dekker 2002). Display Conventions These are multi-view composite tracks that contains multiple data types controllable using the 'Select view' function as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Further details on display conventions and data interpretation are available in the subtrack descriptions. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15;295(5558):1306-11. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct;16(10):1299-309. Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeGisChiaPetSignal Signal Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetNb4Pol2SigRep1 NB4 Pol2 Sig 1 Pol2 NB4 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2012-04-23 wgEncodeEH001431 1431 GSM970214 Ruan GIS-Ruan IHN009M_hg19 1 wgEncodeGisChiaPetNb4Pol2SigRep1 Signal RNA Polymerase II acute promyelocytic leukemia cell line. (PMID: 1995093) Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal NB4 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetHct116Pol2SigRep1 HCT116 Pol2 Sig 1 Pol2 HCT-116 ChiaPet ENCODE Mar 2012 Freeze 2011-09-23 2012-04-23 wgEncodeEH001427 1427 GSM970210 Ruan GIS-Ruan CHH524M 1 wgEncodeGisChiaPetHct116Pol2SigRep1 Signal RNA Polymerase II colorectal carcinoma (PMID: 7214343) Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal HCT-116 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2SigRep4 MCF7 Pol2 Sig 4 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-27 2012-04-23 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM163M_L4 4 wgEncodeGisChiaPetMcf7Pol2SigRep4 Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 Pol2 ChIA-PET Signal Rep 4 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2SigRep3 MCF7 Pol2 Sig 3 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-27 2011-06-08 2012-03-08 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM160M_L4 3 wgEncodeGisChiaPetMcf7Pol2SigRep3 Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 Pol2 ChIA-PET Signal Rep 3 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2SigRep2 MCF7 Pol2 Sig 2 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-23 2012-04-23 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM053T_hg19 2 wgEncodeGisChiaPetMcf7Pol2SigRep2 Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 Pol2 ChIA-PET Signal Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2SigRep1 MCF7 Pol2 Sig 1 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-26 2012-04-23 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM040M_hg19 1 wgEncodeGisChiaPetMcf7Pol2SigRep1 Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaSigRep3 MCF7 ERa Sig 3 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2012-04-23 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHM096M 3 wgEncodeGisChiaPetMcf7EraaSigRep3 Signal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 ERalpha a ChIA-PET Signal Rep 3 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaSigRep2 MCF7 ERa Sig 2 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-21 2012-04-21 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHH015T_hg19 2 wgEncodeGisChiaPetMcf7EraaSigRep2 Signal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 ERalpha a ChIA-PET Signal Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaSigRep1 MCF7 ERa Sig 1 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-20 2012-04-20 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHM001T_hg19 1 wgEncodeGisChiaPetMcf7EraaSigRep1 Signal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 ERalpha a ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7CtcfSigRep2 MCF7 CTCF Sig 2 CTCF MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002076 2076 GSM970215 Ruan GIS-Ruan CHM077M 2 wgEncodeGisChiaPetMcf7CtcfSigRep2 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 CTCF ChIA-PET Signal Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7CtcfSigRep1 MCF7 CTCF Sig 1 CTCF MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002076 2076 GSM970215 Ruan GIS-Ruan CHM076M 1 wgEncodeGisChiaPetMcf7CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 CTCF ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetHelas3Pol2SigRep1 HeLaS3 Pol2 Sig 1 Pol2 HeLa-S3 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2012-04-23 wgEncodeEH001426 1426 GSM970211 Ruan GIS-Ruan IHH025M_hg19 1 wgEncodeGisChiaPetHelas3Pol2SigRep1 Signal RNA Polymerase II cervical carcinoma Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal HeLa-S3 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562Pol2SigRep2 K562 Pol2 Sig 2 Pol2 K562 ChiaPet ENCODE Mar 2012 Freeze 2011-08-19 2011-02-05 2011-11-04 wgEncodeEH001428 1428 GSM970213 Ruan GIS-Ruan CHK019M_L2_lane24 2 wgEncodeGisChiaPetK562Pol2SigRep2 Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal K562 Pol2 ChIA-PET Signal Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562Pol2SigRep1 K562 Pol2 Sig 1 Pol2 K562 ChiaPet ENCODE Mar 2012 Freeze 2011-08-23 2011-02-05 2011-11-04 wgEncodeEH001428 1428 GSM970213 Ruan GIS-Ruan CHK019M_L2_lane13 1 wgEncodeGisChiaPetK562Pol2SigRep1 Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal K562 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562CtcfSigRep1 K562 CTCF Sig 1 CTCF K562 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002075 2075 GSM970216 Ruan GIS-Ruan CTCF_K562M_L7 1 wgEncodeGisChiaPetK562CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal K562 CTCF ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetInteractions Interactions Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetNb4Pol2InteractionsRep1 NB4 Pol2 Int 1 Pol2 NB4 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2011-01-20 2011-10-20 wgEncodeEH001431 1431 GSM970214 Ruan GIS-Ruan IHN009M_hg19 1 wgEncodeGisChiaPetNb4Pol2InteractionsRep1 Interactions RNA Polymerase II acute promyelocytic leukemia cell line. (PMID: 1995093) Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. NB4 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetHct116Pol2InteractionsRep1 HCT116 Pol2 Int 1 Pol2 HCT-116 ChiaPet ENCODE Mar 2012 Freeze 2011-09-23 2011-01-20 2011-10-20 wgEncodeEH001427 1427 GSM970210 Ruan GIS-Ruan CHH524M 1 wgEncodeGisChiaPetHct116Pol2InteractionsRep1 Interactions RNA Polymerase II colorectal carcinoma (PMID: 7214343) Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. HCT-116 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2InteractionsRep4 MCF7 Pol2 Int 4 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-27 2011-01-20 2011-10-20 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM163M_L4 4 wgEncodeGisChiaPetMcf7Pol2InteractionsRep4 Interactions RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 Pol2 ChIA-PET Interactions Rep 4 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2InteractionsRep3 MCF7 Pol2 Int 3 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-27 2011-06-08 2012-03-08 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM160M_L4 3 wgEncodeGisChiaPetMcf7Pol2InteractionsRep3 Interactions RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 Pol2 ChIA-PET Interactions Rep 3 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2InteractionsRep2 MCF7 Pol2 Int 2 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-23 2011-01-20 2011-10-20 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM053T_hg19 2 wgEncodeGisChiaPetMcf7Pol2InteractionsRep2 Interactions RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 Pol2 ChIA-PET Interactions Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2InteractionsRep1 MCF7 Pol2 Int 1 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-26 2011-01-20 2011-10-20 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM040M_hg19 1 wgEncodeGisChiaPetMcf7Pol2InteractionsRep1 Interactions RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaInteractionsRep3 MCF7 ERa Int 3 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2012-04-23 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHM096M 3 wgEncodeGisChiaPetMcf7EraaInteractionsRep3 Interactions This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 ERalpha a ChIA-PET Interactions Rep 3 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaInteractionsRep2 MCF7 ERa Int 2 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-21 2012-04-21 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHH015T_hg19 2 wgEncodeGisChiaPetMcf7EraaInteractionsRep2 Interactions This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 ERalpha a ChIA-PET Interactions Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaInteractionsRep1 MCF7 ERa Int 1 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-20 2012-04-20 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHM001T_hg19 1 wgEncodeGisChiaPetMcf7EraaInteractionsRep1 Interactions This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 ERalpha a ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7CtcfInteractionsRep2 MCF7 CTCF Int 2 CTCF MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002076 2076 GSM970215 Ruan GIS-Ruan CHM077M 2 wgEncodeGisChiaPetMcf7CtcfInteractionsRep2 Interactions CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 CTCF ChIA-PET Interactions Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7CtcfInteractionsRep1 MCF7 CTCF Int 1 CTCF MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002076 2076 GSM970215 Ruan GIS-Ruan CHM076M 1 wgEncodeGisChiaPetMcf7CtcfInteractionsRep1 Interactions CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 CTCF ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetHelas3Pol2InteractionsRep1 HeLaS3 Pol2 Int 1 Pol2 HeLa-S3 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2011-01-20 2011-10-20 wgEncodeEH001426 1426 GSM970211 Ruan GIS-Ruan IHH025M_hg19 1 wgEncodeGisChiaPetHelas3Pol2InteractionsRep1 Interactions RNA Polymerase II cervical carcinoma Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. HeLa-S3 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562Pol2InteractionsRep2 K562 Pol2 Int 2 Pol2 K562 ChiaPet ENCODE Mar 2012 Freeze 2011-02-05 2011-01-20 2011-10-20 wgEncodeEH001428 1428 GSM970213 Ruan GIS-Ruan CHK019M_L2_lane24 2 wgEncodeGisChiaPetK562Pol2InteractionsRep2 Interactions RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. K562 Pol2 ChIA-PET Interactions Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562Pol2InteractionsRep1 K562 Pol2 Int 1 Pol2 K562 ChiaPet ENCODE Mar 2012 Freeze 2011-02-05 2011-01-20 2011-10-20 wgEncodeEH001428 1428 GSM970213 Ruan GIS-Ruan CHK019M_L2_lane13 1 wgEncodeGisChiaPetK562Pol2InteractionsRep1 Interactions RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. K562 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562CtcfInteractionsRep1 K562 CTCF Int 1 CTCF K562 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002075 2075 GSM970216 Ruan GIS-Ruan CTCF_K562M_L7 1 wgEncodeGisChiaPetK562CtcfInteractionsRep1 Interactions CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. K562 CTCF ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisRnaSeq GIS RNA-seq GSE27221 RNA-seq from ENCODE/Genome Institute of Singapore Expression Description This track is produced as part of the ENCODE Transcriptome Project. It shows high throughput sequencing of RNA samples from tissues or sub cellular compartments from cell lines included in the ENCODE Transcriptome subproject. The overall goal of the ENCODE project is to identify and characterize all functional elements in the sequence of the human genome. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types. Plus Raw Signal The Plus Raw Signal view graphs the base-by-base density of alignments on the + strand. Minus Raw Signal The Minus Raw Signal view graphs the base-by-base density of alignments on the - strand. Alignments The Alignments view shows reads mapped to the genome, both split alignments and alignments mapped to one exon. Sequences determined to be transcribed on the positive strand are shown in blue. Sequences determined to be transcribed on the negative strand are shown in red. Sequences for which the direction of transcription was not able to be determined are shown in black. For more information on the XL XJ and XU custom tags used in these files, please contact the producing lab. Please see the Bowtie Manual for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format. Methods The RNA-Seq data were generated from high quality polyA RNA, and the RNA-Seq libraries were constructed using SOLiD Whole Transcriptome (WT) protocol and reagent kit. Total RNA in good quality was used as starting materials and purified twice through MACs polyT column aimed to enrich polyA and remove any contaminants (e.g., rRNA, tRNA, DNA, protein etc.). A one microgram enriched polyA RNA sample was then fragmented to small pieces, and a gel-based selection method was performed to collect fragmented random polyA at a size-range of 50-150 nt in length. The collected fragmental RNA was then hybridized and ligated to a mix of adapters provided from ABI, followed by reverse transcription to generate corresponding cDNAs. The resulting cDNA library was further amplified by PCR and sequenced by SOLiD platform for single reads at 35 bp length (new version in 50 bp length). Cells were grown according to the approved ENCODE cell culture protocols. Data: The SOLiD-generated RNA-Seq reads were 35 bp in length. An initial filtering process was performed to remove any non-desirable contamination sequences, such as rRNA, tRNA, and repeats etc. A read-split mapping approach was developed to map the 35 bp reads onto the reference genome (GRCh37/hg19) excluding mitochondrion, haplotypes, randoms and chromosome Y. Mapping parameters: Strand specific mapping was done using Applied Biosystems' SOLiD alignment where all the reads were mapped to the genome, and to exon-exon junction database. Seed and extend strategy is adopted where initial seed length of 25 is mapped with maximum of 2 mismatches and then extended to read length, each color space match is awarded a score of +1 and each mismatch is awarded a penalty of -2. After extension each read is trimmed to its maximum score, shortest length. The color space sequences are then converted into base space and checked to ensure that each sequence has a maximum of 2 base pair mismatches. If any sequence has more than 2 mismatches, then that sequence is discarded. Credits The GIS RNA-seq libraries and sequence data for transcriptome analysis were produced at the Genome Institute of Singapore. The data were mapped and analyzed by scientists from the Genome Institute of Singapore. Contact: RUAN Xiaoan Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeGisRnaSeqViewPlusRawSignal Plus Raw Signal RNA-seq from ENCODE/Genome Institute of Singapore Expression 
wgEncodeGisRnaSeqK562CytosolPapPlusRawRep2 K562 cyto pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672835 Gingeras GIS crg-55 cytosol hg18 2 longPolyA wgEncodeGisRnaSeqK562CytosolPapPlusRawRep2 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus raw signal rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqK562CytosolPapPlusRawRep1 K562 cyto pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672833 Gingeras GIS crg-48 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqK562CytosolPapPlusRawRep1 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus raw signal rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqH1hescCellPapPlusRawRep1 H1ES cell pA+ + 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000270 270 GSM672836 Gingeras GIS crg-16 cell hg18 1 longPolyA wgEncodeGisRnaSeqH1hescCellPapPlusRawRep1 PlusRawSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore Whole cell Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ RNA-seq Plus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqGm12878CytosolPapPlusRawRep1 GM12 cyto pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000269 269 GSM672834 Gingeras GIS crg-9 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqGm12878CytosolPapPlusRawRep1 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ RNA-seq Plus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqViewMinusRawSignal Minus Raw Signal RNA-seq from ENCODE/Genome Institute of Singapore Expression 
wgEncodeGisRnaSeqK562CytosolPapMinusRawRep2 K562 cyto pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672835 Gingeras GIS crg-55 cytosol hg18 2 longPolyA wgEncodeGisRnaSeqK562CytosolPapMinusRawRep2 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus raw signal rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqK562CytosolPapMinusRawRep1 K562 cyto pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672833 Gingeras GIS crg-48 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqK562CytosolPapMinusRawRep1 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqH1hescCellPapMinusRawRep1 H1ES cell pA+ - 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000270 270 GSM672836 Gingeras GIS crg-16 cell hg18 1 longPolyA wgEncodeGisRnaSeqH1hescCellPapMinusRawRep1 MinusRawSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore Whole cell Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ RNA-seq Minus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqGm12878CytosolPapMinusRawRep1 GM12 cyto pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000269 269 GSM672834 Gingeras GIS crg-9 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqGm12878CytosolPapMinusRawRep1 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ RNA-seq Minus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqViewAlignments Alignments RNA-seq from ENCODE/Genome Institute of Singapore Expression 
wgEncodeGisRnaSeqK562CytosolPapAlnRep2 K562 cyto pA+ 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672835 Gingeras GIS crg-55 cytosol hg18 2 longPolyA wgEncodeGisRnaSeqK562CytosolPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ RNA-seq Alignments rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqK562CytosolPapAlnRep1 K562 cyto pA+ 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672833 Gingeras GIS crg-48 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqK562CytosolPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ RNA-seq Alignments rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqH1hescCellPapAlnRep1 H1ES cell pA+ 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000270 270 GSM672836 Gingeras GIS crg-16 cell hg18 1 longPolyA wgEncodeGisRnaSeqH1hescCellPapAlnRep1 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore Whole cell Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC polyA+ RNA-seq Alignments rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqGm12878CytosolPapAlnRep1 GM12 cyto pA+ 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000269 269 GSM672834 Gingeras GIS crg-9 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqGm12878CytosolPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA+ RNA-seq Alignments rep 1 from ENCODE/GIS Expression 
wgEncodeHaibMethylRrbs HAIB Methyl RRBS GSE27584 DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha Regulation Description This track was produced as part of the ENCODE project. The track reports the percentage of DNA molecules that exhibit cytosine methylation at specific CpG dinucleotides. In general, DNA methylation within a gene's promoter is associated with gene silencing and DNA methylation within the exons and introns of a gene is associated with gene expression. Proper regulation of DNA methylation is essential during development and aberrant DNA methylation is a hallmark of cancer. DNA methylation status was assayed at more than 500,000 CpG dinucleotides in the genome using Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA was digested with the methyl-insensitive restriction enzyme MspI and then small genomic DNA fragments were purified by gel electrophoresis and used to construct an Illumina sequencing library. The library fragments were treated with sodium bisulfite and amplified by PCR to convert every unmethylated cytosine to a thymidine while leaving methylated cytosines intact. The sequenced fragments were aligned to a customized reference genome sequence. For each assayed CpG, the number of sequencing reads covering that CpG and the percentage of those reads that were methylated were reported. Display Conventions and Configuration Methylation status is represented with an 11-color gradient using the following convention: red = 100% of molecules sequenced are methylated yellow = 50% of molecules sequenced are methylated green = 0% of molecules sequenced are methylated The score in this track reports the number of sequencing reads obtained for each CpG, which is often called 'coverage'. The score is capped at 1000, so any CpGs that were covered by more than 1000 sequencing reads have a score of 1000. The BED files available for download contain two extra columns: one with the uncapped coverage (number of reads at that site) and one with the percentage of those reads that show methylation. High reproducibility was obtained, with correlation coefficients greater than 0.9 between biological replicates, when only considering CpGs represented by at least 10 sequencing reads (10X coverage, score=10). Therefore, the default view for this track is set to 10X coverage, or a score of 10. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods DNA methylation at CpG sites was assayed with a modified version of Reduced Representation Bisulfite Sequencing (Meissner et al., 2008). RRBS was performed on cell lines grown by many ENCODE production groups. The production group that grew the cells and isolated genomic DNA is indicated in the "obtainedBy" field of the metadata. When a cell type was provided by more than one lab, the data from only one lab are available for immediate display. However, the data for every cell type from every lab is available from the Downloads page. RRBS was also performed on genomic DNA from tissue samples provided by BioChain. The replicates for the BioChain tissues are technical replicates (rather than biological replicates) beginning at the bisulfite treatment step. RRBS was carried out by the Myers production group at the HudsonAlpha Institute for Biotechnology. Isolation of Genomic DNA Genomic DNA was isolated from biological replicates of each cell line using the QIAGEN DNeasy Blood &amp; Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations for each genomic DNA preparation were determined using fluorescent DNA binding dye and a fluorometer (Invitrogen Quant-iT dsDNA High Sensitivity Kit and Qubit Fluorometer). Typically, 1 &micro;g of DNA is used to make an RRBS library; however, there has been success in making libraries with 200 ng genomic DNA from rare or precious samples. RRBS Library Construction and Sequencing RRBS library construction started with MspI digestion of genomic DNA, which cut at every CCGG regardless of methylation status. Klenow exo- DNA Polymerase was then used to fill in the recessed end of the genomic DNA and add an adenosine as a 3' overhang. Next, a methylated version of the Illumina paired-end adapters was ligated onto the DNA. Adapter-ligated genomic DNA fragments between 105 and 185 base pairs were selected using agarose gel electrophoresis and a Qiagen Qiaquick Gel Extraction Kit. The selected adapter-ligated fragments were treated with sodium bisulfite using the Zymo Research EZ DNA Methylation Gold Kit, which converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged. Bisulfite treated DNA was amplified in a final PCR reaction which was optimized to uniformly amplify diverse fragment sizes and sequence contexts in the same reaction. During this final PCR reaction, uracils were copied as thymines resulting in a thymine in the PCR products wherever an unmethylated cytosine existed in the genomic DNA. The sample was then ready for sequencing on the Illumina sequencing platform. These libraries were sequenced with an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. The full RRBS protocol can be found here. Data Analysis To analyze the sequence data, a reference genome was created that contained only the 36 base pairs adjacent to every MspI site and in which every C was changed to a T. A converted sequence read file was then created by changing each C in the original sequence reads to a T. The converted sequence reads were aligned to the converted reference genome and only reads that mapped uniquely to the reference genome were kept. Once the reads were aligned, the percent methylation was calculated for each CpG using the original sequence reads. The percent methylation and number of reads were reported for each CpG. Release Notes This is Release 3 (July 2012) of this track which adds the MCF-7 cell line with shRNA knockdowns obtained from the Crawford Lab at Duke University. Credits These data were produced by the Dr. Richard Myers Lab at the HudsonAlpha Institute for Biotechnology. Cells were grown by the Myers Lab and other ENCODE production groups. Contact: Dr. Florencia Pauli References Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008 Aug 7;454(7205):766-70. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeDnaMethylSuper ENC DNA Methyl ENCODE DNA Methylation Regulation Description DNA methylation is essential for normal development and is associated with silencing large regions of DNA through processes such as imprinting and X-chromosome inactivation. The majority of CpG dinucleotides are methylated in mammals. Unmethylated CpGs occur in segments called "CpG islands", which often lie upstream of genes in the regulatory regions and impact transcription. Display Conventions These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Illingworth RS, Bird AP. CpG islands--'a rough guide'. FEBS Lett. 2009 Jun 5;583(11):1713-20. Caiafa P, Zampieri M. DNA methylation and chromatin structure: the puzzling CpG islands. J Cell Biochem. 2005 Feb 1;94(2):257-65. Latham T, Gilbert N, Ramsahoye B. DNA methylation in mouse embryonic stem cells and development. Cell Tissue Res. 2008 Jan;331(1):31-55. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep2 Uterus_BC 2 BC_Uterus_BN0765 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001400 1400 GSM683911 Myers HudsonAlpha SL3414 BioChain 2 wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep2 None Sites uterus, donor BN0765, age 44, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Uterus BC BN0765 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep1 Uterus_BC 1 BC_Uterus_BN0765 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001400 1400 GSM683803 Myers HudsonAlpha SL1671 BioChain 1 wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep1 None Sites uterus, donor BN0765, age 44, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Uterus BC BN0765 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsUch1DukeSitesRep2 UCH-1 2 UCH-1 MethylRrbs ENCODE Mar 2012 Freeze 2011-08-31 2012-05-31 wgEncodeEH002063 2063 GSM980581 Myers HudsonAlpha SL1821 Duke 2 wgEncodeHaibMethylRrbsUch1DukeSitesRep2 None Sites chordoma cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites UCH-1 Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsUch1DukeSitesRep1 UCH-1 1 UCH-1 MethylRrbs ENCODE Mar 2012 Freeze 2011-08-31 2012-05-31 wgEncodeEH002063 2063 GSM980581 Myers HudsonAlpha SL1814 Duke 1 wgEncodeHaibMethylRrbsUch1DukeSitesRep1 None Sites chordoma cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites UCH-1 Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsU87HaibSitesRep2 U87 2 U87 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001414 1414 GSM683890 Myers HudsonAlpha SL3558 HudsonAlpha 2 F wgEncodeHaibMethylRrbsU87HaibSitesRep2 None Sites glioblastoma, astrocytoma, (PMID: 4332744) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Female Sites U87 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsU87HaibSitesRep1 U87 1 U87 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001414 1414 GSM683917 Myers HudsonAlpha SL3557 HudsonAlpha 1 F wgEncodeHaibMethylRrbsU87HaibSitesRep1 None Sites glioblastoma, astrocytoma, (PMID: 4332744) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Female Sites U87 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep2 Testis_BC 2 BC_Testis_N30 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001399 1399 GSM683850 Myers HudsonAlpha SL3416 BioChain 2 wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep2 None Sites testis, donor N30, age 41, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Testis BC N30 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep1 Testis_BC  1 BC_Testis_N30 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001399 1399 GSM683781 Myers HudsonAlpha SL1677 BioChain 1 wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep1 None Sites testis, donor N30, age 41, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Testis BC N30 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep2 T-47D Estra 2 T-47D MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001413 1413 GSM683842 Myers HudsonAlpha SL1435 HudsonAlpha 2 wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep2 Estradiol_10nM_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 24 hr with 10 nM Estradiol (Myers) Sites T-47D Estradiol Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep2 T-47D DMSO 2 T-47D MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001412 1412 GSM683771 Myers HudsonAlpha SL1436 HudsonAlpha 2 wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep2 DMSO_0.02pct_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 24 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites T-47D DMSO 0.02% 24 h Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep1 T-47D Estra 1 T-47D MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001413 1413 GSM683904 Myers HudsonAlpha SL3484 HudsonAlpha 1 wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep1 Estradiol_10nM_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 24 hr with 10 nM Estradiol (Myers) Sites T-47D Estradiol Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep1 T-47D DMSO 1 T-47D MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001412 1412 GSM683937 Myers HudsonAlpha SL3485 HudsonAlpha 1 wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep1 DMSO_0.02pct_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 24 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites T-47D DMSO 0.02% 24 h Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep2 Stomach_BC 2 BC_Stomach_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001398 1398 GSM683877 Myers HudsonAlpha SL3431 BioChain 2 wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep2 None Sites stomach, donor 01-11002, age 83, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Stomach BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep1 Stomach_BC 1 BC_Stomach_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001398 1398 GSM683947 Myers HudsonAlpha SL1997 BioChain 1 wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep1 None Sites stomach, donor 01-11002, age 83, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Stomach BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknshraUwSitesRep2 SK-N-SH_RA 2 SK-N-SH_RA MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001370 1370 GSM683919 Myers HudsonAlpha SL1628 UW 2 wgEncodeHaibMethylRrbsSknshraUwSitesRep2 None Sites neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH BC RA Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknshraUwSitesRep1 SK-N-SH_RA 1 SK-N-SH_RA MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001370 1370 GSM683800 Myers HudsonAlpha SL863 UW 1 wgEncodeHaibMethylRrbsSknshraUwSitesRep1 None Sites neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH BC RA Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknmcHaibSitesRep2 SK-N-MC 2 SK-N-MC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001411 1411 GSM683918 Myers HudsonAlpha SL3554 HudsonAlpha 2 wgEncodeHaibMethylRrbsSknmcHaibSitesRep2 None Sites neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-MC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknmcHaibSitesRep1 SK-N-MC 1 SK-N-MC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001411 1411 GSM683884 Myers HudsonAlpha SL3553 HudsonAlpha 1 wgEncodeHaibMethylRrbsSknmcHaibSitesRep1 None Sites neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-MC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSkmcUwSitesRep2 SKMC 2 SKMC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001354 1354 GSM683784 Myers HudsonAlpha SL1419 UW 2 wgEncodeHaibMethylRrbsSkmcUwSitesRep2 None Sites skeletal muscle cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SKMC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSkmcUwSitesRep1 SKMC 1 SKMC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001354 1354 GSM683894 Myers HudsonAlpha SL886 UW 1 wgEncodeHaibMethylRrbsSkmcUwSitesRep1 None Sites skeletal muscle cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SKMC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep2 Skin BC 2 BC_Skin_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001397 1397 GSM683892 Myers HudsonAlpha SL3436 BioChain 2 wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep2 None Sites skin, donor 01-11002, age 83, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skin BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep1 Skin BC 1 BC_Skin_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001397 1397 GSM683865 Myers HudsonAlpha SL1727 BioChain 1 wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep1 None Sites skin, donor 01-11002, age 83, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skin BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep2 Skeletal_7N 2 BC_Skeletal_Muscle_H12817N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001396 1396 GSM683868 Myers HudsonAlpha SL3441 BioChain 2 wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep2 None Sites skeletal muscle, donor H12817N, age 71, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skeletal Muscle BC H12817N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep1 Skeletal_7N 1 BC_Skeletal_Muscle_H12817N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001396 1396 GSM683931 Myers HudsonAlpha SL1758 BioChain 1 wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep1 None Sites skeletal muscle, donor H12817N, age 71, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skeletal Muscle BC H12817N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep2 Skeletal_02 2 BC_Skeletal_Muscle_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001395 1395 GSM683811 Myers HudsonAlpha SL3439 BioChain 2 wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep2 None Sites skeletal muscle, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skeletal Muscle BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep1 Skeletal_02 1 BC_Skeletal_Muscle_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001395 1395 GSM683789 Myers HudsonAlpha SL1752 BioChain 1 wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep1 None Sites skeletal muscle, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skeletal Muscle BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSaecUwSitesRep2 SAEC 2 SAEC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001369 1369 GSM683833 Myers HudsonAlpha SL1342 UW 2 wgEncodeHaibMethylRrbsSaecUwSitesRep2 None Sites small airway epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SAEC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSaecUwSitesRep1 SAEC 1 SAEC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001369 1369 GSM683916 Myers HudsonAlpha SL864 UW 1 wgEncodeHaibMethylRrbsSaecUwSitesRep1 None Sites small airway epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SAEC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsRptecSitesRep2 RPTEC 2 RPTEC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001375 1375 GSM683772 Myers HudsonAlpha SL1346 UW 2 wgEncodeHaibMethylRrbsRptecSitesRep2 None Sites renal proximal tubule epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites RPTEC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsRptecSitesRep1 RPTEC 1 RPTEC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001375 1375 GSM683802 Myers HudsonAlpha SL876 UW 1 wgEncodeHaibMethylRrbsRptecSitesRep1 None Sites renal proximal tubule epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites RPTEC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsProgfibSitesRep2 ProgFib 2 ProgFib MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001374 1374 GSM683783 Myers HudsonAlpha SL1802 Duke 2 wgEncodeHaibMethylRrbsProgfibSitesRep2 None Sites fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites ProgFib Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsProgfibSitesRep1 ProgFib 1 ProgFib MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001374 1374 GSM683875 Myers HudsonAlpha SL938 Duke 1 wgEncodeHaibMethylRrbsProgfibSitesRep1 None Sites fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites ProgFib Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPrecUwSitesRep2 PrEC 2 PrEC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001410 1410 GSM683760 Myers HudsonAlpha SL869 UW 2 wgEncodeHaibMethylRrbsPrecUwSitesRep2 None Sites prostate epithelial cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PrEC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPrecUwSitesRep1 PrEC 1 PrEC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001410 1410 GSM683838 Myers HudsonAlpha SL868 UW 1 wgEncodeHaibMethylRrbsPrecUwSitesRep1 None Sites prostate epithelial cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PrEC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep2 Placenta_BC 2 BC_Placenta_UHN00189 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001394 1394 GSM683893 Myers HudsonAlpha SL3413 BioChain 2 wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep2 None Sites placenta, donor UHN00189, age 29 DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Placenta BC UHN00189 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep1 Placenta_BC 1 BC_Placenta_UHN00189 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001394 1394 GSM683796 Myers HudsonAlpha SL1675 BioChain 1 wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep1 None Sites placenta, donor UHN00189, age 29 DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Placenta BC UHN00189 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPfsk1HaibSitesRep2 PFSK-1 2 PFSK-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001409 1409 GSM683909 Myers HudsonAlpha SL3548 HudsonAlpha 2 wgEncodeHaibMethylRrbsPfsk1HaibSitesRep2 None Sites neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PFSK-1 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPfsk1HaibSitesRep1 PFSK-1 1 PFSK-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001409 1409 GSM683810 Myers HudsonAlpha SL3547 HudsonAlpha 1 wgEncodeHaibMethylRrbsPfsk1HaibSitesRep1 None Sites neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PFSK-1 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep2 Pericardium_BC 2 BC_Pericardium_H12529N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001393 1393 GSM683820 Myers HudsonAlpha SL3266 BioChain 2 wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep2 None Sites pericardium, donor H12529N, age 70, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Pericardium BC H12529N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep1 Pericardium_BC 1 BC_Pericardium_H12529N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001393 1393 GSM683899 Myers HudsonAlpha SL1674 BioChain 1 wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep1 None Sites pericardium, donor H12529N, age 70, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Pericardium BC H12529N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanisletsSitesRep2 PanIslets 2 PanIslets MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001373 1373 GSM683934 Myers HudsonAlpha SL1941 Duke 2 wgEncodeHaibMethylRrbsPanisletsSitesRep2 None Sites pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PanIslets Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanisletsSitesRep1 PanIslets 1 PanIslets MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001373 1373 GSM683874 Myers HudsonAlpha SL1937 Duke 1 wgEncodeHaibMethylRrbsPanisletsSitesRep1 None Sites pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PanIslets Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep2 Pancreas_BC 2 BC_Pancreas_H12817N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001392 1392 GSM683819 Myers HudsonAlpha SL3442 BioChain 2 wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep2 None Sites pancreas, donor H12817N, age 71, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Pancreas BC H12817N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep1 Pancreas_BC 1 BC_Pancreas_H12817N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001392 1392 GSM683848 Myers HudsonAlpha SL1726 BioChain 1 wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep1 None Sites pancreas, donor H12817N, age 71, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Pancreas BC H12817N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanc1UwSitesRep2 PANC-1 UW 2 PANC-1 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001408 1408 GSM1048458 Myers HudsonAlpha SL4743 UW 2 wgEncodeHaibMethylRrbsPanc1UwSitesRep2 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 UW Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanc1HaibSitesRep2 PANC-1 HA 2 PANC-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001408 1408 GSM683920 Myers HudsonAlpha SL3552 HudsonAlpha 2 wgEncodeHaibMethylRrbsPanc1HaibSitesRep2 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 HAIB Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanc1UwSitesRep1 PANC-1 UW 1 PANC-1 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001408 1408 GSM1048458 Myers HudsonAlpha SL861 UW 1 wgEncodeHaibMethylRrbsPanc1UwSitesRep1 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 UW Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanc1HaibSitesRep1 PANC-1 HA 1 PANC-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001408 1408 GSM683866 Myers HudsonAlpha SL3551 HudsonAlpha 1 wgEncodeHaibMethylRrbsPanc1HaibSitesRep1 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 HAIB Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsOvcar3UwSitesRep2 Ovcar-3 2 ovcar-3 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001419 1419 GSM980577 Myers HudsonAlpha SL4746 UW 2 wgEncodeHaibMethylRrbsOvcar3UwSitesRep2 None Sites ovarian adenocarcinoma, "the NIH: OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID: 6604576) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Ovcar-3 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsOvcar3UwSitesRep1 Ovcar-3 1 ovcar-3 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001419 1419 GSM980577 Myers HudsonAlpha SL904 UW 1 wgEncodeHaibMethylRrbsOvcar3UwSitesRep1 None Sites ovarian adenocarcinoma, "the NIH: OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID: 6604576) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Ovcar-3 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsOsteoblDukeSitesRep2 Osteobl 2 Osteobl MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001381 1381 GSM683928 Myers HudsonAlpha SL1806 Duke 2 wgEncodeHaibMethylRrbsOsteoblDukeSitesRep2 None Sites osteoblasts (NHOst) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Osteoblasts Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsOsteoblDukeSitesRep1 Osteobl 1 Osteobl MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001381 1381 GSM683881 Myers HudsonAlpha SL767 Duke 1 wgEncodeHaibMethylRrbsOsteoblDukeSitesRep1 None Sites osteoblasts (NHOst) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Osteoblasts Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep2 NT2-D1 2 NT2-D1 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001353 1353 GSM683929 Myers HudsonAlpha SL1899 Stanford 2 wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep2 None Sites malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NT2-D1 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep1 NT2-D1 1 NT2-D1 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001353 1353 GSM720349 Myers HudsonAlpha SL758 Stanford 1 wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep1 None Sites malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NT2-D1 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhdfneoUwSitesRep2 NHDF-neo 2 NHDF-neo MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001368 1368 GSM683861 Myers HudsonAlpha SL1376 UW 2 wgEncodeHaibMethylRrbsNhdfneoUwSitesRep2 None Sites neonatal dermal fibroblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHDF-neo Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhdfneoUwSitesRep1 NHDF-neo 1 NHDF-neo MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001368 1368 GSM683797 Myers HudsonAlpha SL895 UW 1 wgEncodeHaibMethylRrbsNhdfneoUwSitesRep1 None Sites neonatal dermal fibroblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHDF-neo Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhbeUwSitesRep2 NHBE 2 NHBE MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001352 1352 GSM683785 Myers HudsonAlpha SL1420 UW 2 wgEncodeHaibMethylRrbsNhbeUwSitesRep2 None Sites bronchial epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHBE Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhbeUwSitesRep1 NHBE 1 NHBE MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001352 1352 GSM683859 Myers HudsonAlpha SL871 UW 1 wgEncodeHaibMethylRrbsNhbeUwSitesRep1 None Sites bronchial epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHBE Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhaUwSitesRep2 NH-A 2 NH-A MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001380 1380 GSM683923 Myers HudsonAlpha SL1621 UW 2 wgEncodeHaibMethylRrbsNhaUwSitesRep2 None Sites astrocytes (also called Astrocy) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NH-A Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhaUwSitesRep1 NH-A 1 NH-A MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001380 1380 GSM683873 Myers HudsonAlpha SL887 UW 1 wgEncodeHaibMethylRrbsNhaUwSitesRep1 None Sites astrocytes (also called Astrocy) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NH-A Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNb4UwSitesRep2 NB4 2 NB4 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001351 1351 GSM683827 Myers HudsonAlpha SL1442 UW 2 wgEncodeHaibMethylRrbsNb4UwSitesRep2 None Sites acute promyelocytic leukemia cell line. (PMID: 1995093) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NB4 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNb4UwSitesRep1 NB4 1 NB4 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001351 1351 GSM683857 Myers HudsonAlpha SL872 UW 1 wgEncodeHaibMethylRrbsNb4UwSitesRep1 None Sites acute promyelocytic leukemia cell line. (PMID: 1995093) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NB4 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMyometrDukeSitesRep2 Myometr 2 Myometr MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001407 1407 GSM683762 Myers HudsonAlpha SL3476 Duke 2 wgEncodeHaibMethylRrbsMyometrDukeSitesRep2 None Sites myometrial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Myometr Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMyometrDukeSitesRep1 Myometr 1 Myometr MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001407 1407 GSM683889 Myers HudsonAlpha SL3475 Duke 1 wgEncodeHaibMethylRrbsMyometrDukeSitesRep1 None Sites myometrial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Myometr Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMelanoSitesRep2 Melano 2 Melano MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001372 1372 GSM683840 Myers HudsonAlpha SL1809 Duke 2 wgEncodeHaibMethylRrbsMelanoSitesRep2 None Sites epidermal melanocytes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Melano Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMelanoSitesRep1 Melano 1 Melano MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001372 1372 GSM683860 Myers HudsonAlpha SL1820 Duke 1 wgEncodeHaibMethylRrbsMelanoSitesRep1 None Sites epidermal melanocytes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Melano Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2 MCF-7 CTCF 2 MCF-7 MethylRrbs ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEH003032 3032 GSM980574 Myers HudsonAlpha SL14362 Duke 2 wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2 CTCF_shRNA_knockdown Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Sites MCF-7 shRNA CTCF knockdown Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2 MCF-7 Cont 2 MCF-7 MethylRrbs ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEH003033 3033 GSM980575 Myers HudsonAlpha SL14364 Duke 2 wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2 Randomized_shRNA_control Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Sites MCF-7 shRNA Control Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1 MCF-7 CTCF 1 MCF-7 MethylRrbs ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEH003032 3032 GSM980574 Myers HudsonAlpha SL14361 Duke 1 wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1 CTCF_shRNA_knockdown Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Sites MCF-7 shRNA CTCF knockdown Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1 MCF-7 Cont 1 MCF-7 MethylRrbs ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEH003033 3033 GSM980575 Myers HudsonAlpha SL14363 Duke 1 wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1 Randomized_shRNA_control Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Sites MCF-7 shRNA Control Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep2 MCF10A 2 MCF10A-Er-Src MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001378 1378 GSM683822 Myers HudsonAlpha SL730 Stanford 2 wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep2 None Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF10A Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep2 MCF10A Tam 2 MCF10A-Er-Src MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001379 1379 GSM683791 Myers HudsonAlpha SL733 Stanford 2 wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep2 4OHTAM_1uM_36hr Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Sites MCF10A Tamoxifen Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep1 MCF10A 1 MCF10A-Er-Src MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001378 1378 GSM683896 Myers HudsonAlpha SL729 Stanford 1 wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep1 None Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF10A Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep1 MCF10A Tam 1 MCF10A-Er-Src MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001379 1379 GSM683853 Myers HudsonAlpha SL732 Stanford 1 wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep1 4OHTAM_1uM_36hr Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Sites MCF10A Tamoxifen Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep2 Lung BC 2 BC_Lung_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001391 1391 GSM683940 Myers HudsonAlpha SL3433 BioChain 2 wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep2 None Sites lung, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Lung BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep1 Lung BC 1 BC_Lung_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001391 1391 GSM683821 Myers HudsonAlpha SL1725 BioChain 1 wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep1 None Sites lung, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Lung BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapUwSitesRep2 LNCaP UW 2 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001406 1406 GSM683768 Myers HudsonAlpha SL3561 UW 2 wgEncodeHaibMethylRrbsLncapUwSitesRep2 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP UW Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapDukeSitesRep2 LNCaP Duke 2 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001406 1406 GSM683924 Myers HudsonAlpha SL3545 Duke 2 wgEncodeHaibMethylRrbsLncapDukeSitesRep2 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP Duke Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep2 LNCaP Andro 2 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001367 1367 GSM683776 Myers HudsonAlpha SL1805 Duke 2 wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep2 androgen Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Sites LNCaP Androgen Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapUwSitesRep1 LNCaP UW 1 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001406 1406 GSM683863 Myers HudsonAlpha SL907 UW 1 wgEncodeHaibMethylRrbsLncapUwSitesRep1 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP UW Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapDukeSitesRep1 LNCaP Duke 1 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001406 1406 GSM683862 Myers HudsonAlpha SL787 Duke 1 wgEncodeHaibMethylRrbsLncapDukeSitesRep1 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP Duke Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep1 LNCaP Andro 1 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001367 1367 GSM683946 Myers HudsonAlpha SL1903 Duke 1 wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep1 androgen Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Sites LNCaP Androgen Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep2 Liver_BC 2 BC_Liver_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001390 1390 GSM683782 Myers HudsonAlpha SL3438 BioChain 2 wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep2 None Sites liver, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Liver BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep1 Liver BC 1 BC_Liver_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001390 1390 GSM683914 Myers HudsonAlpha SL1996 BioChain 1 wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep1 None Sites liver, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Liver BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep2 Leukocyte_BC 2 BC_Leukocyte_UHN00204 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001389 1389 GSM683759 Myers HudsonAlpha SL3261 BioChain 2 wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep2 None Sites peripheral blood mononuclear cell, donor UHN00204, age 54, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Leukocyte BC UHN00204 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep1 Leukocyte_BC 1 BC_Leukocyte_UHN00204 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001389 1389 GSM683876 Myers HudsonAlpha SL1755 BioChain 1 wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep1 None Sites peripheral blood mononuclear cell, donor UHN00204, age 54, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Leukocyte BC UHN00204 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep2 Ventricle_BC 2 BC_Left_Ventricle_N41 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001388 1388 GSM683895 Myers HudsonAlpha SL3264 BioChain 2 wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep2 None Sites left ventricle, donor N41, age 26, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Left Ventricle BC N41 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep1 Ventricle 1 BC_Left_Ventricle_N41 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001388 1388 GSM683846 Myers HudsonAlpha SL1722 BioChain 1 wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep1 None Sites left ventricle, donor N41, age 26, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Left Ventricle BC N41 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep2 Kidney_BC 2 BC_Kidney_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001387 1387 GSM683878 Myers HudsonAlpha SL3435 BioChain 2 wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep2 None Sites kidney, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Kidney BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep1 Kidney_BC 1 BC_Kidney_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001387 1387 GSM683870 Myers HudsonAlpha SL1751 BioChain 1 wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep1 None Sites kidney, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Kidney BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsJurkatUwSitesRep2 Jurkat 2 Jurkat MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001359 1359 GSM683806 Myers HudsonAlpha SL1345 UW 2 wgEncodeHaibMethylRrbsJurkatUwSitesRep2 None Sites T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Jurkati Methyl-RRBS Rep 2  from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsJurkatUwSitesRep1 Jurkat 1 Jurkat MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001359 1359 GSM683792 Myers HudsonAlpha SL899 UW 1 wgEncodeHaibMethylRrbsJurkatUwSitesRep1 None Sites T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Jurkat Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHtr8DukeSitesRep3 HTR8svn 2 HTR8svn MethylRrbs ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001415 1415 GSM683867 Myers HudsonAlpha SL1811 Duke 3 wgEncodeHaibMethylRrbsHtr8DukeSitesRep3 None Sites trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HTR-8svn Methyl-RRBS Rep 2 (Lab Rep 3) from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHtr8DukeSitesRep1 HTR8svn 1 HTR8svn MethylRrbs ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001415 1415 GSM683939 Myers HudsonAlpha SL3474 Duke 1 wgEncodeHaibMethylRrbsHtr8DukeSitesRep1 None Sites trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HTR-8svn Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep3 HSMMtube_FSHD 3 HSMMtube_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002061 2061 GSM980579 Myers HudsonAlpha SL1918 Duke 3 wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep3 None Sites myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube FSHD Methyl RRBS Rep 3 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep2 HSMMtube_FSHD 2 HSMMtube_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002061 2061 GSM980579 Myers HudsonAlpha SL1921 Duke 2 wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep2 None Sites myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube FSHD Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep1 HSMMtube_FSHD 1 HSMMtube_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002061 2061 GSM980579 Myers HudsonAlpha SL1920 Duke 1 wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep1 None Sites myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube FSHD Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtDukeSitesRep3 HSMMtube 3 HSMMtube MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001348 1348 GSM683801 Myers HudsonAlpha SL1915 Duke 3 wgEncodeHaibMethylRrbsHsmmtDukeSitesRep3 None Sites skeletal muscle myotubes differentiated from the HSMM cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube Methyl-RRBS Rep 3 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtDukeSitesRep2 HSMMtube 2 HSMMtube MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001348 1348 GSM683799 Myers HudsonAlpha SL1935 Duke 2 wgEncodeHaibMethylRrbsHsmmtDukeSitesRep2 None Sites skeletal muscle myotubes differentiated from the HSMM cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtDukeSitesRep1 HSMMtube 1 HSMMtube MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001348 1348 GSM683945 Myers HudsonAlpha SL1916 Duke 1 wgEncodeHaibMethylRrbsHsmmtDukeSitesRep1 None Sites skeletal muscle myotubes differentiated from the HSMM cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep3 HSMM_FSHD 3 HSMM_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002060 2060 GSM980578 Myers HudsonAlpha SL1917 Duke 3 wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep3 None Sites primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM FSHD Methyl RRBS Rep 3 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep2 HSMM_FSHD 2 HSMM_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002060 2060 GSM980578 Myers HudsonAlpha SL1936 Duke 2 wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep2 None Sites primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM FSHD Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep1 HSMM_FSHD 1 HSMM_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002060 2060 GSM980578 Myers HudsonAlpha SL1919 Duke 1 wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep1 None Sites primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM FSHD Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmDukeSitesRep2 HSMM 2 HSMM MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001371 1371 GSM683907 Myers HudsonAlpha SL940 Duke 2 wgEncodeHaibMethylRrbsHsmmDukeSitesRep2 None Sites skeletal muscle myoblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmDukeSitesRep1 HSMM 1 HSMM MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001371 1371 GSM683818 Myers HudsonAlpha SL939 Duke 1 wgEncodeHaibMethylRrbsHsmmDukeSitesRep1 None Sites skeletal muscle myoblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHrpeUwSitesRep2 HRPEpiC 2 HRPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001358 1358 GSM683905 Myers HudsonAlpha SL1443 UW 2 wgEncodeHaibMethylRrbsHrpeUwSitesRep2 None Sites retinal pigment epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRPEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHrpeUwSitesRep1 HRPEpiC 1 HRPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001358 1358 GSM683773 Myers HudsonAlpha SL874 UW 1 wgEncodeHaibMethylRrbsHrpeUwSitesRep1 None Sites retinal pigment epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRPEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHreUwSitesRep2 HRE 2 HRE MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001357 1357 GSM683943 Myers HudsonAlpha SL1343 UW 2 wgEncodeHaibMethylRrbsHreUwSitesRep2 None Sites renal epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRE Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHreUwSitesRep1 HRE 1 HRE MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001357 1357 GSM683831 Myers HudsonAlpha SL865 UW 1 wgEncodeHaibMethylRrbsHreUwSitesRep1 None Sites renal epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRE Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHrceUwSitesRep2 HRCEpiC 2 HRCEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001347 1347 GSM683851 Myers HudsonAlpha SL1344 UW 2 wgEncodeHaibMethylRrbsHrceUwSitesRep2 None Sites renal cortical epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRCEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHrceUwSitesRep1 HRCEpiC 1 HRCEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001347 1347 GSM683901 Myers HudsonAlpha SL866 UW 1 wgEncodeHaibMethylRrbsHrceUwSitesRep1 None Sites renal cortical epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRCEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHpaeUwSitesRep2 HPAEpiC 2 HPAEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001366 1366 GSM683913 Myers HudsonAlpha SL1347 UW 2 wgEncodeHaibMethylRrbsHpaeUwSitesRep2 None Sites pulmonary alveolar epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HPAEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHpaeUwSitesRep1 HPAEpiC 1 HPAEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001366 1366 GSM683794 Myers HudsonAlpha SL897 UW 1 wgEncodeHaibMethylRrbsHpaeUwSitesRep1 None Sites pulmonary alveolar epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HPAEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHnpceUwSitesRep2 HNPCEpiC 2 HNPCEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001346 1346 GSM683808 Myers HudsonAlpha SL1440 UW 2 wgEncodeHaibMethylRrbsHnpceUwSitesRep2 None Sites non-pigment ciliary epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HNPCEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHnpceUwSitesRep1 HNPCEpiC 1 HNPCEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001346 1346 GSM683844 Myers HudsonAlpha SL877 UW 1 wgEncodeHaibMethylRrbsHnpceUwSitesRep1 None Sites non-pigment ciliary epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HNPCEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHmecUwSitesRep2 HMEC 2 HMEC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001345 1345 GSM683854 Myers HudsonAlpha SL1421 UW 2 wgEncodeHaibMethylRrbsHmecUwSitesRep2 None Sites mammary epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HMEC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHmecUwSitesRep1 HMEC 1 HMEC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001345 1345 GSM683944 Myers HudsonAlpha SL867 UW 1 wgEncodeHaibMethylRrbsHmecUwSitesRep1 None Sites mammary epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HMEC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHl60UwSitesRep2 HL-60 2 HL-60 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001418 1418 GSM980576 Myers HudsonAlpha SL4742 UW 2 wgEncodeHaibMethylRrbsHl60UwSitesRep2 None Sites promyelocytic leukemia cells, (PMID: 276884) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HL-60 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHl60UwSitesRep1 HL-60 1 HL-60 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001418 1418 GSM980576 Myers HudsonAlpha SL902 UW 1 wgEncodeHaibMethylRrbsHl60UwSitesRep1 None Sites promyelocytic leukemia cells, (PMID: 276884) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HL-60 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHipeUwSitesRep2 HIPEpiC 2 HIPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001344 1344 GSM683942 Myers HudsonAlpha SL1619 UW 2 wgEncodeHaibMethylRrbsHipeUwSitesRep2 None Sites iris pigment epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HIPEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHipeUwSitesRep1 HIPEpiC 1 HIPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001344 1344 GSM683816 Myers HudsonAlpha SL875 UW 1 wgEncodeHaibMethylRrbsHipeUwSitesRep1 None Sites iris pigment epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HIPEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep2 Hepatocytes 2 Hepatocytes MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001405 1405 GSM683872 Myers HudsonAlpha SL1807 Duke 2 wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep2 None Sites primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Hepatocytes Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep1 Hepatocytes 1 Hepatocytes MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001405 1405 GSM683764 Myers HudsonAlpha SL1819 Duke 1 wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep1 None Sites primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Hepatocytes Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHek293UwSitesRep2 HEK293 UW 2 HEK293 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001343 1343 GSM683769 Myers HudsonAlpha SL1422 UW 2 wgEncodeHaibMethylRrbsHek293UwSitesRep2 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 UW Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHek293StanfordSitesRep2 HEK293 St 2 HEK293 MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001343 1343 GSM720354 Myers HudsonAlpha SL1901 Stanford 2 wgEncodeHaibMethylRrbsHek293StanfordSitesRep2 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 St Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHek293UwSitesRep1 HEK293 UW 1 HEK293 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001343 1343 GSM683825 Myers HudsonAlpha SL860 UW 1 wgEncodeHaibMethylRrbsHek293UwSitesRep1 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 UW Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHek293StanfordSitesRep1 HEK293 St 1 HEK293 MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001343 1343 GSM720355 Myers HudsonAlpha SL759 Stanford 1 wgEncodeHaibMethylRrbsHek293StanfordSitesRep1 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 St Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHeeUwSitesRep2 HEEpiC 2 HEEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001342 1342 GSM683807 Myers HudsonAlpha SL1620 UW 2 wgEncodeHaibMethylRrbsHeeUwSitesRep2 None Sites esophageal epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHeeUwSitesRep1 HEEpiC 1 HEEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001342 1342 GSM683839 Myers HudsonAlpha SL896 UW 1 wgEncodeHaibMethylRrbsHeeUwSitesRep1 None Sites esophageal epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHct116StanfordSitesRep2 HCT-116 2 HCT-116 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001356 1356 GSM683898 Myers HudsonAlpha SL1902 Stanford 2 wgEncodeHaibMethylRrbsHct116StanfordSitesRep2 None Sites colorectal carcinoma (PMID: 7214343) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCT-116 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHct116StanfordSitesRep1 HCT-116 1 HCT-116 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001356 1356 GSM683788 Myers HudsonAlpha SL757 Stanford 1 wgEncodeHaibMethylRrbsHct116StanfordSitesRep1 None Sites colorectal carcinoma (PMID: 7214343) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCT-116 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcpeUwSitesRep2 HCPEpiC 2 HCPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001365 1365 GSM683849 Myers HudsonAlpha SL1439 UW 2 wgEncodeHaibMethylRrbsHcpeUwSitesRep2 None Sites choroid plexus epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCPEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcpeUwSitesRep1 HCPEpiC 1 HCPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001365 1365 GSM683936 Myers HudsonAlpha SL892 UW 1 wgEncodeHaibMethylRrbsHcpeUwSitesRep1 None Sites choroid plexus epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCPEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcmUwSitesRep2 HCM 2 HCM MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001341 1341 GSM683922 Myers HudsonAlpha SL1626 UW 2 wgEncodeHaibMethylRrbsHcmUwSitesRep2 None Sites cardiac myocytes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCM Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcmUwSitesRep1 HCM 1 HCM MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001341 1341 GSM683852 Myers HudsonAlpha SL873 UW 1 wgEncodeHaibMethylRrbsHcmUwSitesRep1 None Sites cardiac myocytes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCM Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcfUwSitesRep2 HCF 2 HCF MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001340 1340 GSM683829 Myers HudsonAlpha SL1441 UW 2 wgEncodeHaibMethylRrbsHcfUwSitesRep2 None Sites cardiac fibroblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCF Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcfUwSitesRep1 HCF 1 HCF MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001340 1340 GSM683837 Myers HudsonAlpha SL898 UW 1 wgEncodeHaibMethylRrbsHcfUwSitesRep1 None Sites cardiac fibroblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCF Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHaeUwSitesRep2 HAEpiC 2 HAEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001339 1339 GSM683858 Myers HudsonAlpha SL1618 UW 2 wgEncodeHaibMethylRrbsHaeUwSitesRep2 None Sites amniotic epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HAEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHaeUwSitesRep1 HAEpiC 1 HAEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001339 1339 GSM683824 Myers HudsonAlpha SL889 UW 1 wgEncodeHaibMethylRrbsHaeUwSitesRep1 None Sites amniotic epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HAEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm19240DukeSitesRep2 GM19240 2 GM19240 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001338 1338 GSM683938 Myers HudsonAlpha SL1803 Duke 2 wgEncodeHaibMethylRrbsGm19240DukeSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19240 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm19240DukeSitesRep1 GM19240 1 GM19240 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001338 1338 GSM683777 Myers HudsonAlpha SL943 Duke 1 wgEncodeHaibMethylRrbsGm19240DukeSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19240 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm19239DukeSitesRep2 GM19239 2 GM19239 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001337 1337 GSM683843 Myers HudsonAlpha SL793 Duke 2 wgEncodeHaibMethylRrbsGm19239DukeSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19239 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm19239DukeSitesRep1 GM19239 1 GM19239 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001337 1337 GSM683903 Myers HudsonAlpha SL1804 Duke 1 wgEncodeHaibMethylRrbsGm19239DukeSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19239 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12892HaibSitesRep2 GM12892 2 GM12892 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001361 1361 GSM683887 Myers HudsonAlpha SL760 HudsonAlpha 2 wgEncodeHaibMethylRrbsGm12892HaibSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12892 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12892HaibSitesRep1 GM12892 1 GM12892 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001361 1361 GSM683902 Myers HudsonAlpha SL761 HudsonAlpha 1 wgEncodeHaibMethylRrbsGm12892HaibSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12892 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12891HaibSitesRep2 GM12891 2 GM12891 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001360 1360 GSM683921 Myers HudsonAlpha SL1233 HudsonAlpha 2 wgEncodeHaibMethylRrbsGm12891HaibSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12891 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12891HaibSitesRep1 GM12891 1 GM12891 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001360 1360 GSM683835 Myers HudsonAlpha SL1232 HudsonAlpha 1 wgEncodeHaibMethylRrbsGm12891HaibSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12891 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep2 GM12878-XiM 2 GM12878-XiMat MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001376 1376 GSM683841 Myers HudsonAlpha SL1614 HudsonAlpha 2 wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep2 None Sites B-lymphocyte, lymphoblastoid, cloned for maternal X inactivation, International HapMap Project, CEPH/Utah, Epstein-Barr Virus DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878-XiMat Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep1 GM12878-XiM 1 GM12878-XiMat MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001376 1376 GSM683774 Myers HudsonAlpha SL1615 HudsonAlpha 1 wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep1 None Sites B-lymphocyte, lymphoblastoid, cloned for maternal X inactivation, International HapMap Project, CEPH/Utah, Epstein-Barr Virus DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878-XiMat Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm06990UwSitesRep2 GM06990 2 GM06990 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001417 1417 GSM980583 Myers HudsonAlpha SL4745 UW 2 wgEncodeHaibMethylRrbsGm06990UwSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM06990 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm06990UwSitesRep1 GM06990 1 GM06990 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001417 1417 GSM980583 Myers HudsonAlpha SL901 UW 1 wgEncodeHaibMethylRrbsGm06990UwSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM06990 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsFibroblDukeSitesRep2 Fibrobl 2 Fibrobl MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001336 1336 GSM683847 Myers HudsonAlpha SL1818 Duke 2 wgEncodeHaibMethylRrbsFibroblDukeSitesRep2 None Sites child fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Fibrobl Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsFibroblDukeSitesRep1 Fibrobl 1 Fibrobl MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001336 1336 GSM683766 Myers HudsonAlpha SL765 Duke 1 wgEncodeHaibMethylRrbsFibroblDukeSitesRep1 None Sites child fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Fibrobl Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsEcc1HaibSitesRep2 ECC-1 2 ECC-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001403 1403 GSM683925 Myers HudsonAlpha SL3483 HudsonAlpha 2 wgEncodeHaibMethylRrbsEcc1HaibSitesRep2 None Sites epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites ECC-1 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsEcc1HaibSitesRep1 ECC-1 1 ECC-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001403 1403 GSM683845 Myers HudsonAlpha SL3482 HudsonAlpha 1 wgEncodeHaibMethylRrbsEcc1HaibSitesRep1 None Sites epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites ECC-1 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsCmkUwSitesRep2 CMK 2 CMK MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001335 1335 GSM683930 Myers HudsonAlpha SL1341 UW 2 wgEncodeHaibMethylRrbsCmkUwSitesRep2 None Sites acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites CMK Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsCmkUwSitesRep1 CMK 1 CMK MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001335 1335 GSM683778 Myers HudsonAlpha SL870 UW 1 wgEncodeHaibMethylRrbsCmkUwSitesRep1 None Sites acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites CMK Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsCaco2UwSitesRep2 Caco-2 2 Caco-2 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001416 1416 GSM980582 Myers HudsonAlpha SL4744 UW 2 wgEncodeHaibMethylRrbsCaco2UwSitesRep2 None Sites colorectal adenocarcinoma. (PMID: 1939345) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Caco-2 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsCaco2UwSitesRep1 Caco-2 1 Caco-2 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001416 1416 GSM980582 Myers HudsonAlpha SL862 UW 1 wgEncodeHaibMethylRrbsCaco2UwSitesRep1 None Sites colorectal adenocarcinoma. (PMID: 1939345) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Caco-2 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep2 Breast BC 2 BC_Breast_02-03015 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001386 1386 GSM683761 Myers HudsonAlpha SL3430 BioChain 2 wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep2 None Sites breast, donor 02-03015, age 21, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Breast BC 02-03015 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep1 Breast_BC 1 BC_Breast_02-03015 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001386 1386 GSM683834 Myers HudsonAlpha SL1673 BioChain 1 wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep1 None Sites breast, donor 02-03015, age 21, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Breast BC 02-03015 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep2 Brain_BC 2 BC_Brain_H11058N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001385 1385 GSM683798 Myers HudsonAlpha SL3267 BioChain 2 wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep2 None Sites brain, donor H11058N, age 66, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Brain BC H11058N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep1 Brain_BC 1 BC_Brain_H11058N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001385 1385 GSM683908 Myers HudsonAlpha SL1672 BioChain 1 wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep1 None Sites brain, donor H11058N, age 66, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Brain BC H11058N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBjUwSitesRep2 BJ 2 BJ MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001402 1402 GSM683763 Myers HudsonAlpha SL3560 UW 2 wgEncodeHaibMethylRrbsBjUwSitesRep2 None Sites skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites BJ Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBjUwSitesRep1 BJ 1 BJ MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001402 1402 GSM683779 Myers HudsonAlpha SL903 UW 1 wgEncodeHaibMethylRrbsBjUwSitesRep1 None Sites skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites BJ Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBe2cHaibSitesRep2 BE2_C 2 BE2_C MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001401 1401 GSM683869 Myers HudsonAlpha SL3556 HudsonAlpha 2 wgEncodeHaibMethylRrbsBe2cHaibSitesRep2 None Sites neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites BE2 C Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBe2cHaibSitesRep1 BE2_C 1 BE2_C MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001401 1401 GSM683885 Myers HudsonAlpha SL3555 HudsonAlpha 1 wgEncodeHaibMethylRrbsBe2cHaibSitesRep1 None Sites neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites BE2 C Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAosmcDukeSitesRep2 AoSMC 2 AoSMC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001382 1382 GSM683910 Myers HudsonAlpha SL3546 Duke 2 wgEncodeHaibMethylRrbsAosmcDukeSitesRep2 None Sites aortic smooth muscle cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AoSMC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAosmcDukeSitesRep1 AoSMC 1 AoSMC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001382 1382 GSM683814 Myers HudsonAlpha SL766 Duke 1 wgEncodeHaibMethylRrbsAosmcDukeSitesRep1 None Sites aortic smooth muscle cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AoSMC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg10803UwSitesRep2 AG10803 2 AG10803 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001334 1334 GSM683912 Myers HudsonAlpha SL1438 UW 2 wgEncodeHaibMethylRrbsAg10803UwSitesRep2 None Sites abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG10803 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg10803UwSitesRep1 AG10803 1 AG10803 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001334 1334 GSM683809 Myers HudsonAlpha SL891 UW 1 wgEncodeHaibMethylRrbsAg10803UwSitesRep1 None Sites abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG10803 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg09319UwSitesRep2 AG09319 2 AG09319 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001333 1333 GSM683864 Myers HudsonAlpha SL1418 UW 2 wgEncodeHaibMethylRrbsAg09319UwSitesRep2 None Sites gum tissue fibroblasts from apparently heathly 24 year old DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09319 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg09319UwSitesRep1 AG09319 1 AG09319 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001333 1333 GSM683915 Myers HudsonAlpha SL894 UW 1 wgEncodeHaibMethylRrbsAg09319UwSitesRep1 None Sites gum tissue fibroblasts from apparently heathly 24 year old DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09319 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg09309UwSitesRep2 AG09309 2 AG09309 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001332 1332 GSM683886 Myers HudsonAlpha SL1437 UW 2 wgEncodeHaibMethylRrbsAg09309UwSitesRep2 None Sites adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09309 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg09309UwSitesRep1 AG09309 1 AG09309 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001332 1332 GSM683767 Myers HudsonAlpha SL888 UW 1 wgEncodeHaibMethylRrbsAg09309UwSitesRep1 None Sites adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09309 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg04450UwSitesRep2 AG04450 2 AG04450 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001331 1331 GSM683880 Myers HudsonAlpha SL1417 UW 2 wgEncodeHaibMethylRrbsAg04450UwSitesRep2 None Sites fetal lung fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04450 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg04450UwSitesRep1 AG04450 1 AG04450 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001331 1331 GSM683817 Myers HudsonAlpha SL893 UW 1 wgEncodeHaibMethylRrbsAg04450UwSitesRep1 None Sites fetal lung fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04450 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg04449UwSitesRep2 AG04449 2 AG04449 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001330 1330 GSM683897 Myers HudsonAlpha SL1625 UW 2 wgEncodeHaibMethylRrbsAg04449UwSitesRep2 None Sites fetal buttock/thigh fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04449 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg04449UwSitesRep1 AG04449 1 AG04449 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001330 1330 GSM683830 Myers HudsonAlpha SL890 UW 1 wgEncodeHaibMethylRrbsAg04449UwSitesRep1 None Sites fetal buttock/thigh fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04449 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep2 Adrenal_BC 2 BC_Adrenal_Gland_H12803N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001384 1384 GSM683883 Myers HudsonAlpha SL3265 BioChain 2 wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep2 None Sites adrenal gland, donor H12803N, age 88, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Adrenal Gland BC H12803N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep1 Adrenal_BC 1 BC_Adrenal_Gland_H12803N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001384 1384 GSM683786 Myers HudsonAlpha SL1676 BioChain 1 wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep1 None Sites adrenal gland, donor H12803N, age 88, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Adrenal Gland BC H12803N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknshHaibSitesRep2 SK-N-SH 2 SK-N-SH MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001404 1404 GSM683775 Myers HudsonAlpha SL3550 HudsonAlpha 2 wgEncodeHaibMethylRrbsSknshHaibSitesRep2 None Sites neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknshHaibSitesRep1 SK-N-SH 1 SK-N-SH MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001404 1404 GSM683888 Myers HudsonAlpha SL3549 HudsonAlpha 1 wgEncodeHaibMethylRrbsSknshHaibSitesRep1 None Sites neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7DukeSitesRep2 MCF-7 2 MCF-7 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001350 1350 GSM683793 Myers HudsonAlpha SL1813 Duke 2 wgEncodeHaibMethylRrbsMcf7DukeSitesRep2 None Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF-7 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7DukeSitesRep1 MCF-7 1 MCF-7 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001350 1350 GSM683787 Myers HudsonAlpha SL1812 Duke 1 wgEncodeHaibMethylRrbsMcf7DukeSitesRep1 None Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF-7 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsImr90UwSitesRep2 IMR90 2 IMR90 MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001377 1377 GSM683815 Myers HudsonAlpha SL1375 UW 2 wgEncodeHaibMethylRrbsImr90UwSitesRep2 None Sites fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites IMR90 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsImr90UwSitesRep1 IMR90 1 IMR90 MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001377 1377 GSM683823 Myers HudsonAlpha SL900 UW 1 wgEncodeHaibMethylRrbsImr90UwSitesRep1 None Sites fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites IMR90 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHepg2DukeSitesRep2 HepG2 2 HepG2 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001349 1349 GSM683855 Myers HudsonAlpha SL1816 Duke 2 wgEncodeHaibMethylRrbsHepg2DukeSitesRep2 None Sites hepatocellular carcinoma DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HepG2 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHepg2DukeSitesRep1 HepG2 1 HepG2 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001349 1349 GSM683795 Myers HudsonAlpha SL1815 Duke 1 wgEncodeHaibMethylRrbsHepg2DukeSitesRep1 None Sites hepatocellular carcinoma DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HepG2 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHelas3HaibSitesRep2 HeLa-S3 2 HeLa-S3 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001363 1363 GSM683828 Myers HudsonAlpha SL712 HudsonAlpha 2 wgEncodeHaibMethylRrbsHelas3HaibSitesRep2 None Sites cervical carcinoma DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HeLa-S3 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHelas3HaibSitesRep1 HeLa-S3 1 HeLa-S3 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001363 1363 GSM683926 Myers HudsonAlpha SL657 HudsonAlpha 1 wgEncodeHaibMethylRrbsHelas3HaibSitesRep1 None Sites cervical carcinoma DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HeLa-S3 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep2 A549 2 A549 MethylRrbs ENCODE Mar 2012 Freeze 2011-08-31 2012-05-31 wgEncodeEH002062 2062 GSM980580 Myers HudsonAlpha SL3656 HudsonAlpha 2 wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep2 DMSO_0.02pct_7d Sites epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 7 d with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites A549 DMSO 0.02% 7 d Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep1 A549 1 A549 MethylRrbs ENCODE Mar 2012 Freeze 2011-08-31 2012-05-31 wgEncodeEH002062 2062 GSM980580 Myers HudsonAlpha SL3655 HudsonAlpha 1 wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep1 DMSO_0.02pct_7d Sites epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 7 d with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites A549 DMSO 0.02% 7 d Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsK562HaibSitesRep2 K562 2 K562 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001364 1364 GSM683780 Myers HudsonAlpha SL726 HudsonAlpha 2 wgEncodeHaibMethylRrbsK562HaibSitesRep2 None Sites leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites K562 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsK562HaibSitesRep1 K562 1 K562 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001364 1364 GSM683856 Myers HudsonAlpha SL725 HudsonAlpha 1 wgEncodeHaibMethylRrbsK562HaibSitesRep1 None Sites leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites K562 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsH1hescHaibSitesRep2 H1-hESC 2 H1-hESC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001362 1362 GSM683879 Myers HudsonAlpha SL713 HudsonAlpha 2 wgEncodeHaibMethylRrbsH1hescHaibSitesRep2 None Sites embryonic stem cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites H1-hESC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsH1hescHaibSitesRep1 H1-hESC 1 H1-hESC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001362 1362 GSM683770 Myers HudsonAlpha SL716 HudsonAlpha 1 wgEncodeHaibMethylRrbsH1hescHaibSitesRep1 None Sites embryonic stem cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites H1-hESC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12878HaibSitesRep2 GM12878 2 GM12878 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001355 1355 GSM683927 Myers HudsonAlpha SL728 HudsonAlpha 2 wgEncodeHaibMethylRrbsGm12878HaibSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12878HaibSitesRep1 GM12878 1 GM12878 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001355 1355 GSM683906 Myers HudsonAlpha SL727 HudsonAlpha 1 wgEncodeHaibMethylRrbsGm12878HaibSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethyl450 HAIB Methyl450 GSE40699 CpG Methylation by Methyl 450K  Bead Arrays from ENCODE/HAIB Regulation Description This track is produced as part of the ENCODE project. The track displays the methylation status of specific CpG dinucleotides in the given cell types as identified by the Illumina Infinium Human Methylation 450 Bead Array platform. In general, methylation of CpG sites within a promoter causes silencing of the gene associated with that promoter. The Infinium Human Methylation 450 platform uses bisulfite treated genomic DNA to assay the methylation status of more than 450,000 CpG sites covering all designatable RefSeq genes, including promoter, 5' and 3' regions, without bias against those lacking CpG islands. Additionally, the assay includes CpG islands and shores, CpG sites outside of CpG islands, non-CpG methylated sites identified in human stem cells, differentially methylated sites identified in tumor versus normal (multiple forms of cancer) and across several tissue types, CpG islands outside of coding regions, miRNA promoter regions, and disease-associated regions identified through GWAS. The detailed protocol, information for CpG targets, and beta values are available from the supplemental directory. Display Conventions and Configuration Scores associated with each site are beta values (see Methods) multiplied by 1000. Methylation status is color-coded as: orange = methylated (score &gt;= 600) purple = partially methylated (200 &lt; score &lt; 600) bright blue = unmethylated (0 &lt; score &lt;= 200) black = NA (score = 0) Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Genomic DNA was isolated from each cell line with the QIAGEN DNeasy Blood &amp; Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations and a level of quality of each preparation was determined by fluorescence with the Qubit Fluorometer (Invitrogen). Genomic DNA was treated with sodium bisulfite, converting unmethylated cytosines of CpG dinucleotides into uracils; methylated cytosines did not get converted. After bisulfite treatment, the methylation status of a site was assayed by single base-pair extension with a Cy3 or Cy5 labeled nucleotide on oligo-beads specific for the methylated or unmethylated state. The bisulfite conversion reaction was done using the Zymo Research EZ-96 DNA MethylationTM Kit. One step of the protocol was modified. During the incubation, a 30 second 95oC denaturing step every hour was included to increase reaction efficiency as recommended by the Illumina Infinium Human Methylation27 protocol. The bead arrays were run according to the protocol provided by Illumina. A beta value was calculated for each CpG target with Illumina's Bead Studio software with the Methylation Module v3.2. Beta-value = intensity value from the methylated bead type/(intensity values from the methylated + intensity value from unmethylated bead types + 100). The data was then quality-filtered using p-values. Beta values with p-value greater than 0.01 are considered to fall below the minimum intensity and threshold are displayed as "NA". Any beta value equal to or greater than 0.6 was considered fully methylated. Any beta value equal to or less than 0.2 was considered to be fully unmethylated. Beta values between 0.2 and 0.6 were considered to be partially methylated. Release Notes This is Release 1 (Dec 2011) of the 450K bead array data, with data corrections applied to the displayed data tables in May 2012. A perl script to correct coordinates in the download files has been included in the download directory. The initial release had incorrect probe mappings. The data providers also requested these annotations be limited to the first nucleotide in the probe, so the single CpG assayed is displayed instead of the full probe. When the Infinium platform was first released, it was thought that methylation states of CpG's within the 50 bp window could be assigned by assaying a single nucleotide, but it has since been determined that methylation states vary even at close distances. Credits These data were produced by the Dr. Richard Myers Lab and the Dr. Devin Absher lab at the HudsonAlpha Institute for Biotechnology. Cells were grown by the Myers Lab and other ENCODE production groups. Contact: Dr. Florencia Pauli. References --> Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeHaibMethyl450U87SitesRep1 U87 U87 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002233 2233 GSM999396 Myers HudsonAlpha Methyl450K HudsonAlpha 1 F wgEncodeHaibMethyl450U87SitesRep1 None Sites glioblastoma, astrocytoma, (PMID: 4332744) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Female Sites U87 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450T47dDm002p24hSitesRep1 T-47D DMSO T-47D MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002184 2184 GSM999377 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450T47dDm002p24hSitesRep1 DMSO_0.02pct_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology 24 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites T-47D DMSO Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SknshraSitesRep1 SK-N-SH_RA SK-N-SH_RA MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002231 2231 GSM999388 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450SknshraSitesRep1 None Sites neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH_RA Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SknmcSitesRep1 SK-N-MC SK-N-MC MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002183 2183 GSM999370 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450SknmcSitesRep1 None Sites neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-MC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SkmcSitesRep1 SKMC SKMC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002232 2232 GSM999335 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450SkmcSitesRep1 None Sites skeletal muscle cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SKMC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SaecSitesRep1 SAEC SAEC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002229 2229 GSM999346 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450SaecSitesRep1 None Sites small airway epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SAEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450RptecSitesRep1 RPTEC RPTEC MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002197 2197 GSM999343 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450RptecSitesRep1 None Sites renal proximal tubule epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites RPTEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450ProgfibSitesRep1 ProgFib ProgFib MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002196 2196 GSM999342 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450ProgfibSitesRep1 None Sites fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites ProgFib Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450PrecSitesRep1 PrEC PrEC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002228 2228 GSM999369 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450PrecSitesRep1 None Sites prostate epithelial cell line DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites PrEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Pfsk1SitesRep1 PFSK-1 PFSK-1 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002182 2182 GSM999371 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Pfsk1SitesRep1 None Sites neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites PFSK-1 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Panc1SitesRep1 PANC-1 PANC-1 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002227 2227 GSM999395 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Panc1SitesRep1 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ovcar3SitesRep1 ovcar-3 ovcar-3 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002234 2234 GSM999393 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ovcar3SitesRep1 None Sites ovarian adenocarcinoma, "the NIH: OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID: 6604576) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites ovcar-3 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Nt2d1SitesRep1 NT2-D1 NT2-D1 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002181 2181 GSM999372 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Nt2d1SitesRep1 None Sites malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NT2-D1 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450NhdfneoSitesRep1 NHDF-neo NHDF-neo MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002226 2226 GSM999394 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450NhdfneoSitesRep1 None Sites neonatal dermal fibroblasts DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHDF-neo Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450NhbeSitesRep1 NHBE NHBE MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002225 2225 GSM999358 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450NhbeSitesRep1 None Sites bronchial epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHBE Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450NhaSitesRep1 NH-A NH-A MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002224 2224 GSM999357 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450NhaSitesRep1 None Sites astrocytes (also called Astrocy) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NH-A Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Nb4SitesRep1 NB4 NB4 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002223 2223 GSM999360 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Nb4SitesRep1 None Sites acute promyelocytic leukemia cell line. (PMID: 1995093) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NB4 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Mcf10aesSitesRep1 MCF10A MCF10A-Er-Src MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002222 2222 GSM999359 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Mcf10aesSitesRep1 None Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF10A Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Mcf10aesTamSitesRep1 MCF10A TAM MCF10A-Er-Src MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002235 2235 GSM999392 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Mcf10aesTamSitesRep1 4OHTAM_1uM_36hr Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Sites MCF10A TAM Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450LncapSitesRep1 LNCaP LNCaP MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002179 2179 GSM999368 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450LncapSitesRep1 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450JurkatSitesRep1 Jurkat Jurkat MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002178 2178 GSM999367 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450JurkatSitesRep1 None Sites T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites Jurkat Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HrpeSitesRep1 HRPEpiC HRPEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002221 2221 GSM999362 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HrpeSitesRep1 None Sites retinal pigment epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRPEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HreSitesRep1 HRE HRE MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002220 2220 GSM999361 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HreSitesRep1 None Sites renal epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRE Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HrceSitesRep1 HRCEpiC HRCEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002219 2219 GSM999390 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HrceSitesRep1 None Sites renal cortical epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRCEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HpaeSitesRep1 HPAEpiC HPAEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002218 2218 GSM999391 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HpaeSitesRep1 None Sites pulmonary alveolar epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HPAEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HnpceSitesRep1 HNPCEpiC HNPCEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002217 2217 GSM999384 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HnpceSitesRep1 None Sites non-pigment ciliary epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HNPCEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HmecSitesRep1 HMEC HMEC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002216 2216 GSM999385 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HmecSitesRep1 None Sites mammary epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HMEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hl60SitesRep1 HL-60 HL-60 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002215 2215 GSM999386 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Hl60SitesRep1 None Sites promyelocytic leukemia cells, (PMID: 276884) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HL-60 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HipeSitesRep1 HIPEpiC HIPEpiC MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002190 2190 GSM999336 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HipeSitesRep1 None Sites iris pigment epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HIPEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HepatoSitesRep1 Hepatocyte Hepatocytes MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002193 2193 GSM999339 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450HepatoSitesRep1 None Sites primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites Hepatocyte Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hek293SitesRep1 HEK293 HEK293 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002176 2176 GSM999363 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Hek293SitesRep1 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HeeSitesRep1 HEEpiC HEEpiC MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002189 2189 GSM999378 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HeeSitesRep1 None Sites esophageal epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hct116StanfordSitesRep1 HCT-116 Stanford HCT-116 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002214 2214 GSM999387 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Hct116StanfordSitesRep1 None Sites colorectal carcinoma (PMID: 7214343) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCT-116 Stanford Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hct116HaibSitesRep1 HCT-116 HAIB HCT-116 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002214 2214 GSM999387 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Hct116HaibSitesRep1 None Sites colorectal carcinoma (PMID: 7214343) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCT-116 HAIB Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HcpeSitesRep1 HCPEpiC HCPEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002213 2213 GSM999380 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HcpeSitesRep1 None Sites choroid plexus epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCPEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HcmSitesRep1 HCM HCM MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002212 2212 GSM999381 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HcmSitesRep1 None Sites cardiac myocytes DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCM Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HcfSitesRep1 HCF HCF MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002211 2211 GSM999382 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HcfSitesRep1 None Sites cardiac fibroblasts DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCF Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HaeSitesRep1 HAEpiC HAEpiC MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002208 2208 GSM999355 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HaeSitesRep1 None Sites amniotic epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HAEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm19239SitesRep1 GM19239 GM19239 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002207 2207 GSM999354 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450Gm19239SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19239 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm12892SitesRep1 GM12892 GM12892 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002187 2187 GSM999374 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Gm12892SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12892 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm12891SitesRep1 GM12891 GM12891 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002186 2186 GSM999375 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Gm12891SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12891 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm06990SitesRep1 GM06990 GM06990 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002206 2206 GSM999353 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Gm06990SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM06990 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ecc1SitesRep1 ECC-1 ECC-1 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002175 2175 GSM999366 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Ecc1SitesRep1 None Sites epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites ECC-1 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450CmkSitesRep1 CMK CMK MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002204 2204 GSM999351 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450CmkSitesRep1 None Sites acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites CMK Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Caco2SitesRep1 Caco-2 Caco-2 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002205 2205 GSM999352 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Caco2SitesRep1 None Sites colorectal adenocarcinoma. (PMID: 1939345) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites Caco-2 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450BjSitesRep1 BJ BJ MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002203 2203 GSM999350 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450BjSitesRep1 None Sites skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites BJ Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Be2cSitesRep1 BE2_C BE2_C MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002210 2210 GSM999383 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Be2cSitesRep1 None Sites neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites BE2_C Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450AosmcSitesRep1 AoSMC AoSMC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002209 2209 GSM999356 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450AosmcSitesRep1 None Sites aortic smooth muscle cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AoSMC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag10803SitesRep1 AG10803 AG10803 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002202 2202 GSM999349 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag10803SitesRep1 None Sites abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG10803 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag09319SitesRep1 AG09319 AG09319 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002201 2201 GSM999348 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag09319SitesRep1 None Sites gum tissue fibroblasts from apparently heathly 24 year old DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09319 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag09309SitesRep1 AG09309 AG09309 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002200 2200 GSM999347 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag09309SitesRep1 None Sites adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09309 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag04450SitesRep1 AG04450 AG04450 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002199 2199 GSM999345 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag04450SitesRep1 None Sites fetal lung fibroblast DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04450 Methylation  450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag04449SitesRep1 AG04449 AG04449 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002198 2198 GSM999344 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag04449SitesRep1 None Sites fetal buttock/thigh fibroblast DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04449 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SknshSitesRep1 SK-N-SH SK-N-SH MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002230 2230 GSM999389 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450SknshSitesRep1 None Sites neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Mcf7SitesRep1 MCF-7 MCF-7 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002180 2180 GSM999373 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450Mcf7SitesRep1 None Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF-7 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Imr90SitesRep1 IMR90 IMR90 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002194 2194 GSM999340 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Imr90SitesRep1 None Sites fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites IMR90 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HuvecSitesRep1 HUVEC HUVEC MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002177 2177 GSM999364 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450HuvecSitesRep1 None Sites umbilical vein endothelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HUVEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hepg2SitesRep1 HepG2 HepG2 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002192 2192 GSM999338 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Hepg2SitesRep1 None Sites hepatocellular carcinoma DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HepG2 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Helas3SitesRep1 HeLa-S3 HeLa-S3 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002191 2191 GSM999337 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Helas3SitesRep1 None Sites cervical carcinoma DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HeLa-S3 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450A549Etoh02SitesRep1 A549 ETOH A549 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002174 2174 GSM999365 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450A549Etoh02SitesRep1 EtOH_0.02pct Sites epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Sites A549 EtOH Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450K562SitesRep1 K562 K562 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002195 2195 GSM999341 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450K562SitesRep1 None Sites leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites K562 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450H1hescSitesRep1 H1-hESC H1-hESC MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002188 2188 GSM999379 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450H1hescSitesRep1 None Sites embryonic stem cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites H1-hESC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm12878SitesRep1 GM12878 GM12878 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002185 2185 GSM999376 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Gm12878SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibRnaSeq HAIB RNA-seq GSE35584 RNA-seq from ENCODE/HAIB Expression Description This track was produced as part of the ENCODE Project. RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly (Mortazavi et al., 2008). Biological replicates of ENCODE cell lines were grown on separate culture plates, total RNA was purified and polyA selected two times. The mRNA extract was then fragmented by magnesium-catalyzed hydrolysis and reverse transcribed to cDNA by random priming and amplification. The cDNA was sequenced on an Illumina Genome Analyzer (GAI or GAIIx). The DNA sequences were aligned to the NCBI Build37 (hg19) version of the human genome using the sequence alignment programs ELAND (Illumina) or Bowtie (Langmead et al., 2009). The first 10 residues of sequencing have a weak characteristic nucleotide bias of unknown origin. This RNA-seq protocol does not specify the coding strand. As a result, there will be ambiguity at loci where both strands are transcribed. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks (cell lines, replicates and growth conditions) that display individually on the browser. Instructions for configuring multi-view tracks are here. The following views are in this track: Alignments The Alignments view shows reads mapped to the genome. See the Bowtie Manual for more information about the SAM Bowtie output (including tag definitions) and the SAM Format Specification for more information on the SAM/BAM file format. The reads are named using the following convention: Lane &#35;:Tile &#35;:X-coordinate:Y-coordinate Raw Signal Density graph of signal enrichment based on a normalized aligned read density (Read Per Million, RPM). RPM is reported in the score field and is equal to the number of reads at that position divided by the total number of reads divided by one million. The Raw Signal view displays dense, continuous data as a graph and the RPM measure assists in visualizing the relative amount of a given transcript across multiple samples. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Experimental Procedures Cells were grown according to the approved ENCODE cell culture protocols. Cells were lysed in RLT buffer (Qiagen RNEasy kit) and processed on RNEasy midi columns according to the manufacturer's protocol, with the inclusion of the "on-column" DNase digestion step to remove residual genomic DNA. The mRNA was isolated from at least 10 ug of total RNA with oligo(dT) two times (Dynabeads mRNA PurificationgKit, Invitrogen). Alternatively, cells were lysed and mRNA was purified directly two times with oligo(dT) (Dynabeads mRNA DIRECT Kit, Invitrogen). A quantity of 100 ng of mRNA was fragmented by magnesium-catalyzed hydrolysis and reverse transcribed to cDNA by random priming according to the protocol in Mortazavi et al. (2008). The cDNA was prepared for sequencing on the Genome Analyzer flowcell according to the protocol for the ChIPSeq DNA genomic DNA kit (Illumina). The sequencing libraries were size-selected around 225 bp and amplified with 15 rounds of PCR. Libraries were sequenced with an Illumina Genome Analyzer I or an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. Single end reads of 36 nt in length were obtained. Data Processing and Analysis FastQ files were made from qseq files generated by the Illumina pipeline (Casava 1.7). The Raw Signal files (bigWig) were generated from bedgraph files and the score was calculated as the number of reads at that position divided by the total number of reads divided by one million. Casava export files were aligned to the NCBI Build37 (hg19) version of the human genome with ELAND (Illumina), generating SAM files. FastQ files of experiments that were previously aligned to NCBI Build36 (hg18) were aligned to NCBI Build37 (hg19) using Bowtie (Langmead et al., 2009; parameters: -S -n 2 -k 11 -m 10 --best), also generating SAM files. SAM files were converted to BAM files with SAMtools (Li et al., 2009). Gene expression within GENCODE V7 (Harrow et al., 2006) gene models was estimated using Cufflinks v0.9.3 (Roberts et al., 2011). Estimates of transcript abundance were reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM). FPKM is calculated by dividing the total number of fragments that align to the gene model by the size of the spliced transcript (exons) in kilobases. This number is then divided by the total number of reads in millions for the experiment. FPKM is reported in the last column of the GTF (TranscriptGencV7) files. Raw Data (fastQ), Raw Signal (bigWig), Alignments (BAM) and Transcript GENCODE V7 (GTF) files are available from the Downloads page. Verification The mapped data were visually inspected to verify the majority of the reads fell within known exons. Biological replicates confirm expression measurements with r &gt; 0.90. Release Notes Update (May 2012): the labels of the Raw Signal subtracks have been updated because they were originally labeled as Signals instead of Raw Signals. This is the first NCBI Build37 (hg19) release of this track (Feb 2012). This release includes the 3 datasets (Jurkat, A549/DEX100nm, and A549/EtOH2pct) previously released on NCBI Build36 (hg18) and adds data for several more cell types and growth conditions in replicate. Four types of download files are available for each replicate including the Raw Data (fastQ), Transcript GENCODE V7 (GTF), Raw Signal (bigWig), and Alignments (BAM). Credits These data were produced by the Dr. Richard Myers Lab at the HudsonAlpha Institute for Biotechnology. Contact: Dr. Florencia Pauli References Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 2011;12(3):R22. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeHaibRnaSeqViewSignal Signal RNA-seq from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqU87RawRep2V2 U87 2 U87 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-09 wgEncodeEH001253 1253 GSM923437 Myers HudsonAlpha SL533 cufflinks_v_0.9 bow125 hg18 1x36 2 longPolyA wgEncodeHaibRnaSeqU87RawRep2V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqU87RawRep1V2 U87 1 U87 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-09 wgEncodeEH001253 1253 GSM923437 Myers HudsonAlpha SL532 cufflinks_v_0.9 bow125 hg18 1x36 1 longPolyA wgEncodeHaibRnaSeqU87RawRep1V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dGen4hRawRep2 T-47D GEN 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001245 1245 GSM923436 Myers HudsonAlpha SL1549 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dGen4hRawRep2 Genistein_100nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D GENISTEIN 4 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dGen4hRawRep1 T-47D GEN 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001245 1245 GSM923436 Myers HudsonAlpha SL1246 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dGen4hRawRep1 Genistein_100nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D GENISTEIN 4 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dEstradia4hRawRep2 T-47D EST 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001244 1244 GSM923431 Myers HudsonAlpha SL1548 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dEstradia4hRawRep2 Estradiol_10nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ESTRADIOL 4 hr 10 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dEstradia4hRawRep1 T-47D EST 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001244 1244 GSM923431 Myers HudsonAlpha SL1245 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dEstradia4hRawRep1 Estradiol_10nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ESTRADIOL 4 hr 10 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dDm002p4hRawRep2 T-47D DMSO 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001243 1243 GSM923428 Myers HudsonAlpha SL1547 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dDm002p4hRawRep2 DMSO_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D DMSO 4 hr 0.02% RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dDm002p4hRawRep1 T-47D DMSO 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001243 1243 GSM923428 Myers HudsonAlpha SL1244 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dDm002p4hRawRep1 DMSO_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D DMSO 4 hr 0.02% RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dBpa14hRawRep2 T-47D BPA 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001242 1242 GSM923429 Myers HudsonAlpha SL1911 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dBpa14hRawRep2 BPA_100nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D BPA 4 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dBpa14hRawRep1 T-47D BPA 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001242 1242 GSM923429 Myers HudsonAlpha SL1550 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dBpa14hRawRep1 BPA_100nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D BPA 4 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPfsk1RawRep2 PFSK-1 2 PFSK-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001252 1252 GSM923430 Myers HudsonAlpha SL531 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqPfsk1RawRep2 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPfsk1RawRep1 PFSK-1 1 PFSK-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001252 1252 GSM923430 Myers HudsonAlpha SL530 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqPfsk1RawRep1 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPanc1RawRep2 PANC-1 2 PANC-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001251 1251 GSM923421 Myers HudsonAlpha SL529 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqPanc1RawRep2 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPanc1RawRep1 PANC-1 1 PANC-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001251 1251 GSM923421 Myers HudsonAlpha SL528 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqPanc1RawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqJurkatRawRep2 Jurkat 2 Jurkat RnaSeq ENCODE Mar 2012 Freeze 2011-04-05 2012-01-04 wgEncodeEH000315 315 GSM923424 Myers HudsonAlpha SL317 cufflinks_v_0.9 bow125 hg18 1x36 2 longPolyA wgEncodeHaibRnaSeqJurkatRawRep2 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqJurkatRawRep1 Jurkat 1 Jurkat RnaSeq ENCODE Mar 2012 Freeze 2012-01-24 2012-10-24 wgEncodeEH000315 315 GSM923424 Myers HudsonAlpha SL316 cufflinks_v_0.9 bow125 hg18 1x36 1 longPolyA wgEncodeHaibRnaSeqJurkatRawRep1 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Gen4hRawRep2 ECC-1 GEN 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001241 1241 GSM923426 Myers HudsonAlpha SL2860 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Gen4hRawRep2 Genistein_100nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GENISTEIN 4 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Gen4hRawRep1 ECC-1 GEN 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001241 1241 GSM923426 Myers HudsonAlpha SL991 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Gen4hRawRep1 Genistein_100nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GENISTEIN 4 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Estradia4hRawRep2 ECC-1 EST 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001240 1240 GSM923427 Myers HudsonAlpha SL2932 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Estradia4hRawRep2 Estradiol_10nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ESTRADIOL 4 hr 10 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Estradia4hRawRep1 ECC-1 EST 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001240 1240 GSM923427 Myers HudsonAlpha SL990 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Estradia4hRawRep1 Estradiol_10nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ESTRADIOL 4 hr 10 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Dm002p4hRawRep2 ECC-1 DMSO 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001239 1239 GSM923423 Myers HudsonAlpha SL2861 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Dm002p4hRawRep2 DMSO_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 DMSO 4 hr 0.02% RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Dm002p4hRawRep1 ECC-1 DMSO 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001239 1239 GSM923423 Myers HudsonAlpha SL989 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Dm002p4hRawRep1 DMSO_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 DMSO 4 hr 0.02% RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Bpa14hRawRep2 ECC-1 BPA 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001238 1238 GSM923422 Myers HudsonAlpha SL2859 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Bpa14hRawRep2 BPA_100nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 BPA 4 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Bpa14hRawRep1 ECC-1 BPA 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001238 1238 GSM923422 Myers HudsonAlpha SL1552 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Bpa14hRawRep1 BPA_100nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 BPA 4 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqBe2cRawRep2 BE2_C 2 BE2_C RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001249 1249 GSM923434 Myers HudsonAlpha SL525 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqBe2cRawRep2 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqBe2cRawRep1 BE2_C 1 BE2_C RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001249 1249 GSM923434 Myers HudsonAlpha SL524 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqBe2cRawRep1 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqSknshRawRep2 SK-N-SH 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001250 1250 GSM923419 Myers HudsonAlpha SL527 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqSknshRawRep2 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqSknshRawRep1 SK-N-SH 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001250 1250 GSM923419 Myers HudsonAlpha SL526 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqSknshRawRep1 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02RawRep4 A549 ETOH 4 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000314 314 GSM923425 Myers HudsonAlpha SL1260 cufflinks_v_0.9 bow125 hg19 1x36 4 longPolyA wgEncodeHaibRnaSeqA549Etoh02RawRep4 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETOH 1 hr 0.02% RNA-seq Raw Signal Rep 4 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02RawRep3 A549 ETOH 3 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000314 314 GSM923425 Myers HudsonAlpha SL1255 cufflinks_v_0.9 bow125 hg19 1x36 3 longPolyA wgEncodeHaibRnaSeqA549Etoh02RawRep3 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETOH 1 hr 0.02% RNA-seq Raw Signal Rep 3 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02RawRep2 A549 ETOH 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000314 314 GSM923425 Myers HudsonAlpha SL333 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Etoh02RawRep2 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETOH 1 hr 0.02% RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02RawRep1 A549 ETOH 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000314 314 GSM923425 Myers HudsonAlpha SL331 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Etoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETOH 1 hr 0.02% RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex5nmRawRep2 A549 DEX5nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001248 1248 GSM923435 Myers HudsonAlpha SL1264 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex5nmRawRep2 DEX_5nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 5 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 5 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex5nmRawRep1 A549 DEX5nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001248 1248 GSM923435 Myers HudsonAlpha SL1259 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex5nmRawRep1 DEX_5nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 5 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 5 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex500pmRawRep2 A549 DEX500pM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001247 1247 GSM923432 Myers HudsonAlpha SL1262 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex500pmRawRep2 DEX_500pM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 500 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 500 pM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex500pmRawRep1 A549 DEX500pM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001247 1247 GSM923432 Myers HudsonAlpha SL1257 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex500pmRawRep1 DEX_500pM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 500 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 500 pM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex1nmRawRep2 A549 DEX1nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001246 1246 GSM923433 Myers HudsonAlpha SL1263 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex1nmRawRep2 DEX_1nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 1 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 1 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex1nmRawRep1 A549 DEX1nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001246 1246 GSM923433 Myers HudsonAlpha SL1258 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex1nmRawRep1 DEX_1nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 1 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 1 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100pmRawRep2 A549 DEX100pM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001237 1237 GSM923418 Myers HudsonAlpha SL1261 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex100pmRawRep2 DEX_100pM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 100 pM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100pmRawRep1 A549 DEX100pM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001237 1237 GSM923418 Myers HudsonAlpha SL1256 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex100pmRawRep1 DEX_100pM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 100 pM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100nmRawRep2 A549 DEX100nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000313 313 GSM923420 Myers HudsonAlpha SL332 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex100nmRawRep2 DEX_100nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100nmRawRep1 A549 DEX100nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000313 313 GSM923420 Myers HudsonAlpha SL330 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex100nmRawRep1 DEX_100nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqViewAlignments Alignments RNA-seq from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqU87AlnRep2V2 U87 2 U87 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-09 wgEncodeEH001253 1253 Myers HudsonAlpha SL533 cufflinks_v_0.9 bow125 hg18 1x36 2 longPolyA wgEncodeHaibRnaSeqU87AlnRep2V2 None Alignments glioblastoma, astrocytoma, (PMID: 4332744) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch U87 RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqU87AlnRep1V2 U87 1 U87 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-09 wgEncodeEH001253 1253 Myers HudsonAlpha SL532 cufflinks_v_0.9 bow125 hg18 1x36 1 longPolyA wgEncodeHaibRnaSeqU87AlnRep1V2 None Alignments glioblastoma, astrocytoma, (PMID: 4332744) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch U87 RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dGen4hAlnRep2 T-47D GEN 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001245 1245 Myers HudsonAlpha SL1549 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dGen4hAlnRep2 Genistein_100nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D GENISTEIN 4 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dGen4hAlnRep1 T-47D GEN 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001245 1245 Myers HudsonAlpha SL1246 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dGen4hAlnRep1 Genistein_100nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D GENISTEIN 4 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dEstradia4hAlnRep2 T-47D EST 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001244 1244 Myers HudsonAlpha SL1548 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dEstradia4hAlnRep2 Estradiol_10nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D ESTRADIOL 4 hr 10 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dEstradia4hAlnRep1 T-47D EST 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001244 1244 Myers HudsonAlpha SL1245 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dEstradia4hAlnRep1 Estradiol_10nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D ESTRADIOL 4 hr 10 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dDm002p4hAlnRep2 T-47D DMSO 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001243 1243 Myers HudsonAlpha SL1547 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dDm002p4hAlnRep2 DMSO_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D DMSO 4 hr 0.02% RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dDm002p4hAlnRep1 T-47D DMSO 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001243 1243 Myers HudsonAlpha SL1244 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dDm002p4hAlnRep1 DMSO_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D DMSO 4 hr 0.02% RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dBpa14hAlnRep2 T-47D BPA 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001242 1242 Myers HudsonAlpha SL1911 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dBpa14hAlnRep2 BPA_100nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D BPA 4 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dBpa14hAlnRep1 T-47D BPA 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001242 1242 Myers HudsonAlpha SL1550 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dBpa14hAlnRep1 BPA_100nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D BPA 4 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPfsk1AlnRep2 PFSK-1 2 PFSK-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001252 1252 Myers HudsonAlpha SL531 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqPfsk1AlnRep2 None Alignments neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch PFSK-1 RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPfsk1AlnRep1 PFSK-1 1 PFSK-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001252 1252 Myers HudsonAlpha SL530 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqPfsk1AlnRep1 None Alignments neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch PFSK-1 RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPanc1AlnRep2 PANC-1 2 PANC-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001251 1251 Myers HudsonAlpha SL529 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqPanc1AlnRep2 None Alignments pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch PANC-1 RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPanc1AlnRep1 PANC-1 1 PANC-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001251 1251 Myers HudsonAlpha SL528 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqPanc1AlnRep1 None Alignments pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch PANC-1 RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqJurkatAlnRep2 Jurkat 2 Jurkat RnaSeq ENCODE Mar 2012 Freeze 2011-04-05 2012-01-04 wgEncodeEH000315 315 Myers HudsonAlpha SL317 cufflinks_v_0.9 bow125 hg18 1x36 2 longPolyA wgEncodeHaibRnaSeqJurkatAlnRep2 None Alignments T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch Jurkat RNA-seq Alignments Replicate 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqJurkatAlnRep1V2 Jurkat 1 Jurkat RnaSeq ENCODE Mar 2012 Freeze 2012-01-24 2012-10-24 wgEncodeEH000315 315 Myers HudsonAlpha SL316 cufflinks_v_0.9 bow125 hg18 1x36 1 longPolyA wgEncodeHaibRnaSeqJurkatAlnRep1V2 None Alignments T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch Jurkat RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Gen4hAlnRep2 ECC-1 GEN 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001241 1241 Myers HudsonAlpha SL2860 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Gen4hAlnRep2 Genistein_100nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 GENISTEIN 4 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Gen4hAlnRep1 ECC-1 GEN 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001241 1241 Myers HudsonAlpha SL991 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Gen4hAlnRep1 Genistein_100nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 GENISTEIN 4 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Estradia4hAlnRep2 ECC-1 EST 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001240 1240 Myers HudsonAlpha SL2932 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Estradia4hAlnRep2 Estradiol_10nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 ESTRADIOL 4 hr 10 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Estradia4hAlnRep1 ECC-1 EST 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001240 1240 Myers HudsonAlpha SL990 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Estradia4hAlnRep1 Estradiol_10nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 ESTRADIOL 4 hr 10 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Dm002p4hAlnRep2 ECC-1 DMSO 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001239 1239 Myers HudsonAlpha SL2861 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Dm002p4hAlnRep2 DMSO_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 DMSO 4 hr 0.02% RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Dm002p4hAlnRep1 ECC-1 DMSO 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001239 1239 Myers HudsonAlpha SL989 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Dm002p4hAlnRep1 DMSO_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 DMSO 4 hr 0.02% RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Bpa14hAlnRep2 ECC-1 BPA 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001238 1238 Myers HudsonAlpha SL2859 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Bpa14hAlnRep2 BPA_100nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 BPA 4 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Bpa14hAlnRep1 ECC-1 BPA 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001238 1238 Myers HudsonAlpha SL1552 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Bpa14hAlnRep1 BPA_100nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 BPA 4 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqBe2cAlnRep2 BE2_C 2 BE2_C RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001249 1249 Myers HudsonAlpha SL525 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqBe2cAlnRep2 None Alignments neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch BE2_C RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqBe2cAlnRep1 BE2_C 1 BE2_C RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001249 1249 Myers HudsonAlpha SL524 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqBe2cAlnRep1 None Alignments neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch BE2_C RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqSknshAlnRep2 SK-N-SH 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001250 1250 Myers HudsonAlpha SL527 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqSknshAlnRep2 None Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqSknshAlnRep1 SK-N-SH 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001250 1250 Myers HudsonAlpha SL526 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqSknshAlnRep1 None Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02AlnRep4 A549 ETOH 4 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000314 314 Myers HudsonAlpha SL1260 cufflinks_v_0.9 bow125 hg19 1x36 4 longPolyA wgEncodeHaibRnaSeqA549Etoh02AlnRep4 EtOH_0.02pct Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 ETOH 1 hr 0.02% RNA-seq Alignments Rep 4 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02AlnRep3 A549 ETOH 3 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000314 314 Myers HudsonAlpha SL1255 cufflinks_v_0.9 bow125 hg19 1x36 3 longPolyA wgEncodeHaibRnaSeqA549Etoh02AlnRep3 EtOH_0.02pct Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 ETOH 1 hr 0.02% RNA-seq Alignments Rep 3 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02AlnRep2 A549 ETOH 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000314 314 Myers HudsonAlpha SL333 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Etoh02AlnRep2 EtOH_0.02pct Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 ETOH 1 hr 0.02% RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02AlnRep1 A549 ETOH 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000314 314 Myers HudsonAlpha SL331 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Etoh02AlnRep1 EtOH_0.02pct Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 ETOH 1 hr 0.02% RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex5nmAlnRep2 A549 DEX5nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001248 1248 Myers HudsonAlpha SL1264 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex5nmAlnRep2 DEX_5nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 5 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 5 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex5nmAlnRep1 A549 DEX5nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001248 1248 Myers HudsonAlpha SL1259 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex5nmAlnRep1 DEX_5nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 5 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 5 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex500pmAlnRep2 A549 DEX500pM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001247 1247 Myers HudsonAlpha SL1262 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex500pmAlnRep2 DEX_500pM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 500 pM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 500 pM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex500pmAlnRep1 A549 DEX500pM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001247 1247 Myers HudsonAlpha SL1257 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex500pmAlnRep1 DEX_500pM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 500 pM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 500 pM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex1nmAlnRep2 A549 DEX1nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001246 1246 Myers HudsonAlpha SL1263 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex1nmAlnRep2 DEX_1nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 1 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 1 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex1nmAlnRep1 A549 DEX1nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001246 1246 Myers HudsonAlpha SL1258 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex1nmAlnRep1 DEX_1nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 1 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 1 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100pmAlnRep2 A549 DEX100pM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001237 1237 Myers HudsonAlpha SL1261 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex100pmAlnRep2 DEX_100pM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 pM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 100 pM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100pmAlnRep1 A549 DEX100pM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001237 1237 Myers HudsonAlpha SL1256 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex100pmAlnRep1 DEX_100pM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 pM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 100 pM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100nmAlnRep2 A549 DEX100nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000313 313 Myers HudsonAlpha SL332 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex100nmAlnRep2 DEX_100nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100nmAlnRep1 A549 DEX100nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000313 313 Myers HudsonAlpha SL330 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex100nmAlnRep1 DEX_100nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibTfbs HAIB TFBS GSE32465 Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB Regulation Description This track displays binding sites of the specified transcription factors in the given cell types as identified by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq &mdash; see Johnson et al., 2007 and Fields, 2007). ChIP-seq was used to assay chromatin fragments bound by specific or general transcription factors as described below. DNA enriched by chromatin immunoprecipitation was sequenced and short sequence reads of 25-36 nt were mapped to the human reference genome. Enriched regions (peaks) of high sequence read density relative to input chromatin control sequence reads were identified with a peak calling algorithm. The sequence reads with quality scores (fastq files) and alignment coordinates (BAM files) from these experiments are available for download. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. The subtracks in this track are grouped by transcription factor targeted antibody and by cell type. For each experiment (cell type vs. antibody), the following views are included: Peaks Sites with the greatest evidence of transcription factor binding, calculated using the MACS peak caller (Zhang et al., 2008), as enriched regions of high read density in the ChIP experiment relative to total input chromatin control reads. Raw Signal A continuous signal which indicates density of aligned reads. The sequence reads were extended to the size-selected length (225 bp), and the read density computed as reads per million. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Cross-linked chromatin was immunoprecipitated with an antibody, the protein-DNA crosslinks were reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and check here for the most current version of the protocol. Biological replicates from each experiment were completed. Libraries were sequenced with an Illumina Genome Analyzer I or IIx according to the manufacturer's recommendations. Sequence data produced by the Illumina data pipeline software were quality-filtered and then mapped to NCBI GRCh37 (hg19) using the integrated Eland software; 32 nt of the sequence reads were used for alignment. Up to two mismatches were tolerated; reads that mapped to multiple sites in the genome were discarded. To identify likely transcription factor occupancy sites, peak calling was applied to the aligned sequence data sets using MACS (Zhang et al., 2008). The MACS method models the shift size of ChIP-seq tags empirically, and uses the shift to improve the spatial resolution of predicted binding sites. The MACS method also uses a dynamic Poisson distribution to capture local biases in the genome, allowing for more robust predictions (Zhang et al., 2008). Protocol Notes Several changes and improvements were made to the original ChIP-seq protocol (Jonshon et al., 2008). The major differences between protocols are the number of cells and magnetic beads used for IP, the method of sonication used to fragment DNA, the method used for fragment size selection, and the number of cycles of PCR used to amplify the sequencing library. The protocol field for each file denotes the version of the protocol used as being PCR1x, PCR2x or a version number (e.g., v041610.1). The sequencing libraries labeled as PCR2x were made with two rounds of amplification (25 and 15 cycles) and those labeled as PCR1x were made with one 15-cycle round of amplification. Experiments that were completed prior to January 2010 were originally aligned to NCBI36 (hg18). They have been re-aligned to NCBI GRCh37 (hg19) with the Bowtie software (Langmead et al., 2009) for this data release. The libraries labeled with a protocol version number were competed after January 2010 and were only aligned to NCBI GRCh37 (hg19). Please refer to the Myers Lab website for details on each protocol version and the most current protocol in use. Verification The MACS peak caller was used to call significant peaks on the individual replicates of a ChIP-seq experiment. Next, the irreproducible discovery rate (IDR) method developed by Li et al. (2011), was used to quantify the consistency between pairs of ranked peaks lists from replicates. The IDR methods uses a model that assumes that the ranked lists of peaks in a pair of replicates consist of two groups: a reproducible group and an irreproducible group. In general, the signals in the reproducible group are more consistent (i.e. with a larger rank correlation coefficient) and are ranked higher than the irreproducible group. The proportion of peaks that belong to the irreproducible component and the correlation of the reproducible component are estimated adaptively from the data. The model also provides an IDR score for each peak, which reflects the posterior probability of the peak belonging to the irreproducible group. The aligned reads were pooled from all replicates and the MACS peak caller was used to call significant peaks on the pooled data. Only datasets containing at least 100 peaks passing the IDR threshold were considered valid and submitted for release. As part of the validation of ChIP-seq antibodies and to study the downstream targets of several transcription factors, inducible short hairpin RNA (shRNA) cell lines were generated to knock down the expression of these factors. K562 cells (non-adherent, human erythromyeloblastoid leukemia cell line; ENCODE Tier 1) were transduced with lentiviral vectors carrying an inducible shRNA to a specific transcription factor as described in this protocol. Expression of shRNA was induced with doxycycline in the growth media. Only cell lines that exhibited at least 70% reduction in expression of the targeted transcription factor (determined by qPCR) were used. The cell lines were designated K562-shX, where X is the transcription factor targeted by shRNA and K562 denotes the parent cell line. For example, K562-shATF3 cells are K562 cells selected for stable integration of shRNA targeting the ATF3 gene. Gene expression in doxycycline-induced and uninduced cells were measured and profiled using RNA-seq. The RNA-seq data were submitted to GEO (Accession:GSE33816). Release Notes This is Release 3 (Sept 2012). It contains 110 new experiments including 3 new cell lines and 1 new antibodies. The entire HepG2/HEY1 (Accession: wgEncodeEH001502) and K562/HEY1 (Accession: wgEncodeEH001481) datasets have been revoked due to problems with the quality of the antibody. All experiments with the U87 cell line were remapped. Previously, the sex of the cell was unknown and was mapped to the male genome. It was discovered that the cell line is female. Other files from the previous releases also contained errors. They have been corrected with a version number appended to the name (e.g., V2). shRNA validation data have been included in previous releases. The Verification section above provides a more in-depth explanation of the method. Credits These data were provided by the Myers Lab at the HudsonAlpha Institute for Biotechnology. Contact: Flo Pauli References Fields S. Molecular biology. Site-seeing by sequencing. Science. 2007 Jun 8;316(5830):1441-2. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007 Jun 8;316(5830):1497-502. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Li Q, Brown JB, Huang H, Bickel PJ. Measuring Reproducibility of High-throughput experiments. Ann. Appl. Stat. Volume 5, Number 3 (2011), 1752-1779. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeTfBindingSuper ENC TF Binding ENCODE Transcription Factor Binding Regulation Description Transcription is regulated through the binding of transcription factor proteins to specific cis-level regulatory sites in the DNA. The nature of this regulation depends on the transcription factor. For example, some proteins activate transcription by recruiting RNA polymerase, some repress transcription by suppressing this recruitment, and others insulate proximal regions from the activity of nearby transcriptional activators or repressors. A key characteristic of each transcription factor protein is its DNA binding domain. Each DNA binding domain recognizes and interacts with DNA that matches a specific nucleotide pattern, or motif. These motifs tend to be short and degenerate, so even when the DNA binding motif is known, one cannot generally predict where a given transcription factor may bind. In general, transcription factor binding is determined experimentally. These tracks contain transcription factor binding sites determined by ChIP-seq. This process involves fragmenting DNA, selecting the fragments of DNA that are bound by a certain transcription factor, and sequencing those DNA fragments. This generally yields a large library of DNA sequences, including some that were bound by the transcription factor directly, some that were bound indirectly via interactions with other molecules, and some false positives (such as cases of nonspecific binding). With the appropriate analysis methods, ChIP-seq can be a valuable approach for elucidating transcription factor binding and cis-level regulation. Display Conventions These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun;17(6):898-909. Hudson ME, Snyder M. High-throughput methods of regulatory element discovery. Biotechniques. 2006 Dec;41(6):673, 675, 677 passim. Data Use Policy External data users may freely download, analyze and publish results based on any ENCODE data without restrictions as soon as they are released. The full policy is available here: ENCODE Data Use Policy for External Users 
wgEncodeHaibTfbsViewRawSignal Raw Signal Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87RxlchV0416101RawRep2V2 U87 RvXL V101 2 RevXlinkChromatin U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-23 2012-02-23 wgEncodeEH001676 1676 GSM803491 Myers HudsonAlpha SL3777 v041610.1 2 input wgEncodeHaibTfbsU87RxlchV0416101RawRep2V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87RxlchV0416101RawRep1V2 U87 RvXL V101 1 RevXlinkChromatin U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-23 2012-02-23 wgEncodeEH001676 1676 GSM803491 Myers HudsonAlpha SL2338 v041610.1 1 input wgEncodeHaibTfbsU87RxlchV0416101RawRep1V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87RxlchPcr2xRawRep2V2 U87 RvXL PCR2 2 RevXlinkChromatin U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-01-21 2011-10-20 wgEncodeEH001559 1559 GSM803375 Myers HudsonAlpha SL414 PCR2x 2 input wgEncodeHaibTfbsU87RxlchPcr2xRawRep2V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87RxlchPcr2xRawRep1V2 U87 RvXL PCR2 1 RevXlinkChromatin U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-03-08 2011-12-08 wgEncodeEH001559 1559 GSM803375 Myers HudsonAlpha SL103 PCR2x 1 input wgEncodeHaibTfbsU87RxlchPcr2xRawRep1V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87Pol24h8V0416101RawRep2V2 U87 Pol2-4H8 V101 2 Pol2-4H8 U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-20 2012-02-20 wgEncodeEH001674 1674 GSM803459 Myers HudsonAlpha SL3773 v041610.1 2 exp wgEncodeHaibTfbsU87Pol24h8V0416101RawRep2V2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87Pol24h8V0416101RawRep1V2 U87 Pol2-4H8 V101 1 Pol2-4H8 U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-20 2012-02-23 wgEncodeEH001674 1674 GSM803459 Myers HudsonAlpha SL1962 v041610.1 1 exp wgEncodeHaibTfbsU87Pol24h8V0416101RawRep1V2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87NrsfPcr2xRawRep2V2 U87 NRSF PCR2 2 NRSF U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-01-21 2011-10-20 wgEncodeEH001554 1554 GSM803372 Myers HudsonAlpha SL413 PCR2x 2 exp wgEncodeHaibTfbsU87NrsfPcr2xRawRep2V2 None RawSignal Neuron-restrictive silencer transcription factor glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87NrsfPcr2xRawRep1V2 U87 NRSF PCR2 1 NRSF U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-03-08 2011-12-08 wgEncodeEH001554 1554 GSM803372 Myers HudsonAlpha SL88 PCR2x 1 exp wgEncodeHaibTfbsU87NrsfPcr2xRawRep1V2 None RawSignal Neuron-restrictive silencer transcription factor glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dRxlchV0422111RawRep1 T47D RvXL V11 1 RevXlinkChromatin T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003431 3431 GSM1010884 Myers HudsonAlpha SL13294 v042211.1 1 input wgEncodeHaibTfbsT47dRxlchV0422111RawRep1 None RawSignal epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dRxlchV0416102Dm002p1hRawRep1 T47D RvXL DMSO 1 RevXlinkChromatin T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001631 1631 GSM803433 Myers HudsonAlpha SL1881 v041610.2 1 input wgEncodeHaibTfbsT47dRxlchV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D Control DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dP300V0416102Dm002p1hRawRep2 T47D p300 DMSO 2 p300 T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001602 1602 GSM803522 Myers HudsonAlpha SL3015 v041610.2 2 exp wgEncodeHaibTfbsT47dP300V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal EP300(c-20) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D p300 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dP300V0416102Dm002p1hRawRep1 T47D p300 DMSO 1 p300 T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001602 1602 GSM803522 Myers HudsonAlpha SL2633 v041610.2 1 exp wgEncodeHaibTfbsT47dP300V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal EP300(c-20) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D p300 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dJundV0422111RawRep2 T47D JunD V11 2 JunD T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003321 3321 GSM1010718 Myers HudsonAlpha SL11657 v042211.1 2 exp wgEncodeHaibTfbsT47dJundV0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D JunD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dJundV0422111RawRep1 T47D JunD V11 1 JunD T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003321 3321 GSM1010718 Myers HudsonAlpha SL11656 v042211.1 1 exp wgEncodeHaibTfbsT47dJundV0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D JunD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hRawRep2 T47D GATA3 DMSO 2 GATA3_(SC-268) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001639 1639 GSM803514 Myers HudsonAlpha SL3013 v041610.2 2 exp wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D GATA3 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hRawRep1 T47D GATA3 DMSO 1 GATA3_(SC-268) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001639 1639 GSM803514 Myers HudsonAlpha SL2636 v041610.2 1 exp wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D GATA3 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hRawRep2 T47D FOXA1 DMSO 2 FOXA1_(SC-6553) T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001588 1588 GSM803409 Myers HudsonAlpha SL2081 v041610.2 2 exp wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D FOXA1 6553 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hRawRep1 T47D FOXA1 DMSO 1 FOXA1_(SC-6553) T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001588 1588 GSM803409 Myers HudsonAlpha SL1878 v041610.2 1 exp wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D FOXA1 6553 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Gen1hRawRep2 T47 ERa Gen 102 2 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001556 1556 GSM803374 Myers HudsonAlpha SL1492 v041610.2 2 exp wgEncodeHaibTfbsT47dEralphaaV0416102Gen1hRawRep2 Genistein_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a Genistein v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Gen1hRawRep1 T47 ERa Gen 102 1 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001556 1556 GSM803374 Myers HudsonAlpha SL1218 v041610.2 1 exp wgEncodeHaibTfbsT47dEralphaaV0416102Gen1hRawRep1 Genistein_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a Genistein v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hRawRep2 T47D ERa Estra 2 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001577 1577 GSM803539 Myers HudsonAlpha SL1491 v041610.2 2 exp wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hRawRep2 Estradiol_10nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a Estradiol v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hRawRep1 T47D ERa Estra 1 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001577 1577 GSM803539 Myers HudsonAlpha SL1217 v041610.2 1 exp wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hRawRep1 Estradiol_10nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a Estradiol v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Dm002p1hRawRep2 T47D ERa DMSO 2 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001601 1601 GSM803519 Myers HudsonAlpha SL1490 v041610.2 2 input wgEncodeHaibTfbsT47dEralphaaV0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Dm002p1hRawRep1 T47D ERa DMSO 1 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001601 1601 GSM803519 Myers HudsonAlpha SL1216 v041610.2 1 input wgEncodeHaibTfbsT47dEralphaaV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEraaV0416102Bpa1hRawRep2 T47D ERa BPA 2 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002299 2299 GSM1010823 Myers HudsonAlpha SL1877 v041610.2 2 exp wgEncodeHaibTfbsT47dEraaV0416102Bpa1hRawRep2 BPA_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a BPA v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEraaV0416102Bpa1hRawRep1 T47D ERa BPA 1 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002299 2299 GSM1010823 Myers HudsonAlpha SL1493 v041610.2 1 exp wgEncodeHaibTfbsT47dEraaV0416102Bpa1hRawRep1 BPA_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a BPA v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hRawRep2 T47D CTCF DMSO 2 CTCF_(SC-5916) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001656 1656 GSM803348 Myers HudsonAlpha SL3014 v041610.2 2 exp wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D CTCF 5916 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hRawRep1 T47D CTCF DMSO 1 CTCF_(SC-5916) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001656 1656 GSM803348 Myers HudsonAlpha SL2634 v041610.2 1 exp wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D CTCF 5916 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRxlchV0416102RawRep1 SKRA RvXL V102 1 RevXlinkChromatin SK-N-SH_RA ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001606 1606 GSM803526 Myers HudsonAlpha SL2905 v041610.2 1 input wgEncodeHaibTfbsSknshraRxlchV0416102RawRep1 None RawSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA Control v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraYy1sc281V0416102RawRep2 SKRA YY1 V102 2 YY1_(SC-281) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001615 1615 GSM803498 Myers HudsonAlpha SL3640 v041610.2 2 exp wgEncodeHaibTfbsSknshraYy1sc281V0416102RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA YY1 281 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraYy1sc281V0416102RawRep1 SKRA YY1 V102 1 YY1_(SC-281) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001615 1615 GSM803498 Myers HudsonAlpha SL3639 v041610.2 1 exp wgEncodeHaibTfbsSknshraYy1sc281V0416102RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA YY1 281 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraUsf1sc8983V0416102RawRep2 SKRA USF1 V102 2 USF1_(SC-8983) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001621 1621 GSM803472 Myers HudsonAlpha SL2919 v041610.2 2 exp wgEncodeHaibTfbsSknshraUsf1sc8983V0416102RawRep2 None RawSignal This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq). neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA USF-1 8983 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraUsf1sc8983V0416102RawRep1 SKRA USF1 V102 1 USF1_(SC-8983) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001621 1621 GSM803472 Myers HudsonAlpha SL2911 v041610.2 1 exp wgEncodeHaibTfbsSknshraUsf1sc8983V0416102RawRep1 None RawSignal This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq). neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA USF-1 8983 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRad21V0416102RawRep2 SKRA RAD21 V102 2 Rad21 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001614 1614 GSM803497 Myers HudsonAlpha SL2915 v041610.2 2 exp wgEncodeHaibTfbsSknshraRad21V0416102RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA RAD21 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRad21V0416102RawRep1 SKRA RAD21 V102 1 Rad21 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001614 1614 GSM803497 Myers HudsonAlpha SL2907 v041610.2 1 exp wgEncodeHaibTfbsSknshraRad21V0416102RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA RAD21 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraP300V0416102RawRep2 SKRA p300 V102 2 p300 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001616 1616 GSM803495 Myers HudsonAlpha SL2918 v041610.2 2 exp wgEncodeHaibTfbsSknshraP300V0416102RawRep2 None RawSignal EP300(c-20) neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA p300 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraP300V0416102RawRep1 SKRA p300 V102 1 p300 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001616 1616 GSM803495 Myers HudsonAlpha SL2910 v041610.2 1 exp wgEncodeHaibTfbsSknshraP300V0416102RawRep1 None RawSignal EP300(c-20) neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA p300 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraCtcfV0416102RawRep2 SKRA CTCF V102 2 CTCF SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001613 1613 GSM803333 Myers HudsonAlpha SL2914 v041610.2 2 exp wgEncodeHaibTfbsSknshraCtcfV0416102RawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA CTCF v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraCtcfV0416102RawRep1 SKRA CTCF V102 1 CTCF SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001613 1613 GSM803333 Myers HudsonAlpha SL2906 v041610.2 1 exp wgEncodeHaibTfbsSknshraCtcfV0416102RawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA CTCF v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcRxlchV0416101RawRep1 SKMC RvXL V101 1 RevXlinkChromatin SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001535 1535 GSM803423 Myers HudsonAlpha SL1714 v041610.1 1 input wgEncodeHaibTfbsSknmcRxlchV0416101RawRep1 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcRxlchPcr2xRawRep1 SKMC RvXL PCR2 1 RevXlinkChromatin SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-02 2012-03-02 wgEncodeEH001677 1677 GSM803492 Myers HudsonAlpha SL102 PCR2x 1 input wgEncodeHaibTfbsSknmcRxlchPcr2xRawRep1 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcPol24h8V0416101RawRep2 SKMC Pol2-4H8 V101 2 Pol2-4H8 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002281 2281 GSM1010793 Myers HudsonAlpha SL5611 v041610.1 2 exp wgEncodeHaibTfbsSknmcPol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcPol24h8V0416101RawRep1 SKMC Pol2-4H8 V101 1 Pol2-4H8 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002281 2281 GSM1010793 Myers HudsonAlpha SL1963 v041610.1 1 exp wgEncodeHaibTfbsSknmcPol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcFoxp2Pcr2xRawRep2 SKMC FOXP2 PCR2 2 FOXP2 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2008-10-31 2009-07-31 wgEncodeEH001461 1461 GSM803353 Myers HudsonAlpha SL167 PCR2x 2 exp wgEncodeHaibTfbsSknmcFoxp2Pcr2xRawRep2 None RawSignal This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC FOXP2 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcFoxp2Pcr2xRawRep1 SKMC FOXP2 PCR2 1 FOXP2 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001461 1461 GSM803353 Myers HudsonAlpha SL144 PCR2x 1 exp wgEncodeHaibTfbsSknmcFoxp2Pcr2xRawRep1 None RawSignal This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC FOXP2 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1RxlchV0416101RawRep1 PFSK RvXL V101 1 RevXlinkChromatin PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002286 2286 GSM1010797 Myers HudsonAlpha SL2339 v041610.1 1 input wgEncodeHaibTfbsPfsk1RxlchV0416101RawRep1 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep3 PFSK RvXL PCR2 3 RevXlinkChromatin PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001558 1558 GSM803376 Myers HudsonAlpha SL16 PCR2x 3 input wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep3 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Control PCR2x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep2 PFSK RvXL PCR2 2 RevXlinkChromatin PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001558 1558 GSM803376 Myers HudsonAlpha SL412 PCR2x 2 input wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep2 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep1 PFSK RvXL PCR2 1 RevXlinkChromatin PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001558 1558 GSM803376 Myers HudsonAlpha SL150 PCR2x 1 input wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep1 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Taf1V0416101RawRep2 PFSK TAF1 V101 2 TAF1 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002309 2309 GSM1010770 Myers HudsonAlpha SL6969 v041610.1 2 exp wgEncodeHaibTfbsPfsk1Taf1V0416101RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 TAF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Taf1V0416101RawRep1 PFSK TAF1 V101 1 TAF1 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002309 2309 GSM1010770 Myers HudsonAlpha SL3772 v041610.1 1 exp wgEncodeHaibTfbsPfsk1Taf1V0416101RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 TAF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Sin3ak20V0416101RawRep2 PFSK Sin3A V101 2 Sin3Ak-20 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002268 2268 GSM1010781 Myers HudsonAlpha SL5041 v041610.1 2 exp wgEncodeHaibTfbsPfsk1Sin3ak20V0416101RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Sin3ak20V0416101RawRep1 PFSK Sin3A V101 1 Sin3Ak-20 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002268 2268 GSM1010781 Myers HudsonAlpha SL2354 v041610.1 1 exp wgEncodeHaibTfbsPfsk1Sin3ak20V0416101RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Pol24h8V0416101RawRep2 PFSK Pol2-4H8 V101 2 Pol2-4H8 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH002272 2272 GSM1010819 Myers HudsonAlpha SL5610 v041610.1 2 exp wgEncodeHaibTfbsPfsk1Pol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Pol24h8V0416101RawRep1 PFSK Pol2-4H8 V101 1 Pol2-4H8 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH002272 2272 GSM1010819 Myers HudsonAlpha SL2353 v041610.1 1 exp wgEncodeHaibTfbsPfsk1Pol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfV0416101RawRep2 PFSK NRSF V101 2 NRSF PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002267 2267 GSM1010786 Myers HudsonAlpha SL5497 v041610.1 2 exp wgEncodeHaibTfbsPfsk1NrsfV0416101RawRep2 None RawSignal Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 NRSF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfV0416101RawRep1 PFSK NRSF V101 1 NRSF PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002267 2267 GSM1010786 Myers HudsonAlpha SL5496 v041610.1 1 exp wgEncodeHaibTfbsPfsk1NrsfV0416101RawRep1 None RawSignal Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 NRSF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfPcr2xRawRep2 PFSK NRSF PCR2 2 NRSF PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001553 1553 GSM803369 Myers HudsonAlpha SL411 PCR2x 2 exp wgEncodeHaibTfbsPfsk1NrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfPcr2xRawRep1 PFSK NRSF PCR2 1 NRSF PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001553 1553 GSM803369 Myers HudsonAlpha SL149 PCR2x 1 exp wgEncodeHaibTfbsPfsk1NrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Foxp2Pcr2xRawRep2 PFSK FOXP2 PCR2 2 FOXP2 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2008-10-31 2009-07-31 wgEncodeEH001460 1460 GSM803480 Myers HudsonAlpha SL14 PCR2x 2 exp wgEncodeHaibTfbsPfsk1Foxp2Pcr2xRawRep2 None RawSignal This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 FOXP2 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Foxp2Pcr2xRawRep1 PFSK FOXP2 PCR2 1 FOXP2 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001460 1460 GSM803480 Myers HudsonAlpha SL13 PCR2x 1 exp wgEncodeHaibTfbsPfsk1Foxp2Pcr2xRawRep1 None RawSignal This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 FOXP2 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchV0422111RawRep1 PANC RvXL V11 1 RevXlinkChromatin PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003429 3429 GSM1010853 Myers HudsonAlpha SL16762 v042211.1 1 input wgEncodeHaibTfbsPanc1RxlchV0422111RawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchV0416101RawRep2 PANC RvXL V101 2 RevXlinkChromatin PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002285 2285 GSM1010796 Myers HudsonAlpha SL3776 v041610.1 2 input wgEncodeHaibTfbsPanc1RxlchV0416101RawRep2 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchV0416101RawRep1 PANC RvXL V101 1 RevXlinkChromatin PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002285 2285 GSM1010796 Myers HudsonAlpha SL2340 v041610.1 1 input wgEncodeHaibTfbsPanc1RxlchV0416101RawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchPcr2xRawRep2 PANC RvXL PCR2 2 RevXlinkChromatin PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001525 1525 GSM803394 Myers HudsonAlpha SL523 PCR2x 2 input wgEncodeHaibTfbsPanc1RxlchPcr2xRawRep2 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchPcr2xRawRep1 PANC RvXL PCR2 1 RevXlinkChromatin PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001525 1525 GSM803394 Myers HudsonAlpha SL117 PCR2x 1 input wgEncodeHaibTfbsPanc1RxlchPcr2xRawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Sin3ak20V0416101RawRep2 PANC Sin3A V101 2 Sin3Ak-20 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002266 2266 GSM1010785 Myers HudsonAlpha SL5042 v041610.1 2 exp wgEncodeHaibTfbsPanc1Sin3ak20V0416101RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Sin3ak20V0416101RawRep1 PANC Sin3A V101 1 Sin3Ak-20 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002266 2266 GSM1010785 Myers HudsonAlpha SL2344 v041610.1 1 exp wgEncodeHaibTfbsPanc1Sin3ak20V0416101RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Pol24h8V0416101RawRep2 PANC Pol2-4H8 V101 2 Pol2-4H8 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002265 2265 GSM1010788 Myers HudsonAlpha SL5609 v041610.1 2 exp wgEncodeHaibTfbsPanc1Pol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Pol24h8V0416101RawRep1 PANC Pol2-4H8 V101 1 Pol2-4H8 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002265 2265 GSM1010788 Myers HudsonAlpha SL2343 v041610.1 1 exp wgEncodeHaibTfbsPanc1Pol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0422111RawRep2 PANC NRSF V11 2 NRSF PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003285 3285 GSM1010859 Myers HudsonAlpha SL16342 v042211.1 2 exp wgEncodeHaibTfbsPanc1NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0422111RawRep1 PANC NRSF V11 1 NRSF PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003285 3285 GSM1010859 Myers HudsonAlpha SL14681 v042211.1 1 exp wgEncodeHaibTfbsPanc1NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0416101RawRep2 PANC NRSF V101 2 NRSF PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002280 2280 GSM1010792 Myers HudsonAlpha SL5495 v041610.1 2 exp wgEncodeHaibTfbsPanc1NrsfV0416101RawRep2 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0416101RawRep1 PANC NRSF V101 1 NRSF PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002280 2280 GSM1010792 Myers HudsonAlpha SL4437 v041610.1 1 exp wgEncodeHaibTfbsPanc1NrsfV0416101RawRep1 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfPcr2xRawRep2 PANC NRSF PCR2 2 NRSF PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001552 1552 GSM803370 Myers HudsonAlpha SL522 PCR2x 2 exp wgEncodeHaibTfbsPanc1NrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfPcr2xRawRep1 PANC NRSF PCR2 1 NRSF PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001552 1552 GSM803370 Myers HudsonAlpha SL116 PCR2x 1 exp wgEncodeHaibTfbsPanc1NrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60RxlchV0422111RawRep2 HL-60 RvXL V11 2 RevXlinkChromatin HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003427 3427 GSM1010870 Myers HudsonAlpha SL16759 v042211.1 2 input wgEncodeHaibTfbsHl60RxlchV0422111RawRep2 None RawSignal promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60RxlchV0422111RawRep1 HL-60 RvXL V11 1 RevXlinkChromatin HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003427 3427 GSM1010870 Myers HudsonAlpha SL12792 v042211.1 1 input wgEncodeHaibTfbsHl60RxlchV0422111RawRep1 None RawSignal promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pu1V0422111RawRep2 HL-60 PU.1 V11 2 PU.1 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003292 3292 GSM1010843 Myers HudsonAlpha SL14712 v042211.1 2 exp wgEncodeHaibTfbsHl60Pu1V0422111RawRep2 None RawSignal PU.1 (H-135) promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 PU.1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pu1V0422111RawRep1 HL-60 PU.1 V11 1 PU.1 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003292 3292 GSM1010843 Myers HudsonAlpha SL12629 v042211.1 1 exp wgEncodeHaibTfbsHl60Pu1V0422111RawRep1 None RawSignal PU.1 (H-135) promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 PU.1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep2 HL-60 Pol2-4H8 V11 2 Pol2-4H8 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003253 3253 GSM1010737 Myers HudsonAlpha SL16322 v042211.1 2 exp wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Pol2-4H8 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep1 HL-60 Pol2-4H8 V11 1 Pol2-4H8 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003253 3253 GSM1010737 Myers HudsonAlpha SL12628 v042211.1 1 exp wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Pol2-4H8 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60NrsfV0422111RawRep2 HL-60 NRSF V11 2 NRSF HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003247 3247 GSM1010754 Myers HudsonAlpha SL13747 v042211.1 2 exp wgEncodeHaibTfbsHl60NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60NrsfV0422111RawRep1 HL-60 NRSF V11 1 NRSF HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003247 3247 GSM1010754 Myers HudsonAlpha SL12632 v042211.1 1 exp wgEncodeHaibTfbsHl60NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60GabpV0422111RawRep2 HL-60 GABP V11 2 GABP HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003252 3252 GSM1010822 Myers HudsonAlpha SL16321 v042211.1 2 exp wgEncodeHaibTfbsHl60GabpV0422111RawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 GABP v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60GabpV0422111RawRep1 HL-60 GABP V11 1 GABP HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003252 3252 GSM1010822 Myers HudsonAlpha SL12633 v042211.1 1 exp wgEncodeHaibTfbsHl60GabpV0422111RawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 GABP v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116RxlchV0422111RawRep2 HCT RvXL V11 2 RevXlinkChromatin HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003426 3426 GSM1010872 Myers HudsonAlpha SL12247 v042211.1 2 input wgEncodeHaibTfbsHct116RxlchV0422111RawRep2 None RawSignal colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116RxlchV0422111RawRep1 HCT RvXL V11 1 RevXlinkChromatin HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003426 3426 GSM1010872 Myers HudsonAlpha SL12246 v042211.1 1 input wgEncodeHaibTfbsHct116RxlchV0422111RawRep1 None RawSignal colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116RxlchV0416101RawRep1 HCT RvXL V101 1 RevXlinkChromatin HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001626 1626 GSM803475 Myers HudsonAlpha SL3457 v041610.1 1 input wgEncodeHaibTfbsHct116RxlchV0416101RawRep1 None RawSignal colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Zbtb33V0416101RawRep2 HCT ZBTB33 2 ZBTB33 HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001672 1672 GSM803458 Myers HudsonAlpha SL3970 v041610.1 2 exp wgEncodeHaibTfbsHct116Zbtb33V0416101RawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ZBTB33 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Zbtb33V0416101RawRep1 HCT ZBTB33 1 ZBTB33 HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001672 1672 GSM803458 Myers HudsonAlpha SL3646 v041610.1 1 exp wgEncodeHaibTfbsHct116Zbtb33V0416101RawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ZBTB33 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Yy1sc281V0416101RawRep2 HCT YY1 V101 2 YY1_(SC-281) HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001671 1671 GSM803354 Myers HudsonAlpha SL4500 v041610.1 2 exp wgEncodeHaibTfbsHct116Yy1sc281V0416101RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Yy1sc281V0416101RawRep1 HCT YY1 V101 1 YY1_(SC-281) HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001671 1671 GSM803354 Myers HudsonAlpha SL3971 v041610.1 1 exp wgEncodeHaibTfbsHct116Yy1sc281V0416101RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Usf1V0422111RawRep2 HCT USF1 V11 2 USF-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003310 3310 GSM1010836 Myers HudsonAlpha SL16733 v042211.1 2 exp wgEncodeHaibTfbsHct116Usf1V0422111RawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 USF-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Usf1V0422111RawRep1 HCT USF1 V11 1 USF-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003310 3310 GSM1010836 Myers HudsonAlpha SL12238 v042211.1 1 exp wgEncodeHaibTfbsHct116Usf1V0422111RawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 USF-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Tead4sc101184V0422111RawRep2 HCT TEAD4 V11 2 TEAD4_(SC-101184) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003309 3309 GSM1010772 Myers HudsonAlpha SL14570 v042211.1 2 exp wgEncodeHaibTfbsHct116Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Tead4sc101184V0422111RawRep1 HCT TEAD4 V11 1 TEAD4_(SC-101184) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003309 3309 GSM1010772 Myers HudsonAlpha SL16313 v042211.1 1 exp wgEncodeHaibTfbsHct116Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116SrfV0422111RawRep2 HCT SRF V11 2 SRF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003218 3218 GSM1010851 Myers HudsonAlpha SL13070 v042211.1 2 exp wgEncodeHaibTfbsHct116SrfV0422111RawRep2 None RawSignal Serum response transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 SRF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116SrfV0422111RawRep1 HCT SRF V11 1 SRF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003218 3218 GSM1010851 Myers HudsonAlpha SL12237 v042211.1 1 exp wgEncodeHaibTfbsHct116SrfV0422111RawRep1 None RawSignal Serum response transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 SRF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sp1V0422111RawRep2 HCT SP1 V11 2 SP1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003221 3221 GSM1010902 Myers HudsonAlpha SL13072 v042211.1 2 exp wgEncodeHaibTfbsHct116Sp1V0422111RawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 SP1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sp1V0422111RawRep1 HCT SP1 V11 1 SP1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003221 3221 GSM1010902 Myers HudsonAlpha SL12239 v042211.1 1 exp wgEncodeHaibTfbsHct116Sp1V0422111RawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 SP1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sin3ak20V0422111RawRep2 HCT Sin3A V11 2 Sin3Ak-20 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003222 3222 GSM1010905 Myers HudsonAlpha SL13076 v042211.1 2 exp wgEncodeHaibTfbsHct116Sin3ak20V0422111RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Sin3Ak-20 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sin3ak20V0422111RawRep1 HCT Sin3A V11 1 Sin3Ak-20 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003222 3222 GSM1010905 Myers HudsonAlpha SL12244 v042211.1 1 exp wgEncodeHaibTfbsHct116Sin3ak20V0422111RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Sin3Ak-20 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Rad21V0422111RawRep2 HCT RAD21 V11 2 Rad21 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003217 3217 GSM1010848 Myers HudsonAlpha SL13067 v042211.1 2 exp wgEncodeHaibTfbsHct116Rad21V0422111RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 RAD21 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Rad21V0422111RawRep1 HCT RAD21 V11 1 Rad21 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003217 3217 GSM1010848 Myers HudsonAlpha SL12230 v042211.1 1 exp wgEncodeHaibTfbsHct116Rad21V0422111RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 RAD21 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Pol24h8V0416101RawRep2 HCT Pol2-4H8 V101 2 Pol2-4H8 HCT-116 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001627 1627 GSM803474 Myers HudsonAlpha SL3830 v041610.1 2 exp wgEncodeHaibTfbsHct116Pol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Pol24h8V0416101RawRep1 HCT Pol2-4H8 V101 1 Pol2-4H8 HCT-116 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001627 1627 GSM803474 Myers HudsonAlpha SL3456 v041610.1 1 exp wgEncodeHaibTfbsHct116Pol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116NrsfV0422111RawRep2 HCT NRSF V11 2 NRSF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003308 3308 GSM1010869 Myers HudsonAlpha SL14560 v042211.1 2 exp wgEncodeHaibTfbsHct116NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116NrsfV0422111RawRep1 HCT NRSF V11 1 NRSF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003308 3308 GSM1010869 Myers HudsonAlpha SL16310 v042211.1 1 exp wgEncodeHaibTfbsHct116NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116MaxV0422111RawRep2 HCT Max V11 2 Max HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003223 3223 GSM1010904 Myers HudsonAlpha SL13075 v042211.1 2 exp wgEncodeHaibTfbsHct116MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116MaxV0422111RawRep1 HCT Max V11 1 Max HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003223 3223 GSM1010904 Myers HudsonAlpha SL12243 v042211.1 1 exp wgEncodeHaibTfbsHct116MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116JundV0422111RawRep2 HCT JunD V11 2 JunD HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003216 3216 GSM1010847 Myers HudsonAlpha SL13069 v042211.1 2 exp wgEncodeHaibTfbsHct116JundV0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 JunD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116JundV0422111RawRep1 HCT JunD V11 1 JunD HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003216 3216 GSM1010847 Myers HudsonAlpha SL12233 v042211.1 1 exp wgEncodeHaibTfbsHct116JundV0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 JunD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Fosl1V0422111RawRep2 HCT FOSL1 V11 2 FOSL1_(SC-183) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003246 3246 GSM1010756 Myers HudsonAlpha SL13068 v042211.1 2 exp wgEncodeHaibTfbsHct116Fosl1V0422111RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 FOSL1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Fosl1V0422111RawRep1 HCT FOSL1 V11 1 FOSL1_(SC-183) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003246 3246 GSM1010756 Myers HudsonAlpha SL12231 v042211.1 1 exp wgEncodeHaibTfbsHct116Fosl1V0422111RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 FOSL1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Elf1V0422111RawRep2 HCT ELF1 V11 2 ELF1_(SC-631) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003307 3307 GSM1010765 Myers HudsonAlpha SL13733 v042211.1 2 exp wgEncodeHaibTfbsHct116Elf1V0422111RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ELF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Elf1V0422111RawRep1 HCT ELF1 V11 1 ELF1_(SC-631) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003307 3307 GSM1010765 Myers HudsonAlpha SL14719 v042211.1 1 exp wgEncodeHaibTfbsHct116Elf1V0422111RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ELF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Egr1V0422111RawRep2 HCT Egr-1 V11 2 Egr-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003215 3215 GSM1010846 Myers HudsonAlpha SL13065 v042211.1 2 exp wgEncodeHaibTfbsHct116Egr1V0422111RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Egr1V0422111RawRep1 HCT Egr-1 V11 1 Egr-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003215 3215 GSM1010846 Myers HudsonAlpha SL12228 v042211.1 1 exp wgEncodeHaibTfbsHct116Egr1V0422111RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116CtcfcV0422111RawRep2 HCT CTCF V11 2 CTCF_(SC-5916) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003220 3220 GSM1010903 Myers HudsonAlpha SL13074 v042211.1 2 exp wgEncodeHaibTfbsHct116CtcfcV0422111RawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CTCF 5916 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116CtcfcV0422111RawRep1 HCT CTCF V11 1 CTCF_(SC-5916) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003220 3220 GSM1010903 Myers HudsonAlpha SL12242 v042211.1 1 exp wgEncodeHaibTfbsHct116CtcfcV0422111RawRep1 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CTCF 5916 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep2 HCT CEBPB V11 2 CEBPB_(SC-150) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003219 3219 GSM1010852 Myers HudsonAlpha SL13073 v042211.1 2 exp wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep1 HCT CEBPB V11 1 CEBPB_(SC-150) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003219 3219 GSM1010852 Myers HudsonAlpha SL12240 v042211.1 1 exp wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep2 HCT CBX3 V11 2 CBX3_(SC-101004) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003277 3277 GSM1010758 Myers HudsonAlpha SL13066 v042211.1 2 exp wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep2 None RawSignal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CBX3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep1 HCT CBX3 V11 1 CBX3_(SC-101004) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003277 3277 GSM1010758 Myers HudsonAlpha SL12229 v042211.1 1 exp wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep1 None RawSignal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CBX3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Atf3V0422111RawRep2 HCT ATF3 V11 2 ATF3 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003276 3276 GSM1010757 Myers HudsonAlpha SL16874 v042211.1 2 exp wgEncodeHaibTfbsHct116Atf3V0422111RawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ATF3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Atf3V0422111RawRep1 HCT ATF3 V11 1 ATF3 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003276 3276 GSM1010757 Myers HudsonAlpha SL12234 v042211.1 1 exp wgEncodeHaibTfbsHct116Atf3V0422111RawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ATF3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892RxlchV0416102RawRep1 GM92 RvXL V102 1 RevXlinkChromatin GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001510 1510 GSM803488 Myers HudsonAlpha SL818 v041610.2 1 input wgEncodeHaibTfbsGm12892RxlchV0416102RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Control v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892RxlchV0416101RawRep1 GM92 RvXL V101 1 RevXlinkChromatin GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001518 1518 GSM803482 Myers HudsonAlpha SL1783 v041610.1 1 input wgEncodeHaibTfbsGm12892RxlchV0416101RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Yy1V0416101RawRep2 GM92 YY1 V101 2 YY1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001609 1609 GSM803516 Myers HudsonAlpha SL3584 v041610.1 2 exp wgEncodeHaibTfbsGm12892Yy1V0416101RawRep2 None RawSignal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 YY1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Yy1V0416101RawRep1 GM92 YY1 V101 1 YY1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001609 1609 GSM803516 Myers HudsonAlpha SL2132 v041610.1 1 exp wgEncodeHaibTfbsGm12892Yy1V0416101RawRep1 None RawSignal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 YY1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Taf1V0416102RawRep2 GM92 TAF1 V102 2 TAF1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001513 1513 GSM803489 Myers HudsonAlpha SL945 v041610.2 2 exp wgEncodeHaibTfbsGm12892Taf1V0416102RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 TAF1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Taf1V0416102RawRep1 GM92 TAF1 V102 1 TAF1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001513 1513 GSM803489 Myers HudsonAlpha SL736 v041610.2 1 exp wgEncodeHaibTfbsGm12892Taf1V0416102RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 TAF1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep2 GM92 Pol2-4H8 V102 2 Pol2-4H8 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001512 1512 GSM803490 Myers HudsonAlpha SL946 v041610.2 2 exp wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep1 GM92 Pol2-4H8 V102 1 Pol2-4H8 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001512 1512 GSM803490 Myers HudsonAlpha SL911 v041610.2 1 exp wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol2V0416102RawRep2 GM92 Pol2 V102 2 Pol2 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001511 1511 GSM803487 Myers HudsonAlpha SL944 v041610.2 2 exp wgEncodeHaibTfbsGm12892Pol2V0416102RawRep2 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Pol2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol2V0416102RawRep1 GM92 Pol2 V102 1 Pol2 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001511 1511 GSM803487 Myers HudsonAlpha SL909 v041610.2 1 exp wgEncodeHaibTfbsGm12892Pol2V0416102RawRep1 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Pol2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep2 GM92 PAX5 V101 2 PAX5-C20 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001546 1546 GSM803334 Myers HudsonAlpha SL2133 v041610.1 2 exp wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep2 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 PAX5-C20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep1 GM92 PAX5 V101 1 PAX5-C20 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001546 1546 GSM803334 Myers HudsonAlpha SL1664 v041610.1 1 exp wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep1 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 PAX5-C20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891RxlchV0416101RawRep1 GM91 RvXL V101 1 RevXlinkChromatin GM12891 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001592 1592 GSM803467 Myers HudsonAlpha SL1782 v041610.1 1 input wgEncodeHaibTfbsGm12891RxlchV0416101RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891RxlchPcr1xRawRep1 GM91 RvXL PCR1 1 RevXlinkChromatin GM12891 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001519 1519 GSM803481 Myers HudsonAlpha SL817 PCR1x 1 input wgEncodeHaibTfbsGm12891RxlchPcr1xRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Yy1sc281V0416101RawRep2 GM91 YY1 V101 2 YY1_(SC-281) GM12891 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001573 1573 GSM803535 Myers HudsonAlpha SL2130 v041610.1 2 exp wgEncodeHaibTfbsGm12891Yy1sc281V0416101RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Yy1sc281V0416101RawRep1 GM91 YY1 V101 1 YY1_(SC-281) GM12891 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001573 1573 GSM803535 Myers HudsonAlpha SL2388 v041610.1 1 exp wgEncodeHaibTfbsGm12891Yy1sc281V0416101RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Taf1Pcr1xRawRep2 GM91 TAF1 PCR1 2 TAF1 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001524 1524 GSM803393 Myers HudsonAlpha SL920 PCR1x 2 exp wgEncodeHaibTfbsGm12891Taf1Pcr1xRawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 TAF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Taf1Pcr1xRawRep1 GM91 TAF1 PCR1 1 TAF1 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001524 1524 GSM803393 Myers HudsonAlpha SL749 PCR1x 1 exp wgEncodeHaibTfbsGm12891Taf1Pcr1xRawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 TAF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pu1Pcr1xRawRep2 GM91 PU.1 PCR1 2 PU.1 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001521 1521 GSM803398 Myers HudsonAlpha SL948 PCR1x 2 exp wgEncodeHaibTfbsGm12891Pu1Pcr1xRawRep2 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 PU.1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pu1Pcr1xRawRep1 GM91 PU.1 PCR1 1 PU.1 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001521 1521 GSM803398 Myers HudsonAlpha SL977 PCR1x 1 exp wgEncodeHaibTfbsGm12891Pu1Pcr1xRawRep1 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 PU.1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep2 GM91 POU2F2 2 POU2F2 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001520 1520 GSM803397 Myers HudsonAlpha SL918 PCR1x 2 exp wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep2 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 POU2F2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep1 GM91 POU2F2 1 POU2F2 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001520 1520 GSM803397 Myers HudsonAlpha SL802 PCR1x 1 exp wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep1 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 POU2F2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol24h8Pcr1xRawRep2 GM91 Pol2-4H8 PCR1 2 Pol2-4H8 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001523 1523 GSM803400 Myers HudsonAlpha SL922 PCR1x 2 exp wgEncodeHaibTfbsGm12891Pol24h8Pcr1xRawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Pol2-4H8 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol24h8Pcr1xRawRep1 GM91 Pol2-4H8 PCR1 1 Pol2-4H8 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001523 1523 GSM803400 Myers HudsonAlpha SL910 PCR1x 1 exp wgEncodeHaibTfbsGm12891Pol24h8Pcr1xRawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Pol2-4H8 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol2Pcr1xRawRep2 GM91 Pol2 PCR1 2 Pol2 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001522 1522 GSM803399 Myers HudsonAlpha SL921 PCR1x 2 exp wgEncodeHaibTfbsGm12891Pol2Pcr1xRawRep2 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Pol2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol2Pcr1xRawRep1 GM91 Pol2 PCR1 1 Pol2 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001522 1522 GSM803399 Myers HudsonAlpha SL908 PCR1x 1 exp wgEncodeHaibTfbsGm12891Pol2Pcr1xRawRep1 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Pol2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pax5c20V0416101RawRep2 GM91 PAX5 V101 2 PAX5-C20 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001545 1545 GSM803337 Myers HudsonAlpha SL2131 v041610.1 2 exp wgEncodeHaibTfbsGm12891Pax5c20V0416101RawRep2 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 PAX5-C20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pax5c20V0416101RawRep1 GM91 PAX5 V101 1 PAX5-C20 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001545 1545 GSM803337 Myers HudsonAlpha SL1662 v041610.1 1 exp wgEncodeHaibTfbsGm12891Pax5c20V0416101RawRep1 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 PAX5-C20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1RxlchV0422111RawRep2 ECC1 RvXL V11 2 RevXlinkChromatin ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003424 3424 GSM1010874 Myers HudsonAlpha SL16754 v042211.1 2 input wgEncodeHaibTfbsEcc1RxlchV0422111RawRep2 None RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1RxlchV0422111RawRep1 ECC1 RvXL V11 1 RevXlinkChromatin ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003424 3424 GSM1010874 Myers HudsonAlpha SL13506 v042211.1 1 input wgEncodeHaibTfbsEcc1RxlchV0422111RawRep1 None RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1RxlchV0416102Dm002p1hRawRep1 ECC1 RvXL DMSO 1 RevXlinkChromatin ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001587 1587 GSM803445 Myers HudsonAlpha SL1882 v041610.2 1 input wgEncodeHaibTfbsEcc1RxlchV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Control DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Zbtb7aV0422111RawRep2 ECC1 ZBTB7A 2 ZBTB7A_(SC-34508) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003241 3241 GSM1010752 Myers HudsonAlpha SL14586 v042211.1 2 exp wgEncodeHaibTfbsEcc1Zbtb7aV0422111RawRep2 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ZBTB7A v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Zbtb7aV0422111RawRep1 ECC1 ZBTB7A 1 ZBTB7A_(SC-34508) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003241 3241 GSM1010752 Myers HudsonAlpha SL13275 v042211.1 1 exp wgEncodeHaibTfbsEcc1Zbtb7aV0422111RawRep1 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ZBTB7A v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Yy1sc281V0422111RawRep2 ECC1 YY1 V11 2 YY1_(SC-281) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003240 3240 GSM1010753 Myers HudsonAlpha SL14584 v042211.1 2 exp wgEncodeHaibTfbsEcc1Yy1sc281V0422111RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 YY1 281 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Yy1sc281V0422111RawRep1 ECC1 YY1 V11 1 YY1_(SC-281) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003240 3240 GSM1010753 Myers HudsonAlpha SL13273 v042211.1 1 exp wgEncodeHaibTfbsEcc1Yy1sc281V0422111RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 YY1 281 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Usf1V0422111RawRep2 ECC1 USF1 V11 2 USF-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003239 3239 GSM1010886 Myers HudsonAlpha SL14589 v042211.1 2 exp wgEncodeHaibTfbsEcc1Usf1V0422111RawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 USF-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Usf1V0422111RawRep1 ECC1 USF1 V11 1 USF-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003239 3239 GSM1010886 Myers HudsonAlpha SL13279 v042211.1 1 exp wgEncodeHaibTfbsEcc1Usf1V0422111RawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 USF-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tead4sc101184V0422111RawRep2 ECC1 TEAD4 V11 2 TEAD4_(SC-101184) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003238 3238 GSM1010885 Myers HudsonAlpha SL14591 v042211.1 2 exp wgEncodeHaibTfbsEcc1Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tead4sc101184V0422111RawRep1 ECC1 TEAD4 V11 1 TEAD4_(SC-101184) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003238 3238 GSM1010885 Myers HudsonAlpha SL13281 v042211.1 1 exp wgEncodeHaibTfbsEcc1Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tcf12V0422111RawRep2 ECC1 TCF12 V11 2 TCF12 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003291 3291 GSM1010842 Myers HudsonAlpha SL14063 v042211.1 2 exp wgEncodeHaibTfbsEcc1Tcf12V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TCF12 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tcf12V0422111RawRep1 ECC1 TCF12 V11 1 TCF12 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003291 3291 GSM1010842 Myers HudsonAlpha SL16025 v042211.1 1 exp wgEncodeHaibTfbsEcc1Tcf12V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TCF12 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Taf1V0422111RawRep2 ECC1 TAF1 V11 2 TAF1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003256 3256 GSM1010733 Myers HudsonAlpha SL14721 v042211.1 2 exp wgEncodeHaibTfbsEcc1Taf1V0422111RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TAF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Taf1V0422111RawRep1 ECC1 TAF1 V11 1 TAF1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003256 3256 GSM1010733 Myers HudsonAlpha SL13751 v042211.1 1 exp wgEncodeHaibTfbsEcc1Taf1V0422111RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TAF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1SrfV0422111RawRep2 ECC1 SRF V11 2 SRF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003245 3245 GSM1010762 Myers HudsonAlpha SL14583 v042211.1 2 exp wgEncodeHaibTfbsEcc1SrfV0422111RawRep2 None RawSignal Serum response transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 SRF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1SrfV0422111RawRep1 ECC1 SRF V11 1 SRF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003245 3245 GSM1010762 Myers HudsonAlpha SL13272 v042211.1 1 exp wgEncodeHaibTfbsEcc1SrfV0422111RawRep1 None RawSignal Serum response transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 SRF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Rad21V0422111RawRep2 ECC1 RAD21 V11 2 Rad21 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003263 3263 GSM1010801 Myers HudsonAlpha SL16305 v042211.1 2 exp wgEncodeHaibTfbsEcc1Rad21V0422111RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 RAD21 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Rad21V0422111RawRep1 ECC1 RAD21 V11 1 Rad21 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003263 3263 GSM1010801 Myers HudsonAlpha SL13270 v042211.1 1 exp wgEncodeHaibTfbsEcc1Rad21V0422111RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 RAD21 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hRawRep2 ECC1 Pol2 DMSO 2 Pol2 ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001572 1572 GSM803536 Myers HudsonAlpha SL2085 v041610.2 2 exp wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal RNA Polymerase II epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Pol2 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hRawRep1 ECC1 Pol2 DMSO 1 Pol2 ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001572 1572 GSM803536 Myers HudsonAlpha SL1176 v041610.2 1 exp wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal RNA Polymerase II epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Pol2 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1P300V0422111RawRep2 ECC1 p300 V11 2 p300 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003274 3274 GSM1010759 Myers HudsonAlpha SL14585 v042211.1 2 exp wgEncodeHaibTfbsEcc1P300V0422111RawRep2 None RawSignal EP300(c-20) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 p300 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1P300V0422111RawRep1 ECC1 p300 V11 1 p300 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003274 3274 GSM1010759 Myers HudsonAlpha SL13274 v042211.1 1 exp wgEncodeHaibTfbsEcc1P300V0422111RawRep1 None RawSignal EP300(c-20) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 p300 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1NrsfV0422111RawRep2 ECC1 NRSF V11 2 NRSF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003290 3290 GSM1010841 Myers HudsonAlpha SL14057 v042211.1 2 exp wgEncodeHaibTfbsEcc1NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1NrsfV0422111RawRep1 ECC1 NRSF V11 1 NRSF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003290 3290 GSM1010841 Myers HudsonAlpha SL16023 v042211.1 1 exp wgEncodeHaibTfbsEcc1NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Nficsc81335V0422111RawRep2 ECC1 NFIC V11 2 NFIC_(SC-81335) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003289 3289 GSM1010855 Myers HudsonAlpha SL16022 v042211.1 2 exp wgEncodeHaibTfbsEcc1Nficsc81335V0422111RawRep2 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 NFIC v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Nficsc81335V0422111RawRep1 ECC1 NFIC V11 1 NFIC_(SC-81335) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003289 3289 GSM1010855 Myers HudsonAlpha SL14056 v042211.1 1 exp wgEncodeHaibTfbsEcc1Nficsc81335V0422111RawRep1 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 NFIC v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1MaxV0422111RawRep2 ECC1 Max V11 2 Max ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003268 3268 GSM1010807 Myers HudsonAlpha SL16021 v042211.1 2 exp wgEncodeHaibTfbsEcc1MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1MaxV0422111RawRep1 ECC1 Max V11 1 Max ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003268 3268 GSM1010807 Myers HudsonAlpha SL14054 v042211.1 1 exp wgEncodeHaibTfbsEcc1MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Etoh02RawRep2 ECC1 GR EtOH 2 GR ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001591 1591 GSM803464 Myers HudsonAlpha SL1087 v041610.2 2 input wgEncodeHaibTfbsEcc1GrV0416102Etoh02RawRep2 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GR EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Etoh02RawRep1 ECC1 GR EtOH 1 GR ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001591 1591 GSM803464 Myers HudsonAlpha SL1035 v041610.2 1 input wgEncodeHaibTfbsEcc1GrV0416102Etoh02RawRep1 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GR EtOH v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Dex100nmRawRep2 ECC1 GR DEX 102 2 GR ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001540 1540 GSM803340 Myers HudsonAlpha SL1088 v041610.2 2 exp wgEncodeHaibTfbsEcc1GrV0416102Dex100nmRawRep2 DEX_100nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GR DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Dex100nmRawRep1 ECC1 GR DEX 102 1 GR ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001540 1540 GSM803340 Myers HudsonAlpha SL1012 v041610.2 1 exp wgEncodeHaibTfbsEcc1GrV0416102Dex100nmRawRep1 DEX_100nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GR DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep2 ECC1 FOXM1 V11 2 FOXM1_(SC-502) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003288 3288 GSM1010856 Myers HudsonAlpha SL14725 v042211.1 2 exp wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep2 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep1 ECC1 FOXM1 V11 1 FOXM1_(SC-502) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003288 3288 GSM1010856 Myers HudsonAlpha SL14051 v042211.1 1 exp wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep1 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hRawRep2 ECC1 FOXA1 DMSO 2 FOXA1_(SC-6553) ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001586 1586 GSM803444 Myers HudsonAlpha SL2080 v041610.2 2 exp wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 FOXA1 6553 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hRawRep1 ECC1 FOXA1 DMSO 1 FOXA1_(SC-6553) ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001586 1586 GSM803444 Myers HudsonAlpha SL1880 v041610.2 1 exp wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 FOXA1 6553 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hRawRep2 ECC1 ERa Geni 2 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001575 1575 GSM803541 Myers HudsonAlpha SL1122 v041610.2 2 exp wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hRawRep2 Genistein_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a Genistein v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hRawRep1 ECC1 ERa Geni 1 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001575 1575 GSM803541 Myers HudsonAlpha SL1049 v041610.2 1 exp wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hRawRep1 Genistein_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a Genistein v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hRawRep2 ECC1 ERa Estra 2 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001536 1536 GSM803422 Myers HudsonAlpha SL1093 v041610.2 2 exp wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hRawRep2 Estradiol_10nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a Estradiol v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hRawRep1 ECC1 ERa Estra 1 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001536 1536 GSM803422 Myers HudsonAlpha SL1011 v041610.2 1 exp wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hRawRep1 Estradiol_10nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a Estradiol v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Dm002p1hRawRep2 ECC1 ERa DMSO 2 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001537 1537 GSM803421 Myers HudsonAlpha SL1092 v041610.2 2 input wgEncodeHaibTfbsEcc1EralphaaV0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Dm002p1hRawRep1 ECC1 ERa DMSO 1 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001537 1537 GSM803421 Myers HudsonAlpha SL1034 v041610.2 1 input wgEncodeHaibTfbsEcc1EralphaaV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hRawRep2 ECC1 ERa BPA 2 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002313 2313 GSM1010747 Myers HudsonAlpha SL2082 v041610.2 2 exp wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hRawRep2 BPA_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a BPA v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hRawRep1 ECC1 ERa BPA 1 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002313 2313 GSM1010747 Myers HudsonAlpha SL1050 v041610.2 1 exp wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hRawRep1 BPA_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a BPA v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Egr1V0422111RawRep2 ECC1 Egr-1 V11 2 Egr-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003232 3232 GSM1010888 Myers HudsonAlpha SL14590 v042211.1 2 exp wgEncodeHaibTfbsEcc1Egr1V0422111RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Egr1V0422111RawRep1 ECC1 Egr-1 V11 1 Egr-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003232 3232 GSM1010888 Myers HudsonAlpha SL13280 v042211.1 1 exp wgEncodeHaibTfbsEcc1Egr1V0422111RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hRawRep2 ECC1 CTCF DMSO 2 CTCF_(SC-5916) ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002300 2300 GSM1010774 Myers HudsonAlpha SL3447 v041610.2 2 exp wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CTCF 5916 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hRawRep1 ECC1 CTCF DMSO 1 CTCF_(SC-5916) ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002300 2300 GSM1010774 Myers HudsonAlpha SL2630 v041610.2 1 exp wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CTCF 5916 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Creb1sc240V0422111RawRep2 ECC1 CREB1 V11 2 CREB1_(SC-240) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003287 3287 GSM1010857 Myers HudsonAlpha SL14723 v042211.1 2 exp wgEncodeHaibTfbsEcc1Creb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Creb1sc240V0422111RawRep1 ECC1 CREB1 V11 1 CREB1_(SC-240) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003287 3287 GSM1010857 Myers HudsonAlpha SL14048 v042211.1 1 exp wgEncodeHaibTfbsEcc1Creb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Cebpbsc150V0422111RawRep2 ECC1 CEBPB V11 2 CEBPB_(SC-150) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003262 3262 GSM1010802 Myers HudsonAlpha SL16302 v042211.1 2 exp wgEncodeHaibTfbsEcc1Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Cebpbsc150V0422111RawRep1 ECC1 CEBPB V11 1 CEBPB_(SC-150) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003262 3262 GSM1010802 Myers HudsonAlpha SL13276 v042211.1 1 exp wgEncodeHaibTfbsEcc1Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0422111RawRep4 SKSH RvXL V11 4 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003430 3430 GSM1010883 Myers HudsonAlpha SL16761 v042211.1 4 input wgEncodeHaibTfbsSknshRxlchV0422111RawRep4 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v042211.1 ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0422111RawRep3 SKSH RvXL V11 3 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003430 3430 GSM1010883 Myers HudsonAlpha SL13505 v042211.1 3 input wgEncodeHaibTfbsSknshRxlchV0422111RawRep3 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0422111RawRep2 SKSH RvXL V11 2 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003430 3430 GSM1010883 Myers HudsonAlpha SL16760 v042211.1 2 input wgEncodeHaibTfbsSknshRxlchV0422111RawRep2 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0422111RawRep1 SKSH RvXL V11 1 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003430 3430 GSM1010883 Myers HudsonAlpha SL12791 v042211.1 1 input wgEncodeHaibTfbsSknshRxlchV0422111RawRep1 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0416101RawRep3 SKSH RvXL V101 3 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002287 2287 GSM1010798 Myers HudsonAlpha SL3775 v041610.1 3 input wgEncodeHaibTfbsSknshRxlchV0416101RawRep3 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v041610.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0416101RawRep2 SKSH RvXL V101 2 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002287 2287 GSM1010798 Myers HudsonAlpha SL3774 v041610.1 2 input wgEncodeHaibTfbsSknshRxlchV0416101RawRep2 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0416101RawRep1 SKSH RvXL V101 1 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002287 2287 GSM1010798 Myers HudsonAlpha SL2134 v041610.1 1 input wgEncodeHaibTfbsSknshRxlchV0416101RawRep1 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchPcr2xRawRep2 SKSH RvXL PCR2 2 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001473 1473 GSM803528 Myers HudsonAlpha SL410 PCR2x 2 input wgEncodeHaibTfbsSknshRxlchPcr2xRawRep2 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchPcr2xRawRep1 SKSH RvXL PCR2 1 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001473 1473 GSM803528 Myers HudsonAlpha SL108 PCR2x 1 input wgEncodeHaibTfbsSknshRxlchPcr2xRawRep1 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshZbtb33V0422111RawRep2 SKSH ZBTB33 V11 2 ZBTB33 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003261 3261 GSM1010799 Myers HudsonAlpha SL14711 v042211.1 2 exp wgEncodeHaibTfbsSknshZbtb33V0422111RawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH ZBTB33 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshZbtb33V0422111RawRep1 SKSH ZBTB33 V11 1 ZBTB33 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003261 3261 GSM1010799 Myers HudsonAlpha SL13502 v042211.1 1 exp wgEncodeHaibTfbsSknshZbtb33V0422111RawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH ZBTB33 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshYy1sc281V0422111RawRep2 SKSH YY1 V11 2 YY1_(SC-281) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003228 3228 GSM1010897 Myers HudsonAlpha SL14045 v042211.1 2 exp wgEncodeHaibTfbsSknshYy1sc281V0422111RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH YY1 281 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshYy1sc281V0422111RawRep1 SKSH YY1 V11 1 YY1_(SC-281) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003228 3228 GSM1010897 Myers HudsonAlpha SL13085 v042211.1 1 exp wgEncodeHaibTfbsSknshYy1sc281V0422111RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH YY1 281 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshUsf1V0422111RawRep2 SKSH USF1 V11 2 USF-1 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003269 3269 GSM1010806 Myers HudsonAlpha SL14597 v042211.1 2 exp wgEncodeHaibTfbsSknshUsf1V0422111RawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH USF-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshUsf1V0422111RawRep1 SKSH USF1 V11 1 USF-1 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003269 3269 GSM1010806 Myers HudsonAlpha SL13084 v042211.1 1 exp wgEncodeHaibTfbsSknshUsf1V0422111RawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH USF-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTead4sc101184V0422111RawRep2 SKSH TEAD4 V11 2 TEAD4_(SC-101184) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003286 3286 GSM1010858 Myers HudsonAlpha SL14710 v042211.1 2 exp wgEncodeHaibTfbsSknshTead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTead4sc101184V0422111RawRep1 SKSH TEAD4 V11 1 TEAD4_(SC-101184) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003286 3286 GSM1010858 Myers HudsonAlpha SL13501 v042211.1 1 exp wgEncodeHaibTfbsSknshTead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTcf12V0422111RawRep2 SKSH TCF12 V11 2 TCF12 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003227 3227 GSM1010900 Myers HudsonAlpha SL14046 v042211.1 2 exp wgEncodeHaibTfbsSknshTcf12V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TCF12 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTcf12V0422111RawRep1 SKSH TCF12 V11 1 TCF12 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003227 3227 GSM1010900 Myers HudsonAlpha SL13086 v042211.1 1 exp wgEncodeHaibTfbsSknshTcf12V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TCF12 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTaf1V0416101RawRep2 SKSH TAF1 V101 2 TAF1 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002301 2301 GSM1010773 Myers HudsonAlpha SL6462 v041610.1 2 exp wgEncodeHaibTfbsSknshTaf1V0416101RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TAF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTaf1V0416101RawRep1 SKSH TAF1 V101 1 TAF1 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002301 2301 GSM1010773 Myers HudsonAlpha SL5612 v041610.1 1 exp wgEncodeHaibTfbsSknshTaf1V0416101RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TAF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshSin3ak20V0416101RawRep2 SKSH Sin3A V101 2 Sin3Ak-20 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002271 2271 GSM1010816 Myers HudsonAlpha SL5895 v041610.1 2 exp wgEncodeHaibTfbsSknshSin3ak20V0416101RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshSin3ak20V0416101RawRep1 SKSH Sin3A V101 1 Sin3Ak-20 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002271 2271 GSM1010816 Myers HudsonAlpha SL5043 v041610.1 1 exp wgEncodeHaibTfbsSknshSin3ak20V0416101RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxraV0422111RawRep2 SKSH RXRA V11 2 RXRA SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003302 3302 GSM1010767 Myers HudsonAlpha SL14708 v042211.1 2 exp wgEncodeHaibTfbsSknshRxraV0422111RawRep2 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RXRA v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxraV0422111RawRep1 SKSH RXRA V11 1 RXRA SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003302 3302 GSM1010767 Myers HudsonAlpha SL13497 v042211.1 1 exp wgEncodeHaibTfbsSknshRxraV0422111RawRep1 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RXRA v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPol24h8V0416101RawRep2 SKSH Pol2-4H8 V101 2 Pol2-4H8 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002270 2270 GSM1010817 Myers HudsonAlpha SL5607 v041610.1 2 exp wgEncodeHaibTfbsSknshPol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPol24h8V0416101RawRep1 SKSH Pol2-4H8 V101 1 Pol2-4H8 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002270 2270 GSM1010817 Myers HudsonAlpha SL3768 v041610.1 1 exp wgEncodeHaibTfbsSknshPol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPbx3V0422111RawRep2 SKSH PBx3 V11 2 Pbx3 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003300 3300 GSM1010887 Myers HudsonAlpha SL16042 v042211.1 2 exp wgEncodeHaibTfbsSknshPbx3V0422111RawRep2 None RawSignal Pbx 3 (D-17) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH PBx3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPbx3V0422111RawRep1 SKSH PBx3 V11 1 Pbx3 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003300 3300 GSM1010887 Myers HudsonAlpha SL13495 v042211.1 1 exp wgEncodeHaibTfbsSknshPbx3V0422111RawRep1 None RawSignal Pbx 3 (D-17) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH PBx3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshP300V0422111RawRep2 SKSH p300 V11 2 p300 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003270 3270 GSM1010763 Myers HudsonAlpha SL14705 v042211.1 2 exp wgEncodeHaibTfbsSknshP300V0422111RawRep2 None RawSignal EP300(c-20) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH p300 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshP300V0422111RawRep1 SKSH p300 V11 1 p300 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003270 3270 GSM1010763 Myers HudsonAlpha SL13494 v042211.1 1 exp wgEncodeHaibTfbsSknshP300V0422111RawRep1 None RawSignal EP300(c-20) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH p300 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfV0416101RawRep2 SKSH NRSF V101 2 NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002269 2269 GSM1010735 Myers HudsonAlpha SL5896 v041610.1 2 exp wgEncodeHaibTfbsSknshNrsfV0416101RawRep2 None RawSignal Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NRSF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfV0416101RawRep1 SKSH NRSF V101 1 NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002269 2269 GSM1010735 Myers HudsonAlpha SL5494 v041610.1 1 exp wgEncodeHaibTfbsSknshNrsfV0416101RawRep1 None RawSignal Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NRSF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfPcr2xRawRep2 SKSH NRSF PCR2 2 NRSF SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001547 1547 GSM803335 Myers HudsonAlpha SL409 PCR2x 2 exp wgEncodeHaibTfbsSknshNrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfPcr2xRawRep1 SKSH NRSF PCR2 1 NRSF SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001547 1547 GSM803335 Myers HudsonAlpha SL83 PCR2x 1 exp wgEncodeHaibTfbsSknshNrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNficsc81335V0422111RawRep2 SKSH NFIC V11 2 NFIC_(SC-81335) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEH003237 3237 GSM1010880 Myers HudsonAlpha SL14603 v042211.1 2 exp wgEncodeHaibTfbsSknshNficsc81335V0422111RawRep2 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NFIC v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNficsc81335V0422111RawRep1 SKSH NFIC V11 1 NFIC_(SC-81335) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEH003237 3237 GSM1010880 Myers HudsonAlpha SL13313 v042211.1 1 exp wgEncodeHaibTfbsSknshNficsc81335V0422111RawRep1 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NFIC v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMef2aV0422111RawRep2 SKSH MEF2A V11 2 MEF2A SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003298 3298 GSM1010834 Myers HudsonAlpha SL14704 v042211.1 2 exp wgEncodeHaibTfbsSknshMef2aV0422111RawRep2 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH MEF2A v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMef2aV0422111RawRep1 SKSH MEF2A V11 1 MEF2A SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003298 3298 GSM1010834 Myers HudsonAlpha SL13493 v042211.1 1 exp wgEncodeHaibTfbsSknshMef2aV0422111RawRep1 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH MEF2A v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMaxV0422111RawRep2 SKSH Max V11 2 Max SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003299 3299 GSM1010835 Myers HudsonAlpha SL16738 v042211.1 2 exp wgEncodeHaibTfbsSknshMaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMaxV0422111RawRep1 SKSH Max V11 1 Max SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003299 3299 GSM1010835 Myers HudsonAlpha SL14602 v042211.1 1 exp wgEncodeHaibTfbsSknshMaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshJundV0422111RawRep2 SKSH JunD V11 2 JunD SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003226 3226 GSM1010901 Myers HudsonAlpha SL14042 v042211.1 2 exp wgEncodeHaibTfbsSknshJundV0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH JunD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshJundV0422111RawRep1 SKSH JunD V11 1 JunD SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003226 3226 GSM1010901 Myers HudsonAlpha SL13079 v042211.1 1 exp wgEncodeHaibTfbsSknshJundV0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH JunD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGata3V0422111RawRep2 SKSH GATA3 V11 2 GATA3_(SC-268) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003249 3249 GSM1010738 Myers HudsonAlpha SL14041 v042211.1 2 exp wgEncodeHaibTfbsSknshGata3V0422111RawRep2 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH GATA3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGata3V0422111RawRep1 SKSH GATA3 V11 1 GATA3_(SC-268) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003249 3249 GSM1010738 Myers HudsonAlpha SL13078 v042211.1 1 exp wgEncodeHaibTfbsSknshGata3V0422111RawRep1 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH GATA3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGabpV0422111RawRep2 SKSH GABP V11 2 GABP SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003248 3248 GSM1010739 Myers HudsonAlpha SL13752 v042211.1 2 exp wgEncodeHaibTfbsSknshGabpV0422111RawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH GABP v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGabpV0422111RawRep1 SKSH GABP V11 1 GABP SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003248 3248 GSM1010739 Myers HudsonAlpha SL12627 v042211.1 1 exp wgEncodeHaibTfbsSknshGabpV0422111RawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH GABP v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFoxm1sc502V0422111RawRep2 SKSH FOXM1 V11 2 FOXM1_(SC-502) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003243 3243 GSM1010750 Myers HudsonAlpha SL14596 v042211.1 2 exp wgEncodeHaibTfbsSknshFoxm1sc502V0422111RawRep2 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH FOXM1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFoxm1sc502V0422111RawRep1 SKSH FOXM1 V11 1 FOXM1_(SC-502) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003243 3243 GSM1010750 Myers HudsonAlpha SL13083 v042211.1 1 exp wgEncodeHaibTfbsSknshFoxm1sc502V0422111RawRep1 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH FOXM1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFosl2V0422111RawRep2 SKSH FOSL2 V11 2 FOSL2 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003297 3297 GSM1010840 Myers HudsonAlpha SL16737 v042211.1 2 exp wgEncodeHaibTfbsSknshFosl2V0422111RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH FOSL2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFosl2V0422111RawRep1 SKSH FOSL2 V11 1 FOSL2 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003297 3297 GSM1010840 Myers HudsonAlpha SL13310 v042211.1 1 exp wgEncodeHaibTfbsSknshFosl2V0422111RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH FOSL2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshElf1V0422111RawRep2 SKSH ELF1 V11 2 ELF1_(SC-631) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003242 3242 GSM1010751 Myers HudsonAlpha SL14600 v042211.1 2 exp wgEncodeHaibTfbsSknshElf1V0422111RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH ELF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshElf1V0422111RawRep1 SKSH ELF1 V11 1 ELF1_(SC-631) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003242 3242 GSM1010751 Myers HudsonAlpha SL13309 v042211.1 1 exp wgEncodeHaibTfbsSknshElf1V0422111RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH ELF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7RxlchV0422111RawRep4 MCF-7 RvXL V11 4 RevXlinkChromatin MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003428 3428 GSM1010854 Myers HudsonAlpha SL16758 v042211.1 4 input wgEncodeHaibTfbsMcf7RxlchV0422111RawRep4 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Control v042211.1 ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7RxlchV0422111RawRep3 MCF-7 RvXL V11 3 RevXlinkChromatin MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003428 3428 GSM1010854 Myers HudsonAlpha SL16757 v042211.1 3 input wgEncodeHaibTfbsMcf7RxlchV0422111RawRep3 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7RxlchV0422111RawRep2 MCF-7 RvXL V11 2 RevXlinkChromatin MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003428 3428 GSM1010854 Myers HudsonAlpha SL16756 v042211.1 2 input wgEncodeHaibTfbsMcf7RxlchV0422111RawRep2 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7RxlchV0422111RawRep1 MCF-7 RvXL V11 1 RevXlinkChromatin MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003428 3428 GSM1010854 Myers HudsonAlpha SL13504 v042211.1 1 input wgEncodeHaibTfbsMcf7RxlchV0422111RawRep1 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep2 MCF-7 TEAD4 V11 2 TEAD4_(SC-101184) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003284 3284 GSM1010860 Myers HudsonAlpha SL16341 v042211.1 2 exp wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep1 MCF-7 TEAD4 V11 1 TEAD4_(SC-101184) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003284 3284 GSM1010860 Myers HudsonAlpha SL14575 v042211.1 1 exp wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep2 MCF-7 TCF12 V11 2 TCF12 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003283 3283 GSM1010861 Myers HudsonAlpha SL16340 v042211.1 2 exp wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TCF12 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep1 MCF-7 TCF12 V11 1 TCF12 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003283 3283 GSM1010861 Myers HudsonAlpha SL14574 v042211.1 1 exp wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TCF12 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Taf1V0422111RawRep2 MCF-7 TAF1 V11 2 TAF1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003317 3317 GSM1010811 Myers HudsonAlpha SL16339 v042211.1 2 exp wgEncodeHaibTfbsMcf7Taf1V0422111RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TAF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Taf1V0422111RawRep1 MCF-7 TAF1 V11 1 TAF1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003317 3317 GSM1010811 Myers HudsonAlpha SL14572 v042211.1 1 exp wgEncodeHaibTfbsMcf7Taf1V0422111RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TAF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7SrfV0422111RawRep2 MCF-7 SRF V11 2 SRF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003296 3296 GSM1010839 Myers HudsonAlpha SL16044 v042211.1 2 exp wgEncodeHaibTfbsMcf7SrfV0422111RawRep2 None RawSignal Serum response transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 SRF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7SrfV0422111RawRep1 MCF-7 SRF V11 1 SRF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003296 3296 GSM1010839 Myers HudsonAlpha SL13723 v042211.1 1 exp wgEncodeHaibTfbsMcf7SrfV0422111RawRep1 None RawSignal Serum response transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 SRF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep2 MCF-7 Sin3A V11 2 Sin3Ak-20 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003282 3282 GSM1010862 Myers HudsonAlpha SL14716 v042211.1 2 exp wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Sin3Ak-20 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep1 MCF-7 Sin3A V11 1 Sin3Ak-20 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003282 3282 GSM1010862 Myers HudsonAlpha SL13726 v042211.1 1 exp wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Sin3Ak-20 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Rad21V0422111RawRep2 MCF-7 RAD21 V11 2 Rad21 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003259 3259 GSM1010791 Myers HudsonAlpha SL16336 v042211.1 2 exp wgEncodeHaibTfbsMcf7Rad21V0422111RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 RAD21 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Rad21V0422111RawRep1 MCF-7 RAD21 V11 1 Rad21 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003259 3259 GSM1010791 Myers HudsonAlpha SL13724 v042211.1 1 exp wgEncodeHaibTfbsMcf7Rad21V0422111RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 RAD21 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep2 MCF-7 PML V11 2 PML_(SC-71910) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003295 3295 GSM1010838 Myers HudsonAlpha SL16026 v042211.1 2 exp wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 PML v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep1 MCF-7 PML V11 1 PML_(SC-71910) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003295 3295 GSM1010838 Myers HudsonAlpha SL13722 v042211.1 1 exp wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 PML v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7P300V0422111RawRep2 MCF-7 p300 V11 2 p300 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003260 3260 GSM1010800 Myers HudsonAlpha SL16335 v042211.1 2 exp wgEncodeHaibTfbsMcf7P300V0422111RawRep2 None RawSignal EP300(c-20) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 p300 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7P300V0422111RawRep1 MCF-7 p300 V11 1 p300 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003260 3260 GSM1010800 Myers HudsonAlpha SL13492 v042211.1 1 exp wgEncodeHaibTfbsMcf7P300V0422111RawRep1 None RawSignal EP300(c-20) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 p300 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7NrsfV0422111RawRep2 MCF-7 NRSF V11 2 NRSF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003231 3231 GSM1010891 Myers HudsonAlpha SL14698 v042211.1 2 exp wgEncodeHaibTfbsMcf7NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7NrsfV0422111RawRep1 MCF-7 NRSF V11 1 NRSF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003231 3231 GSM1010891 Myers HudsonAlpha SL13491 v042211.1 1 exp wgEncodeHaibTfbsMcf7NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep2 MCF-7 NR2F2 V11 2 NR2F2_(SC-271940) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003294 3294 GSM1010837 Myers HudsonAlpha SL14697 v042211.1 2 exp wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep2 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep1 MCF-7 NR2F2 V11 1 NR2F2_(SC-271940) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003294 3294 GSM1010837 Myers HudsonAlpha SL13490 v042211.1 1 exp wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep1 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7MaxV0422111RawRep2 MCF-7 Max V11 2 Max MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003281 3281 GSM1010863 Myers HudsonAlpha SL14695 v042211.1 2 exp wgEncodeHaibTfbsMcf7MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7MaxV0422111RawRep1 MCF-7 Max V11 1 Max MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003281 3281 GSM1010863 Myers HudsonAlpha SL13485 v042211.1 1 exp wgEncodeHaibTfbsMcf7MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7JundV0422111RawRep2 MCF-7 JunD V11 2 JunD MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003236 3236 GSM1010892 Myers HudsonAlpha SL14694 v042211.1 2 exp wgEncodeHaibTfbsMcf7JundV0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 JunD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7JundV0422111RawRep1 MCF-7 JunD V11 1 JunD MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003236 3236 GSM1010892 Myers HudsonAlpha SL13484 v042211.1 1 exp wgEncodeHaibTfbsMcf7JundV0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 JunD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep2 MCF-7 HDAC2 V11 2 HDAC2_(SC-6296) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003258 3258 GSM1010825 Myers HudsonAlpha SL16334 v042211.1 2 exp wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep2 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 HDAC2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep1 MCF-7 HDAC2 V11 1 HDAC2_(SC-6296) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003258 3258 GSM1010825 Myers HudsonAlpha SL13483 v042211.1 1 exp wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep1 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 HDAC2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Gata3V0422111RawRep2 MCF-7 GATA3 V11 2 GATA3_(SC-268) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003235 3235 GSM1010783 Myers HudsonAlpha SL14692 v042211.1 2 exp wgEncodeHaibTfbsMcf7Gata3V0422111RawRep2 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 GATA3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Gata3V0422111RawRep1 MCF-7 GATA3 V11 1 GATA3_(SC-268) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003235 3235 GSM1010783 Myers HudsonAlpha SL13482 v042211.1 1 exp wgEncodeHaibTfbsMcf7Gata3V0422111RawRep1 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 GATA3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7GabpV0422111RawRep2 MCF-7 GABP V11 2 GABP MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003280 3280 GSM1010864 Myers HudsonAlpha SL14683 v042211.1 2 exp wgEncodeHaibTfbsMcf7GabpV0422111RawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 GABP v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7GabpV0422111RawRep1 MCF-7 GABP V11 1 GABP MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003280 3280 GSM1010864 Myers HudsonAlpha SL13459 v042211.1 1 exp wgEncodeHaibTfbsMcf7GabpV0422111RawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 GABP v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep2 MCF-7 FOXM1 V11 2 FOXM1_(SC-502) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003279 3279 GSM1010769 Myers HudsonAlpha SL14686 v042211.1 2 exp wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep2 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep1 MCF-7 FOXM1 V11 1 FOXM1_(SC-502) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003279 3279 GSM1010769 Myers HudsonAlpha SL13462 v042211.1 1 exp wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep1 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep2 MCF-7 FOSL2 V11 2 FOSL2 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003278 3278 GSM1010768 Myers HudsonAlpha SL14682 v042211.1 2 exp wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 FOSL2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep1 MCF-7 FOSL2 V11 1 FOSL2 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003278 3278 GSM1010768 Myers HudsonAlpha SL13457 v042211.1 1 exp wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 FOSL2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Elf1V0422111RawRep2 MCF-7 ELF1 V11 2 ELF1_(SC-631) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003234 3234 GSM1010764 Myers HudsonAlpha SL14690 v042211.1 2 exp wgEncodeHaibTfbsMcf7Elf1V0422111RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 ELF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Elf1V0422111RawRep1 MCF-7 ELF1 V11 1 ELF1_(SC-631) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003234 3234 GSM1010764 Myers HudsonAlpha SL13466 v042211.1 1 exp wgEncodeHaibTfbsMcf7Elf1V0422111RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 ELF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Egr1V0422111RawRep2 MCF-7 Egr-1 V11 2 Egr-1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003293 3293 GSM1010844 Myers HudsonAlpha SL14689 v042211.1 2 exp wgEncodeHaibTfbsMcf7Egr1V0422111RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Egr1V0422111RawRep1 MCF-7 Egr-1 V11 1 Egr-1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003293 3293 GSM1010844 Myers HudsonAlpha SL13465 v042211.1 1 exp wgEncodeHaibTfbsMcf7Egr1V0422111RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep2 MCF-7 CTCF V11 2 CTCF_(SC-5916) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003257 3257 GSM1010734 Myers HudsonAlpha SL16333 v042211.1 2 exp wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CTCF 5916 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep1 MCF-7 CTCF V11 1 CTCF_(SC-5916) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003257 3257 GSM1010734 Myers HudsonAlpha SL13463 v042211.1 1 exp wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep1 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CTCF 5916 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep2 MCF-7 CEBPB V11 2 CEBPB_(SC-150) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003233 3233 GSM1010889 Myers HudsonAlpha SL14684 v042211.1 2 exp wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep1 MCF-7 CEBPB V11 1 CEBPB_(SC-150) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003233 3233 GSM1010889 Myers HudsonAlpha SL13460 v042211.1 1 exp wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecRxlchPcr1xRawRep1 HUVEC RvXL PCR1 1 RevXlinkChromatin HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001675 1675 GSM1010736 Myers HudsonAlpha SL1106 PCR1x 1 input wgEncodeHaibTfbsHuvecRxlchPcr1xRawRep1 None RawSignal umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep2 HUVEC Pol2-4H8 V101 2 Pol2-4H8 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002298 2298 GSM1010824 Myers HudsonAlpha SL2387 v041610.1 2 exp wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep1 HUVEC Pol2-4H8 V101 1 Pol2-4H8 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002298 2298 GSM1010824 Myers HudsonAlpha SL1104 v041610.1 1 exp wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep2 HUVEC Pol2 PCR1 2 Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002297 2297 GSM1010830 Myers HudsonAlpha SL6966 PCR1x 2 exp wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep2 None RawSignal RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Pol2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep1 HUVEC Pol2 PCR1 1 Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002297 2297 GSM1010830 Myers HudsonAlpha SL1103 PCR1x 1 exp wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep1 None RawSignal RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Pol2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0422111RawRep3 HepG RvXL V11 3 RevXlinkChromatin HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002277 2277 GSM1010814 Myers HudsonAlpha SL12795 v042211.1 3 input wgEncodeHaibTfbsHepg2RxlchV0422111RawRep3 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0422111RawRep2 HepG RvXL V11 2 RevXlinkChromatin HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002277 2277 GSM1010814 Myers HudsonAlpha SL12050 v042211.1 2 input wgEncodeHaibTfbsHepg2RxlchV0422111RawRep2 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0422111RawRep1 HepG RvXL V11 1 RevXlinkChromatin HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002277 2277 GSM1010814 Myers HudsonAlpha SL6019 v042211.1 1 input wgEncodeHaibTfbsHepg2RxlchV0422111RawRep1 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0416101RawRep2 HepG RvXL V101 2 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001596 1596 GSM803463 Myers HudsonAlpha SL3976 v041610.1 2 input wgEncodeHaibTfbsHepg2RxlchV0416101RawRep2 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0416101RawRep1 HepG RvXL V101 1 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001596 1596 GSM803463 Myers HudsonAlpha SL1781 v041610.1 1 input wgEncodeHaibTfbsHepg2RxlchV0416101RawRep1 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep2 HepG RvXL PCR2 2 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001597 1597 GSM803462 Myers HudsonAlpha SL295 PCR2x 2 input wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep2 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep1 HepG RvXL PCR2 1 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001597 1597 GSM803462 Myers HudsonAlpha SL294 PCR2x 1 input wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep1 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep4 HepG RvXL PCR1 4 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001603 1603 GSM803521 Myers HudsonAlpha SL1401 PCR1x 4 input wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep4 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR1x ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep3 HepG RvXL PCR1 3 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001603 1603 GSM803521 Myers HudsonAlpha SL1400 PCR1x 3 input wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep3 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep2 HepG RvXL PCR1 2 RevXlinkChromatin HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001603 1603 GSM803521 Myers HudsonAlpha SL819 PCR1x 2 input wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep2 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep1 HepG RvXL PCR1 1 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001603 1603 GSM803521 Myers HudsonAlpha SL593 PCR1x 1 input wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep1 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep2 HepG ZEB1 V11 2 ZEB1_(SC-25388) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003315 3315 GSM1010809 Myers HudsonAlpha SL16318 v042211.1 2 exp wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep2 None RawSignal This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZEB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep1 HepG ZEB1 V11 1 ZEB1_(SC-25388) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003315 3315 GSM1010809 Myers HudsonAlpha SL13301 v042211.1 1 exp wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep1 None RawSignal This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZEB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep2 HepG ZBTB7A 2 ZBTB7A_(SC-34508) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002296 2296 GSM1010831 Myers HudsonAlpha SL6464 v041610.1 2 exp wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep2 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB7A v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep1 HepG ZBTB7A 1 ZBTB7A_(SC-34508) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002296 2296 GSM1010831 Myers HudsonAlpha SL3973 v041610.1 1 exp wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep1 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB7A v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep2 HepG ZBTB33 2 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001642 1642 GSM803418 Myers HudsonAlpha SL3987 v041610.1 2 exp wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB33 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep1 HepG ZBTB33 1 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001642 1642 GSM803418 Myers HudsonAlpha SL3929 v041610.1 1 exp wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB33 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep2 HepG ZBTB33 2 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001503 1503 GSM803449 Myers HudsonAlpha SL1055 PCR1x 2 exp wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep1 HepG ZBTB33 1 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001503 1503 GSM803449 Myers HudsonAlpha SL981 PCR1x 1 exp wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep2 HepG YY1 V101 2 YY1_(SC-281) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001661 1661 GSM803381 Myers HudsonAlpha SL3927 v041610.1 2 exp wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep1 HepG YY1 V101 1 YY1_(SC-281) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001661 1661 GSM803381 Myers HudsonAlpha SL2195 v041610.1 1 exp wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep2 HepG USF1 PCR1 2 USF-1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001472 1472 GSM803527 Myers HudsonAlpha SL636 PCR1x 2 exp wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 USF-1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep1 HepG USF1 PCR1 1 USF-1 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-21 2011-12-21 wgEncodeEH001472 1472 GSM803527 Myers HudsonAlpha SL582 PCR1x 1 exp wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 USF-1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep2 HepG TEAD4 V11 2 TEAD4_(SC-101184) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002345 2345 GSM1010875 Myers HudsonAlpha SL9545 v042211.1 2 exp wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep1 HepG TEAD4 V11 1 TEAD4_(SC-101184) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002345 2345 GSM1010875 Myers HudsonAlpha SL8584 v042211.1 1 exp wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep2 HepG TCF12 PCR1 2 TCF12 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001544 1544 GSM803336 Myers HudsonAlpha SL1167 PCR1x 2 exp wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TCF12 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep1 HepG TCF12 PCR1 1 TCF12 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001544 1544 GSM803336 Myers HudsonAlpha SL1060 PCR1x 1 exp wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TCF12 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep2 HepG TAF1 PCR2 2 TAF1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001551 1551 GSM803367 Myers HudsonAlpha SL359 PCR2x 2 exp wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TAF1 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep1 HepG TAF1 PCR2 1 TAF1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001551 1551 GSM803367 Myers HudsonAlpha SL358 PCR2x 1 exp wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TAF1 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2SrfV0416101RawRep2 HepG SRF V101 2 SRF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001611 1611 GSM803502 Myers HudsonAlpha SL3275 v041610.1 2 exp wgEncodeHaibTfbsHepg2SrfV0416101RawRep2 None RawSignal Serum response transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SRF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2SrfV0416101RawRep1 HepG SRF V101 1 SRF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001611 1611 GSM803502 Myers HudsonAlpha SL3156 v041610.1 1 exp wgEncodeHaibTfbsHepg2SrfV0416101RawRep1 None RawSignal Serum response transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SRF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp2V0422111RawRep2 HepG SP2 V11 2 SP2_(SC-643) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002264 2264 GSM1010787 Myers HudsonAlpha SL6006 v042211.1 2 exp wgEncodeHaibTfbsHepg2Sp2V0422111RawRep2 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SP2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp2V0422111RawRep1 HepG SP2 V11 1 SP2_(SC-643) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002264 2264 GSM1010787 Myers HudsonAlpha SL5688 v042211.1 1 exp wgEncodeHaibTfbsHepg2Sp2V0422111RawRep1 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SP2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep2 HepG SP1 PCR1 2 SP1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001561 1561 GSM803507 Myers HudsonAlpha SL1194 PCR1x 2 exp wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SP1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep1 HepG SP1 PCR1 1 SP1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001561 1561 GSM803507 Myers HudsonAlpha SL1056 PCR1x 1 exp wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SP1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep2 HepG Sin3A PCR1 2 Sin3Ak-20 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001471 1471 GSM803530 Myers HudsonAlpha SL637 PCR1x 2 exp wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Sin3Ak-20 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep1 HepG Sin3A PCR1 1 Sin3Ak-20 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001471 1471 GSM803530 Myers HudsonAlpha SL583 PCR1x 1 exp wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Sin3Ak-20 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxraPcr1xRawRep2 HepG RXRA PCR1 2 RXRA HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001506 1506 GSM803452 Myers HudsonAlpha SL1054 PCR1x 2 exp wgEncodeHaibTfbsHepg2RxraPcr1xRawRep2 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 RXRA PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxraPcr1xRawRep1 HepG RXRA PCR1 1 RXRA HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001506 1506 GSM803452 Myers HudsonAlpha SL984 PCR1x 1 exp wgEncodeHaibTfbsHepg2RxraPcr1xRawRep1 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 RXRA PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Rad21V0416101RawRep2 HepG RAD21 V101 2 Rad21 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001608 1608 GSM803517 Myers HudsonAlpha SL3586 v041610.1 2 exp wgEncodeHaibTfbsHepg2Rad21V0416101RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 RAD21 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Rad21V0416101RawRep1 HepG RAD21 V101 1 Rad21 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001608 1608 GSM803517 Myers HudsonAlpha SL3179 v041610.1 1 exp wgEncodeHaibTfbsHepg2Rad21V0416101RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 RAD21 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep2 HepG Pol2-4H8 V102 2 Pol2-4H8 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002278 2278 GSM1010821 Myers HudsonAlpha SL5604 v041610.2 2 exp wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep1 HepG Pol2-4H8 V102 1 Pol2-4H8 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002278 2278 GSM1010821 Myers HudsonAlpha SL1363 v041610.2 1 exp wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep2 HepG Pol2 PCR2 2 Pol2 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001550 1550 GSM803368 Myers HudsonAlpha SL349 PCR2x 2 exp wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep2 None RawSignal RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Pol2 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep1 HepG Pol2 PCR2 1 Pol2 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001550 1550 GSM803368 Myers HudsonAlpha SL348 PCR2x 1 exp wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep1 None RawSignal RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Pol2 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2P300V0416101RawRep2 HepG p300 V101 2 p300 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001612 1612 GSM803499 Myers HudsonAlpha SL3644 v041610.1 2 exp wgEncodeHaibTfbsHepg2P300V0416101RawRep2 None RawSignal EP300(c-20) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 p300 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2P300V0416101RawRep1 HepG p300 V101 1 p300 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001612 1612 GSM803499 Myers HudsonAlpha SL3154 v041610.1 1 exp wgEncodeHaibTfbsHepg2P300V0416101RawRep1 None RawSignal EP300(c-20) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 p300 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfV0416101RawRep2 HepG NRSF V101 2 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002263 2263 GSM1010784 Myers HudsonAlpha SL5897 v041610.1 2 exp wgEncodeHaibTfbsHepg2NrsfV0416101RawRep2 None RawSignal Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NRSF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfV0416101RawRep1 HepG NRSF V101 1 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002263 2263 GSM1010784 Myers HudsonAlpha SL5040 v041610.1 1 exp wgEncodeHaibTfbsHepg2NrsfV0416101RawRep1 None RawSignal Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NRSF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep2 HepG NRSF PCR2 2 NRSF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001549 1549 GSM803344 Myers HudsonAlpha SL274 PCR2x 2 exp wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep1 HepG NRSF PCR2 1 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2010-12-14 2011-09-14 wgEncodeEH001549 1549 GSM803344 Myers HudsonAlpha SL273 PCR2x 1 exp wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep2 HepG NR2F2 V11 2 NR2F2_(SC-271940) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003314 3314 GSM1010810 Myers HudsonAlpha SL16316 v042211.1 2 exp wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep2 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep1 HepG NR2F2 V11 1 NR2F2_(SC-271940) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003314 3314 GSM1010810 Myers HudsonAlpha SL12644 v042211.1 1 exp wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep1 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep2 HepG NFIC V11 2 NFIC_(SC-81335) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002319 2319 GSM1010741 Myers HudsonAlpha SL7554 v042211.1 2 exp wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep2 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NFIC v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep1 HepG NFIC V11 1 NFIC_(SC-81335) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002319 2319 GSM1010741 Myers HudsonAlpha SL7102 v042211.1 1 exp wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep1 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NFIC v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep2 HepG MYBL2 V11 2 MYBL2_(SC-81192) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002344 2344 GSM1010876 Myers HudsonAlpha SL7564 v042211.1 2 exp wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep2 None RawSignal The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 MYBL2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep1 HepG MYBL2 V11 1 MYBL2_(SC-81192) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002344 2344 GSM1010876 Myers HudsonAlpha SL7101 v042211.1 1 exp wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep1 None RawSignal The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 MYBL2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep2 HepG MBD4 V11 2 MBD4_(SC-271530) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002318 2318 GSM1010740 Myers HudsonAlpha SL8132 v042211.1 2 exp wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep2 None RawSignal MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 MBD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep1 HepG MBD4 V11 1 MBD4_(SC-271530) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002318 2318 GSM1010740 Myers HudsonAlpha SL7901 v042211.1 1 exp wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep1 None RawSignal MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 MBD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2MaxV0422111RawRep2 HepG Max V11 2 Max HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003254 3254 GSM1010865 Myers HudsonAlpha SL13292 v042211.1 2 exp wgEncodeHaibTfbsHepg2MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2MaxV0422111RawRep1 HepG Max V11 1 Max HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003254 3254 GSM1010865 Myers HudsonAlpha SL12422 v042211.1 1 exp wgEncodeHaibTfbsHepg2MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2JundPcr1xRawRep2 HepG JunD PCR1 2 JunD HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001470 1470 GSM803500 Myers HudsonAlpha SL629 PCR1x 2 exp wgEncodeHaibTfbsHepg2JundPcr1xRawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 JunD PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2JundPcr1xRawRep1 HepG JunD PCR1 1 JunD HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001470 1470 GSM803500 Myers HudsonAlpha SL635 PCR1x 1 exp wgEncodeHaibTfbsHepg2JundPcr1xRawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 JunD PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep2 HepG HNF4G V101 2 HNF4G_(SC-6558) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001651 1651 GSM803404 Myers HudsonAlpha SL3463 v041610.1 2 exp wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep2 None RawSignal Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HNF4G v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep1 HepG HNF4G V101 1 HNF4G_(SC-6558) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001651 1651 GSM803404 Myers HudsonAlpha SL3178 v041610.1 1 exp wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep1 None RawSignal Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HNF4G v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep2 HepG HNF4A V101 2 HNF4A_(SC-8987) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001595 1595 GSM803460 Myers HudsonAlpha SL2125 v041610.1 2 exp wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep2 None RawSignal The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HNF4A v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep1 HepG HNF4A V101 1 HNF4A_(SC-8987) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001595 1595 GSM803460 Myers HudsonAlpha SL1481 v041610.1 1 exp wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep1 None RawSignal The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HNF4A v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep2 HepG HDAC2 V101 2 HDAC2_(SC-6296) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001618 1618 GSM803493 Myers HudsonAlpha SL3583 v041610.1 2 exp wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep2 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HDAC2 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep1 HepG HDAC2 V101 1 HDAC2_(SC-6296) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001618 1618 GSM803493 Myers HudsonAlpha SL3177 v041610.1 1 exp wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep1 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HDAC2 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2GabpPcr2xRawRep2 HepG GABP PCR2 2 GABP HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001548 1548 GSM803343 Myers HudsonAlpha SL276 PCR2x 2 exp wgEncodeHaibTfbsHepg2GabpPcr2xRawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 GABP PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2GabpPcr2xRawRep1 HepG GABP PCR2 1 GABP HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001548 1548 GSM803343 Myers HudsonAlpha SL275 PCR2x 1 exp wgEncodeHaibTfbsHepg2GabpPcr2xRawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 GABP PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep2 HepG FOXA2 V101 2 FOXA2_(SC-6554) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001650 1650 GSM803403 Myers HudsonAlpha SL3175 v041610.1 2 exp wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep2 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA2 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep1 HepG FOXA2 V101 1 FOXA2_(SC-6554) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001650 1650 GSM803403 Myers HudsonAlpha SL2196 v041610.1 1 exp wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep1 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA2 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep2 HepG FOXA1 V101 2 FOXA1_(SC-6553) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001594 1594 GSM803461 Myers HudsonAlpha SL2124 v041610.1 2 exp wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep2 None RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA1 6553 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep1 HepG FOXA1 V101 1 FOXA1_(SC-6553) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001594 1594 GSM803461 Myers HudsonAlpha SL1786 v041610.1 1 exp wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep1 None RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA1 6553 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep2 HepG FOXA1 V101 2 FOXA1_(SC-101058) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001630 1630 GSM803432 Myers HudsonAlpha SL2194 v041610.1 2 exp wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep2 None RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA1 101058 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep1 HepG FOXA1 V101 1 FOXA1_(SC-101058) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001630 1630 GSM803432 Myers HudsonAlpha SL1788 v041610.1 1 exp wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep1 None RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA1 101058 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep2 HepG FOSL2 V101 2 FOSL2 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001501 1501 GSM803451 Myers HudsonAlpha SL1107 v041610.1 2 exp wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOSL2 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep1 HepG FOSL2 V101 1 FOSL2 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001501 1501 GSM803451 Myers HudsonAlpha SL632 v041610.1 1 exp wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOSL2 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep2 HepG ELF1 V101 2 ELF1_(SC-631) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001641 1641 GSM803415 Myers HudsonAlpha SL3986 v041610.1 2 exp wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ELF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep1 HepG ELF1 V101 1 ELF1_(SC-631) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001641 1641 GSM803415 Myers HudsonAlpha SL3645 v041610.1 1 exp wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ELF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep2 HepG CTCF V101 2 CTCF_(SC-5916) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2010-01-06 2010-10-06 wgEncodeEH001516 1516 GSM803486 Myers HudsonAlpha SL3582 v041610.1 2 exp wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CTCF 5916 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep1 HepG CTCF V101 1 CTCF_(SC-5916) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2010-01-06 2010-10-06 wgEncodeEH001516 1516 GSM803486 Myers HudsonAlpha SL3176 v041610.1 1 exp wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep1 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CTCF 5916 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep2 HepG CREB1 V11 2 CREB1_(SC-240) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003312 3312 GSM1010808 Myers HudsonAlpha SL13290 v042211.1 2 exp wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep1 HepG CREB1 V11 1 CREB1_(SC-240) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003312 3312 GSM1010808 Myers HudsonAlpha SL12405 v042211.1 1 exp wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep2 HepG CEBPD V101 2 CEBPD_(SC-636) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002305 2305 GSM1010777 Myers HudsonAlpha SL4940 v041610.1 2 exp wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep2 None RawSignal The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CEBPD v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep1 HepG CEBPD V101 1 CEBPD_(SC-636) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002305 2305 GSM1010777 Myers HudsonAlpha SL4210 v041610.1 1 exp wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep1 None RawSignal The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CEBPD v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep2 HepG CEBPB V101 2 CEBPB_(SC-150) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002304 2304 GSM1010778 Myers HudsonAlpha SL4939 v041610.1 2 exp wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CEBPB v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep1 HepG CEBPB V101 1 CEBPB_(SC-150) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002304 2304 GSM1010778 Myers HudsonAlpha SL4209 v041610.1 1 exp wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CEBPB v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep2 HepG BHLHE40 2 BHLHE40 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001515 1515 GSM803483 Myers HudsonAlpha SL3460 v041610.1 2 exp wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep2 None RawSignal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 BHLHE40 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep1 HepG BHLHE40 1 BHLHE40 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001515 1515 GSM803483 Myers HudsonAlpha SL1059 v041610.1 1 exp wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep1 None RawSignal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 BHLHE40 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Atf3V0416101RawRep2 HepG ATF3 V101 2 ATF3 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001568 1568 GSM803503 Myers HudsonAlpha SL1787 v041610.1 2 exp wgEncodeHaibTfbsHepg2Atf3V0416101RawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ATF3 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Atf3V0416101RawRep1 HepG ATF3 V101 1 ATF3 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001568 1568 GSM803503 Myers HudsonAlpha SL2386 v041610.1 1 exp wgEncodeHaibTfbsHepg2Atf3V0416101RawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ATF3 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3RxlchPcr1xRawRep1 HeLa RvXL PCR1 1 RevXlinkChromatin HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001628 1628 GSM803479 Myers HudsonAlpha SL592 PCR1x 1 input wgEncodeHaibTfbsHelas3RxlchPcr1xRawRep1 None RawSignal cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep2 HeLa TAF1 PCR1 2 TAF1 HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001505 1505 GSM803455 Myers HudsonAlpha SL706 PCR1x 2 exp wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 TAF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep1 HeLa TAF1 PCR1 1 TAF1 HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001505 1505 GSM803455 Myers HudsonAlpha SL590 PCR1x 1 exp wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 TAF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep2 HeLa Pol2 PCR1 2 Pol2 HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001474 1474 GSM803533 Myers HudsonAlpha SL672 PCR1x 2 exp wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep2 None RawSignal RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Pol2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep1 HeLa Pol2 PCR1 1 Pol2 HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001474 1474 GSM803533 Myers HudsonAlpha SL631 PCR1x 1 exp wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep1 None RawSignal RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Pol2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep2 HeLa NRSF PCR1 2 NRSF HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001629 1629 GSM803478 Myers HudsonAlpha SL1322 PCR1x 2 exp wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 NRSF PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep1 HeLa NRSF PCR1 1 NRSF HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001629 1629 GSM803478 Myers HudsonAlpha SL679 PCR1x 1 exp wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 NRSF PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3GabpPcr1xRawRep2 HeLa GABP PCR1 2 GABP HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001504 1504 GSM803454 Myers HudsonAlpha SL611 PCR1x 2 exp wgEncodeHaibTfbsHelas3GabpPcr1xRawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 GABP PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3GabpPcr1xRawRep1 HeLa GABP PCR1 1 GABP HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001504 1504 GSM803454 Myers HudsonAlpha SL610 PCR1x 1 exp wgEncodeHaibTfbsHelas3GabpPcr1xRawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 GABP PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep2 H1-neu RvXL 2 RevXlinkChromatin H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003425 3425 GSM1010873 Myers HudsonAlpha SL16755 v042211.1 2 input wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep2 None RawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep1 H1-neu RvXL 1 RevXlinkChromatin H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003425 3425 GSM1010873 Myers HudsonAlpha SL13320 v042211.1 1 input wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep1 None RawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep2 H1-neu TAF1 2 TAF1 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003266 3266 GSM1010805 Myers HudsonAlpha SL14594 v042211.1 2 exp wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons TAF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep1 H1-neu TAF1 1 TAF1 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003266 3266 GSM1010805 Myers HudsonAlpha SL13300 v042211.1 1 exp wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons TAF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep2 H1-neu Pol2-4H8 2 Pol2-4H8 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003265 3265 GSM1010803 Myers HudsonAlpha SL14592 v042211.1 2 exp wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons Pol2-4H8 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep1 H1-neu Pol2-4H8 1 Pol2-4H8 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003265 3265 GSM1010803 Myers HudsonAlpha SL13298 v042211.1 1 exp wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons Pol2-4H8 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep2 H1-neu NRSF 2 NRSF H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003264 3264 GSM1010804 Myers HudsonAlpha SL14593 v042211.1 2 exp wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep1 H1-neu NRSF 1 NRSF H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003264 3264 GSM1010804 Myers HudsonAlpha SL13299 v042211.1 1 exp wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0422111RawRep3 A549 RvXL V11 3 RevXlinkChromatin A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003423 3423 GSM1010866 Myers HudsonAlpha SL12790 v042211.1 3 input wgEncodeHaibTfbsA549RxlchV0422111RawRep3 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0422111RawRep2 A549 RvXL V11 2 RevXlinkChromatin A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003423 3423 GSM1010866 Myers HudsonAlpha SL16753 v042211.1 2 input wgEncodeHaibTfbsA549RxlchV0422111RawRep2 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0422111RawRep1 A549 RvXL V11 1 RevXlinkChromatin A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003423 3423 GSM1010866 Myers HudsonAlpha SL13321 v042211.1 1 input wgEncodeHaibTfbsA549RxlchV0422111RawRep1 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0422111Etoh02RawRep1 A549 RX Eth V11 1 RevXlinkChromatin A549 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002273 2273 GSM1010818 Myers HudsonAlpha SL6021 v042211.1 1 input wgEncodeHaibTfbsA549RxlchV0422111Etoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0416101Etoh02RawRep1 A549 RvXL V101 1 RevXlinkChromatin A549 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002283 2283 GSM1010795 Myers HudsonAlpha SL3978 v041610.1 1 input wgEncodeHaibTfbsA549RxlchV0416101Etoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control EtOH v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchPcr2xEtoh02RawRep1 A549 RX Eth PC2 1 RevXlinkChromatin A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001589 1589 GSM803435 Myers HudsonAlpha SL307 PCR2x 1 input wgEncodeHaibTfbsA549RxlchPcr2xEtoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control EtOH PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchPcr1xEtoh02RawRep1 A549 RX Eth PC1 1 RevXlinkChromatin A549 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001644 1644 GSM803412 Myers HudsonAlpha SL475 PCR1x 1 input wgEncodeHaibTfbsA549RxlchPcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchPcr2xDex100nmRawRep1 A549 RX DEX PC2 1 RevXlinkChromatin A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001590 1590 GSM803465 Myers HudsonAlpha SL335 PCR2x 1 input wgEncodeHaibTfbsA549RxlchPcr2xDex100nmRawRep1 DEX_100nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control DEX 100nM PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchPcr1xDex100nmRawRep1 A549 RX DEX PC1 1 RevXlinkChromatin A549 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001643 1643 GSM803417 Myers HudsonAlpha SL474 PCR1x 1 input wgEncodeHaibTfbsA549RxlchPcr1xDex100nmRawRep1 DEX_100nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control DEX 100nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02RawRep2 A549 ZBTB33 ETH 2 ZBTB33 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002295 2295 GSM1010832 Myers HudsonAlpha SL6592 v042211.1 2 exp wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ZBTB33 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02RawRep1 A549 ZBTB33 ETH 1 ZBTB33 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002295 2295 GSM1010832 Myers HudsonAlpha SL6016 v042211.1 1 exp wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ZBTB33 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Yy1cV0422111Etoh02RawRep2 A549 YY1 EtOH 2 YY1_(SC-281) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002282 2282 GSM1010794 Myers HudsonAlpha SL5699 v042211.1 2 exp wgEncodeHaibTfbsA549Yy1cV0422111Etoh02RawRep2 EtOH_0.02pct RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 YY1 281 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Yy1cV0422111Etoh02RawRep1 A549 YY1 EtOH 1 YY1_(SC-281) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002282 2282 GSM1010794 Myers HudsonAlpha SL5357 v042211.1 1 exp wgEncodeHaibTfbsA549Yy1cV0422111Etoh02RawRep1 EtOH_0.02pct RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 YY1 281 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1V0422111Etoh02RawRep2 A549 USF Et V11 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002291 2291 GSM1010828 Myers HudsonAlpha SL7279 v042211.1 2 exp wgEncodeHaibTfbsA549Usf1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1V0422111Etoh02RawRep1 A549 USF Et V11 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002291 2291 GSM1010828 Myers HudsonAlpha SL6593 v042211.1 1 exp wgEncodeHaibTfbsA549Usf1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02RawRep2 A549 USF1 Et P1 2 USF-1 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001539 1539 GSM803429 Myers HudsonAlpha SL1207 PCR1x 2 exp wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02RawRep2 EtOH_0.02pct RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 EtOH PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02RawRep1 A549 USF1 Et P1 1 USF-1 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001539 1539 GSM803429 Myers HudsonAlpha SL1080 PCR1x 1 exp wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmRawRep2 A549 USF1 DEX 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001509 1509 GSM803457 Myers HudsonAlpha SL1206 PCR1x 2 exp wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmRawRep2 DEX_100nM RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 DEX 100nM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmRawRep1 A549 USF1 DEX 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001509 1509 GSM803457 Myers HudsonAlpha SL1079 PCR1x 1 exp wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmRawRep1 DEX_100nM RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 DEX 100nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tead4sc101184V0422111RawRep2 A549 TEAD4 V11 2 TEAD4_(SC-101184) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003273 3273 GSM1010868 Myers HudsonAlpha SL14702 v042211.1 2 exp wgEncodeHaibTfbsA549Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tead4sc101184V0422111RawRep1 A549 TEAD4 V11 1 TEAD4_(SC-101184) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003273 3273 GSM1010868 Myers HudsonAlpha SL13479 v042211.1 1 exp wgEncodeHaibTfbsA549Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tcf12V0422111Etoh02RawRep2 A549 TCF12 EtOH 2 TCF12 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002312 2312 GSM1010746 Myers HudsonAlpha SL8076 v042211.1 2 exp wgEncodeHaibTfbsA549Tcf12V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TCF12 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tcf12V0422111Etoh02RawRep1 A549 TCF12 EtOH 1 TCF12 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002312 2312 GSM1010746 Myers HudsonAlpha SL7114 v042211.1 1 exp wgEncodeHaibTfbsA549Tcf12V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TCF12 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Taf1V0422111Etoh02RawRep2 A549 TAF1 EtOH 2 TAF1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002275 2275 GSM1010812 Myers HudsonAlpha SL5700 v042211.1 2 exp wgEncodeHaibTfbsA549Taf1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TAF1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Taf1V0422111Etoh02RawRep1 A549 TAF1 EtOH 1 TAF1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002275 2275 GSM1010812 Myers HudsonAlpha SL5358 v042211.1 1 exp wgEncodeHaibTfbsA549Taf1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TAF1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sp1V0422111Etoh02RawRep2 A549 SP1 EtOH 2 SP1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002274 2274 GSM1010813 Myers HudsonAlpha SL5701 v042211.1 2 exp wgEncodeHaibTfbsA549Sp1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 SP1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sp1V0422111Etoh02RawRep1 A549 SP1 EtOH 1 SP1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002274 2274 GSM1010813 Myers HudsonAlpha SL5360 v042211.1 1 exp wgEncodeHaibTfbsA549Sp1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 SP1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Six5V0422111Etoh02RawRep2 A549 SIX5 EtOH 2 SIX5 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002341 2341 GSM1010879 Myers HudsonAlpha SL8400 v042211.1 2 exp wgEncodeHaibTfbsA549Six5V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 SIX5 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Six5V0422111Etoh02RawRep1 A549 SIX5 EtOH 1 SIX5 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002341 2341 GSM1010879 Myers HudsonAlpha SL7277 v042211.1 1 exp wgEncodeHaibTfbsA549Six5V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 SIX5 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02RawRep2 A549 Sin3A EtOH 2 Sin3Ak-20 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002342 2342 GSM1010882 Myers HudsonAlpha SL8401 v042211.1 2 exp wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Sin3Ak-20 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02RawRep1 A549 Sin3A EtOH 1 Sin3Ak-20 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002342 2342 GSM1010882 Myers HudsonAlpha SL7275 v042211.1 1 exp wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Sin3Ak-20 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Rad21V0422111RawRep2 A549 RAD21 V11 2 Rad21 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003272 3272 GSM1010761 Myers HudsonAlpha SL16300 v042211.1 2 exp wgEncodeHaibTfbsA549Rad21V0422111RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 RAD21 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Rad21V0422111RawRep1 A549 RAD21 V11 1 Rad21 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003272 3272 GSM1010761 Myers HudsonAlpha SL12634 v042211.1 1 exp wgEncodeHaibTfbsA549Rad21V0422111RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 RAD21 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02RawRep2 A549 Pol2 EtOH 2 Pol2 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001493 1493 GSM803360 Myers HudsonAlpha SL334 PCR2x 2 exp wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02RawRep2 EtOH_0.02pct RawSignal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Pol2 EtOH PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02RawRep1 A549 Pol2 EtOH 1 Pol2 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001493 1493 GSM803360 Myers HudsonAlpha SL245 PCR2x 1 exp wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02RawRep1 EtOH_0.02pct RawSignal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Pol2 EtOH PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmRawRep2 A549 Pol2 DEX 2 Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2010-12-20 2011-09-20 wgEncodeEH001494 1494 GSM803361 Myers HudsonAlpha SL306 PCR2x 2 exp wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmRawRep2 DEX_100nM RawSignal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Pol2 DEX 100nM PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmRawRep1 A549 Pol2 DEX 1 Pol2 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001494 1494 GSM803361 Myers HudsonAlpha SL244 PCR2x 1 exp wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmRawRep1 DEX_100nM RawSignal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Pol2 DEX 100nM PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pbx3V0422111RawRep2 A549 PBx3 V11 2 Pbx3 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003255 3255 GSM1010755 Myers HudsonAlpha SL16043 v042211.1 2 exp wgEncodeHaibTfbsA549Pbx3V0422111RawRep2 None RawSignal Pbx 3 (D-17) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 PBx3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pbx3V0422111RawRep1 A549 PBx3 V11 1 Pbx3 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003255 3255 GSM1010755 Myers HudsonAlpha SL13476 v042211.1 1 exp wgEncodeHaibTfbsA549Pbx3V0422111RawRep1 None RawSignal Pbx 3 (D-17) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 PBx3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549P300V0422111Etoh02RawRep2 A549 p300 EtOH 2 p300 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002292 2292 GSM1010827 Myers HudsonAlpha SL7115 v042211.1 2 exp wgEncodeHaibTfbsA549P300V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal EP300(c-20) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 p300 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549P300V0422111Etoh02RawRep1 A549 p300 EtOH 1 p300 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002292 2292 GSM1010827 Myers HudsonAlpha SL6437 v042211.1 1 exp wgEncodeHaibTfbsA549P300V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal EP300(c-20) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 p300 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawRep2 A549 NRSF EtOH 2 NRSF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002311 2311 GSM1010749 Myers HudsonAlpha SL8075 v042211.1 2 exp wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawRep2 EtOH_0.02pct RawSignal Neuron-restrictive silencer transcription factor epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 NRSF EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawRep1 A549 NRSF EtOH 1 NRSF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002311 2311 GSM1010749 Myers HudsonAlpha SL7110 v042211.1 1 exp wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawRep1 EtOH_0.02pct RawSignal Neuron-restrictive silencer transcription factor epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 NRSF EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549MaxV0422111RawRep2 A549 Max V11 2 Max A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003251 3251 GSM1010728 Myers HudsonAlpha SL13754 v042211.1 2 exp wgEncodeHaibTfbsA549MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549MaxV0422111RawRep1 A549 Max V11 1 Max A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003251 3251 GSM1010728 Myers HudsonAlpha SL12638 v042211.1 1 exp wgEncodeHaibTfbsA549MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549JundV0416102Etoh02RawRep2 A549 JunD EtOH 2 JunD A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002327 2327 GSM1010723 Myers HudsonAlpha SL4698 v041610.2 2 exp wgEncodeHaibTfbsA549JundV0416102Etoh02RawRep2 EtOH_0.02pct RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 JunD EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549JundV0416102Etoh02RawRep1 A549 JunD EtOH 1 JunD A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002327 2327 GSM1010723 Myers HudsonAlpha SL3900 v041610.2 1 exp wgEncodeHaibTfbsA549JundV0416102Etoh02RawRep1 EtOH_0.02pct RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 JunD EtOH v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xEtoh02RawRep2 A549 GR Eth PC2 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001557 1557 GSM803373 Myers HudsonAlpha SL305 PCR2x 2 input wgEncodeHaibTfbsA549GrPcr2xEtoh02RawRep2 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR EtOH PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xEtoh02RawRep1 A549 GR Eth PC2 1 GR A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001557 1557 GSM803373 Myers HudsonAlpha SL247 PCR2x 1 input wgEncodeHaibTfbsA549GrPcr2xEtoh02RawRep1 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR EtOH PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xEtoh02RawRep2 A549 GR Eth PC1 2 GR A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001526 1526 GSM803395 Myers HudsonAlpha SL879 PCR1x 2 input wgEncodeHaibTfbsA549GrPcr1xEtoh02RawRep2 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR EtOH PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xEtoh02RawRep1 A549 GR Eth PC1 1 GR A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001526 1526 GSM803395 Myers HudsonAlpha SL878 PCR1x 1 input wgEncodeHaibTfbsA549GrPcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex5nmRawRep2 A549 GR DX5nM 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001492 1492 GSM803359 Myers HudsonAlpha SL881 PCR1x 2 exp wgEncodeHaibTfbsA549GrPcr1xDex5nmRawRep2 DEX_5nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 5 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 5nM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex5nmRawRep1 A549 GR DX5nM 1 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001492 1492 GSM803359 Myers HudsonAlpha SL880 PCR1x 1 exp wgEncodeHaibTfbsA549GrPcr1xDex5nmRawRep1 DEX_5nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 5 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 5nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex50nmRawRep2 A549 GR DX50nM 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001491 1491 GSM803358 Myers HudsonAlpha SL883 PCR1x 2 exp wgEncodeHaibTfbsA549GrPcr1xDex50nmRawRep2 DEX_50nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 50 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 50nM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex50nmRawRep1 A549 GR DX50nM 1 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001491 1491 GSM803358 Myers HudsonAlpha SL882 PCR1x 1 exp wgEncodeHaibTfbsA549GrPcr1xDex50nmRawRep1 DEX_50nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 50 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 50nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex500pmRawRep2 A549 GR DX.5nM 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001490 1490 GSM803357 Myers HudsonAlpha SL885 PCR1x 2 exp wgEncodeHaibTfbsA549GrPcr1xDex500pmRawRep2 DEX_500pM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 500 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 500pM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex500pmRawRep1 A549 GR DX.5nM 1 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001490 1490 GSM803357 Myers HudsonAlpha SL884 PCR1x 1 exp wgEncodeHaibTfbsA549GrPcr1xDex500pmRawRep1 DEX_500pM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 500 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 500pM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xDex100nmRawRep2 A549 GR DX100nM 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001555 1555 GSM803371 Myers HudsonAlpha SL304 PCR2x 2 exp wgEncodeHaibTfbsA549GrPcr2xDex100nmRawRep2 DEX_100nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 100nM PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xDex100nmRawRep1 A549 GR DX100nM 1 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001555 1555 GSM803371 Myers HudsonAlpha SL246 PCR2x 1 exp wgEncodeHaibTfbsA549GrPcr2xDex100nmRawRep1 DEX_100nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 100nM PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Gata3V0422111RawRep2 A549 GATA3 V11 2 GATA3_(SC-268) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003250 3250 GSM1010727 Myers HudsonAlpha SL13283 v042211.1 2 exp wgEncodeHaibTfbsA549Gata3V0422111RawRep2 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GATA3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Gata3V0422111RawRep1 A549 GATA3 V11 1 GATA3_(SC-268) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003250 3250 GSM1010727 Myers HudsonAlpha SL12399 v042211.1 1 exp wgEncodeHaibTfbsA549Gata3V0422111RawRep1 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GATA3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GabpV0422111Etoh02RawRep2 A549 GABP EtOH 2 GABP A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002294 2294 GSM1010833 Myers HudsonAlpha SL6595 v042211.1 2 exp wgEncodeHaibTfbsA549GabpV0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GABP EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GabpV0422111Etoh02RawRep1 A549 GABP EtOH 1 GABP A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002294 2294 GSM1010833 Myers HudsonAlpha SL6015 v042211.1 1 exp wgEncodeHaibTfbsA549GabpV0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GABP EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa2V0416102Etoh02RawRep2 A549 FOXA2 EtOH 2 FOXA2_(SC-6554) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002326 2326 GSM1010724 Myers HudsonAlpha SL3253 v041610.2 2 exp wgEncodeHaibTfbsA549Foxa2V0416102Etoh02RawRep2 EtOH_0.02pct RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA2 EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa2V0416102Etoh02RawRep1 A549 FOXA2 EtOH 1 FOXA2_(SC-6554) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002326 2326 GSM1010724 Myers HudsonAlpha SL3077 v041610.2 1 exp wgEncodeHaibTfbsA549Foxa2V0416102Etoh02RawRep1 EtOH_0.02pct RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA2 EtOH v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Etoh02RawRep2 A549 FOXA1 EtOH 2 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002325 2325 GSM1010725 Myers HudsonAlpha SL3251 v041610.2 2 input wgEncodeHaibTfbsA549Foxa1V0416102Etoh02RawRep2 EtOH_0.02pct RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA1 101058 EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Etoh02RawRep1 A549 FOXA1 EtOH 1 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002325 2325 GSM1010725 Myers HudsonAlpha SL2665 v041610.2 1 input wgEncodeHaibTfbsA549Foxa1V0416102Etoh02RawRep1 EtOH_0.02pct RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA1 101058 EtOH v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmRawRep2 A549 FOXA1 DEX 2 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002293 2293 GSM1010826 Myers HudsonAlpha SL3250 v041610.2 2 exp wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmRawRep2 DEX_100nM RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA1 101058 DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmRawRep1 A549 FOXA1 DEX 1 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002293 2293 GSM1010826 Myers HudsonAlpha SL2666 v041610.2 1 exp wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmRawRep1 DEX_100nM RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA1 101058 DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Fosl2V0422111Etoh02RawRep2 A549 FOSL2 EtOH 2 FOSL2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002310 2310 GSM1010748 Myers HudsonAlpha SL8077 v042211.1 2 exp wgEncodeHaibTfbsA549Fosl2V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOSL2 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Fosl2V0422111Etoh02RawRep1 A549 FOSL2 EtOH 1 FOSL2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002310 2310 GSM1010748 Myers HudsonAlpha SL7116 v042211.1 1 exp wgEncodeHaibTfbsA549Fosl2V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOSL2 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ets1V0422111Etoh02RawRep2 A549 ETS1 EtOH 2 ETS1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002290 2290 GSM1010829 Myers HudsonAlpha SL7108 v042211.1 2 exp wgEncodeHaibTfbsA549Ets1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETS1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ets1V0422111Etoh02RawRep1 A549 ETS1 EtOH 1 ETS1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002290 2290 GSM1010829 Myers HudsonAlpha SL6600 v042211.1 1 exp wgEncodeHaibTfbsA549Ets1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETS1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Elf1V0422111Etoh02RawRep2 A549 ELF1 EtOH 2 ELF1_(SC-631) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002289 2289 GSM1010790 Myers HudsonAlpha SL7113 v042211.1 2 exp wgEncodeHaibTfbsA549Elf1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ELF1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Elf1V0422111Etoh02RawRep1 A549 ELF1 EtOH 1 ELF1_(SC-631) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002289 2289 GSM1010790 Myers HudsonAlpha SL6436 v042211.1 1 exp wgEncodeHaibTfbsA549Elf1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ELF1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549E2f6V0422111RawRep2 A549 E2F6 V11 2 E2F6 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003244 3244 GSM1010766 Myers HudsonAlpha SL14581 v042211.1 2 exp wgEncodeHaibTfbsA549E2f6V0422111RawRep2 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 E2F6 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549E2f6V0422111RawRep1 A549 E2F6 V11 1 E2F6 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003244 3244 GSM1010766 Myers HudsonAlpha SL13319 v042211.1 1 exp wgEncodeHaibTfbsA549E2f6V0422111RawRep1 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 E2F6 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02RawRep2 A549 CTCF EtOH 2 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001508 1508 GSM803456 Myers HudsonAlpha SL1078 PCR1x 2 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02RawRep2 EtOH_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF 5916 EtOH PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02RawRep1 A549 CTCF EtOH 1 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001508 1508 GSM803456 Myers HudsonAlpha SL1205 PCR1x 1 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF 5916 EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmRawRep2 A549 CTCF DEX 2 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001507 1507 GSM803453 Myers HudsonAlpha SL1077 PCR1x 2 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmRawRep2 DEX_100nM RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF 5916 DEX 100nM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmRawRep1 A549 CTCF DEX 1 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001507 1507 GSM803453 Myers HudsonAlpha SL1204 PCR1x 1 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmRawRep1 DEX_100nM RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF 5916 DEX 100nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Etoh02RawRep2 A549 CREB1 EtOH 2 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002324 2324 GSM1010726 Myers HudsonAlpha SL3898 v041610.2 2 input wgEncodeHaibTfbsA549Creb1sc240V0416102Etoh02RawRep2 EtOH_0.02pct RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CREB1 EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240Pcr1xEtoh02RawRep1 A549 CREB1 EtOH 1 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002322 2322 GSM1010720 Myers HudsonAlpha SL1668 PCR1x 1 input wgEncodeHaibTfbsA549Creb1sc240Pcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CREB1 EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmRawRep2 A549 CREB1 DEX 2 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002323 2323 GSM1010719 Myers HudsonAlpha SL3897 v041610.2 2 exp wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmRawRep2 DEX_100nM RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CREB1 DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmRawRep1 A549 CREB1 DEX 1 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002323 2323 GSM1010719 Myers HudsonAlpha SL1667 v041610.2 1 exp wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmRawRep1 DEX_100nM RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CREB1 DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Cebpbsc150V0422111RawRep2 A549 CEBPB V11 2 CEBPB_(SC-150) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003271 3271 GSM1010871 Myers HudsonAlpha SL16299 v042211.1 2 exp wgEncodeHaibTfbsA549Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Cebpbsc150V0422111RawRep1 A549 CEBPB V11 1 CEBPB_(SC-150) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003271 3271 GSM1010871 Myers HudsonAlpha SL12637 v042211.1 1 exp wgEncodeHaibTfbsA549Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Bcl3V0422111Etoh02RawRep2 A549 BCL3 EtOH 2 BCL3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002303 2303 GSM1010775 Myers HudsonAlpha SL7109 v042211.1 2 exp wgEncodeHaibTfbsA549Bcl3V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 BCL3 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Bcl3V0422111Etoh02RawRep1 A549 BCL3 EtOH 1 BCL3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002303 2303 GSM1010775 Myers HudsonAlpha SL6596 v042211.1 1 exp wgEncodeHaibTfbsA549Bcl3V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 BCL3 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Atf3V0422111Etoh02RawRep2 A549 ATF3 EtOH 2 ATF3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002288 2288 GSM1010789 Myers HudsonAlpha SL7273 v042211.1 2 exp wgEncodeHaibTfbsA549Atf3V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ATF3 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Atf3V0422111Etoh02RawRep1 A549 ATF3 EtOH 1 ATF3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002288 2288 GSM1010789 Myers HudsonAlpha SL6010 v042211.1 1 exp wgEncodeHaibTfbsA549Atf3V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ATF3 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0422111RawRep4 K562 RvXL V11 4 RevXlinkChromatin K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002332 2332 GSM1010894 Myers HudsonAlpha SL12793 v042211.1 4 input wgEncodeHaibTfbsK562RxlchV0422111RawRep4 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v042211.1 ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0422111RawRep3 K562 RvXL V11 3 RevXlinkChromatin K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002332 2332 GSM1010894 Myers HudsonAlpha SL11659 v042211.1 3 input wgEncodeHaibTfbsK562RxlchV0422111RawRep3 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0422111RawRep2 K562 RvXL V11 2 RevXlinkChromatin K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002332 2332 GSM1010894 Myers HudsonAlpha SL9103 v042211.1 2 input wgEncodeHaibTfbsK562RxlchV0422111RawRep2 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0422111RawRep1 K562 RvXL V11 1 RevXlinkChromatin K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002332 2332 GSM1010894 Myers HudsonAlpha SL6023 v042211.1 1 input wgEncodeHaibTfbsK562RxlchV0422111RawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0416101RawRep2 K562 RvXL V101 2 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001599 1599 GSM803468 Myers HudsonAlpha SL3980 v041610.1 2 input wgEncodeHaibTfbsK562RxlchV0416101RawRep2 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0416101RawRep1 K562 RvXL V101 1 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001599 1599 GSM803468 Myers HudsonAlpha SL2455 v041610.1 1 input wgEncodeHaibTfbsK562RxlchV0416101RawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchPcr1xRawRep4 K562 RvXL PCR1 4 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001466 1466 GSM803352 Myers HudsonAlpha SL1397 PCR1x 4 input wgEncodeHaibTfbsK562RxlchPcr1xRawRep4 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control PCR1x ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchPcr1xRawRep3 K562 RvXL PCR1 3 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001466 1466 GSM803352 Myers HudsonAlpha SL1396 PCR1x 3 input wgEncodeHaibTfbsK562RxlchPcr1xRawRep3 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchPcr1xRawRep2 K562 RvXL PCR1 2 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001466 1466 GSM803352 Myers HudsonAlpha SL519 PCR1x 2 input wgEncodeHaibTfbsK562RxlchPcr1xRawRep2 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchPcr1xRawRep1 K562 RvXL PCR1 1 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001466 1466 GSM803352 Myers HudsonAlpha SL518 PCR1x 1 input wgEncodeHaibTfbsK562RxlchPcr1xRawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep2 K562 ZBTB7A 2 ZBTB7A_(SC-34508) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001620 1620 GSM803473 Myers HudsonAlpha SL3183 v041610.1 2 exp wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep2 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ZBTB7A v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep1 K562 ZBTB7A 1 ZBTB7A_(SC-34508) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001620 1620 GSM803473 Myers HudsonAlpha SL2265 v041610.1 1 exp wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep1 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ZBTB7A v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep2 K562 ZBTB33 2 ZBTB33 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001569 1569 GSM803504 Myers HudsonAlpha SL1320 PCR1x 2 exp wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep1 K562 ZBTB33 1 ZBTB33 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001569 1569 GSM803504 Myers HudsonAlpha SL1114 PCR1x 1 exp wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep2 K562 YY1 V101 2 YY1_(SC-281) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEH001584 1584 GSM803446 Myers HudsonAlpha SL2944 v041610.1 2 exp wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep1 K562 YY1 V101 1 YY1_(SC-281) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEH001584 1584 GSM803446 Myers HudsonAlpha SL2203 v041610.1 1 exp wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1V0416102RawRep2 K562 YY1 V102 2 YY1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001623 1623 GSM803470 Myers HudsonAlpha SL3071 v041610.2 2 exp wgEncodeHaibTfbsK562Yy1V0416102RawRep2 None RawSignal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 YY1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1V0416102RawRep1 K562 YY1 V102 1 YY1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001623 1623 GSM803470 Myers HudsonAlpha SL2946 v041610.2 1 exp wgEncodeHaibTfbsK562Yy1V0416102RawRep1 None RawSignal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 YY1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Usf1V0416101RawRep2 K562 USF1 V101 2 USF-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001583 1583 GSM803441 Myers HudsonAlpha SL3166 v041610.1 2 exp wgEncodeHaibTfbsK562Usf1V0416101RawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 USF-1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Usf1V0416101RawRep1 K562 USF1 V101 1 USF-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001583 1583 GSM803441 Myers HudsonAlpha SL3163 v041610.1 1 exp wgEncodeHaibTfbsK562Usf1V0416101RawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 USF-1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep2 K562 TRIM28 V11 2 TRIM28_(SC-81411) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH003210 3210 GSM1010849 Myers HudsonAlpha SL9830 v042211.1 2 exp wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep2 None RawSignal The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TRIM28 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep1 K562 TRIM28 V11 1 TRIM28_(SC-81411) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH003210 3210 GSM1010849 Myers HudsonAlpha SL8672 v042211.1 1 exp wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep1 None RawSignal The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TRIM28 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep2 K562 THAP1 V101 2 THAP1_(SC-98174) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001655 1655 GSM803408 Myers HudsonAlpha SL3186 v041610.1 2 exp wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep2 None RawSignal The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 THAP1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep1 K562 THAP1 V101 1 THAP1_(SC-98174) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001655 1655 GSM803408 Myers HudsonAlpha SL2202 v041610.1 1 exp wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep1 None RawSignal The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 THAP1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep2 K562 TEAD4 V11 2 TEAD4_(SC-101184) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002333 2333 GSM1010895 Myers HudsonAlpha SL7841 v042211.1 2 exp wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep1 K562 TEAD4 V11 1 TEAD4_(SC-101184) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002333 2333 GSM1010895 Myers HudsonAlpha SL7571 v042211.1 1 exp wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep2 K562 TAF7 V101 2 TAF7_(SC-101167) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001654 1654 GSM803407 Myers HudsonAlpha SL3568 v041610.1 2 exp wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep2 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TAF7 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep1 K562 TAF7 V101 1 TAF7_(SC-101167) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001654 1654 GSM803407 Myers HudsonAlpha SL3274 v041610.1 1 exp wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep1 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TAF7 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf1V0416101RawRep2 K562 TAF1 V101 2 TAF1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001582 1582 GSM803431 Myers HudsonAlpha SL2942 v041610.1 2 exp wgEncodeHaibTfbsK562Taf1V0416101RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TAF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf1V0416101RawRep1 K562 TAF1 V101 1 TAF1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001582 1582 GSM803431 Myers HudsonAlpha SL2941 v041610.1 1 exp wgEncodeHaibTfbsK562Taf1V0416101RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TAF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Stat5asc74442V0422111RawRep2 K562 STAT5A V11 2 STAT5A_(SC-74442) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002347 2347 GSM1010877 Myers HudsonAlpha SL9116 v042211.1 2 exp wgEncodeHaibTfbsK562Stat5asc74442V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 STAT5A v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Stat5asc74442V0422111RawRep1 K562 STAT5A V11 1 STAT5A_(SC-74442) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002347 2347 GSM1010877 Myers HudsonAlpha SL8673 v042211.1 1 exp wgEncodeHaibTfbsK562Stat5asc74442V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 STAT5A v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562SrfV0416101RawRep2 K562 SRF V101 2 SRF K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001600 1600 GSM803520 Myers HudsonAlpha SL3272 v041610.1 2 exp wgEncodeHaibTfbsK562SrfV0416101RawRep2 None RawSignal Serum response transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SRF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562SrfV0416101RawRep1 K562 SRF V101 1 SRF K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001600 1600 GSM803520 Myers HudsonAlpha SL3162 v041610.1 1 exp wgEncodeHaibTfbsK562SrfV0416101RawRep1 None RawSignal Serum response transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SRF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp2sc643V0416102RawRep2 K562 SP2 V102 2 SP2_(SC-643) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001653 1653 GSM803402 Myers HudsonAlpha SL3361 v041610.2 2 exp wgEncodeHaibTfbsK562Sp2sc643V0416102RawRep2 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SP2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp2sc643V0416102RawRep1 K562 SP2 V102 1 SP2_(SC-643) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001653 1653 GSM803402 Myers HudsonAlpha SL2951 v041610.2 1 exp wgEncodeHaibTfbsK562Sp2sc643V0416102RawRep1 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SP2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp1Pcr1xRawRep2 K562 SP1 PCR1 2 SP1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001578 1578 GSM803505 Myers HudsonAlpha SL1510 PCR1x 2 exp wgEncodeHaibTfbsK562Sp1Pcr1xRawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SP1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp1Pcr1xRawRep1 K562 SP1 PCR1 1 SP1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001578 1578 GSM803505 Myers HudsonAlpha SL1197 PCR1x 1 exp wgEncodeHaibTfbsK562Sp1Pcr1xRawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SP1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5V0416101RawRep2 K562 SIX5 V101 2 SIX5 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001664 1664 GSM803378 Myers HudsonAlpha SL3990 v041610.1 2 exp wgEncodeHaibTfbsK562Six5V0416101RawRep2 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SIX5 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5V0416101RawRep1 K562 SIX5 V101 1 SIX5 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001664 1664 GSM803378 Myers HudsonAlpha SL3924 v041610.1 1 exp wgEncodeHaibTfbsK562Six5V0416101RawRep1 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SIX5 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5Pcr1xRawRep2 K562 SIX5 PCR1 2 SIX5 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001483 1483 GSM803383 Myers HudsonAlpha SL986 PCR1x 2 exp wgEncodeHaibTfbsK562Six5Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SIX5 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5Pcr1xRawRep1 K562 SIX5 PCR1 1 SIX5 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001483 1483 GSM803383 Myers HudsonAlpha SL842 PCR1x 1 exp wgEncodeHaibTfbsK562Six5Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SIX5 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sin3ak20V0416101RawRep2 K562 Sin3A V101 2 Sin3Ak-20 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-03 2011-09-03 wgEncodeEH001607 1607 GSM803525 Myers HudsonAlpha SL3496 v041610.1 2 exp wgEncodeHaibTfbsK562Sin3ak20V0416101RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sin3ak20V0416101RawRep1 K562 Sin3A V101 1 Sin3Ak-20 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-03 2011-09-03 wgEncodeEH001607 1607 GSM803525 Myers HudsonAlpha SL3273 v041610.1 1 exp wgEncodeHaibTfbsK562Sin3ak20V0416101RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Rad21V0416102RawRep2 K562 RAD21 V102 2 Rad21 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001585 1585 GSM803447 Myers HudsonAlpha SL3072 v041610.2 2 exp wgEncodeHaibTfbsK562Rad21V0416102RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 RAD21 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Rad21V0416102RawRep1 K562 RAD21 V102 1 Rad21 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001585 1585 GSM803447 Myers HudsonAlpha SL2947 v041610.2 1 exp wgEncodeHaibTfbsK562Rad21V0416102RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 RAD21 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pu1Pcr1xRawRep2 K562 PU.1 PCR1 2 PU.1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001482 1482 GSM803384 Myers HudsonAlpha SL705 PCR1x 2 exp wgEncodeHaibTfbsK562Pu1Pcr1xRawRep2 None RawSignal PU.1 (H-135) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 PU.1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pu1Pcr1xRawRep1 K562 PU.1 PCR1 1 PU.1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001482 1482 GSM803384 Myers HudsonAlpha SL646 PCR1x 1 exp wgEncodeHaibTfbsK562Pu1Pcr1xRawRep1 None RawSignal PU.1 (H-135) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 PU.1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol24h8V0416101RawRep2 K562 Pol2-4H8 V101 2 Pol2-4H8 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001581 1581 GSM803443 Myers HudsonAlpha SL2940 v041610.1 2 exp wgEncodeHaibTfbsK562Pol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol24h8V0416101RawRep1 K562 Pol2-4H8 V101 1 Pol2-4H8 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001581 1581 GSM803443 Myers HudsonAlpha SL2939 v041610.1 1 exp wgEncodeHaibTfbsK562Pol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol2V0416101RawRep2 K562 Pol2 V101 2 Pol2 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001633 1633 GSM803410 Myers HudsonAlpha SL3820 v041610.1 2 exp wgEncodeHaibTfbsK562Pol2V0416101RawRep2 None RawSignal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Pol2 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol2V0416101RawRep1 K562 Pol2 V101 1 Pol2 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001633 1633 GSM803410 Myers HudsonAlpha SL3819 v041610.1 1 exp wgEncodeHaibTfbsK562Pol2V0416101RawRep1 None RawSignal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Pol2 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pmlsc71910V0422111RawRep2 K562 PML V11 2 PML_(SC-71910) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002320 2320 GSM1010722 Myers HudsonAlpha SL8137 v042211.1 2 exp wgEncodeHaibTfbsK562Pmlsc71910V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 PML v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pmlsc71910V0422111RawRep1 K562 PML V11 1 PML_(SC-71910) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002320 2320 GSM1010722 Myers HudsonAlpha SL7894 v042211.1 1 exp wgEncodeHaibTfbsK562Pmlsc71910V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 PML v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562NrsfV0416102RawRep2 K562 NRSF V102 2 NRSF K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001638 1638 GSM803440 Myers HudsonAlpha SL3822 v041610.2 2 exp wgEncodeHaibTfbsK562NrsfV0416102RawRep2 None RawSignal Neuron-restrictive silencer transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 NRSF v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562NrsfV0416102RawRep1 K562 NRSF V102 1 NRSF K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001638 1638 GSM803440 Myers HudsonAlpha SL3821 v041610.2 1 exp wgEncodeHaibTfbsK562NrsfV0416102RawRep1 None RawSignal Neuron-restrictive silencer transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 NRSF v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Nr2f2sc271940V0422111RawRep2 K562 NR2F2 V11 2 NR2F2_(SC-271940) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002382 2382 GSM1010782 Myers HudsonAlpha SL8577 v042211.1 2 exp wgEncodeHaibTfbsK562Nr2f2sc271940V0422111RawRep2 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Nr2f2sc271940V0422111RawRep1 K562 NR2F2 V11 1 NR2F2_(SC-271940) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002382 2382 GSM1010782 Myers HudsonAlpha SL8143 v042211.1 1 exp wgEncodeHaibTfbsK562Nr2f2sc271940V0422111RawRep1 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Mef2aV0416101RawRep2 K562 MEF2A V101 2 MEF2A K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001663 1663 GSM803379 Myers HudsonAlpha SL3925 v041610.1 2 exp wgEncodeHaibTfbsK562Mef2aV0416101RawRep2 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 MEF2A v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Mef2aV0416101RawRep1 K562 MEF2A V101 1 MEF2A K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001663 1663 GSM803379 Myers HudsonAlpha SL1794 v041610.1 1 exp wgEncodeHaibTfbsK562Mef2aV0416101RawRep1 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 MEF2A v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562MaxV0416102RawRep2 K562 Max V102 2 Max K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001605 1605 GSM803523 Myers HudsonAlpha SL3070 v041610.2 2 exp wgEncodeHaibTfbsK562MaxV0416102RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Max v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562MaxV0416102RawRep1 K562 Max V102 1 Max K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001605 1605 GSM803523 Myers HudsonAlpha SL2945 v041610.2 1 exp wgEncodeHaibTfbsK562MaxV0416102RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Max v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep2 K562 HDAC2 V102 2 HDAC2_(SC-6296) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001622 1622 GSM803471 Myers HudsonAlpha SL3359 v041610.2 2 exp wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep2 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 HDAC2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep1 K562 HDAC2 V102 1 HDAC2_(SC-6296) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001622 1622 GSM803471 Myers HudsonAlpha SL2952 v041610.2 1 exp wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep1 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 HDAC2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep2 K562 GATA2 PCR1 2 GATA2_(SC-267) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001576 1576 GSM803540 Myers HudsonAlpha SL1665 PCR1x 2 exp wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep2 None RawSignal This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 GATA2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep1 K562 GATA2 PCR1 1 GATA2_(SC-267) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001576 1576 GSM803540 Myers HudsonAlpha SL1430 PCR1x 1 exp wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep1 None RawSignal This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 GATA2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562GabpV0416101RawRep2 K562 GABP V101 2 GABP K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001604 1604 GSM803524 Myers HudsonAlpha SL3356 v041610.1 2 exp wgEncodeHaibTfbsK562GabpV0416101RawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 GABP v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562GabpV0416101RawRep1 K562 GABP V101 1 GABP K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001604 1604 GSM803524 Myers HudsonAlpha SL2943 v041610.1 1 exp wgEncodeHaibTfbsK562GabpV0416101RawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 GABP v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep2 K562 FOSL1 V101 2 FOSL1_(SC-183) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001637 1637 GSM803439 Myers HudsonAlpha SL3187 v041610.1 2 exp wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 FOSL1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep1 K562 FOSL1 V101 1 FOSL1_(SC-183) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001637 1637 GSM803439 Myers HudsonAlpha SL2349 v041610.1 1 exp wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 FOSL1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ets1V0416101RawRep2 K562 ETS1 V101 2 ETS1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001580 1580 GSM803442 Myers HudsonAlpha SL3182 v041610.1 2 exp wgEncodeHaibTfbsK562Ets1V0416101RawRep2 None RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ETS1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ets1V0416101RawRep1 K562 ETS1 V101 1 ETS1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001580 1580 GSM803442 Myers HudsonAlpha SL2262 v041610.1 1 exp wgEncodeHaibTfbsK562Ets1V0416101RawRep1 None RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ETS1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep2 K562 ELF1 V102 2 ELF1_(SC-631) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001619 1619 GSM803494 Myers HudsonAlpha SL3360 v041610.2 2 exp wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ELF1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep1 K562 ELF1 V102 1 ELF1_(SC-631) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001619 1619 GSM803494 Myers HudsonAlpha SL2950 v041610.2 1 exp wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ELF1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Egr1V0416101RawRep2 K562 Egr-1 V101 2 Egr-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001646 1646 GSM803414 Myers HudsonAlpha SL3497 v041610.1 2 exp wgEncodeHaibTfbsK562Egr1V0416101RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Egr-1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Egr1V0416101RawRep1 K562 Egr-1 V101 1 Egr-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001646 1646 GSM803414 Myers HudsonAlpha SL3164 v041610.1 1 exp wgEncodeHaibTfbsK562Egr1V0416101RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Egr-1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562E2f6V0416102RawRep2 K562 E2F6 V102 2 E2F6 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001598 1598 GSM803469 Myers HudsonAlpha SL3073 v041610.2 2 exp wgEncodeHaibTfbsK562E2f6V0416102RawRep2 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 E2F6 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562E2f6V0416102RawRep1 K562 E2F6 V102 1 E2F6 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001598 1598 GSM803469 Myers HudsonAlpha SL2948 v041610.2 1 exp wgEncodeHaibTfbsK562E2f6V0416102RawRep1 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 E2F6 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562CtcfcPcr1xRawRep2 K562 CTCF PCR1 2 CTCF_(SC-5916) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002279 2279 GSM1010820 Myers HudsonAlpha SL5605 PCR1x 2 exp wgEncodeHaibTfbsK562CtcfcPcr1xRawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCF 5916 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562CtcfcPcr1xRawRep1V2 K562 CTCF PCR1 1 CTCF_(SC-5916) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-21 wgEncodeEH002279 2279 GSM1010820 Myers HudsonAlpha SL3075 PCR1x 1 exp wgEncodeHaibTfbsK562CtcfcPcr1xRawRep1V2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCF 5916 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ctcflsc98982V0416101RawRep2 K562 CTCFL V101 2 CTCFL_(SC-98982) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001652 1652 GSM803401 Myers HudsonAlpha SL3972 v041610.1 2 exp wgEncodeHaibTfbsK562Ctcflsc98982V0416101RawRep2 None RawSignal CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCFL v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ctcflsc98982V0416101RawRep1 K562 CTCFL V101 1 CTCFL_(SC-98982) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001652 1652 GSM803401 Myers HudsonAlpha SL3189 v041610.1 1 exp wgEncodeHaibTfbsK562Ctcflsc98982V0416101RawRep1 None RawSignal CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCFL v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep2 K562 CREB1 V11 2 CREB1_(SC-240) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003230 3230 GSM1010890 Myers HudsonAlpha SL13293 v042211.1 2 exp wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep1 K562 CREB1 V11 1 CREB1_(SC-240) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003230 3230 GSM1010890 Myers HudsonAlpha SL12420 v042211.1 1 exp wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep2 K562 CEBPD V11 2 CEBPD_(SC-636) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003432 3432 GSM1010906 Myers HudsonAlpha SL13317 v042211.1 2 exp wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CEBPD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIBd Regulation 
wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep1 K562 CEBPD V11 1 CEBPD_(SC-636) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003432 3432 GSM1010906 Myers HudsonAlpha SL11280 v042211.1 1 exp wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CEBPD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIBd Regulation 
wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep2 K562 CEBPB V11 2 CEBPB_(SC-150) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002346 2346 GSM1010878 Myers HudsonAlpha SL9547 v042211.1 2 exp wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep1 K562 CEBPB V11 1 CEBPB_(SC-150) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002346 2346 GSM1010878 Myers HudsonAlpha SL8085 v042211.1 1 exp wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep2 K562 CBX3 V11 2 CBX3_(SC-101004) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002383 2383 GSM1010732 Myers HudsonAlpha SL7568 v042211.1 2 exp wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep2 None RawSignal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CBX3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep1 K562 CBX3 V11 1 CBX3_(SC-101004) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002383 2383 GSM1010732 Myers HudsonAlpha SL7105 v042211.1 1 exp wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep1 None RawSignal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CBX3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep2 K562 BCLAF1 2 BCLAF1_(SC-101388) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001571 1571 GSM803515 Myers HudsonAlpha SL1512 PCR1x 2 exp wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep2 None RawSignal This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 BCLAF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep1 K562 BCLAF1 1 BCLAF1_(SC-101388) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001571 1571 GSM803515 Myers HudsonAlpha SL1273 PCR1x 1 exp wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep1 None RawSignal This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 BCLAF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Atf3V0416101RawRep2 K562 ATF3 V101 2 ATF3 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001662 1662 GSM803380 Myers HudsonAlpha SL3926 v041610.1 2 exp wgEncodeHaibTfbsK562Atf3V0416101RawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ATF3 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Atf3V0416101RawRep1 K562 ATF3 V101 1 ATF3 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001662 1662 GSM803380 Myers HudsonAlpha SL3184 v041610.1 1 exp wgEncodeHaibTfbsK562Atf3V0416101RawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ATF3 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxlchV0422111RawRep2 hESC RvXL V11 2 RevXlinkChromatin H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002276 2276 GSM1010815 Myers HudsonAlpha SL12796 v042211.1 2 input wgEncodeHaibTfbsH1hescRxlchV0422111RawRep2 None RawSignal embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxlchV0422111RawRep1 hESC RvXL V11 1 RevXlinkChromatin H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002276 2276 GSM1010815 Myers HudsonAlpha SL6018 v042211.1 1 input wgEncodeHaibTfbsH1hescRxlchV0422111RawRep1 None RawSignal embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxlchV0416102RawRep1 hESC RvXL V102 1 RevXlinkChromatin H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001497 1497 GSM803364 Myers HudsonAlpha SL969 v041610.2 1 input wgEncodeHaibTfbsH1hescRxlchV0416102RawRep1 None RawSignal embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Control v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxlchPcr1xRawRep1 hESC RvXL PCR1 1 RevXlinkChromatin H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001543 1543 GSM803339 Myers HudsonAlpha SL1398 PCR1x 1 input wgEncodeHaibTfbsH1hescRxlchPcr1xRawRep1 None RawSignal embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep2 hESC YY1 V102 2 YY1_(SC-281) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001567 1567 GSM803513 Myers HudsonAlpha SL1967 v041610.2 2 exp wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC YY1 281 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep1 hESC YY1 V102 1 YY1_(SC-281) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001567 1567 GSM803513 Myers HudsonAlpha SL1657 v041610.2 1 exp wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC YY1 281 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep2 hESC USF1 PCR1 2 USF-1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001532 1532 GSM803426 Myers HudsonAlpha SL1319 PCR1x 2 exp wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC USF-1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep1 hESC USF1 PCR1 1 USF-1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001532 1532 GSM803426 Myers HudsonAlpha SL1159 PCR1x 1 exp wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC USF-1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep2 hESC TEAD4 V11 2 TEAD4_(SC-101184) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003214 3214 GSM1010845 Myers HudsonAlpha SL12417 v042211.1 2 exp wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep1 hESC TEAD4 V11 1 TEAD4_(SC-101184) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003214 3214 GSM1010845 Myers HudsonAlpha SL10882 v042211.1 1 exp wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep2 hESC TCF12 PCR1 2 TCF12 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001531 1531 GSM803427 Myers HudsonAlpha SL1315 PCR1x 2 exp wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TCF12 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep1 hESC TCF12 PCR1 1 TCF12 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001531 1531 GSM803427 Myers HudsonAlpha SL1158 PCR1x 1 exp wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TCF12 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf7sc101167V0416102RawRep2 hESC TAF7 V102 2 TAF7_(SC-101167) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-13 2011-09-13 wgEncodeEH001610 1610 GSM803501 Myers HudsonAlpha SL3062 v041610.2 2 exp wgEncodeHaibTfbsH1hescTaf7sc101167V0416102RawRep2 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TAF7 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf7sc101167V0416102RawRep1 hESC TAF7 V102 1 TAF7_(SC-101167) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-13 2011-09-13 wgEncodeEH001610 1610 GSM803501 Myers HudsonAlpha SL2697 v041610.2 1 exp wgEncodeHaibTfbsH1hescTaf7sc101167V0416102RawRep1 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TAF7 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf1V0416102RawRep2 hESC TAF1 V102 2 TAF1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001500 1500 GSM803450 Myers HudsonAlpha SL964 v041610.2 2 exp wgEncodeHaibTfbsH1hescTaf1V0416102RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TAF1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf1V0416102RawRep1 hESC TAF1 V102 1 TAF1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001500 1500 GSM803450 Myers HudsonAlpha SL853 v041610.2 1 exp wgEncodeHaibTfbsH1hescTaf1V0416102RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TAF1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSrfPcr1xRawRep2 hESC SRF PCR1 2 SRF H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001533 1533 GSM803425 Myers HudsonAlpha SL1659 PCR1x 2 exp wgEncodeHaibTfbsH1hescSrfPcr1xRawRep2 None RawSignal Serum response transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SRF PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSrfPcr1xRawRep1 hESC SRF PCR1 1 SRF H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001533 1533 GSM803425 Myers HudsonAlpha SL1483 PCR1x 1 exp wgEncodeHaibTfbsH1hescSrfPcr1xRawRep1 None RawSignal Serum response transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SRF PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp4v20V0422111RawRep2 hESC SP4 V11 2 SP4_(V-20) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002317 2317 GSM1010743 Myers HudsonAlpha SL8135 v042211.1 2 exp wgEncodeHaibTfbsH1hescSp4v20V0422111RawRep2 None RawSignal Binds to GT and GC boxes promoters elements. Probable transcriptional activator. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp4v20V0422111RawRep1 hESC SP4 V11 1 SP4_(V-20) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002317 2317 GSM1010743 Myers HudsonAlpha SL7836 v042211.1 1 exp wgEncodeHaibTfbsH1hescSp4v20V0422111RawRep1 None RawSignal Binds to GT and GC boxes promoters elements. Probable transcriptional activator. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp2V0422111RawRep2 hESC SP2 V11 2 SP2_(SC-643) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-07 2012-06-07 wgEncodeEH002302 2302 GSM1010776 Myers HudsonAlpha SL6005 v042211.1 2 exp wgEncodeHaibTfbsH1hescSp2V0422111RawRep2 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp2V0422111RawRep1 hESC SP2 V11 1 SP2_(SC-643) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-07 2012-06-07 wgEncodeEH002302 2302 GSM1010776 Myers HudsonAlpha SL5690 v042211.1 1 exp wgEncodeHaibTfbsH1hescSp2V0422111RawRep1 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp1Pcr1xRawRep2 hESC SP1 PCR1 2 SP1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001529 1529 GSM803377 Myers HudsonAlpha SL1318 PCR1x 2 exp wgEncodeHaibTfbsH1hescSp1Pcr1xRawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp1Pcr1xRawRep1 hESC SP1 PCR1 1 SP1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001529 1529 GSM803377 Myers HudsonAlpha SL1166 PCR1x 1 exp wgEncodeHaibTfbsH1hescSp1Pcr1xRawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSix5Pcr1xRawRep2 hESC SIX5 PCR1 2 SIX5 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001528 1528 GSM803405 Myers HudsonAlpha SL1317 PCR1x 2 exp wgEncodeHaibTfbsH1hescSix5Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SIX5 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSix5Pcr1xRawRep1 hESC SIX5 PCR1 1 SIX5 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001528 1528 GSM803405 Myers HudsonAlpha SL1162 PCR1x 1 exp wgEncodeHaibTfbsH1hescSix5Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SIX5 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSin3ak20Pcr1xRawRep2 hESC Sin3A PCR1 2 Sin3Ak-20 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001530 1530 GSM803428 Myers HudsonAlpha SL1313 PCR1x 2 exp wgEncodeHaibTfbsH1hescSin3ak20Pcr1xRawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Sin3Ak-20 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSin3ak20Pcr1xRawRep1 hESC Sin3A PCR1 1 Sin3Ak-20 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001530 1530 GSM803428 Myers HudsonAlpha SL1157 PCR1x 1 exp wgEncodeHaibTfbsH1hescSin3ak20Pcr1xRawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Sin3Ak-20 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxraV0416102RawRep2 hESC RXRA V102 2 RXRA H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001560 1560 GSM803506 Myers HudsonAlpha SL2346 v041610.2 2 exp wgEncodeHaibTfbsH1hescRxraV0416102RawRep2 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC RXRA v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxraV0416102RawRep1 hESC RXRA V102 1 RXRA H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001560 1560 GSM803506 Myers HudsonAlpha SL1163 v041610.2 1 exp wgEncodeHaibTfbsH1hescRxraV0416102RawRep1 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC RXRA v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRad21V0416102RawRep2 hESC RAD21 V102 2 Rad21 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001593 1593 GSM803466 Myers HudsonAlpha SL3066 v041610.2 2 exp wgEncodeHaibTfbsH1hescRad21V0416102RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC RAD21 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRad21V0416102RawRep1 hESC RAD21 V102 1 Rad21 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001593 1593 GSM803466 Myers HudsonAlpha SL2689 v041610.2 1 exp wgEncodeHaibTfbsH1hescRad21V0416102RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC RAD21 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102RawRep2 hESC POU5F1 2 POU5F1_(SC-9081) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001636 1636 GSM803438 Myers HudsonAlpha SL3453 v041610.2 2 exp wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102RawRep2 None RawSignal This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC POU5F1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102RawRep1 hESC POU5F1 1 POU5F1_(SC-9081) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001636 1636 GSM803438 Myers HudsonAlpha SL2548 v041610.2 1 exp wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102RawRep1 None RawSignal This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC POU5F1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol24h8V0416102RawRep2 hESC Pol2-4H8 V102 2 Pol2-4H8 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001514 1514 GSM803484 Myers HudsonAlpha SL1051 v041610.2 2 exp wgEncodeHaibTfbsH1hescPol24h8V0416102RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol24h8V0416102RawRep1 hESC Pol2-4H8 V102 1 Pol2-4H8 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001514 1514 GSM803484 Myers HudsonAlpha SL979 v041610.2 1 exp wgEncodeHaibTfbsH1hescPol24h8V0416102RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol2V0416102RawRep2 hESC Pol2 V102 2 Pol2 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001499 1499 GSM803366 Myers HudsonAlpha SL1052 v041610.2 2 exp wgEncodeHaibTfbsH1hescPol2V0416102RawRep2 None RawSignal RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Pol2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol2V0416102RawRep1 hESC Pol2 V102 1 Pol2 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001499 1499 GSM803366 Myers HudsonAlpha SL980 v041610.2 1 exp wgEncodeHaibTfbsH1hescPol2V0416102RawRep1 None RawSignal RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Pol2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescP300V0416102RawRep2 hESC p300 V102 2 p300 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001574 1574 GSM803542 Myers HudsonAlpha SL1883 v041610.2 2 exp wgEncodeHaibTfbsH1hescP300V0416102RawRep2 None RawSignal EP300(c-20) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC p300 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescP300V0416102RawRep1 hESC p300 V102 1 p300 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001574 1574 GSM803542 Myers HudsonAlpha SL2250 v041610.2 1 exp wgEncodeHaibTfbsH1hescP300V0416102RawRep1 None RawSignal EP300(c-20) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC p300 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNrsfV0416102RawRep2 hESC NRSF V102 2 NRSF H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001498 1498 GSM803365 Myers HudsonAlpha SL1053 v041610.2 2 exp wgEncodeHaibTfbsH1hescNrsfV0416102RawRep2 None RawSignal Neuron-restrictive silencer transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC NRSF v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNrsfV0416102RawRep1 hESC NRSF V102 1 NRSF H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001498 1498 GSM803365 Myers HudsonAlpha SL978 v041610.2 1 exp wgEncodeHaibTfbsH1hescNrsfV0416102RawRep1 None RawSignal Neuron-restrictive silencer transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC NRSF v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNanogsc33759V0416102RawRep2 hESC NANOG V102 2 NANOG_(SC-33759) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001635 1635 GSM803437 Myers HudsonAlpha SL3068 v041610.2 2 exp wgEncodeHaibTfbsH1hescNanogsc33759V0416102RawRep2 None RawSignal Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC NANOG v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNanogsc33759V0416102RawRep1 hESC NANOG V102 1 NANOG_(SC-33759) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001635 1635 GSM803437 Myers HudsonAlpha SL2687 v041610.2 1 exp wgEncodeHaibTfbsH1hescNanogsc33759V0416102RawRep1 None RawSignal Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC NANOG v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescMaxV0422111RawRep2 hESC Max V11 2 Max H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003225 3225 GSM1010898 Myers HudsonAlpha SL13302 v042211.1 2 exp wgEncodeHaibTfbsH1hescMaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescMaxV0422111RawRep1 hESC Max V11 1 Max H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003225 3225 GSM1010898 Myers HudsonAlpha SL12411 v042211.1 1 exp wgEncodeHaibTfbsH1hescMaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescJundV0416102RawRep2 hESC JunD V102 2 JunD H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001579 1579 GSM803529 Myers HudsonAlpha SL3065 v041610.2 2 exp wgEncodeHaibTfbsH1hescJundV0416102RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC JunD v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescJundV0416102RawRep1 hESC JunD V102 1 JunD H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001579 1579 GSM803529 Myers HudsonAlpha SL2690 v041610.2 1 exp wgEncodeHaibTfbsH1hescJundV0416102RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC JunD v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep2 hESC HDAC2 V102 2 HDAC2_(SC-6296) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2011-12-02 wgEncodeEH001659 1659 GSM803345 Myers HudsonAlpha SL3454 v041610.2 2 exp wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep2 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC HDAC2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep1 hESC HDAC2 V102 1 HDAC2_(SC-6296) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2011-12-02 wgEncodeEH001659 1659 GSM803345 Myers HudsonAlpha SL3935 v041610.2 1 exp wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep1 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC HDAC2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescGabpPcr1xRawRep2 hESC GABP PCR1 2 GABP H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001534 1534 GSM803424 Myers HudsonAlpha SL1660 PCR1x 2 exp wgEncodeHaibTfbsH1hescGabpPcr1xRawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC GABP PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescGabpPcr1xRawRep1 hESC GABP PCR1 1 GABP H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001534 1534 GSM803424 Myers HudsonAlpha SL1518 PCR1x 1 exp wgEncodeHaibTfbsH1hescGabpPcr1xRawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC GABP PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescFosl1sc183V0416102RawRep2 hESC FOSL1 V102 2 FOSL1_(SC-183) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001660 1660 GSM803382 Myers HudsonAlpha SL4211 v041610.2 2 exp wgEncodeHaibTfbsH1hescFosl1sc183V0416102RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC FOSL1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescFosl1sc183V0416102RawRep1 hESC FOSL1 V102 1 FOSL1_(SC-183) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001660 1660 GSM803382 Myers HudsonAlpha SL2692 v041610.2 1 exp wgEncodeHaibTfbsH1hescFosl1sc183V0416102RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC FOSL1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescEgr1V0416102RawRep2 hESC Egr-1 V102 2 Egr-1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001538 1538 GSM803430 Myers HudsonAlpha SL1885 v041610.2 2 exp wgEncodeHaibTfbsH1hescEgr1V0416102RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Egr-1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescEgr1V0416102RawRep1 hESC Egr-1 V102 1 Egr-1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001538 1538 GSM803430 Myers HudsonAlpha SL1482 v041610.2 1 exp wgEncodeHaibTfbsH1hescEgr1V0416102RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Egr-1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescE2f6V0422111RawRep2 hESC E2F6 V11 2 E2F6 H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003224 3224 GSM1010899 Myers HudsonAlpha SL13304 v042211.1 2 exp wgEncodeHaibTfbsH1hescE2f6V0422111RawRep2 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC E2F6 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescE2f6V0422111RawRep1 hESC E2F6 V11 1 E2F6 H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003224 3224 GSM1010899 Myers HudsonAlpha SL12414 v042211.1 1 exp wgEncodeHaibTfbsH1hescE2f6V0422111RawRep1 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC E2F6 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCtcfsc5916V0416102RawRep2 hESC CTCF V102 2 CTCF_(SC-5916) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001649 1649 GSM803419 Myers HudsonAlpha SL3067 v041610.2 2 exp wgEncodeHaibTfbsH1hescCtcfsc5916V0416102RawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC CTCF 5916 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCtcfsc5916V0416102RawRep1 hESC CTCF V102 1 CTCF_(SC-5916) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001649 1649 GSM803419 Myers HudsonAlpha SL2688 v041610.2 1 exp wgEncodeHaibTfbsH1hescCtcfsc5916V0416102RawRep1 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC CTCF 5916 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCreb1sc240V0422111RawRep2 hESC CREB1 V11 2 CREB1_(SC-240) H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003229 3229 GSM1010896 Myers HudsonAlpha SL13303 v042211.1 2 exp wgEncodeHaibTfbsH1hescCreb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCreb1sc240V0422111RawRep1 hESC CREB1 V11 1 CREB1_(SC-240) H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003229 3229 GSM1010896 Myers HudsonAlpha SL12413 v042211.1 1 exp wgEncodeHaibTfbsH1hescCreb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescBcl11aV0416102RawRep2 hESC BCL V102 2 BCL11A H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001625 1625 GSM803476 Myers HudsonAlpha SL3989 v041610.2 2 exp wgEncodeHaibTfbsH1hescBcl11aV0416102RawRep2 None RawSignal This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC BCL11A v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescBcl11aPcr1xRawRep1 hESC BCL11A 1 BCL11A H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001527 1527 GSM803396 Myers HudsonAlpha SL1314 PCR1x 1 exp wgEncodeHaibTfbsH1hescBcl11aPcr1xRawRep1 None RawSignal This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC BCL11A PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf3V0416102RawRep2 hESC ATF3 V102 2 ATF3 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001566 1566 GSM803512 Myers HudsonAlpha SL1968 v041610.2 2 exp wgEncodeHaibTfbsH1hescAtf3V0416102RawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC ATF3 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf3V0416102RawRep1 hESC ATF3 V102 1 ATF3 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001566 1566 GSM803512 Myers HudsonAlpha SL1519 v041610.2 1 exp wgEncodeHaibTfbsH1hescAtf3V0416102RawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC ATF3 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf2sc81188V0422111RawRep2 hESC ATF2 V11 2 ATF2_(SC-81188) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002316 2316 GSM1010742 Myers HudsonAlpha SL8136 v042211.1 2 exp wgEncodeHaibTfbsH1hescAtf2sc81188V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC ATF2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf2sc81188V0422111RawRep1 hESC ATF2 V11 1 ATF2_(SC-81188) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002316 2316 GSM1010742 Myers HudsonAlpha SL7904 v042211.1 1 exp wgEncodeHaibTfbsH1hescAtf2sc81188V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC ATF2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0422111RawRep4 GM78 RvXL V11 4 RevXlinkChromatin GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003422 3422 GSM1010867 Myers HudsonAlpha SL12789 v042211.1 4 input wgEncodeHaibTfbsGm12878RxlchV0422111RawRep4 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v042211.1 ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0422111RawRep3 GM78 RvXL V11 3 RevXlinkChromatin GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003422 3422 GSM1010867 Myers HudsonAlpha SL12049 v042211.1 3 input wgEncodeHaibTfbsGm12878RxlchV0422111RawRep3 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0422111RawRep1 GM78 RvXL V11 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH003422 3422 GSM1010867 Myers HudsonAlpha SL6022 v042211.1 1 input wgEncodeHaibTfbsGm12878RxlchV0422111RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0416102RawRep1 GM78 RvXL V102 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001647 1647 GSM803413 Myers HudsonAlpha SL3979 v041610.2 1 input wgEncodeHaibTfbsGm12878RxlchV0416102RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0416101RawRep1 GM78 RvXL V101 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001634 1634 GSM803436 Myers HudsonAlpha SL1613 v041610.1 1 input wgEncodeHaibTfbsGm12878RxlchV0416101RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr2xRawRep2 GM78 RvXL PCR2 2 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001469 1469 GSM803346 Myers HudsonAlpha SL218 PCR2x 2 input wgEncodeHaibTfbsGm12878RxlchPcr2xRawRep2 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr2xRawRep1 GM78 RvXL PCR2 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001469 1469 GSM803346 Myers HudsonAlpha SL217 PCR2x 1 input wgEncodeHaibTfbsGm12878RxlchPcr2xRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep5 GM78 RvXL PCR1 5 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL1395 PCR1x 5 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep5 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 5 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep4 GM78 RvXL PCR1 4 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL1394 PCR1x 4 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep4 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep3 GM78 RvXL PCR1 3 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL678 PCR1x 3 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep3 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep2 GM78 RvXL PCR1 2 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL517 PCR1x 2 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep2 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep1 GM78 RvXL PCR1 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL516 PCR1x 1 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102RawRep2 GM78 ZEB1 V102 2 ZEB1_(SC-25388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001645 1645 GSM803411 Myers HudsonAlpha SL3254 v041610.2 2 exp wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102RawRep2 None RawSignal This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ZEB1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102RawRep1 GM78 ZEB1 V102 1 ZEB1_(SC-25388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001645 1645 GSM803411 Myers HudsonAlpha SL2957 v041610.2 1 exp wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102RawRep1 None RawSignal This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ZEB1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zbtb33Pcr1xRawRep2 GM78 ZBTB33 2 ZBTB33 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001488 1488 GSM803392 Myers HudsonAlpha SL923 PCR1x 2 exp wgEncodeHaibTfbsGm12878Zbtb33Pcr1xRawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zbtb33Pcr1xRawRep1 GM78 ZBTB33 1 ZBTB33 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001488 1488 GSM803392 Myers HudsonAlpha SL814 PCR1x 1 exp wgEncodeHaibTfbsGm12878Zbtb33Pcr1xRawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xRawRep2 GM78 YY1 PCR1 2 YY1_(SC-281) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-15 2011-11-15 wgEncodeEH001657 1657 GSM803406 Myers HudsonAlpha SL2129 PCR1x 2 exp wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xRawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 YY1 281 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xRawRep1 GM78 YY1 PCR1 1 YY1_(SC-281) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-15 2011-11-15 wgEncodeEH001657 1657 GSM803406 Myers HudsonAlpha SL1475 PCR1x 1 exp wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xRawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 YY1 281 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Usf1Pcr2xRawRep2 GM78 USF1 PCR2 2 USF-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001468 1468 GSM803347 Myers HudsonAlpha SL483 PCR2x 2 exp wgEncodeHaibTfbsGm12878Usf1Pcr2xRawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 USF-1 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Usf1Pcr2xRawRep1 GM78 USF1 PCR2 1 USF-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001468 1468 GSM803347 Myers HudsonAlpha SL448 PCR2x 1 exp wgEncodeHaibTfbsGm12878Usf1Pcr2xRawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 USF-1 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf3Pcr1xRawRep2 GM78 TCF3 PCR1 2 TCF3_(SC-349) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002315 2315 GSM1010745 Myers HudsonAlpha SL633 PCR1x 2 exp wgEncodeHaibTfbsGm12878Tcf3Pcr1xRawRep2 None RawSignal Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TCF3 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf3Pcr1xRawRep1 GM78 TCF3 PCR1 1 TCF3_(SC-349) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002315 2315 GSM1010745 Myers HudsonAlpha SL480 PCR1x 1 exp wgEncodeHaibTfbsGm12878Tcf3Pcr1xRawRep1 None RawSignal Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TCF3 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep2 GM78 TCF12 PCR1 2 TCF12 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001485 1485 GSM803389 Myers HudsonAlpha SL1019 PCR1x 2 exp wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TCF12 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep1 GM78 TCF12 PCR1 1 TCF12 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001485 1485 GSM803389 Myers HudsonAlpha SL673 PCR1x 1 exp wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TCF12 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep2 GM78 TAF1 PCR1 2 TAF1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2009-10-29 2010-07-29 wgEncodeEH001478 1478 GSM803537 Myers HudsonAlpha SL1062 PCR1x 2 exp wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TAF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep1 GM78 TAF1 PCR1 1 TAF1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001478 1478 GSM803537 Myers HudsonAlpha SL805 PCR1x 1 exp wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TAF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Stat5asc74442V0422111RawRep2 GM78 STAT5A V11 2 STAT5A_(SC-74442) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002321 2321 GSM1010721 Myers HudsonAlpha SL8127 v042211.1 2 exp wgEncodeHaibTfbsGm12878Stat5asc74442V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 STAT5A v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Stat5asc74442V0422111RawRep1 GM78 STAT5A V11 1 STAT5A_(SC-74442) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002321 2321 GSM1010721 Myers HudsonAlpha SL7897 v042211.1 1 exp wgEncodeHaibTfbsGm12878Stat5asc74442V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 STAT5A v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfV0416101RawRep2 GM78 SRF V101 2 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001624 1624 GSM803477 Myers HudsonAlpha SL3827 v041610.1 2 exp wgEncodeHaibTfbsGm12878SrfV0416101RawRep2 None RawSignal Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SRF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfV0416101RawRep1 GM78 SRF V101 1 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001624 1624 GSM803477 Myers HudsonAlpha SL3578 v041610.1 1 exp wgEncodeHaibTfbsGm12878SrfV0416101RawRep1 None RawSignal Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SRF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfPcr2xRawRep2 GM78 SRF PCR2 2 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001464 1464 GSM803350 Myers HudsonAlpha SL292 PCR2x 2 exp wgEncodeHaibTfbsGm12878SrfPcr2xRawRep2 None RawSignal Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SRF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfPcr2xRawRep1 GM78 SRF PCR2 1 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001464 1464 GSM803350 Myers HudsonAlpha SL291 PCR2x 1 exp wgEncodeHaibTfbsGm12878SrfPcr2xRawRep1 None RawSignal Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SRF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Sp1Pcr1xRawRep2 GM78 SP1 PCR1 2 SP1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001496 1496 GSM803363 Myers HudsonAlpha SL846 PCR1x 2 exp wgEncodeHaibTfbsGm12878Sp1Pcr1xRawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SP1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Sp1Pcr1xRawRep1 GM78 SP1 PCR1 1 SP1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001496 1496 GSM803363 Myers HudsonAlpha SL746 PCR1x 1 exp wgEncodeHaibTfbsGm12878Sp1Pcr1xRawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SP1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Six5Pcr1xRawRep2 GM78 SIX5 PCR1 2 SIX5 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001542 1542 GSM803338 Myers HudsonAlpha SL1200 PCR1x 2 exp wgEncodeHaibTfbsGm12878Six5Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SIX5 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Six5Pcr1xRawRep1 GM78 SIX5 PCR1 1 SIX5 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001542 1542 GSM803338 Myers HudsonAlpha SL1061 PCR1x 1 exp wgEncodeHaibTfbsGm12878Six5Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SIX5 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxraPcr1xRawRep2 GM78 RXRA PCR1 2 RXRA GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001541 1541 GSM803341 Myers HudsonAlpha SL1265 PCR1x 2 exp wgEncodeHaibTfbsGm12878RxraPcr1xRawRep2 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RXRA PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxraPcr1xRawRep1 GM78 RXRA PCR1 1 RXRA GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001541 1541 GSM803341 Myers HudsonAlpha SL1063 PCR1x 1 exp wgEncodeHaibTfbsGm12878RxraPcr1xRawRep1 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RXRA PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Runx3sc101553V0422111RawRep2 GM78 RUNX3 V11 2 RUNX3_(SC-101553) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002330 2330 GSM1010893 Myers HudsonAlpha SL8128 v042211.1 2 exp wgEncodeHaibTfbsGm12878Runx3sc101553V0422111RawRep2 None RawSignal This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RUNX3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Runx3sc101553V0422111RawRep1 GM78 RUNX3 V11 1 RUNX3_(SC-101553) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002330 2330 GSM1010893 Myers HudsonAlpha SL7898 v042211.1 1 exp wgEncodeHaibTfbsGm12878Runx3sc101553V0422111RawRep1 None RawSignal This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RUNX3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Rad21V0416101RawRep2 GM78 RAD21 V101 2 Rad21 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001640 1640 GSM803416 Myers HudsonAlpha SL3934 v041610.1 2 exp wgEncodeHaibTfbsGm12878Rad21V0416101RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RAD21 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Rad21V0416101RawRep1 GM78 RAD21 V101 1 Rad21 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001640 1640 GSM803416 Myers HudsonAlpha SL3933 v041610.1 1 exp wgEncodeHaibTfbsGm12878Rad21V0416101RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RAD21 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep3 GM78 PU.1 PCR1 3 PU.1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL963 PCR1x 3 exp wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep3 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PU.1 PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep2 GM78 PU.1 PCR1 2 PU.1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL649 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep2 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PU.1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep1 GM78 PU.1 PCR1 1 PU.1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL612 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep1 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PU.1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep3 GM78 POU2F2 3 POU2F2 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL851 PCR1x 3 exp wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep3 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 POU2F2 PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep2 GM78 POU2F2 2 POU2F2 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL648 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep2 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 POU2F2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep1 GM78 POU2F2 1 POU2F2 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL614 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep1 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 POU2F2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep2 GM78 Pol2-4H8 PCR1 2 Pol2-4H8 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-21 2011-12-21 wgEncodeEH001517 1517 GSM803485 Myers HudsonAlpha SL847 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Pol2-4H8 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep1 GM78 Pol2-4H8 PCR1 1 Pol2-4H8 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001517 1517 GSM803485 Myers HudsonAlpha SL748 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Pol2-4H8 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep2 GM78 Pol2 PCR2 2 Pol2 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001463 1463 GSM803355 Myers HudsonAlpha SL209 PCR2x 2 exp wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep2 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Pol2 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep1 GM78 Pol2 PCR2 1 Pol2 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001463 1463 GSM803355 Myers HudsonAlpha SL207 PCR2x 1 exp wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep1 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Pol2 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pmlsc71910V0422111RawRep2 GM78 PML V11 2 PML_(SC-71910) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002308 2308 GSM1010771 Myers HudsonAlpha SL7831 v042211.1 2 exp wgEncodeHaibTfbsGm12878Pmlsc71910V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PML v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pmlsc71910V0422111RawRep1 GM78 PML V11 1 PML_(SC-71910) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002308 2308 GSM1010771 Myers HudsonAlpha SL7281 v042211.1 1 exp wgEncodeHaibTfbsGm12878Pmlsc71910V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PML v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pbx3Pcr1xRawRep2 GM78 PBx3 PCR1 2 Pbx3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001477 1477 GSM803532 Myers HudsonAlpha SL647 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pbx3Pcr1xRawRep2 None RawSignal Pbx 3 (D-17) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PBx3 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pbx3Pcr1xRawRep1 GM78 PBx3 PCR1 1 Pbx3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001477 1477 GSM803532 Myers HudsonAlpha SL615 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pbx3Pcr1xRawRep1 None RawSignal Pbx 3 (D-17) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PBx3 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5n19Pcr1xRawRep2 GM78 PAX5 PCR1 2 PAX5-N19 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001495 1495 GSM803362 Myers HudsonAlpha SL848 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pax5n19Pcr1xRawRep2 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PAX5-N19 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5n19Pcr1xRawRep1 GM78 PAX5 PCR1 1 PAX5-N19 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001495 1495 GSM803362 Myers HudsonAlpha SL677 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pax5n19Pcr1xRawRep1 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PAX5-N19 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5c20Pcr1xRawRep2 GM78 PAX5 PCR1 2 PAX5-C20 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001489 1489 GSM803391 Myers HudsonAlpha SL735 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pax5c20Pcr1xRawRep2 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PAX5-C20 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5c20Pcr1xRawRep1 GM78 PAX5 PCR1 1 PAX5-C20 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001489 1489 GSM803391 Myers HudsonAlpha SL675 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pax5c20Pcr1xRawRep1 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PAX5-C20 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878P300Pcr1xRawRep2 GM78 p300 PCR1 2 p300 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001487 1487 GSM803387 Myers HudsonAlpha SL564 PCR1x 2 exp wgEncodeHaibTfbsGm12878P300Pcr1xRawRep2 None RawSignal EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 p300 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878P300Pcr1xRawRep1 GM78 p300 PCR1 1 p300 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001487 1487 GSM803387 Myers HudsonAlpha SL551 PCR1x 1 exp wgEncodeHaibTfbsGm12878P300Pcr1xRawRep1 None RawSignal EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 p300 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr2xRawRep2 GM78 NRSF PCR2 2 NRSF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001465 1465 GSM803349 Myers HudsonAlpha SL204 PCR2x 2 exp wgEncodeHaibTfbsGm12878NrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr2xRawRep1 GM78 NRSF PCR2 1 NRSF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001465 1465 GSM803349 Myers HudsonAlpha SL202 PCR2x 1 exp wgEncodeHaibTfbsGm12878NrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr1xRawRep2 GM78 NRSF PCR1 2 NRSF GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002314 2314 GSM1010744 Myers HudsonAlpha SL7333 PCR1x 2 exp wgEncodeHaibTfbsGm12878NrsfPcr1xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NRSF PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr1xRawRep1 GM78 NRSF PCR1 1 NRSF GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002314 2314 GSM1010744 Myers HudsonAlpha SL852 PCR1x 1 exp wgEncodeHaibTfbsGm12878NrsfPcr1xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NRSF PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nficsc81335V0422111RawRep2 GM78 NFIC V11 2 NFIC_(SC-81335) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002343 2343 GSM1010881 Myers HudsonAlpha SL8392 v042211.1 2 exp wgEncodeHaibTfbsGm12878Nficsc81335V0422111RawRep2 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NFIC v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nficsc81335V0422111RawRep1 GM78 NFIC V11 1 NFIC_(SC-81335) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002343 2343 GSM1010881 Myers HudsonAlpha SL8083 v042211.1 1 exp wgEncodeHaibTfbsGm12878Nficsc81335V0422111RawRep1 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NFIC v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111RawRep2 GM78 NFATC1 V11 2 NFATC1_(SC-17834) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002307 2307 GSM1010779 Myers HudsonAlpha SL7830 v042211.1 2 exp wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111RawRep2 None RawSignal The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Five transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NFATC1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111RawRep1 GM78 NFATC1 V11 1 NFATC1_(SC-17834) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002307 2307 GSM1010779 Myers HudsonAlpha SL7280 v042211.1 1 exp wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111RawRep1 None RawSignal The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Five transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NFATC1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mta3sc81325V0422111RawRep2 GM78 MTA3 V11 2 MTA3_(SC-81325) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002329 2329 GSM1010729 Myers HudsonAlpha SL8129 v042211.1 2 exp wgEncodeHaibTfbsGm12878Mta3sc81325V0422111RawRep2 None RawSignal Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MTA3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mta3sc81325V0422111RawRep1 GM78 MTA3 V11 1 MTA3_(SC-81325) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002329 2329 GSM1010729 Myers HudsonAlpha SL7899 v042211.1 1 exp wgEncodeHaibTfbsGm12878Mta3sc81325V0422111RawRep1 None RawSignal Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MTA3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep2 GM78 MEFC V101 2 MEF2C_(SC-13268) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001648 1648 GSM803420 Myers HudsonAlpha SL2127 v041610.1 2 exp wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep2 None RawSignal This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MEF2C v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep1 GM78 MEFC V101 1 MEF2C_(SC-13268) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001648 1648 GSM803420 Myers HudsonAlpha SL1654 v041610.1 1 exp wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep1 None RawSignal This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MEF2C v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep2 GM78 MEF2A PCR1 2 MEF2A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001565 1565 GSM803511 Myers HudsonAlpha SL1792 PCR1x 2 exp wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep2 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MEF2A PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep1 GM78 MEF2A PCR1 1 MEF2A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001565 1565 GSM803511 Myers HudsonAlpha SL1425 PCR1x 1 exp wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep1 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MEF2A PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep2 GM78 IRF4 PCR1 2 IRF4_(SC-6059) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001484 1484 GSM803390 Myers HudsonAlpha SL951 PCR1x 2 exp wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep2 None RawSignal The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 IRF4 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep1 GM78 IRF4 PCR1 1 IRF4_(SC-6059) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001484 1484 GSM803390 Myers HudsonAlpha SL838 PCR1x 1 exp wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep1 None RawSignal The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 IRF4 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878GabpPcr2xRawRep2 GM78 GABP PCR2 2 GABP GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001462 1462 GSM803356 Myers HudsonAlpha SL205 PCR2x 2 exp wgEncodeHaibTfbsGm12878GabpPcr2xRawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 GABP PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878GabpPcr2xRawRep1 GM78 GABP PCR2 1 GABP GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001462 1462 GSM803356 Myers HudsonAlpha SL203 PCR2x 1 exp wgEncodeHaibTfbsGm12878GabpPcr2xRawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 GABP PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep2 GM78 FOXM1 V11 2 FOXM1_(SC-502) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002529 2529 GSM1010731 Myers HudsonAlpha SL7834 v042211.1 2 exp wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep2 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep1 GM78 FOXM1 V11 1 FOXM1_(SC-502) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002529 2529 GSM1010731 Myers HudsonAlpha SL7551 v042211.1 1 exp wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep1 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep2 GM78 ETS1 PCR1 2 ETS1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001564 1564 GSM803510 Myers HudsonAlpha SL1655 PCR1x 2 exp wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep2 None RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ETS1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep1 GM78 ETS1 PCR1 1 ETS1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001564 1564 GSM803510 Myers HudsonAlpha SL1507 PCR1x 1 exp wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep1 None RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ETS1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep2 GM78 ELF1 V101 2 ELF1_(SC-631) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001617 1617 GSM803496 Myers HudsonAlpha SL3352 v041610.1 2 exp wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ELF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep1 GM78 ELF1 V101 1 ELF1_(SC-631) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001617 1617 GSM803496 Myers HudsonAlpha SL2253 v041610.1 1 exp wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ELF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1V0416101RawRep2 GM78 Egr-1 V101 2 Egr-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001632 1632 GSM803434 Myers HudsonAlpha SL3828 v041610.1 2 exp wgEncodeHaibTfbsGm12878Egr1V0416101RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Egr-1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1V0416101RawRep1 GM78 Egr-1 V101 1 Egr-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001632 1632 GSM803434 Myers HudsonAlpha SL3579 v041610.1 1 exp wgEncodeHaibTfbsGm12878Egr1V0416101RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Egr-1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1Pcr2xRawRep3 GM78 Egr-1 PCR2 3 Egr-1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002328 2328 GSM1010730 Myers HudsonAlpha SL482 PCR2x 3 exp wgEncodeHaibTfbsGm12878Egr1Pcr2xRawRep3 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Egr-1 PCR2x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep2 GM78 EBF1 PCR1 2 EBF1_(SC-137065) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001480 1480 GSM803386 Myers HudsonAlpha SL988 PCR1x 2 exp wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep2 None RawSignal Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 EBF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep1 GM78 EBF1 PCR1 1 EBF1_(SC-137065) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001480 1480 GSM803386 Myers HudsonAlpha SL745 PCR1x 1 exp wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep1 None RawSignal Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 EBF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep2 GM78 CREB1 V11 2 CREB1_(SC-240) GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003275 3275 GSM1010760 Myers HudsonAlpha SL16741 v042211.1 2 exp wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep1 GM78 CREB1 V11 1 CREB1_(SC-240) GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003275 3275 GSM1010760 Myers HudsonAlpha SL12408 v042211.1 1 exp wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep2 GM78 CEBPB V11 2 CEBPB_(SC-150) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003212 3212 GSM1010850 Myers HudsonAlpha SL9542 v042211.1 2 exp wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep1 GM78 CEBPB V11 1 CEBPB_(SC-150) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003212 3212 GSM1010850 Myers HudsonAlpha SL8084 v042211.1 1 exp wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep2 GM78 BCLAF1 2 BCLAF1_(SC-101388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001563 1563 GSM803509 Myers HudsonAlpha SL2128 v041610.1 2 exp wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep2 None RawSignal This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCLAF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep1 GM78 BCLAF1 1 BCLAF1_(SC-101388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001563 1563 GSM803509 Myers HudsonAlpha SL1509 v041610.1 1 exp wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep1 None RawSignal This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCLAF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep2 GM78 BCL3 V101 2 BCL3 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH001658 1658 GSM803342 Myers HudsonAlpha SL3931 v041610.1 2 exp wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep2 None RawSignal This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCL3 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep1 GM78 BCL3 V101 1 BCL3 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH001658 1658 GSM803342 Myers HudsonAlpha SL3728 v041610.1 1 exp wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep1 None RawSignal This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCL3 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep2 GM78 BCL11A 2 BCL11A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001486 1486 GSM803388 Myers HudsonAlpha SL976 PCR1x 2 exp wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep2 None RawSignal This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCL11A PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep1 GM78 BCL11A 1 BCL11A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001486 1486 GSM803388 Myers HudsonAlpha SL650 PCR1x 1 exp wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep1 None RawSignal This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCL11A PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878BatfPcr1xRawRep2 GM78 BATF PCR1 2 BATF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001479 1479 GSM803538 Myers HudsonAlpha SL985 PCR1x 2 exp wgEncodeHaibTfbsGm12878BatfPcr1xRawRep2 None RawSignal The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BATF PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878BatfPcr1xRawRep1 GM78 BATF PCR1 1 BATF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001479 1479 GSM803538 Myers HudsonAlpha SL839 PCR1x 1 exp wgEncodeHaibTfbsGm12878BatfPcr1xRawRep1 None RawSignal The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BATF PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep2 GM78 ATF3 PCR1 2 ATF3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001562 1562 GSM803508 Myers HudsonAlpha SL1508 PCR1x 2 exp wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ATF3 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep1 GM78 ATF3 PCR1 1 ATF3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001562 1562 GSM803508 Myers HudsonAlpha SL1269 PCR1x 1 exp wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ATF3 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf2sc81188V0422111RawRep2 GM78 ATF2 V11 2 ATF2_(SC-81188) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002306 2306 GSM1010780 Myers HudsonAlpha SL7561 v042211.1 2 exp wgEncodeHaibTfbsGm12878Atf2sc81188V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ATF2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf2sc81188V0422111RawRep1 GM78 ATF2 V11 1 ATF2_(SC-81188) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002306 2306 GSM1010780 Myers HudsonAlpha SL7282 v042211.1 1 exp wgEncodeHaibTfbsGm12878Atf2sc81188V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ATF2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsViewPeaks Peaks Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87Pol24h8V0416101PkRep2V2 U87 Pol2-4H8 V101 2 Pol2-4H8 U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-20 2012-02-20 wgEncodeEH001674 1674 GSM803459 Myers HudsonAlpha SL3773 v041610.1 2 exp MACS wgEncodeHaibTfbsU87Pol24h8V0416101PkRep2V2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment U87 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87Pol24h8V0416101PkRep1V2 U87 Pol2-4H8 V101 1 Pol2-4H8 U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-20 2012-02-23 wgEncodeEH001674 1674 GSM803459 Myers HudsonAlpha SL1962 v041610.1 1 exp MACS wgEncodeHaibTfbsU87Pol24h8V0416101PkRep1V2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment U87 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87NrsfPcr2xPkRep2V2 U87 NRSF PCR2 2 NRSF U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-01-21 2011-10-20 wgEncodeEH001554 1554 GSM803372 Myers HudsonAlpha SL413 PCR2x 2 exp MACS wgEncodeHaibTfbsU87NrsfPcr2xPkRep2V2 None Peaks Neuron-restrictive silencer transcription factor glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment U87 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87NrsfPcr2xPkRep1V2 U87 NRSF PCR2 1 NRSF U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-03-08 2011-12-08 wgEncodeEH001554 1554 GSM803372 Myers HudsonAlpha SL88 PCR2x 1 exp MACS wgEncodeHaibTfbsU87NrsfPcr2xPkRep1V2 None Peaks Neuron-restrictive silencer transcription factor glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment U87 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dP300V0416102Dm002p1hPkRep2 T47D p300 DMSO 2 p300 T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-12-11 2011-09-11 wgEncodeEH001602 1602 GSM803522 Myers HudsonAlpha SL3015 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dP300V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks EP300(c-20) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D p300 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dP300V0416102Dm002p1hPkRep1 T47D p300 DMSO 1 p300 T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-12-11 2011-09-11 wgEncodeEH001602 1602 GSM803522 Myers HudsonAlpha SL2633 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dP300V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks EP300(c-20) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D p300 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dJundV0422111PkRep2 T47D JunD V11 2 JunD T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003321 3321 GSM1010718 Myers HudsonAlpha SL11657 v042211.1 2 exp MACS wgEncodeHaibTfbsT47dJundV0422111PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment T-47D JunD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dJundV0422111PkRep1 T47D JunD V11 1 JunD T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003321 3321 GSM1010718 Myers HudsonAlpha SL11656 v042211.1 1 exp MACS wgEncodeHaibTfbsT47dJundV0422111PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment T-47D JunD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hPkRep2 T47D GATA3 DMSO 2 GATA3_(SC-268) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001639 1639 GSM803514 Myers HudsonAlpha SL3013 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D GATA3 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hPkRep1 T47D GATA3 DMSO 1 GATA3_(SC-268) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001639 1639 GSM803514 Myers HudsonAlpha SL2636 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D GATA3 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hPkRep2 T47D FOXA1 DMSO 2 FOXA1_(SC-6553) T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001588 1588 GSM803409 Myers HudsonAlpha SL2081 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D FOXA1 6553 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hPkRep1 T47D FOXA1 DMSO 1 FOXA1_(SC-6553) T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001588 1588 GSM803409 Myers HudsonAlpha SL1878 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D FOXA1 6553 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hPkRep2 T47 ERa Gen PC2 2 ERalpha_a T-47D ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-22 wgEncodeEH001556 1556 GSM803374 Myers HudsonAlpha SL1492 Genestein 100nM treatment hg19 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hPkRep2 Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment T-47D ERa a Genistein PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hPkRep1 T47 ERa Gen PC2 1 ERalpha_a T-47D ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-22 wgEncodeEH001556 1556 GSM803374 Myers HudsonAlpha SL1218 Genestein 100nM treatment hg19 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hPkRep1 Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment T-47D ERa a Genistein PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hPkRep2 T47D ERa Estra 2 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001577 1577 GSM803539 Myers HudsonAlpha SL1491 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hPkRep2 Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment T-47D ERa a Estradiol v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hPkRep1 T47D ERa Estra 1 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001577 1577 GSM803539 Myers HudsonAlpha SL1217 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hPkRep1 Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment T-47D ERa a Estradiol v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEraaV0416102Bpa1hPkRep2 T47D ERa BPA 2 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002299 2299 GSM1010823 Myers HudsonAlpha SL1877 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dEraaV0416102Bpa1hPkRep2 BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment T-47D ERa a BPA v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEraaV0416102Bpa1hPkRep1 T47D ERa BPA 1 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002299 2299 GSM1010823 Myers HudsonAlpha SL1493 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dEraaV0416102Bpa1hPkRep1 BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment T-47D ERa a BPA v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hPkRep2 T47D CTCF DMSO 2 CTCF_(SC-5916) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001656 1656 GSM803348 Myers HudsonAlpha SL3014 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D CTCF 5916 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hPkRep1 T47D CTCF DMSO 1 CTCF_(SC-5916) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001656 1656 GSM803348 Myers HudsonAlpha SL2634 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D CTCF 5916 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraYy1sc281V0416102PkRep2 SKRA YY1 V102 2 YY1_(SC-281) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001615 1615 GSM803498 Myers HudsonAlpha SL3640 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraYy1sc281V0416102PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA YY1 281 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraYy1sc281V0416102PkRep1 SKRA YY1 V102 1 YY1_(SC-281) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001615 1615 GSM803498 Myers HudsonAlpha SL3639 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraYy1sc281V0416102PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA YY1 281 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraUsf1sc8983V0416102PkRep2 SKRA USF1 V102 2 USF1_(SC-8983) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001621 1621 GSM803472 Myers HudsonAlpha SL2919 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraUsf1sc8983V0416102PkRep2 None Peaks This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq). neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA USF-1 8983 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraUsf1sc8983V0416102PkRep1 SKRA USF1 V102 1 USF1_(SC-8983) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001621 1621 GSM803472 Myers HudsonAlpha SL2911 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraUsf1sc8983V0416102PkRep1 None Peaks This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq). neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA USF-1 8983 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRad21V0416102PkRep2 SKRA RAD21 V102 2 Rad21 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001614 1614 GSM803497 Myers HudsonAlpha SL2915 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraRad21V0416102PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA RAD21 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRad21V0416102PkRep1 SKRA RAD21 V102 1 Rad21 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001614 1614 GSM803497 Myers HudsonAlpha SL2907 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraRad21V0416102PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA RAD21 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraP300V0416102PkRep2 SKRA p300 V102 2 p300 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001616 1616 GSM803495 Myers HudsonAlpha SL2918 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraP300V0416102PkRep2 None Peaks EP300(c-20) neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA p300 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraP300V0416102PkRep1 SKRA p300 V102 1 p300 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001616 1616 GSM803495 Myers HudsonAlpha SL2910 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraP300V0416102PkRep1 None Peaks EP300(c-20) neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA p300 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraCtcfV0416102PkRep2 SKRA CTCF V102 2 CTCF SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001613 1613 GSM803333 Myers HudsonAlpha SL2914 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraCtcfV0416102PkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA CTCF v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraCtcfV0416102PkRep1 SKRA CTCF V102 1 CTCF SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001613 1613 GSM803333 Myers HudsonAlpha SL2906 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraCtcfV0416102PkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA CTCF v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcPol24h8V0416101PkRep2 SKMC Pol2-4H8 V101 2 Pol2-4H8 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002281 2281 GSM1010793 Myers HudsonAlpha SL5611 v041610.1 2 exp MACS wgEncodeHaibTfbsSknmcPol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-MC Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcPol24h8V0416101PkRep1 SKMC Pol2-4H8 V101 1 Pol2-4H8 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002281 2281 GSM1010793 Myers HudsonAlpha SL1963 v041610.1 1 exp MACS wgEncodeHaibTfbsSknmcPol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-MC Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcFoxp2Pcr2xPkRep2 SKMC FOXP2 PCR2 2 FOXP2 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2008-10-31 2009-07-31 wgEncodeEH001461 1461 GSM803353 Myers HudsonAlpha SL167 PCR2x 2 exp wgEncodeHaibTfbsSknmcFoxp2Pcr2xPkRep2 None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment SK-N-MC FOXP2 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcFoxp2Pcr2xPkRep1 SKMC FOXP2 PCR2 1 FOXP2 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-02 2012-03-02 wgEncodeEH001461 1461 GSM803353 Myers HudsonAlpha SL144 PCR2x 1 exp wgEncodeHaibTfbsSknmcFoxp2Pcr2xPkRep1 None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment SK-N-MC FOXP2 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Taf1V0416101PkRep2 PFSK TAF1 V101 2 TAF1 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002309 2309 GSM1010770 Myers HudsonAlpha SL6969 v041610.1 2 exp MACS wgEncodeHaibTfbsPfsk1Taf1V0416101PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 TAF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Taf1V0416101PkRep1 PFSK TAF1 V101 1 TAF1 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002309 2309 GSM1010770 Myers HudsonAlpha SL3772 v041610.1 1 exp MACS wgEncodeHaibTfbsPfsk1Taf1V0416101PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 TAF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Sin3ak20V0416101PkRep2 PFSK Sin3A V101 2 Sin3Ak-20 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002268 2268 GSM1010781 Myers HudsonAlpha SL5041 v041610.1 2 exp MACS wgEncodeHaibTfbsPfsk1Sin3ak20V0416101PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Sin3ak20V0416101PkRep1 PFSK Sin3A V101 1 Sin3Ak-20 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002268 2268 GSM1010781 Myers HudsonAlpha SL2354 v041610.1 1 exp MACS wgEncodeHaibTfbsPfsk1Sin3ak20V0416101PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Pol24h8V0416101PkRep2 PFSK Pol2-4H8 V101 2 Pol2-4H8 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH002272 2272 GSM1010819 Myers HudsonAlpha SL5610 v041610.1 2 exp MACS wgEncodeHaibTfbsPfsk1Pol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Pol24h8V0416101PkRep1 PFSK Pol2-4H8 V101 1 Pol2-4H8 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH002272 2272 GSM1010819 Myers HudsonAlpha SL2353 v041610.1 1 exp MACS wgEncodeHaibTfbsPfsk1Pol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfV0416101PkRep2 PFSK NRSF V101 2 NRSF PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002267 2267 GSM1010786 Myers HudsonAlpha SL5497 v041610.1 2 exp MACS wgEncodeHaibTfbsPfsk1NrsfV0416101PkRep2 None Peaks Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 NRSF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfV0416101PkRep1 PFSK NRSF V101 1 NRSF PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002267 2267 GSM1010786 Myers HudsonAlpha SL5496 v041610.1 1 exp MACS wgEncodeHaibTfbsPfsk1NrsfV0416101PkRep1 None Peaks Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 NRSF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep2 PFSK NRSF PCR2 2 NRSF PFSK-1 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001553 1553 GSM803369 Myers HudsonAlpha SL411 PCR2x 2 exp MACS wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PFSK-1 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep1 PFSK NRSF PCR2 1 NRSF PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2010-08-06 2011-05-06 wgEncodeEH001553 1553 GSM803369 Myers HudsonAlpha SL149 PCR2x 1 exp MACS wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PFSK-1 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Foxp2Pcr2xPkRep2 PFSK FOXP2 PCR2 2 FOXP2 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2008-10-31 2009-07-31 wgEncodeEH001460 1460 GSM803480 Myers HudsonAlpha SL14 PCR2x 2 exp wgEncodeHaibTfbsPfsk1Foxp2Pcr2xPkRep2 None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PFSK-1 FOXP2 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Foxp2Pcr2xPkRep1 PFSK FOXP2 PCR2 1 FOXP2 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-02 2012-03-02 wgEncodeEH001460 1460 GSM803480 Myers HudsonAlpha SL13 PCR2x 1 exp wgEncodeHaibTfbsPfsk1Foxp2Pcr2xPkRep1 None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PFSK-1 FOXP2 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Sin3ak20V0416101PkRep2 PANC Sin3A V101 2 Sin3Ak-20 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002266 2266 GSM1010785 Myers HudsonAlpha SL5042 v041610.1 2 exp MACS wgEncodeHaibTfbsPanc1Sin3ak20V0416101PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Sin3ak20V0416101PkRep1 PANC Sin3A V101 1 Sin3Ak-20 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002266 2266 GSM1010785 Myers HudsonAlpha SL2344 v041610.1 1 exp MACS wgEncodeHaibTfbsPanc1Sin3ak20V0416101PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Pol24h8V0416101PkRep2 PANC Pol2-4H8 V101 2 Pol2-4H8 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002265 2265 GSM1010788 Myers HudsonAlpha SL5609 v041610.1 2 exp MACS wgEncodeHaibTfbsPanc1Pol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Pol24h8V0416101PkRep1 PANC Pol2-4H8 V101 1 Pol2-4H8 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002265 2265 GSM1010788 Myers HudsonAlpha SL2343 v041610.1 1 exp MACS wgEncodeHaibTfbsPanc1Pol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0422111PkRep2 PANC NRSF V11 2 NRSF PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003285 3285 GSM1010859 Myers HudsonAlpha SL16342 v042211.1 2 exp MACS wgEncodeHaibTfbsPanc1NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment PANC-1 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0422111PkRep1 PANC NRSF V11 1 NRSF PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003285 3285 GSM1010859 Myers HudsonAlpha SL14681 v042211.1 1 exp MACS wgEncodeHaibTfbsPanc1NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment PANC-1 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0416101PkRep2 PANC NRSF V101 2 NRSF PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002280 2280 GSM1010792 Myers HudsonAlpha SL5495 v041610.1 2 exp MACS wgEncodeHaibTfbsPanc1NrsfV0416101PkRep2 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 NRSF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0416101PkRep1 PANC NRSF V101 1 NRSF PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002280 2280 GSM1010792 Myers HudsonAlpha SL4437 v041610.1 1 exp MACS wgEncodeHaibTfbsPanc1NrsfV0416101PkRep1 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 NRSF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep2 PANC NRSF PCR2 2 NRSF PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-08-06 2011-05-06 wgEncodeEH001552 1552 GSM803370 Myers HudsonAlpha SL522 PCR2x 2 exp MACS wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PANC-1 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep1 PANC NRSF PCR2 1 NRSF PANC-1 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001552 1552 GSM803370 Myers HudsonAlpha SL116 PCR2x 1 exp MACS wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PANC-1 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pu1V0422111PkRep2 HL-60 PU.1 V11 2 PU.1 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003292 3292 GSM1010843 Myers HudsonAlpha SL14712 v042211.1 2 exp MACS wgEncodeHaibTfbsHl60Pu1V0422111PkRep2 None Peaks PU.1 (H-135) promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 PU.1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pu1V0422111PkRep1 HL-60 PU.1 V11 1 PU.1 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003292 3292 GSM1010843 Myers HudsonAlpha SL12629 v042211.1 1 exp MACS wgEncodeHaibTfbsHl60Pu1V0422111PkRep1 None Peaks PU.1 (H-135) promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 PU.1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep2 HL-60 Pol2-4H8 V11 2 Pol2-4H8 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003253 3253 GSM1010737 Myers HudsonAlpha SL16322 v042211.1 2 exp MACS wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 Pol2-4H8 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep1 HL-60 Pol2-4H8 V11 1 Pol2-4H8 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003253 3253 GSM1010737 Myers HudsonAlpha SL12628 v042211.1 1 exp MACS wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 Pol2-4H8 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60NrsfV0422111PkRep2 HL-60 NRSF V11 2 NRSF HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003247 3247 GSM1010754 Myers HudsonAlpha SL13747 v042211.1 2 exp MACS wgEncodeHaibTfbsHl60NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60NrsfV0422111PkRep1 HL-60 NRSF V11 1 NRSF HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003247 3247 GSM1010754 Myers HudsonAlpha SL12632 v042211.1 1 exp MACS wgEncodeHaibTfbsHl60NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60GabpV0422111PkRep2 HL-60 GABP V11 2 GABP HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003252 3252 GSM1010822 Myers HudsonAlpha SL16321 v042211.1 2 exp MACS wgEncodeHaibTfbsHl60GabpV0422111PkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 GABP v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60GabpV0422111PkRep1 HL-60 GABP V11 1 GABP HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003252 3252 GSM1010822 Myers HudsonAlpha SL12633 v042211.1 1 exp MACS wgEncodeHaibTfbsHl60GabpV0422111PkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 GABP v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Zbtb33V0416101PkRep2 HCT ZBTB33 2 ZBTB33 HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001672 1672 GSM803458 Myers HudsonAlpha SL3970 v041610.1 2 exp MACS wgEncodeHaibTfbsHct116Zbtb33V0416101PkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 ZBTB33 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Zbtb33V0416101PkRep1 HCT ZBTB33 1 ZBTB33 HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001672 1672 GSM803458 Myers HudsonAlpha SL3646 v041610.1 1 exp MACS wgEncodeHaibTfbsHct116Zbtb33V0416101PkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 ZBTB33 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Yy1sc281V0416101PkRep2 HCT YY1 V101 2 YY1_(SC-281) HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001671 1671 GSM803354 Myers HudsonAlpha SL4500 v041610.1 2 exp MACS wgEncodeHaibTfbsHct116Yy1sc281V0416101PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 YY1 281 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Yy1sc281V0416101PkRep1 HCT YY1 V101 1 YY1_(SC-281) HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001671 1671 GSM803354 Myers HudsonAlpha SL3971 v041610.1 1 exp MACS wgEncodeHaibTfbsHct116Yy1sc281V0416101PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 YY1 281 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Usf1V0422111PkRep2 HCT USF1 V11 2 USF-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003310 3310 GSM1010836 Myers HudsonAlpha SL16733 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Usf1V0422111PkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 USF-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Usf1V0422111PkRep1 HCT USF1 V11 1 USF-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003310 3310 GSM1010836 Myers HudsonAlpha SL12238 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Usf1V0422111PkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 USF-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Tead4sc101184V0422111PkRep2 HCT TEAD4 V11 2 TEAD4_(SC-101184) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003309 3309 GSM1010772 Myers HudsonAlpha SL14570 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Tead4sc101184V0422111PkRep1 HCT TEAD4 V11 1 TEAD4_(SC-101184) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003309 3309 GSM1010772 Myers HudsonAlpha SL16313 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116SrfV0422111PkRep2 HCT SRF V11 2 SRF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003218 3218 GSM1010851 Myers HudsonAlpha SL13070 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116SrfV0422111PkRep2 None Peaks Serum response transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 SRF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116SrfV0422111PkRep1 HCT SRF V11 1 SRF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003218 3218 GSM1010851 Myers HudsonAlpha SL12237 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116SrfV0422111PkRep1 None Peaks Serum response transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 SRF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sp1V0422111PkRep2 HCT SP1 V11 2 SP1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003221 3221 GSM1010902 Myers HudsonAlpha SL13072 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Sp1V0422111PkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 SP1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sp1V0422111PkRep1 HCT SP1 V11 1 SP1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003221 3221 GSM1010902 Myers HudsonAlpha SL12239 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Sp1V0422111PkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 SP1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sin3ak20V0422111PkRep2 HCT Sin3A V11 2 Sin3Ak-20 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003222 3222 GSM1010905 Myers HudsonAlpha SL13076 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Sin3ak20V0422111PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Sin3Ak-20 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sin3ak20V0422111PkRep1 HCT Sin3A V11 1 Sin3Ak-20 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003222 3222 GSM1010905 Myers HudsonAlpha SL12244 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Sin3ak20V0422111PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Sin3Ak-20 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Rad21V0422111PkRep2 HCT RAD21 V11 2 Rad21 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003217 3217 GSM1010848 Myers HudsonAlpha SL13067 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Rad21V0422111PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 RAD21 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Rad21V0422111PkRep1 HCT RAD21 V11 1 Rad21 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003217 3217 GSM1010848 Myers HudsonAlpha SL12230 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Rad21V0422111PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 RAD21 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Pol24h8V0416101PkRep2 HCT Pol2-4H8 V101 2 Pol2-4H8 HCT-116 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001627 1627 GSM803474 Myers HudsonAlpha SL3830 v041610.1 2 exp MACS wgEncodeHaibTfbsHct116Pol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Pol24h8V0416101PkRep1 HCT Pol2-4H8 V101 1 Pol2-4H8 HCT-116 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001627 1627 GSM803474 Myers HudsonAlpha SL3456 v041610.1 1 exp MACS wgEncodeHaibTfbsHct116Pol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116NrsfV0422111PkRep2 HCT NRSF V11 2 NRSF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003308 3308 GSM1010869 Myers HudsonAlpha SL14560 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116NrsfV0422111PkRep1 HCT NRSF V11 1 NRSF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003308 3308 GSM1010869 Myers HudsonAlpha SL16310 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116MaxV0422111PkRep2 HCT Max V11 2 Max HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003223 3223 GSM1010904 Myers HudsonAlpha SL13075 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116MaxV0422111PkRep1 HCT Max V11 1 Max HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003223 3223 GSM1010904 Myers HudsonAlpha SL12243 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116JundV0422111PkRep2 HCT JunD V11 2 JunD HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003216 3216 GSM1010847 Myers HudsonAlpha SL13069 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116JundV0422111PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 JunD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116JundV0422111PkRep1 HCT JunD V11 1 JunD HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003216 3216 GSM1010847 Myers HudsonAlpha SL12233 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116JundV0422111PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 JunD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Fosl1V0422111PkRep2 HCT FOSL1 V11 2 FOSL1_(SC-183) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003246 3246 GSM1010756 Myers HudsonAlpha SL13068 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Fosl1V0422111PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 FOSL1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Fosl1V0422111PkRep1 HCT FOSL1 V11 1 FOSL1_(SC-183) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003246 3246 GSM1010756 Myers HudsonAlpha SL12231 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Fosl1V0422111PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 FOSL1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Elf1V0422111PkRep2 HCT ELF1 V11 2 ELF1_(SC-631) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003307 3307 GSM1010765 Myers HudsonAlpha SL13733 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Elf1V0422111PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 ELF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Elf1V0422111PkRep1 HCT ELF1 V11 1 ELF1_(SC-631) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003307 3307 GSM1010765 Myers HudsonAlpha SL14719 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Elf1V0422111PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 ELF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Egr1V0422111PkRep2 HCT Egr-1 V11 2 Egr-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003215 3215 GSM1010846 Myers HudsonAlpha SL13065 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Egr1V0422111PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Egr-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Egr1V0422111PkRep1 HCT Egr-1 V11 1 Egr-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003215 3215 GSM1010846 Myers HudsonAlpha SL12228 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Egr1V0422111PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Egr-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116CtcfcV0422111PkRep2 HCT CTCF V11 2 CTCF_(SC-5916) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003220 3220 GSM1010903 Myers HudsonAlpha SL13074 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116CtcfcV0422111PkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CTCF 5916 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116CtcfcV0422111PkRep1 HCT CTCF V11 1 CTCF_(SC-5916) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003220 3220 GSM1010903 Myers HudsonAlpha SL12242 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116CtcfcV0422111PkRep1 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CTCF 5916 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep2 HCT CEBPB V11 2 CEBPB_(SC-150) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003219 3219 GSM1010852 Myers HudsonAlpha SL13073 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep1 HCT CEBPB V11 1 CEBPB_(SC-150) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003219 3219 GSM1010852 Myers HudsonAlpha SL12240 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep2 HCT CBX3 V11 2 CBX3_(SC-101004) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003277 3277 GSM1010758 Myers HudsonAlpha SL13066 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep2 None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CBX3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep1 HCT CBX3 V11 1 CBX3_(SC-101004) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003277 3277 GSM1010758 Myers HudsonAlpha SL12229 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep1 None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CBX3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Atf3V0422111PkRep2 HCT ATF3 V11 2 ATF3 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003276 3276 GSM1010757 Myers HudsonAlpha SL16874 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Atf3V0422111PkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 ATF3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Atf3V0422111PkRep1 HCT ATF3 V11 1 ATF3 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003276 3276 GSM1010757 Myers HudsonAlpha SL12234 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Atf3V0422111PkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 ATF3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Yy1V0416101PkRep2 GM92 YY1 V101 2 YY1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001609 1609 GSM803516 Myers HudsonAlpha SL3584 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12892Yy1V0416101PkRep2 None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 YY1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Yy1V0416101PkRep1 GM92 YY1 V101 1 YY1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001609 1609 GSM803516 Myers HudsonAlpha SL2132 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12892Yy1V0416101PkRep1 None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 YY1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Taf1V0416102PkRep2 GM92 TAF1 V102 2 TAF1 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001513 1513 GSM803489 Myers HudsonAlpha SL945 v041610.2 2 exp wgEncodeHaibTfbsGm12892Taf1V0416102PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 TAF1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Taf1V0416102PkRep1 GM92 TAF1 V102 1 TAF1 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001513 1513 GSM803489 Myers HudsonAlpha SL736 v041610.2 1 exp wgEncodeHaibTfbsGm12892Taf1V0416102PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 TAF1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep2 GM92 Pol2-4H8 V102 2 Pol2-4H8 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001512 1512 GSM803490 Myers HudsonAlpha SL946 v041610.2 2 exp wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep1 GM92 Pol2-4H8 V102 1 Pol2-4H8 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001512 1512 GSM803490 Myers HudsonAlpha SL911 v041610.2 1 exp wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol2V0416102PkRep2 GM92 Pol2 V102 2 Pol2 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001511 1511 GSM803487 Myers HudsonAlpha SL944 v041610.2 2 exp wgEncodeHaibTfbsGm12892Pol2V0416102PkRep2 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 Pol2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol2V0416102PkRep1 GM92 Pol2 V102 1 Pol2 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001511 1511 GSM803487 Myers HudsonAlpha SL909 v041610.2 1 exp wgEncodeHaibTfbsGm12892Pol2V0416102PkRep1 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 Pol2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep2 GM92 PAX5 V101 2 PAX5-C20 GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2011-03-17 wgEncodeEH001546 1546 GSM803334 Myers HudsonAlpha SL2133 hg19 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep2 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 PAX5-C20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep1 GM92 PAX5 V101 1 PAX5-C20 GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2011-03-17 wgEncodeEH001546 1546 GSM803334 Myers HudsonAlpha SL1664 hg19 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep1 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 PAX5-C20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Yy1sc281V0416101PkRep2 GM91 YY1 V101 2 YY1_(SC-281) GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001573 1573 GSM803535 Myers HudsonAlpha SL2130 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12891Yy1sc281V0416101PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 YY1 281 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Yy1sc281V0416101PkRep1 GM91 YY1 V101 1 YY1_(SC-281) GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001573 1573 GSM803535 Myers HudsonAlpha SL2388 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12891Yy1sc281V0416101PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 YY1 281 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Taf1Pcr1xPkRep2 GM91 TAF1 PCR1 2 TAF1 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001524 1524 GSM803393 Myers HudsonAlpha SL920 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Taf1Pcr1xPkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 TAF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Taf1Pcr1xPkRep1 GM91 TAF1 PCR1 1 TAF1 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001524 1524 GSM803393 Myers HudsonAlpha SL749 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Taf1Pcr1xPkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 TAF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pu1Pcr1xPkRep2 GM91 PU.1 PCR1 2 PU.1 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-10 wgEncodeEH001521 1521 GSM803398 Myers HudsonAlpha SL948 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Pu1Pcr1xPkRep2 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 PU.1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pu1Pcr1xPkRep1 GM91 PU.1 PCR1 1 PU.1 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-10 wgEncodeEH001521 1521 GSM803398 Myers HudsonAlpha SL977 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Pu1Pcr1xPkRep1 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 PU.1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pou2f2Pcr1xPkRep2 GM91 POU2F2 2 POU2F2 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001520 1520 GSM803397 Myers HudsonAlpha SL918 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Pou2f2Pcr1xPkRep2 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 POU2F2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pou2f2Pcr1xPkRep1 GM91 POU2F2 1 POU2F2 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001520 1520 GSM803397 Myers HudsonAlpha SL802 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Pou2f2Pcr1xPkRep1 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 POU2F2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol24h8Pcr1xPkRep2 GM91 Pol2-4H8 PCR1 2 Pol2-4H8 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001523 1523 GSM803400 Myers HudsonAlpha SL922 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Pol24h8Pcr1xPkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 Pol2-4H8 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol24h8Pcr1xPkRep1 GM91 Pol2-4H8 PCR1 1 Pol2-4H8 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001523 1523 GSM803400 Myers HudsonAlpha SL910 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Pol24h8Pcr1xPkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 Pol2-4H8 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol2Pcr1xPkRep2 GM91 Pol2 PCR1 2 Pol2 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001522 1522 GSM803399 Myers HudsonAlpha SL921 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Pol2Pcr1xPkRep2 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 Pol2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol2Pcr1xPkRep1 GM91 Pol2 PCR1 1 Pol2 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001522 1522 GSM803399 Myers HudsonAlpha SL908 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Pol2Pcr1xPkRep1 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 Pol2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pax5c20V0416101PkRep2 GM91 PAX5 V101 2 PAX5-C20 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2011-03-17 wgEncodeEH001545 1545 GSM803337 Myers HudsonAlpha SL2131 hg19 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12891Pax5c20V0416101PkRep2 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 PAX5-C20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pax5c20V0416101PkRep1 GM91 PAX5 V101 1 PAX5-C20 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2011-03-17 wgEncodeEH001545 1545 GSM803337 Myers HudsonAlpha SL1662 hg19 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12891Pax5c20V0416101PkRep1 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 PAX5-C20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Zbtb7aV0422111PkRep2 ECC1 ZBTB7A 2 ZBTB7A_(SC-34508) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003241 3241 GSM1010752 Myers HudsonAlpha SL14586 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Zbtb7aV0422111PkRep2 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 ZBTB7A v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Zbtb7aV0422111PkRep1 ECC1 ZBTB7A 1 ZBTB7A_(SC-34508) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003241 3241 GSM1010752 Myers HudsonAlpha SL13275 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Zbtb7aV0422111PkRep1 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 ZBTB7A v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Yy1sc281V0422111PkRep2 ECC1 YY1 V11 2 YY1_(SC-281) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003240 3240 GSM1010753 Myers HudsonAlpha SL14584 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Yy1sc281V0422111PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 YY1 281 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Yy1sc281V0422111PkRep1 ECC1 YY1 V11 1 YY1_(SC-281) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003240 3240 GSM1010753 Myers HudsonAlpha SL13273 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Yy1sc281V0422111PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 YY1 281 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Usf1V0422111PkRep2 ECC1 USF1 V11 2 USF-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003239 3239 GSM1010886 Myers HudsonAlpha SL14589 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Usf1V0422111PkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 USF-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Usf1V0422111PkRep1 ECC1 USF1 V11 1 USF-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003239 3239 GSM1010886 Myers HudsonAlpha SL13279 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Usf1V0422111PkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 USF-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tead4sc101184V0422111PkRep2 ECC1 TEAD4 V11 2 TEAD4_(SC-101184) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003238 3238 GSM1010885 Myers HudsonAlpha SL14591 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tead4sc101184V0422111PkRep1 ECC1 TEAD4 V11 1 TEAD4_(SC-101184) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003238 3238 GSM1010885 Myers HudsonAlpha SL13281 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tcf12V0422111PkRep2 ECC1 TCF12 V11 2 TCF12 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003291 3291 GSM1010842 Myers HudsonAlpha SL14063 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Tcf12V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TCF12 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tcf12V0422111PkRep1 ECC1 TCF12 V11 1 TCF12 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003291 3291 GSM1010842 Myers HudsonAlpha SL16025 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Tcf12V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TCF12 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Taf1V0422111PkRep2 ECC1 TAF1 V11 2 TAF1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003256 3256 GSM1010733 Myers HudsonAlpha SL14721 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Taf1V0422111PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TAF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Taf1V0422111PkRep1 ECC1 TAF1 V11 1 TAF1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003256 3256 GSM1010733 Myers HudsonAlpha SL13751 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Taf1V0422111PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TAF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1SrfV0422111PkRep2 ECC1 SRF V11 2 SRF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003245 3245 GSM1010762 Myers HudsonAlpha SL14583 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1SrfV0422111PkRep2 None Peaks Serum response transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 SRF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1SrfV0422111PkRep1 ECC1 SRF V11 1 SRF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003245 3245 GSM1010762 Myers HudsonAlpha SL13272 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1SrfV0422111PkRep1 None Peaks Serum response transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 SRF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Rad21V0422111PkRep2 ECC1 RAD21 V11 2 Rad21 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003263 3263 GSM1010801 Myers HudsonAlpha SL16305 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Rad21V0422111PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 RAD21 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Rad21V0422111PkRep1 ECC1 RAD21 V11 1 Rad21 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003263 3263 GSM1010801 Myers HudsonAlpha SL13270 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Rad21V0422111PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 RAD21 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hPkRep2 ECC1 Pol2 DMSO 2 Pol2 ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001572 1572 GSM803536 Myers HudsonAlpha SL2085 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks RNA Polymerase II epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 Pol2 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hPkRep1 ECC1 Pol2 DMSO 1 Pol2 ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001572 1572 GSM803536 Myers HudsonAlpha SL1176 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks RNA Polymerase II epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 Pol2 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1P300V0422111PkRep2 ECC1 p300 V11 2 p300 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003274 3274 GSM1010759 Myers HudsonAlpha SL14585 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1P300V0422111PkRep2 None Peaks EP300(c-20) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 p300 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1P300V0422111PkRep1 ECC1 p300 V11 1 p300 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003274 3274 GSM1010759 Myers HudsonAlpha SL13274 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1P300V0422111PkRep1 None Peaks EP300(c-20) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 p300 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1NrsfV0422111PkRep2 ECC1 NRSF V11 2 NRSF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003290 3290 GSM1010841 Myers HudsonAlpha SL14057 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1NrsfV0422111PkRep1 ECC1 NRSF V11 1 NRSF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003290 3290 GSM1010841 Myers HudsonAlpha SL16023 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Nficsc81335V0422111PkRep2 ECC1 NFIC V11 2 NFIC_(SC-81335) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003289 3289 GSM1010855 Myers HudsonAlpha SL16022 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Nficsc81335V0422111PkRep2 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 NFIC v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Nficsc81335V0422111PkRep1 ECC1 NFIC V11 1 NFIC_(SC-81335) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003289 3289 GSM1010855 Myers HudsonAlpha SL14056 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Nficsc81335V0422111PkRep1 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 NFIC v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1MaxV0422111PkRep2 ECC1 Max V11 2 Max ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003268 3268 GSM1010807 Myers HudsonAlpha SL16021 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1MaxV0422111PkRep1 ECC1 Max V11 1 Max ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003268 3268 GSM1010807 Myers HudsonAlpha SL14054 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Dex100nmPkRep2 ECC1 GR DEX PC2 2 GR ECC-1 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2011-03-07 wgEncodeEH001540 1540 GSM803340 Myers HudsonAlpha SL1088 hg19 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1GrV0416102Dex100nmPkRep2 DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment ECC-1 GR DEX 100nM PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Dex100nmPkRep1 ECC1 GR DEX PC2 1 GR ECC-1 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2011-03-07 wgEncodeEH001540 1540 GSM803340 Myers HudsonAlpha SL1012 hg19 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1GrV0416102Dex100nmPkRep1 DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment ECC-1 GR DEX 100nM PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep2 ECC1 FOXM1 V11 2 FOXM1_(SC-502) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003288 3288 GSM1010856 Myers HudsonAlpha SL14725 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep2 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 FOXM1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep1 ECC1 FOXM1 V11 1 FOXM1_(SC-502) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003288 3288 GSM1010856 Myers HudsonAlpha SL14051 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep1 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 FOXM1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hPkRep2 ECC1 FOXA1 DMSO 2 FOXA1_(SC-6553) ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001586 1586 GSM803444 Myers HudsonAlpha SL2080 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 FOXA1 6553 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hPkRep1 ECC1 FOXA1 DMSO 1 FOXA1_(SC-6553) ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001586 1586 GSM803444 Myers HudsonAlpha SL1880 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 FOXA1 6553 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hPkRep2 ECC1 ERa Geni 2 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001575 1575 GSM803541 Myers HudsonAlpha SL1122 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hPkRep2 Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment ECC-1 ERa a Genistein v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hPkRep1 ECC1 ERa Geni 1 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001575 1575 GSM803541 Myers HudsonAlpha SL1049 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hPkRep1 Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment ECC-1 ERa a Genistein v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hPkRep2 ECC1 ERa Estra 2 ERalpha_a ECC-1 ChipSeq ENCODE June 2010 Freeze 2010-05-27 2011-02-27 wgEncodeEH001536 1536 GSM803422 Myers HudsonAlpha SL1093 hg19 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hPkRep2 Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment ECC-1 ERa a Estradiol v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hPkRep1 ECC1 ERa Estra 1 ERalpha_a ECC-1 ChipSeq ENCODE June 2010 Freeze 2010-05-27 2011-02-27 wgEncodeEH001536 1536 GSM803422 Myers HudsonAlpha SL1011 hg19 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hPkRep1 Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment ECC-1 ERa a Estradiol v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hPkRep2 ECC1 ERa BPA 2 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002313 2313 GSM1010747 Myers HudsonAlpha SL2082 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hPkRep2 BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment ECC-1 ERa a BPA v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hPkRep1 ECC1 ERa BPA 1 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002313 2313 GSM1010747 Myers HudsonAlpha SL1050 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hPkRep1 BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment ECC-1 ERa a BPA v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Egr1V0422111PkRep2 ECC1 Egr-1 V11 2 Egr-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003232 3232 GSM1010888 Myers HudsonAlpha SL14590 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Egr1V0422111PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 Egr-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Egr1V0422111PkRep1 ECC1 Egr-1 V11 1 Egr-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003232 3232 GSM1010888 Myers HudsonAlpha SL13280 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Egr1V0422111PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 Egr-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hPkRep2 ECC1 CTCF DMSO 2 CTCF_(SC-5916) ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002300 2300 GSM1010774 Myers HudsonAlpha SL3447 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 CTCF 5916 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hPkRep1 ECC1 CTCF DMSO 1 CTCF_(SC-5916) ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002300 2300 GSM1010774 Myers HudsonAlpha SL2630 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 CTCF 5916 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Creb1sc240V0422111PkRep2 ECC1 CREB1 V11 2 CREB1_(SC-240) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003287 3287 GSM1010857 Myers HudsonAlpha SL14723 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Creb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Creb1sc240V0422111PkRep1 ECC1 CREB1 V11 1 CREB1_(SC-240) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003287 3287 GSM1010857 Myers HudsonAlpha SL14048 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Creb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Cebpbsc150V0422111PkRep2 ECC1 CEBPB V11 2 CEBPB_(SC-150) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003262 3262 GSM1010802 Myers HudsonAlpha SL16302 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Cebpbsc150V0422111PkRep1 ECC1 CEBPB V11 1 CEBPB_(SC-150) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003262 3262 GSM1010802 Myers HudsonAlpha SL13276 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshZbtb33V0422111PkRep2 SKSH ZBTB33 V11 2 ZBTB33 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003261 3261 GSM1010799 Myers HudsonAlpha SL14711 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshZbtb33V0422111PkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH ZBTB33 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshZbtb33V0422111PkRep1 SKSH ZBTB33 V11 1 ZBTB33 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003261 3261 GSM1010799 Myers HudsonAlpha SL13502 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshZbtb33V0422111PkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH ZBTB33 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshYy1sc281V0422111PkRep2 SKSH YY1 V11 2 YY1_(SC-281) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003228 3228 GSM1010897 Myers HudsonAlpha SL14045 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshYy1sc281V0422111PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH YY1 281 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshYy1sc281V0422111PkRep1 SKSH YY1 V11 1 YY1_(SC-281) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003228 3228 GSM1010897 Myers HudsonAlpha SL13085 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshYy1sc281V0422111PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH YY1 281 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshUsf1V0422111PkRep2 SKSH USF1 V11 2 USF-1 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003269 3269 GSM1010806 Myers HudsonAlpha SL14597 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshUsf1V0422111PkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH USF-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshUsf1V0422111PkRep1 SKSH USF1 V11 1 USF-1 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003269 3269 GSM1010806 Myers HudsonAlpha SL13084 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshUsf1V0422111PkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH USF-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTead4sc101184V0422111PkRep2 SKSH TEAD4 V11 2 TEAD4_(SC-101184) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003286 3286 GSM1010858 Myers HudsonAlpha SL14710 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshTead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTead4sc101184V0422111PkRep1 SKSH TEAD4 V11 1 TEAD4_(SC-101184) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003286 3286 GSM1010858 Myers HudsonAlpha SL13501 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshTead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTcf12V0422111PkRep2 SKSH TCF12 V11 2 TCF12 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003227 3227 GSM1010900 Myers HudsonAlpha SL14046 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshTcf12V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH TCF12 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTcf12V0422111PkRep1 SKSH TCF12 V11 1 TCF12 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003227 3227 GSM1010900 Myers HudsonAlpha SL13086 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshTcf12V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH TCF12 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTaf1V0416101PkRep2 SKSH TAF1 V101 2 TAF1 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002301 2301 GSM1010773 Myers HudsonAlpha SL6462 v041610.1 2 exp MACS wgEncodeHaibTfbsSknshTaf1V0416101PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH TAF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTaf1V0416101PkRep1 SKSH TAF1 V101 1 TAF1 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002301 2301 GSM1010773 Myers HudsonAlpha SL5612 v041610.1 1 exp MACS wgEncodeHaibTfbsSknshTaf1V0416101PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH TAF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshSin3ak20V0416101PkRep2 SKSH Sin3A V101 2 Sin3Ak-20 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002271 2271 GSM1010816 Myers HudsonAlpha SL5895 v041610.1 2 exp MACS wgEncodeHaibTfbsSknshSin3ak20V0416101PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshSin3ak20V0416101PkRep1 SKSH Sin3A V101 1 Sin3Ak-20 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002271 2271 GSM1010816 Myers HudsonAlpha SL5043 v041610.1 1 exp MACS wgEncodeHaibTfbsSknshSin3ak20V0416101PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxraV0422111PkRep2 SKSH RXRA V11 2 RXRA SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003302 3302 GSM1010767 Myers HudsonAlpha SL14708 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshRxraV0422111PkRep2 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH RXRA v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxraV0422111PkRep1 SKSH RXRA V11 1 RXRA SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003302 3302 GSM1010767 Myers HudsonAlpha SL13497 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshRxraV0422111PkRep1 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH RXRA v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPol24h8V0416101PkRep2 SKSH Pol2-4H8 V101 2 Pol2-4H8 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002270 2270 GSM1010817 Myers HudsonAlpha SL5607 v041610.1 2 exp MACS wgEncodeHaibTfbsSknshPol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPol24h8V0416101PkRep1 SKSH Pol2-4H8 V101 1 Pol2-4H8 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002270 2270 GSM1010817 Myers HudsonAlpha SL3768 v041610.1 1 exp MACS wgEncodeHaibTfbsSknshPol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPbx3V0422111PkRep2 SKSH PBx3 V11 2 Pbx3 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003300 3300 GSM1010887 Myers HudsonAlpha SL16042 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshPbx3V0422111PkRep2 None Peaks Pbx 3 (D-17) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH PBx3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPbx3V0422111PkRep1 SKSH PBx3 V11 1 Pbx3 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003300 3300 GSM1010887 Myers HudsonAlpha SL13495 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshPbx3V0422111PkRep1 None Peaks Pbx 3 (D-17) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH PBx3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshP300V0422111PkRep2 SKSH p300 V11 2 p300 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003270 3270 GSM1010763 Myers HudsonAlpha SL14705 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshP300V0422111PkRep2 None Peaks EP300(c-20) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH p300 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshP300V0422111PkRep1 SKSH p300 V11 1 p300 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003270 3270 GSM1010763 Myers HudsonAlpha SL13494 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshP300V0422111PkRep1 None Peaks EP300(c-20) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH p300 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfV0416101PkRep2 SKSH NRSF V101 2 NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002269 2269 GSM1010735 Myers HudsonAlpha SL5896 v041610.1 2 exp MACS wgEncodeHaibTfbsSknshNrsfV0416101PkRep2 None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH NRSF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfV0416101PkRep1 SKSH NRSF V101 1 NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002269 2269 GSM1010735 Myers HudsonAlpha SL5494 v041610.1 1 exp MACS wgEncodeHaibTfbsSknshNrsfV0416101PkRep1 None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH NRSF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfPcr2xPkRep2 SKSH NRSF PCR2 2 NRSF SK-N-SH ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001547 1547 GSM803335 Myers HudsonAlpha SL409 PCR2x 2 exp MACS wgEncodeHaibTfbsSknshNrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment SK-N-SH NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfPcr2xPkRep1 SKSH NRSF PCR2 1 NRSF SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2010-08-06 2011-05-06 wgEncodeEH001547 1547 GSM803335 Myers HudsonAlpha SL83 PCR2x 1 exp MACS wgEncodeHaibTfbsSknshNrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment SK-N-SH NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNficsc81335V0422111PkRep2 SKSH NFIC V11 2 NFIC_(SC-81335) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEH003237 3237 GSM1010880 Myers HudsonAlpha SL14603 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshNficsc81335V0422111PkRep2 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH NFIC v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNficsc81335V0422111PkRep1 SKSH NFIC V11 1 NFIC_(SC-81335) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEH003237 3237 GSM1010880 Myers HudsonAlpha SL13313 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshNficsc81335V0422111PkRep1 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH NFIC v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMef2aV0422111PkRep2 SKSH MEF2A V11 2 MEF2A SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003298 3298 GSM1010834 Myers HudsonAlpha SL14704 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshMef2aV0422111PkRep2 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH MEF2A v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMef2aV0422111PkRep1 SKSH MEF2A V11 1 MEF2A SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003298 3298 GSM1010834 Myers HudsonAlpha SL13493 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshMef2aV0422111PkRep1 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH MEF2A v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMaxV0422111PkRep2 SKSH Max V11 2 Max SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003299 3299 GSM1010835 Myers HudsonAlpha SL16738 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshMaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMaxV0422111PkRep1 SKSH Max V11 1 Max SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003299 3299 GSM1010835 Myers HudsonAlpha SL14602 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshMaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshJundV0422111PkRep2 SKSH JunD V11 2 JunD SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003226 3226 GSM1010901 Myers HudsonAlpha SL14042 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshJundV0422111PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH JunD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshJundV0422111PkRep1 SKSH JunD V11 1 JunD SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003226 3226 GSM1010901 Myers HudsonAlpha SL13079 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshJundV0422111PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH JunD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGata3V0422111PkRep2 SKSH GATA3 V11 2 GATA3_(SC-268) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003249 3249 GSM1010738 Myers HudsonAlpha SL14041 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshGata3V0422111PkRep2 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH GATA3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGata3V0422111PkRep1 SKSH GATA3 V11 1 GATA3_(SC-268) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003249 3249 GSM1010738 Myers HudsonAlpha SL13078 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshGata3V0422111PkRep1 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH GATA3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGabpV0422111PkRep2 SKSH GABP V11 2 GABP SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003248 3248 GSM1010739 Myers HudsonAlpha SL13752 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshGabpV0422111PkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH GABP v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGabpV0422111PkRep1 SKSH GABP V11 1 GABP SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003248 3248 GSM1010739 Myers HudsonAlpha SL12627 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshGabpV0422111PkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH GABP v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFoxm1sc502V0422111PkRep2 SKSH FOXM1 V11 2 FOXM1_(SC-502) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003243 3243 GSM1010750 Myers HudsonAlpha SL14596 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshFoxm1sc502V0422111PkRep2 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH FOXM1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFoxm1sc502V0422111PkRep1 SKSH FOXM1 V11 1 FOXM1_(SC-502) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003243 3243 GSM1010750 Myers HudsonAlpha SL13083 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshFoxm1sc502V0422111PkRep1 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH FOXM1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFosl2V0422111PkRep2 SKSH FOSL2 V11 2 FOSL2 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003297 3297 GSM1010840 Myers HudsonAlpha SL16737 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshFosl2V0422111PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH FOSL2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFosl2V0422111PkRep1 SKSH FOSL2 V11 1 FOSL2 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003297 3297 GSM1010840 Myers HudsonAlpha SL13310 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshFosl2V0422111PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH FOSL2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshElf1V0422111PkRep2 SKSH ELF1 V11 2 ELF1_(SC-631) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003242 3242 GSM1010751 Myers HudsonAlpha SL14600 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshElf1V0422111PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH ELF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshElf1V0422111PkRep1 SKSH ELF1 V11 1 ELF1_(SC-631) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003242 3242 GSM1010751 Myers HudsonAlpha SL13309 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshElf1V0422111PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH ELF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tead4sc101184V0422111PkRep2 MCF-7 TEAD4 V11 2 TEAD4_(SC-101184) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003284 3284 GSM1010860 Myers HudsonAlpha SL16341 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tead4sc101184V0422111PkRep1 MCF-7 TEAD4 V11 1 TEAD4_(SC-101184) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003284 3284 GSM1010860 Myers HudsonAlpha SL14575 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep2 MCF-7 TCF12 V11 2 TCF12 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003283 3283 GSM1010861 Myers HudsonAlpha SL16340 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TCF12 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep1 MCF-7 TCF12 V11 1 TCF12 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003283 3283 GSM1010861 Myers HudsonAlpha SL14574 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TCF12 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Taf1V0422111PkRep2 MCF-7 TAF1 V11 2 TAF1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003317 3317 GSM1010811 Myers HudsonAlpha SL16339 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Taf1V0422111PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TAF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Taf1V0422111PkRep1 MCF-7 TAF1 V11 1 TAF1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003317 3317 GSM1010811 Myers HudsonAlpha SL14572 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Taf1V0422111PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TAF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7SrfV0422111PkRep2 MCF-7 SRF V11 2 SRF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003296 3296 GSM1010839 Myers HudsonAlpha SL16044 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7SrfV0422111PkRep2 None Peaks Serum response transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 SRF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7SrfV0422111PkRep1 MCF-7 SRF V11 1 SRF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003296 3296 GSM1010839 Myers HudsonAlpha SL13723 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7SrfV0422111PkRep1 None Peaks Serum response transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 SRF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep2 MCF-7 Sin3A V11 2 Sin3Ak-20 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003282 3282 GSM1010862 Myers HudsonAlpha SL14716 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Sin3Ak-20 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep1 MCF-7 Sin3A V11 1 Sin3Ak-20 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003282 3282 GSM1010862 Myers HudsonAlpha SL13726 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Sin3Ak-20 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Rad21V0422111PkRep2 MCF-7 RAD21 V11 2 Rad21 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003259 3259 GSM1010791 Myers HudsonAlpha SL16336 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Rad21V0422111PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 RAD21 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Rad21V0422111PkRep1 MCF-7 RAD21 V11 1 Rad21 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003259 3259 GSM1010791 Myers HudsonAlpha SL13724 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Rad21V0422111PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 RAD21 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Pmlsc71910V0422111PkRep2 MCF-7 PML V11 2 PML_(SC-71910) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003295 3295 GSM1010838 Myers HudsonAlpha SL16026 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Pmlsc71910V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 PML v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Pmlsc71910V0422111PkRep1 MCF-7 PML V11 1 PML_(SC-71910) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003295 3295 GSM1010838 Myers HudsonAlpha SL13722 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Pmlsc71910V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 PML v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7P300V0422111PkRep2 MCF-7 p300 V11 2 p300 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003260 3260 GSM1010800 Myers HudsonAlpha SL16335 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7P300V0422111PkRep2 None Peaks EP300(c-20) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 p300 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7P300V0422111PkRep1 MCF-7 p300 V11 1 p300 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003260 3260 GSM1010800 Myers HudsonAlpha SL13492 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7P300V0422111PkRep1 None Peaks EP300(c-20) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 p300 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7NrsfV0422111PkRep2 MCF-7 NRSF V11 2 NRSF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003231 3231 GSM1010891 Myers HudsonAlpha SL14698 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7NrsfV0422111PkRep1 MCF-7 NRSF V11 1 NRSF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003231 3231 GSM1010891 Myers HudsonAlpha SL13491 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111PkRep2 MCF-7 NR2F2 V11 2 NR2F2_(SC-271940) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003294 3294 GSM1010837 Myers HudsonAlpha SL14697 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111PkRep2 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 NR2F2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111PkRep1 MCF-7 NR2F2 V11 1 NR2F2_(SC-271940) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003294 3294 GSM1010837 Myers HudsonAlpha SL13490 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111PkRep1 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 NR2F2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7MaxV0422111PkRep2 MCF-7 Max V11 2 Max MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003281 3281 GSM1010863 Myers HudsonAlpha SL14695 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7MaxV0422111PkRep1 MCF-7 Max V11 1 Max MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003281 3281 GSM1010863 Myers HudsonAlpha SL13485 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7JundV0422111PkRep2 MCF-7 JunD V11 2 JunD MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003236 3236 GSM1010892 Myers HudsonAlpha SL14694 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7JundV0422111PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 JunD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7JundV0422111PkRep1 MCF-7 JunD V11 1 JunD MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003236 3236 GSM1010892 Myers HudsonAlpha SL13484 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7JundV0422111PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 JunD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep2 MCF-7 HDAC2 V11 2 HDAC2_(SC-6296) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003258 3258 GSM1010825 Myers HudsonAlpha SL16334 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep2 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 HDAC2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep1 MCF-7 HDAC2 V11 1 HDAC2_(SC-6296) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003258 3258 GSM1010825 Myers HudsonAlpha SL13483 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep1 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 HDAC2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Gata3V0422111PkRep2 MCF-7 GATA3 V11 2 GATA3_(SC-268) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003235 3235 GSM1010783 Myers HudsonAlpha SL14692 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Gata3V0422111PkRep2 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 GATA3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Gata3V0422111PkRep1 MCF-7 GATA3 V11 1 GATA3_(SC-268) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003235 3235 GSM1010783 Myers HudsonAlpha SL13482 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Gata3V0422111PkRep1 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 GATA3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7GabpV0422111PkRep2 MCF-7 GABP V11 2 GABP MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003280 3280 GSM1010864 Myers HudsonAlpha SL14683 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7GabpV0422111PkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 GABP v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7GabpV0422111PkRep1 MCF-7 GABP V11 1 GABP MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003280 3280 GSM1010864 Myers HudsonAlpha SL13459 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7GabpV0422111PkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 GABP v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Foxm1sc502V0422111PkRep2 MCF-7 FOXM1 V11 2 FOXM1_(SC-502) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003279 3279 GSM1010769 Myers HudsonAlpha SL14686 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Foxm1sc502V0422111PkRep2 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 FOXM1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Foxm1sc502V0422111PkRep1 MCF-7 FOXM1 V11 1 FOXM1_(SC-502) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003279 3279 GSM1010769 Myers HudsonAlpha SL13462 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Foxm1sc502V0422111PkRep1 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 FOXM1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Fosl2V0422111PkRep2 MCF-7 FOSL2 V11 2 FOSL2 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003278 3278 GSM1010768 Myers HudsonAlpha SL14682 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Fosl2V0422111PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 FOSL2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Fosl2V0422111PkRep1 MCF-7 FOSL2 V11 1 FOSL2 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003278 3278 GSM1010768 Myers HudsonAlpha SL13457 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Fosl2V0422111PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 FOSL2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Elf1V0422111PkRep2 MCF-7 ELF1 V11 2 ELF1_(SC-631) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003234 3234 GSM1010764 Myers HudsonAlpha SL14690 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Elf1V0422111PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 ELF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Elf1V0422111PkRep1 MCF-7 ELF1 V11 1 ELF1_(SC-631) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003234 3234 GSM1010764 Myers HudsonAlpha SL13466 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Elf1V0422111PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 ELF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Egr1V0422111PkRep2 MCF-7 Egr-1 V11 2 Egr-1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003293 3293 GSM1010844 Myers HudsonAlpha SL14689 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Egr1V0422111PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Egr-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Egr1V0422111PkRep1 MCF-7 Egr-1 V11 1 Egr-1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003293 3293 GSM1010844 Myers HudsonAlpha SL13465 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Egr1V0422111PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Egr-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep2 MCF-7 CTCF V11 2 CTCF_(SC-5916) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003257 3257 GSM1010734 Myers HudsonAlpha SL16333 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 CTCF 5916 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep1 MCF-7 CTCF V11 1 CTCF_(SC-5916) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003257 3257 GSM1010734 Myers HudsonAlpha SL13463 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep1 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 CTCF 5916 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep2 MCF-7 CEBPB V11 2 CEBPB_(SC-150) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003233 3233 GSM1010889 Myers HudsonAlpha SL14684 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep1 MCF-7 CEBPB V11 1 CEBPB_(SC-150) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003233 3233 GSM1010889 Myers HudsonAlpha SL13460 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep2 HUVEC Pol2-4H8 V101 2 Pol2-4H8 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002298 2298 GSM1010824 Myers HudsonAlpha SL2387 v041610.1 2 exp MACS wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HUVEC Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep1 HUVEC Pol2-4H8 V101 1 Pol2-4H8 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002298 2298 GSM1010824 Myers HudsonAlpha SL1104 v041610.1 1 exp MACS wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HUVEC Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep2 HUVEC Pol2 PCR1 2 Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002297 2297 GSM1010830 Myers HudsonAlpha SL6966 PCR1x 2 exp MACS wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep2 None Peaks RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HUVEC Pol2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep1 HUVEC Pol2 PCR1 1 Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002297 2297 GSM1010830 Myers HudsonAlpha SL1103 PCR1x 1 exp MACS wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep1 None Peaks RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HUVEC Pol2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep2 HepG ZEB1 V11 2 ZEB1_(SC-25388) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003315 3315 GSM1010809 Myers HudsonAlpha SL16318 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep2 None Peaks This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 ZEB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep1 HepG ZEB1 V11 1 ZEB1_(SC-25388) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003315 3315 GSM1010809 Myers HudsonAlpha SL13301 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep1 None Peaks This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 ZEB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep2 HepG ZBTB7A 2 ZBTB7A_(SC-34508) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002296 2296 GSM1010831 Myers HudsonAlpha SL6464 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep2 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB7A v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep1 HepG ZBTB7A 1 ZBTB7A_(SC-34508) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002296 2296 GSM1010831 Myers HudsonAlpha SL3973 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep1 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB7A v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep2 HepG ZBTB33 2 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001642 1642 GSM803418 Myers HudsonAlpha SL3987 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB33 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep1 HepG ZBTB33 1 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001642 1642 GSM803418 Myers HudsonAlpha SL3929 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB33 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep2 HepG ZBTB33 2 ZBTB33 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-17 2010-09-16 wgEncodeEH001503 1503 GSM803449 Myers HudsonAlpha SL1055 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB33 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep1 HepG ZBTB33 1 ZBTB33 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-17 2010-09-16 wgEncodeEH001503 1503 GSM803449 Myers HudsonAlpha SL981 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB33 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep2 HepG YY1 V101 2 YY1_(SC-281) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001661 1661 GSM803381 Myers HudsonAlpha SL3927 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 YY1 281 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep1 HepG YY1 V101 1 YY1_(SC-281) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001661 1661 GSM803381 Myers HudsonAlpha SL2195 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 YY1 281 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep2 HepG USF1 PCR1 2 USF-1 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001472 1472 GSM803527 Myers HudsonAlpha SL636 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 USF-1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep1 HepG USF1 PCR1 1 USF-1 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001472 1472 GSM803527 Myers HudsonAlpha SL582 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 USF-1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep2 HepG TEAD4 V11 2 TEAD4_(SC-101184) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002345 2345 GSM1010875 Myers HudsonAlpha SL9545 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep1 HepG TEAD4 V11 1 TEAD4_(SC-101184) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002345 2345 GSM1010875 Myers HudsonAlpha SL8584 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep2 HepG TCF12 PCR1 2 TCF12 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2011-03-07 wgEncodeEH001544 1544 GSM803336 Myers HudsonAlpha SL1167 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 TCF12 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep1 HepG TCF12 PCR1 1 TCF12 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001544 1544 GSM803336 Myers HudsonAlpha SL1060 PCR1x 1 exp wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 TCF12 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep2 HepG TAF1 PCR2 2 TAF1 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001551 1551 GSM803367 Myers HudsonAlpha SL359 PCR2x 2 exp MACS wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 TAF1 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep1 HepG TAF1 PCR2 1 TAF1 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001551 1551 GSM803367 Myers HudsonAlpha SL358 PCR2x 1 exp MACS wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 TAF1 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2SrfV0416101PkRep2 HepG SRF V101 2 SRF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001611 1611 GSM803502 Myers HudsonAlpha SL3275 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2SrfV0416101PkRep2 None Peaks Serum response transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 SRF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2SrfV0416101PkRep1 HepG SRF V101 1 SRF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001611 1611 GSM803502 Myers HudsonAlpha SL3156 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2SrfV0416101PkRep1 None Peaks Serum response transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 SRF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp2V0422111PkRep2 HepG SP2 V11 2 SP2_(SC-643) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002264 2264 GSM1010787 Myers HudsonAlpha SL6006 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Sp2V0422111PkRep2 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 SP2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp2V0422111PkRep1 HepG SP2 V11 1 SP2_(SC-643) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002264 2264 GSM1010787 Myers HudsonAlpha SL5688 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Sp2V0422111PkRep1 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 SP2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep2 HepG SP1 PCR1 2 SP1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-09-13 2011-06-13 wgEncodeEH001561 1561 GSM803507 Myers HudsonAlpha SL1194 PCR1x 2 exp wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 SP1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep1 HepG SP1 PCR1 1 SP1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-09-13 2011-06-13 wgEncodeEH001561 1561 GSM803507 Myers HudsonAlpha SL1056 PCR1x 1 exp wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 SP1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep2 HepG Sin3A PCR1 2 Sin3Ak-20 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001471 1471 GSM803530 Myers HudsonAlpha SL637 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 Sin3Ak-20 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep1 HepG Sin3A PCR1 1 Sin3Ak-20 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-07-17 2010-04-17 wgEncodeEH001471 1471 GSM803530 Myers HudsonAlpha SL583 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 Sin3Ak-20 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxraPcr1xPkRep2 HepG RXRA PCR1 2 RXRA HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-25 2010-09-25 wgEncodeEH001506 1506 GSM803452 Myers HudsonAlpha SL1054 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2RxraPcr1xPkRep2 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 RXRA PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxraPcr1xPkRep1 HepG RXRA PCR1 1 RXRA HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-25 2010-09-25 wgEncodeEH001506 1506 GSM803452 Myers HudsonAlpha SL984 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2RxraPcr1xPkRep1 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 RXRA PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Rad21V0416101PkRep2 HepG RAD21 V101 2 Rad21 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001608 1608 GSM803517 Myers HudsonAlpha SL3586 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Rad21V0416101PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 RAD21 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Rad21V0416101PkRep1 HepG RAD21 V101 1 Rad21 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001608 1608 GSM803517 Myers HudsonAlpha SL3179 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Rad21V0416101PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 RAD21 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep2 HepG Pol2-4H8 V102 2 Pol2-4H8 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002278 2278 GSM1010821 Myers HudsonAlpha SL5604 v041610.2 2 exp MACS wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep1 HepG Pol2-4H8 V102 1 Pol2-4H8 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002278 2278 GSM1010821 Myers HudsonAlpha SL1363 v041610.2 1 exp MACS wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep2 HepG Pol2 PCR2 2 Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001550 1550 GSM803368 Myers HudsonAlpha SL349 PCR2x 2 exp MACS wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep2 None Peaks RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 Pol2 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep1 HepG Pol2 PCR2 1 Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001550 1550 GSM803368 Myers HudsonAlpha SL348 PCR2x 1 exp MACS wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep1 None Peaks RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 Pol2 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2P300V0416101PkRep2 HepG p300 V101 2 p300 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001612 1612 GSM803499 Myers HudsonAlpha SL3644 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2P300V0416101PkRep2 None Peaks EP300(c-20) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 p300 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2P300V0416101PkRep1 HepG p300 V101 1 p300 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001612 1612 GSM803499 Myers HudsonAlpha SL3154 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2P300V0416101PkRep1 None Peaks EP300(c-20) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 p300 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfV0416101PkRep2 HepG NRSF V101 2 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002263 2263 GSM1010784 Myers HudsonAlpha SL5897 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2NrsfV0416101PkRep2 None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 NRSF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfV0416101PkRep1 HepG NRSF V101 1 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002263 2263 GSM1010784 Myers HudsonAlpha SL5040 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2NrsfV0416101PkRep1 None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 NRSF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep2 HepG NRSF PCR2 2 NRSF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001549 1549 GSM803344 Myers HudsonAlpha SL274 PCR2x 2 exp MACS wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep1 HepG NRSF PCR2 1 NRSF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001549 1549 GSM803344 Myers HudsonAlpha SL273 PCR2x 1 exp MACS wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep2 HepG NR2F2 V11 2 NR2F2_(SC-271940) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003314 3314 GSM1010810 Myers HudsonAlpha SL16316 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep2 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 NR2F2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep1 HepG NR2F2 V11 1 NR2F2_(SC-271940) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003314 3314 GSM1010810 Myers HudsonAlpha SL12644 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep1 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 NR2F2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep2 HepG NFIC V11 2 NFIC_(SC-81335) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002319 2319 GSM1010741 Myers HudsonAlpha SL7554 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep2 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 NFIC v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep1 HepG NFIC V11 1 NFIC_(SC-81335) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002319 2319 GSM1010741 Myers HudsonAlpha SL7102 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep1 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 NFIC v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep2 HepG MYBL2 V11 2 MYBL2_(SC-81192) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002344 2344 GSM1010876 Myers HudsonAlpha SL7564 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep2 None Peaks The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 MYBL2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep1 HepG MYBL2 V11 1 MYBL2_(SC-81192) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002344 2344 GSM1010876 Myers HudsonAlpha SL7101 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep1 None Peaks The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 MYBL2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep2 HepG MBD4 V11 2 MBD4_(SC-271530) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002318 2318 GSM1010740 Myers HudsonAlpha SL8132 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep2 None Peaks MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 MBD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep1 HepG MBD4 V11 1 MBD4_(SC-271530) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002318 2318 GSM1010740 Myers HudsonAlpha SL7901 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep1 None Peaks MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 MBD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2MaxV0422111PkRep2 HepG Max V11 2 Max HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003254 3254 GSM1010865 Myers HudsonAlpha SL13292 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2MaxV0422111PkRep1 HepG Max V11 1 Max HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003254 3254 GSM1010865 Myers HudsonAlpha SL12422 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2JundPcr1xPkRep2 HepG JunD PCR1 2 JunD HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001470 1470 GSM803500 Myers HudsonAlpha SL629 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2JundPcr1xPkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 JunD PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2JundPcr1xPkRep1 HepG JunD PCR1 1 JunD HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001470 1470 GSM803500 Myers HudsonAlpha SL635 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2JundPcr1xPkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 JunD PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep2 HepG HNF4G V101 2 HNF4G_(SC-6558) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001651 1651 GSM803404 Myers HudsonAlpha SL3463 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep2 None Peaks Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HNF4G v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep1 HepG HNF4G V101 1 HNF4G_(SC-6558) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001651 1651 GSM803404 Myers HudsonAlpha SL3178 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep1 None Peaks Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HNF4G v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep2 HepG HNF4A V101 2 HNF4A_(SC-8987) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001595 1595 GSM803460 Myers HudsonAlpha SL2125 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep2 None Peaks The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HNF4A v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep1 HepG HNF4A V101 1 HNF4A_(SC-8987) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001595 1595 GSM803460 Myers HudsonAlpha SL1481 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep1 None Peaks The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HNF4A v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep2 HepG HDAC2 V101 2 HDAC2_(SC-6296) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001618 1618 GSM803493 Myers HudsonAlpha SL3583 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep2 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HDAC2 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep1 HepG HDAC2 V101 1 HDAC2_(SC-6296) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001618 1618 GSM803493 Myers HudsonAlpha SL3177 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep1 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HDAC2 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2GabpPcr2xPkRep2 HepG GABP PCR2 2 GABP HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001548 1548 GSM803343 Myers HudsonAlpha SL276 PCR2x 2 exp MACS wgEncodeHaibTfbsHepg2GabpPcr2xPkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 GABP PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2GabpPcr2xPkRep1 HepG GABP PCR2 1 GABP HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001548 1548 GSM803343 Myers HudsonAlpha SL275 PCR2x 1 exp MACS wgEncodeHaibTfbsHepg2GabpPcr2xPkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 GABP PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep2 HepG FOXA2 V101 2 FOXA2_(SC-6554) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001650 1650 GSM803403 Myers HudsonAlpha SL3175 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep2 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA2 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep1 HepG FOXA2 V101 1 FOXA2_(SC-6554) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001650 1650 GSM803403 Myers HudsonAlpha SL2196 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep1 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA2 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep2 HepG FOXA1 V101 2 FOXA1_(SC-6553) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001594 1594 GSM803461 Myers HudsonAlpha SL2124 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep2 None Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA1 6553 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep1 HepG FOXA1 V101 1 FOXA1_(SC-6553) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001594 1594 GSM803461 Myers HudsonAlpha SL1786 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep1 None Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA1 6553 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep2 HepG FOXA1 V101 2 FOXA1_(SC-101058) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001630 1630 GSM803432 Myers HudsonAlpha SL2194 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep2 None Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA1 101058 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep1 HepG FOXA1 V101 1 FOXA1_(SC-101058) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001630 1630 GSM803432 Myers HudsonAlpha SL1788 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep1 None Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA1 101058 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep2 HepG FOSL2 V101 2 FOSL2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH001501 1501 GSM803451 Myers HudsonAlpha SL1107 hg18 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOSL2 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep1 HepG FOSL2 V101 1 FOSL2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-22 2010-09-22 wgEncodeEH001501 1501 GSM803451 Myers HudsonAlpha SL632 hg18 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOSL2 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep2 HepG ELF1 V101 2 ELF1_(SC-631) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001641 1641 GSM803415 Myers HudsonAlpha SL3986 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ELF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep1 HepG ELF1 V101 1 ELF1_(SC-631) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001641 1641 GSM803415 Myers HudsonAlpha SL3645 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ELF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep2 HepG CTCF V101 2 CTCF_(SC-5916) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2010-01-06 2010-10-06 wgEncodeEH001516 1516 GSM803486 Myers HudsonAlpha SL3582 v041610.1 2 exp wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CTCF 5916 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep1 HepG CTCF V101 1 CTCF_(SC-5916) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2010-01-06 2010-10-06 wgEncodeEH001516 1516 GSM803486 Myers HudsonAlpha SL3176 v041610.1 1 exp wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep1 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CTCF 5916 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep2 HepG CREB1 V11 2 CREB1_(SC-240) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003312 3312 GSM1010808 Myers HudsonAlpha SL13290 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep1 HepG CREB1 V11 1 CREB1_(SC-240) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003312 3312 GSM1010808 Myers HudsonAlpha SL12405 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep2 HepG CEBPD V101 2 CEBPD_(SC-636) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002305 2305 GSM1010777 Myers HudsonAlpha SL4940 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep2 None Peaks The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CEBPD v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep1 HepG CEBPD V101 1 CEBPD_(SC-636) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002305 2305 GSM1010777 Myers HudsonAlpha SL4210 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep1 None Peaks The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CEBPD v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep2 HepG CEBPB V101 2 CEBPB_(SC-150) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002304 2304 GSM1010778 Myers HudsonAlpha SL4939 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CEBPB v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep1 HepG CEBPB V101 1 CEBPB_(SC-150) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002304 2304 GSM1010778 Myers HudsonAlpha SL4209 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CEBPB v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep2 HepG BHLHE40 2 BHLHE40 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001515 1515 GSM803483 Myers HudsonAlpha SL3460 v041610.1 2 exp wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep2 None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 BHLHE40 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep1 HepG BHLHE40 1 BHLHE40 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH001515 1515 GSM803483 Myers HudsonAlpha SL1059 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep1 None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 BHLHE40 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Atf3V0416101PkRep2 HepG ATF3 V101 2 ATF3 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001568 1568 GSM803503 Myers HudsonAlpha SL1787 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Atf3V0416101PkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ATF3 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Atf3V0416101PkRep1 HepG ATF3 V101 1 ATF3 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001568 1568 GSM803503 Myers HudsonAlpha SL2386 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Atf3V0416101PkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ATF3 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep2 HeLa TAF1 PCR1 2 TAF1 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-18 2010-09-18 wgEncodeEH001505 1505 GSM803455 Myers HudsonAlpha SL706 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 TAF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep1 HeLa TAF1 PCR1 1 TAF1 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-18 2010-09-18 wgEncodeEH001505 1505 GSM803455 Myers HudsonAlpha SL590 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 TAF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep2 HeLa Pol2 PCR1 2 Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2009-07-19 2010-04-19 wgEncodeEH001474 1474 GSM803533 Myers HudsonAlpha SL672 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep2 None Peaks RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 Pol2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep1 HeLa Pol2 PCR1 1 Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-19 2010-04-19 wgEncodeEH001474 1474 GSM803533 Myers HudsonAlpha SL631 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep1 None Peaks RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 Pol2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep2 HeLa NRSF PCR1 2 NRSF HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001629 1629 GSM803478 Myers HudsonAlpha SL1322 PCR1x 2 exp wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep2 None Peaks Neuron-restrictive silencer transcription factor cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 NRSF PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep1 HeLa NRSF PCR1 1 NRSF HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001629 1629 GSM803478 Myers HudsonAlpha SL679 PCR1x 1 exp MACS wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep1 None Peaks Neuron-restrictive silencer transcription factor cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 NRSF PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3GabpPcr1xPkRep2 HeLa GABP PCR1 2 GABP HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-18 2010-09-18 wgEncodeEH001504 1504 GSM803454 Myers HudsonAlpha SL611 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHelas3GabpPcr1xPkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 GABP PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3GabpPcr1xPkRep1 HeLa GABP PCR1 1 GABP HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-18 2010-09-18 wgEncodeEH001504 1504 GSM803454 Myers HudsonAlpha SL610 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHelas3GabpPcr1xPkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 GABP PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep2 H1-neu TAF1 2 TAF1 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003266 3266 GSM1010805 Myers HudsonAlpha SL14594 v042211.1 2 exp MACS wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons TAF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep1 H1-neu TAF1 1 TAF1 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003266 3266 GSM1010805 Myers HudsonAlpha SL13300 v042211.1 1 exp MACS wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons TAF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep2 H1-neu Pol2-4H8 2 Pol2-4H8 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003265 3265 GSM1010803 Myers HudsonAlpha SL14592 v042211.1 2 exp MACS wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons Pol2-4H8 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep1 H1-neu Pol2-4H8 1 Pol2-4H8 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003265 3265 GSM1010803 Myers HudsonAlpha SL13298 v042211.1 1 exp MACS wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons Pol2-4H8 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep2 H1-neu NRSF V11 2 NRSF H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003264 3264 GSM1010804 Myers HudsonAlpha SL14593 v042211.1 2 exp MACS wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep1 H1-neu NRSF V11 1 NRSF H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003264 3264 GSM1010804 Myers HudsonAlpha SL13299 v042211.1 1 exp MACS wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02PkRep2 A549 ZBTB33 ETH 2 ZBTB33 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002295 2295 GSM1010832 Myers HudsonAlpha SL6592 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02PkRep2 EtOH_0.02pct Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ZBTB33 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02PkRep1 A549 ZBTB33 ETH 1 ZBTB33 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002295 2295 GSM1010832 Myers HudsonAlpha SL6016 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02PkRep1 EtOH_0.02pct Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ZBTB33 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Yy1cV0422111Etoh02PkRep2 A549 YY1 EtOH 2 YY1_(SC-281) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002282 2282 GSM1010794 Myers HudsonAlpha SL5699 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Yy1cV0422111Etoh02PkRep2 EtOH_0.02pct Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 YY1 281 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Yy1cV0422111Etoh02PkRep1 A549 YY1 EtOH 1 YY1_(SC-281) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002282 2282 GSM1010794 Myers HudsonAlpha SL5357 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Yy1cV0422111Etoh02PkRep1 EtOH_0.02pct Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 YY1 281 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1V0422111Etoh02PkRep2 A549 USF Et V11 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002291 2291 GSM1010828 Myers HudsonAlpha SL7279 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Usf1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 USF-1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1V0422111Etoh02PkRep1 A549 USF Et V11 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002291 2291 GSM1010828 Myers HudsonAlpha SL6593 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Usf1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 USF-1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02PkRep2 A549 USF1 Et P1 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001539 1539 GSM803429 Myers HudsonAlpha SL1207 PCR1x 2 exp wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02PkRep2 EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 USF-1 EtOH PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02PkRep1 A549 USF1 Et P1 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001539 1539 GSM803429 Myers HudsonAlpha SL1080 PCR1x 1 exp wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02PkRep1 EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 USF-1 EtOH PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmPkRep2 A549 USF1 DEX 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001509 1509 GSM803457 Myers HudsonAlpha SL1206 PCR1x 2 exp wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmPkRep2 DEX_100nM Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 USF-1 DEX 100nM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmPkRep1 A549 USF1 DEX 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001509 1509 GSM803457 Myers HudsonAlpha SL1079 PCR1x 1 exp wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmPkRep1 DEX_100nM Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 USF-1 DEX 100nM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep2 A549 TEAD4 V11 2 TEAD4_(SC-101184) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003273 3273 GSM1010868 Myers HudsonAlpha SL14702 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep1 A549 TEAD4 V11 1 TEAD4_(SC-101184) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003273 3273 GSM1010868 Myers HudsonAlpha SL13479 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tcf12V0422111Etoh02PkRep2 A549 TCF12 EtOH 2 TCF12 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002312 2312 GSM1010746 Myers HudsonAlpha SL8076 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Tcf12V0422111Etoh02PkRep2 EtOH_0.02pct Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 TCF12 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tcf12V0422111Etoh02PkRep1 A549 TCF12 EtOH 1 TCF12 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002312 2312 GSM1010746 Myers HudsonAlpha SL7114 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Tcf12V0422111Etoh02PkRep1 EtOH_0.02pct Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 TCF12 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Taf1V0422111Etoh02PkRep2 A549 TAF1 EtOH 2 TAF1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002275 2275 GSM1010812 Myers HudsonAlpha SL5700 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Taf1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 TAF1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Taf1V0422111Etoh02PkRep1 A549 TAF1 EtOH 1 TAF1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002275 2275 GSM1010812 Myers HudsonAlpha SL5358 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Taf1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 TAF1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sp1V0422111Etoh02PkRep2 A549 SP1 EtOH 2 SP1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002274 2274 GSM1010813 Myers HudsonAlpha SL5701 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Sp1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 SP1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sp1V0422111Etoh02PkRep1 A549 SP1 EtOH 1 SP1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002274 2274 GSM1010813 Myers HudsonAlpha SL5360 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Sp1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 SP1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Six5V0422111Etoh02PkRep2 A549 SIX5 EtOH 2 SIX5 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002341 2341 GSM1010879 Myers HudsonAlpha SL8400 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Six5V0422111Etoh02PkRep2 EtOH_0.02pct Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 SIX5 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Six5V0422111Etoh02PkRep1 A549 SIX5 EtOH 1 SIX5 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002341 2341 GSM1010879 Myers HudsonAlpha SL7277 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Six5V0422111Etoh02PkRep1 EtOH_0.02pct Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 SIX5 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02PkRep2 A549 Sin3A EtOH 2 Sin3Ak-20 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002342 2342 GSM1010882 Myers HudsonAlpha SL8401 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02PkRep2 EtOH_0.02pct Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 Sin3Ak-20 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02PkRep1 A549 Sin3A EtOH 1 Sin3Ak-20 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002342 2342 GSM1010882 Myers HudsonAlpha SL7275 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02PkRep1 EtOH_0.02pct Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 Sin3Ak-20 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Rad21V0422111PkRep2 A549 RAD21 V11 2 Rad21 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003272 3272 GSM1010761 Myers HudsonAlpha SL16300 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Rad21V0422111PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 RAD21 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Rad21V0422111PkRep1 A549 RAD21 V11 1 Rad21 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003272 3272 GSM1010761 Myers HudsonAlpha SL12634 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Rad21V0422111PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 RAD21 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02PkRep2 A549 Pol2 EtOH 2 Pol2 A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-15 2011-03-22 wgEncodeEH001493 1493 GSM803360 Myers HudsonAlpha SL334 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02PkRep2 EtOH_0.02pct Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 Pol2 EtOH PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02PkRep1 A549 Pol2 EtOH 1 Pol2 A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-15 2011-03-22 wgEncodeEH001493 1493 GSM803360 Myers HudsonAlpha SL245 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02PkRep1 EtOH_0.02pct Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 Pol2 EtOH PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmPkRep2 A549 Pol2 DEX 2 Pol2 A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-17 2011-03-22 wgEncodeEH001494 1494 GSM803361 Myers HudsonAlpha SL306 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmPkRep2 DEX_100nM Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 Pol2 DEX 100nM PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmPkRep1 A549 Pol2 DEX 1 Pol2 A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-17 2011-03-22 wgEncodeEH001494 1494 GSM803361 Myers HudsonAlpha SL244 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmPkRep1 DEX_100nM Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 Pol2 DEX 100nM PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pbx3V0422111PkRep2 A549 PBx3 V11 2 Pbx3 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003255 3255 GSM1010755 Myers HudsonAlpha SL16043 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Pbx3V0422111PkRep2 None Peaks Pbx 3 (D-17) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 PBx3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pbx3V0422111PkRep1 A549 PBx3 V11 1 Pbx3 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003255 3255 GSM1010755 Myers HudsonAlpha SL13476 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Pbx3V0422111PkRep1 None Peaks Pbx 3 (D-17) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 PBx3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549P300V0422111Etoh02PkRep2 A549 p300 EtOH 2 p300 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002292 2292 GSM1010827 Myers HudsonAlpha SL7115 v042211.1 2 exp MACS wgEncodeHaibTfbsA549P300V0422111Etoh02PkRep2 EtOH_0.02pct Peaks EP300(c-20) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 p300 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549P300V0422111Etoh02PkRep1 A549 p300 EtOH 1 p300 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002292 2292 GSM1010827 Myers HudsonAlpha SL6437 v042211.1 1 exp MACS wgEncodeHaibTfbsA549P300V0422111Etoh02PkRep1 EtOH_0.02pct Peaks EP300(c-20) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 p300 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549NrsfV0422111Etoh02PkRep2 A549 NRSF EtOH 2 NRSF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002311 2311 GSM1010749 Myers HudsonAlpha SL8075 v042211.1 2 exp MACS wgEncodeHaibTfbsA549NrsfV0422111Etoh02PkRep2 EtOH_0.02pct Peaks Neuron-restrictive silencer transcription factor epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 NRSF EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549NrsfV0422111Etoh02PkRep1 A549 NRSF EtOH 1 NRSF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002311 2311 GSM1010749 Myers HudsonAlpha SL7110 v042211.1 1 exp MACS wgEncodeHaibTfbsA549NrsfV0422111Etoh02PkRep1 EtOH_0.02pct Peaks Neuron-restrictive silencer transcription factor epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 NRSF EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549MaxV0422111PkRep2 A549 Max V11 2 Max A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003251 3251 GSM1010728 Myers HudsonAlpha SL13754 v042211.1 2 exp MACS wgEncodeHaibTfbsA549MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549MaxV0422111PkRep1 A549 Max V11 1 Max A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003251 3251 GSM1010728 Myers HudsonAlpha SL12638 v042211.1 1 exp MACS wgEncodeHaibTfbsA549MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549JundV0416102Etoh02PkRep2 A549 JunD EtOH 2 JunD A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-29 2013-05-29 wgEncodeEH002327 2327 GSM1010723 Myers HudsonAlpha SL4698 v041610.2 2 exp MACS wgEncodeHaibTfbsA549JundV0416102Etoh02PkRep2 EtOH_0.02pct Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 JunD EtOH 0.02pct v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549JundV0416102Etoh02PkRep1 A549 JunD EtOH 1 JunD A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-29 2013-05-29 wgEncodeEH002327 2327 GSM1010723 Myers HudsonAlpha SL3900 v041610.2 1 exp MACS wgEncodeHaibTfbsA549JundV0416102Etoh02PkRep1 EtOH_0.02pct Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 JunD EtOH 0.02pct v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex5nmPkRep2 A549 GR DX5nM 2 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-09 2011-03-16 wgEncodeEH001492 1492 GSM803359 Myers HudsonAlpha SL881 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex5nmPkRep2 DEX_5nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 5 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 5nM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex5nmPkRep1 A549 GR DX5nM 1 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001492 1492 GSM803359 Myers HudsonAlpha SL880 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex5nmPkRep1 DEX_5nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 5 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 5nM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex50nmPkRep2 A549 GR DX50nM 2 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001491 1491 GSM803358 Myers HudsonAlpha SL883 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex50nmPkRep2 DEX_50nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 50 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 50nM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex50nmPkRep1 A549 GR DX50nM 1 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001491 1491 GSM803358 Myers HudsonAlpha SL882 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex50nmPkRep1 DEX_50nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 50 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 50nM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex500pmPkRep2 A549 GR DX.5nM 2 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001490 1490 GSM803357 Myers HudsonAlpha SL885 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex500pmPkRep2 DEX_500pM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 500 pM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 500pM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex500pmPkRep1 A549 GR DX.5nM 1 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001490 1490 GSM803357 Myers HudsonAlpha SL884 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex500pmPkRep1 DEX_500pM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 500 pM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 500pM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xDex100nmPkRep2 A549 GR DX100nM 2 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-22 wgEncodeEH001555 1555 GSM803371 Myers HudsonAlpha SL304 hg19 PCR2x 2 exp MACS wgEncodeHaibTfbsA549GrPcr2xDex100nmPkRep2 DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 100nM PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xDex100nmPkRep1 A549 GR DX100nM 1 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-22 wgEncodeEH001555 1555 GSM803371 Myers HudsonAlpha SL246 hg19 PCR2x 1 exp MACS wgEncodeHaibTfbsA549GrPcr2xDex100nmPkRep1 DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 100nM PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Gata3V0422111PkRep2 A549 GATA3 V11 2 GATA3_(SC-268) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003250 3250 GSM1010727 Myers HudsonAlpha SL13283 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Gata3V0422111PkRep2 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 GATA3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Gata3V0422111PkRep1 A549 GATA3 V11 1 GATA3_(SC-268) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003250 3250 GSM1010727 Myers HudsonAlpha SL12399 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Gata3V0422111PkRep1 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 GATA3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GabpV0422111Etoh02PkRep2 A549 GABP EtOH 2 GABP A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002294 2294 GSM1010833 Myers HudsonAlpha SL6595 v042211.1 2 exp MACS wgEncodeHaibTfbsA549GabpV0422111Etoh02PkRep2 EtOH_0.02pct Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 GABP EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GabpV0422111Etoh02PkRep1 A549 GABP EtOH 1 GABP A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002294 2294 GSM1010833 Myers HudsonAlpha SL6015 v042211.1 1 exp MACS wgEncodeHaibTfbsA549GabpV0422111Etoh02PkRep1 EtOH_0.02pct Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 GABP EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa2V0416102Etoh02PkRep2 A549 FOXA2 EtOH 2 FOXA2_(SC-6554) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-29 2013-05-29 wgEncodeEH002326 2326 GSM1010724 Myers HudsonAlpha SL3253 v041610.2 2 exp MACS wgEncodeHaibTfbsA549Foxa2V0416102Etoh02PkRep2 EtOH_0.02pct Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 FOXA2 EtOH v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa2V0416102Etoh02PkRep1 A549 FOXA2 EtOH 1 FOXA2_(SC-6554) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-29 2013-05-29 wgEncodeEH002326 2326 GSM1010724 Myers HudsonAlpha SL3077 v041610.2 1 exp MACS wgEncodeHaibTfbsA549Foxa2V0416102Etoh02PkRep1 EtOH_0.02pct Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 FOXA2 EtOH v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmPkRep2 A549 FOXA1 DEX 2 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002293 2293 GSM1010826 Myers HudsonAlpha SL3250 v041610.2 2 exp MACS wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmPkRep2 DEX_100nM Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 FOXA1 101058 DEX 100nM v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmPkRep1 A549 FOXA1 DEX 1 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002293 2293 GSM1010826 Myers HudsonAlpha SL2666 v041610.2 1 exp MACS wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmPkRep1 DEX_100nM Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 FOXA1 101058 DEX 100nM v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Fosl2V0422111Etoh02PkRep2 A549 FOSL2 EtOH 2 FOSL2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002310 2310 GSM1010748 Myers HudsonAlpha SL8077 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Fosl2V0422111Etoh02PkRep2 EtOH_0.02pct Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 FOSL2 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Fosl2V0422111Etoh02PkRep1 A549 FOSL2 EtOH 1 FOSL2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002310 2310 GSM1010748 Myers HudsonAlpha SL7116 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Fosl2V0422111Etoh02PkRep1 EtOH_0.02pct Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 FOSL2 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ets1V0422111Etoh02PkRep2 A549 ETS1 EtOH 2 ETS1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002290 2290 GSM1010829 Myers HudsonAlpha SL7108 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Ets1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ETS1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ets1V0422111Etoh02PkRep1 A549 ETS1 EtOH 1 ETS1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002290 2290 GSM1010829 Myers HudsonAlpha SL6600 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Ets1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ETS1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Elf1V0422111Etoh02PkRep2 A549 ELF1 EtOH 2 ELF1_(SC-631) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002289 2289 GSM1010790 Myers HudsonAlpha SL7113 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Elf1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ELF1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Elf1V0422111Etoh02PkRep1 A549 ELF1 EtOH 1 ELF1_(SC-631) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002289 2289 GSM1010790 Myers HudsonAlpha SL6436 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Elf1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ELF1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549E2f6V0422111PkRep2 A549 E2F6 V11 2 E2F6 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003244 3244 GSM1010766 Myers HudsonAlpha SL14581 v042211.1 2 exp MACS wgEncodeHaibTfbsA549E2f6V0422111PkRep2 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 E2F6 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549E2f6V0422111PkRep1 A549 E2F6 V11 1 E2F6 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003244 3244 GSM1010766 Myers HudsonAlpha SL13319 v042211.1 1 exp MACS wgEncodeHaibTfbsA549E2f6V0422111PkRep1 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 E2F6 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02PkRep2 A549 CTCF EtOH 2 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001508 1508 GSM803456 Myers HudsonAlpha SL1078 PCR1x 2 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02PkRep2 EtOH_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 CTCF 5916 EtOH PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02PkRep1 A549 CTCF EtOH 1 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001508 1508 GSM803456 Myers HudsonAlpha SL1205 PCR1x 1 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02PkRep1 EtOH_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 CTCF 5916 EtOH PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmPkRep2 A549 CTCF DEX 2 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001507 1507 GSM803453 Myers HudsonAlpha SL1077 PCR1x 2 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmPkRep2 DEX_100nM Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 CTCF 5916 DEX 100nM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmPkRep1 A549 CTCF DEX 1 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001507 1507 GSM803453 Myers HudsonAlpha SL1204 PCR1x 1 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmPkRep1 DEX_100nM Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 CTCF 5916 DEX 100nM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmPkRep2 A549 CREB1 DEX 2 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002323 2323 GSM1010719 Myers HudsonAlpha SL3897 v041610.2 2 exp MACS wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmPkRep2 DEX_100nM Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 CREB1 DEX 100nM v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmPkRep1 A549 CREB1 DEX 1 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002323 2323 GSM1010719 Myers HudsonAlpha SL1667 v041610.2 1 exp MACS wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmPkRep1 DEX_100nM Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 CREB1 DEX 100nM v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Cebpbsc150V0422111PkRep2 A549 CEBPB V11 2 CEBPB_(SC-150) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003271 3271 GSM1010871 Myers HudsonAlpha SL16299 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Cebpbsc150V0422111PkRep1 A549 CEBPB V11 1 CEBPB_(SC-150) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003271 3271 GSM1010871 Myers HudsonAlpha SL12637 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Bcl3V0422111Etoh02PkRep2 A549 BCL3 EtOH 2 BCL3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002303 2303 GSM1010775 Myers HudsonAlpha SL7109 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Bcl3V0422111Etoh02PkRep2 EtOH_0.02pct Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 BCL3 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Bcl3V0422111Etoh02PkRep1 A549 BCL3 EtOH 1 BCL3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002303 2303 GSM1010775 Myers HudsonAlpha SL6596 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Bcl3V0422111Etoh02PkRep1 EtOH_0.02pct Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 BCL3 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Atf3V0422111Etoh02PkRep2 A549 ATF3 EtOH 2 ATF3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002288 2288 GSM1010789 Myers HudsonAlpha SL7273 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Atf3V0422111Etoh02PkRep2 EtOH_0.02pct Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ATF3 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Atf3V0422111Etoh02PkRep1 A549 ATF3 EtOH 1 ATF3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002288 2288 GSM1010789 Myers HudsonAlpha SL6010 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Atf3V0422111Etoh02PkRep1 EtOH_0.02pct Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ATF3 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep2 K562 ZBTB7A 2 ZBTB7A_(SC-34508) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001620 1620 GSM803473 Myers HudsonAlpha SL3183 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep2 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ZBTB7A v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep1 K562 ZBTB7A 1 ZBTB7A_(SC-34508) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001620 1620 GSM803473 Myers HudsonAlpha SL2265 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep1 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ZBTB7A v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep2 K562 ZBTB33 2 ZBTB33 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-16 2011-06-16 wgEncodeEH001569 1569 GSM803504 Myers HudsonAlpha SL1320 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ZBTB33 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep1 K562 ZBTB33 1 ZBTB33 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-16 2011-06-16 wgEncodeEH001569 1569 GSM803504 Myers HudsonAlpha SL1114 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ZBTB33 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep2 K562 YY1 V101 2 YY1_(SC-281) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEH001584 1584 GSM803446 Myers HudsonAlpha SL2944 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 YY1 281 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep1 K562 YY1 V101 1 YY1_(SC-281) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEH001584 1584 GSM803446 Myers HudsonAlpha SL2203 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 YY1 281 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1V0416102PkRep2 K562 YY1 V102 2 YY1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001623 1623 GSM803470 Myers HudsonAlpha SL3071 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Yy1V0416102PkRep2 None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 YY1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1V0416102PkRep1 K562 YY1 V102 1 YY1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001623 1623 GSM803470 Myers HudsonAlpha SL2946 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Yy1V0416102PkRep1 None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 YY1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Usf1V0416101PkRep2 K562 USF1 V101 2 USF-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001583 1583 GSM803441 Myers HudsonAlpha SL3166 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Usf1V0416101PkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 USF-1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Usf1V0416101PkRep1 K562 USF1 V101 1 USF-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001583 1583 GSM803441 Myers HudsonAlpha SL3163 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Usf1V0416101PkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 USF-1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep2 K562 TRIM28 V11 2 TRIM28_(SC-81411) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH003210 3210 GSM1010849 Myers HudsonAlpha SL9830 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep2 None Peaks The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 TRIM28 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep1 K562 TRIM28 V11 1 TRIM28_(SC-81411) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH003210 3210 GSM1010849 Myers HudsonAlpha SL8672 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep1 None Peaks The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 TRIM28 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep2 K562 THAP1 V101 2 THAP1_(SC-98174) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001655 1655 GSM803408 Myers HudsonAlpha SL3186 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep2 None Peaks The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 THAP1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep1 K562 THAP1 V101 1 THAP1_(SC-98174) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001655 1655 GSM803408 Myers HudsonAlpha SL2202 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep1 None Peaks The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 THAP1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep2 K562 TEAD4 V11 2 TEAD4_(SC-101184) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002333 2333 GSM1010895 Myers HudsonAlpha SL7841 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep1 K562 TEAD4 V11 1 TEAD4_(SC-101184) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002333 2333 GSM1010895 Myers HudsonAlpha SL7571 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep2 K562 TAF7 V101 2 TAF7_(SC-101167) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001654 1654 GSM803407 Myers HudsonAlpha SL3568 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep2 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 TAF7 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep1 K562 TAF7 V101 1 TAF7_(SC-101167) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001654 1654 GSM803407 Myers HudsonAlpha SL3274 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep1 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 TAF7 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf1V0416101PkRep2 K562 TAF1 V101 2 TAF1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001582 1582 GSM803431 Myers HudsonAlpha SL2942 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Taf1V0416101PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 TAF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf1V0416101PkRep1 K562 TAF1 V101 1 TAF1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001582 1582 GSM803431 Myers HudsonAlpha SL2941 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Taf1V0416101PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 TAF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Stat5asc74442V0422111PkRep2 K562 STAT5A V11 2 STAT5A_(SC-74442) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002347 2347 GSM1010877 Myers HudsonAlpha SL9116 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Stat5asc74442V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 STAT5A v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Stat5asc74442V0422111PkRep1 K562 STAT5A V11 1 STAT5A_(SC-74442) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002347 2347 GSM1010877 Myers HudsonAlpha SL8673 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Stat5asc74442V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 STAT5A v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562SrfV0416101PkRep2 K562 SRF V101 2 SRF K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001600 1600 GSM803520 Myers HudsonAlpha SL3272 v041610.1 2 exp MACS wgEncodeHaibTfbsK562SrfV0416101PkRep2 None Peaks Serum response transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SRF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562SrfV0416101PkRep1 K562 SRF V101 1 SRF K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001600 1600 GSM803520 Myers HudsonAlpha SL3162 v041610.1 1 exp MACS wgEncodeHaibTfbsK562SrfV0416101PkRep1 None Peaks Serum response transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SRF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp2sc643V0416102PkRep2 K562 SP2 V102 2 SP2_(SC-643) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001653 1653 GSM803402 Myers HudsonAlpha SL3361 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Sp2sc643V0416102PkRep2 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SP2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp2sc643V0416102PkRep1 K562 SP2 V102 1 SP2_(SC-643) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001653 1653 GSM803402 Myers HudsonAlpha SL2951 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Sp2sc643V0416102PkRep1 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SP2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp1Pcr1xPkRep2 K562 SP1 PCR1 2 SP1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH001578 1578 GSM803505 Myers HudsonAlpha SL1510 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Sp1Pcr1xPkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SP1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp1Pcr1xPkRep1 K562 SP1 PCR1 1 SP1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH001578 1578 GSM803505 Myers HudsonAlpha SL1197 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Sp1Pcr1xPkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SP1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5V0416101PkRep2 K562 SIX5 V101 2 SIX5 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001664 1664 GSM803378 Myers HudsonAlpha SL3990 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Six5V0416101PkRep2 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SIX5 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5V0416101PkRep1 K562 SIX5 V101 1 SIX5 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001664 1664 GSM803378 Myers HudsonAlpha SL3924 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Six5V0416101PkRep1 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SIX5 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5Pcr1xPkRep2 K562 SIX5 PCR1 2 SIX5 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001483 1483 GSM803383 Myers HudsonAlpha SL986 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Six5Pcr1xPkRep2 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SIX5 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5Pcr1xPkRep1 K562 SIX5 PCR1 1 SIX5 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-26 2010-07-26 wgEncodeEH001483 1483 GSM803383 Myers HudsonAlpha SL842 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Six5Pcr1xPkRep1 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SIX5 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sin3ak20V0416101PkRep2 K562 Sin3A V101 2 Sin3Ak-20 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-03 2011-09-03 wgEncodeEH001607 1607 GSM803525 Myers HudsonAlpha SL3496 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Sin3ak20V0416101PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sin3ak20V0416101PkRep1 K562 Sin3A V101 1 Sin3Ak-20 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-03 2011-09-03 wgEncodeEH001607 1607 GSM803525 Myers HudsonAlpha SL3273 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Sin3ak20V0416101PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Rad21V0416102PkRep2 K562 RAD21 V102 2 Rad21 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH001585 1585 GSM803447 Myers HudsonAlpha SL3072 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Rad21V0416102PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 RAD21 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Rad21V0416102PkRep1 K562 RAD21 V102 1 Rad21 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH001585 1585 GSM803447 Myers HudsonAlpha SL2947 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Rad21V0416102PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 RAD21 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pu1Pcr1xPkRep2 K562 PU.1 PCR1 2 PU.1 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001482 1482 GSM803384 Myers HudsonAlpha SL705 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Pu1Pcr1xPkRep2 None Peaks PU.1 (H-135) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 PU.1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pu1Pcr1xPkRep1 K562 PU.1 PCR1 1 PU.1 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001482 1482 GSM803384 Myers HudsonAlpha SL646 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Pu1Pcr1xPkRep1 None Peaks PU.1 (H-135) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 PU.1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol24h8V0416101PkRep2 K562 Pol2-4H8 V101 2 Pol2-4H8 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001581 1581 GSM803443 Myers HudsonAlpha SL2940 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Pol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol24h8V0416101PkRep1 K562 Pol2-4H8 V101 1 Pol2-4H8 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001581 1581 GSM803443 Myers HudsonAlpha SL2939 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Pol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol2V0416101PkRep2 K562 Pol2 V101 2 Pol2 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001633 1633 GSM803410 Myers HudsonAlpha SL3820 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Pol2V0416101PkRep2 None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Pol2 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol2V0416101PkRep1 K562 Pol2 V101 1 Pol2 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001633 1633 GSM803410 Myers HudsonAlpha SL3819 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Pol2V0416101PkRep1 None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Pol2 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pmlsc71910V0422111PkRep2 K562 PML V11 2 PML_(SC-71910) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002320 2320 GSM1010722 Myers HudsonAlpha SL8137 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Pmlsc71910V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 PML v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pmlsc71910V0422111PkRep1 K562 PML V11 1 PML_(SC-71910) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002320 2320 GSM1010722 Myers HudsonAlpha SL7894 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Pmlsc71910V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 PML v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562NrsfV0416102PkRep2 K562 NRSF V102 2 NRSF K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001638 1638 GSM803440 Myers HudsonAlpha SL3822 v041610.2 2 exp MACS wgEncodeHaibTfbsK562NrsfV0416102PkRep2 None Peaks Neuron-restrictive silencer transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 NRSF v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562NrsfV0416102PkRep1 K562 NRSF V102 1 NRSF K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001638 1638 GSM803440 Myers HudsonAlpha SL3821 v041610.2 1 exp MACS wgEncodeHaibTfbsK562NrsfV0416102PkRep1 None Peaks Neuron-restrictive silencer transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 NRSF v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Nr2f2sc271940V0422111PkRep2 K562 NR2F2 V11 2 NR2F2_(SC-271940) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002382 2382 GSM1010782 Myers HudsonAlpha SL8577 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Nr2f2sc271940V0422111PkRep2 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 NR2F2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Nr2f2sc271940V0422111PkRep1 K562 NR2F2 V11 1 NR2F2_(SC-271940) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002382 2382 GSM1010782 Myers HudsonAlpha SL8143 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Nr2f2sc271940V0422111PkRep1 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 NR2F2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Mef2aV0416101PkRep2 K562 MEF2A V101 2 MEF2A K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001663 1663 GSM803379 Myers HudsonAlpha SL3925 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Mef2aV0416101PkRep2 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 MEF2A v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Mef2aV0416101PkRep1 K562 MEF2A V101 1 MEF2A K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001663 1663 GSM803379 Myers HudsonAlpha SL1794 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Mef2aV0416101PkRep1 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 MEF2A v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562MaxV0416102PkRep2 K562 Max V102 2 Max K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001605 1605 GSM803523 Myers HudsonAlpha SL3070 v041610.2 2 exp wgEncodeHaibTfbsK562MaxV0416102PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Max v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562MaxV0416102PkRep1 K562 Max V102 1 Max K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001605 1605 GSM803523 Myers HudsonAlpha SL2945 v041610.2 1 exp wgEncodeHaibTfbsK562MaxV0416102PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Max v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep2 K562 HDAC2 V102 2 HDAC2_(SC-6296) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001622 1622 GSM803471 Myers HudsonAlpha SL3359 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep2 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 HDAC2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep1 K562 HDAC2 V102 1 HDAC2_(SC-6296) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001622 1622 GSM803471 Myers HudsonAlpha SL2952 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep1 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 HDAC2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep2 K562 GATA2 PCR1 2 GATA2_(SC-267) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001576 1576 GSM803540 Myers HudsonAlpha SL1665 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep2 None Peaks This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 GATA2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep1 K562 GATA2 PCR1 1 GATA2_(SC-267) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001576 1576 GSM803540 Myers HudsonAlpha SL1430 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep1 None Peaks This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 GATA2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562GabpV0416101PkRep2 K562 GABP V101 2 GABP K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001604 1604 GSM803524 Myers HudsonAlpha SL3356 v041610.1 2 exp wgEncodeHaibTfbsK562GabpV0416101PkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 GABP v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562GabpV0416101PkRep1 K562 GABP V101 1 GABP K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001604 1604 GSM803524 Myers HudsonAlpha SL2943 v041610.1 1 exp wgEncodeHaibTfbsK562GabpV0416101PkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 GABP v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep2 K562 FOSL1 V101 2 FOSL1_(SC-183) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001637 1637 GSM803439 Myers HudsonAlpha SL3187 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 FOSL1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep1 K562 FOSL1 V101 1 FOSL1_(SC-183) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001637 1637 GSM803439 Myers HudsonAlpha SL2349 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 FOSL1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ets1V0416101PkRep2 K562 ETS1 V101 2 ETS1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001580 1580 GSM803442 Myers HudsonAlpha SL3182 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Ets1V0416101PkRep2 None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ETS1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ets1V0416101PkRep1 K562 ETS1 V101 1 ETS1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001580 1580 GSM803442 Myers HudsonAlpha SL2262 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Ets1V0416101PkRep1 None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ETS1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep2 K562 ELF1 V102 2 ELF1_(SC-631) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001619 1619 GSM803494 Myers HudsonAlpha SL3360 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ELF1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep1 K562 ELF1 V102 1 ELF1_(SC-631) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001619 1619 GSM803494 Myers HudsonAlpha SL2950 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ELF1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Egr1V0416101PkRep2 K562 Egr-1 V101 2 Egr-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001646 1646 GSM803414 Myers HudsonAlpha SL3497 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Egr1V0416101PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Egr-1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Egr1V0416101PkRep1 K562 Egr-1 V101 1 Egr-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001646 1646 GSM803414 Myers HudsonAlpha SL3164 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Egr1V0416101PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Egr-1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562E2f6V0416102PkRep2 K562 E2F6 V102 2 E2F6 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001598 1598 GSM803469 Myers HudsonAlpha SL3073 v041610.2 2 exp MACS wgEncodeHaibTfbsK562E2f6V0416102PkRep2 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 E2F6 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562E2f6V0416102PkRep1 K562 E2F6 V102 1 E2F6 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001598 1598 GSM803469 Myers HudsonAlpha SL2948 v041610.2 1 exp MACS wgEncodeHaibTfbsK562E2f6V0416102PkRep1 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 E2F6 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562CtcfcPcr1xPkRep2 K562 CTCF PCR1 2 CTCF_(SC-5916) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002279 2279 GSM1010820 Myers HudsonAlpha SL5605 PCR1x 2 exp MACS wgEncodeHaibTfbsK562CtcfcPcr1xPkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 CTCF 5916 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562CtcfcPcr1xPkRep1V2 K562 CTCF PCR1 1 CTCF_(SC-5916) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-21 wgEncodeEH002279 2279 GSM1010820 Myers HudsonAlpha SL3075 PCR1x 1 exp MACS wgEncodeHaibTfbsK562CtcfcPcr1xPkRep1V2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 CTCF 5916 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ctcflsc98982V0416101PkRep2 K562 CTCFL V101 2 CTCFL_(SC-98982) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001652 1652 GSM803401 Myers HudsonAlpha SL3972 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Ctcflsc98982V0416101PkRep2 None Peaks CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 CTCFL v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ctcflsc98982V0416101PkRep1 K562 CTCFL V101 1 CTCFL_(SC-98982) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001652 1652 GSM803401 Myers HudsonAlpha SL3189 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Ctcflsc98982V0416101PkRep1 None Peaks CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 CTCFL v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep2 K562 CREB1 V11 2 CREB1_(SC-240) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003230 3230 GSM1010890 Myers HudsonAlpha SL13293 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep1 K562 CREB1 V11 1 CREB1_(SC-240) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003230 3230 GSM1010890 Myers HudsonAlpha SL12420 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep2 K562 CEBPD V11 2 CEBPD_(SC-636) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003432 3432 GSM1010906 Myers HudsonAlpha SL13317 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep2 None Peaks The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CEBPD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIBd Regulation 
wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep1 K562 CEBPD V11 1 CEBPD_(SC-636) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003432 3432 GSM1010906 Myers HudsonAlpha SL11280 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep1 None Peaks The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CEBPD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIBd Regulation 
wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep2 K562 CEBPB V11 2 CEBPB_(SC-150) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002346 2346 GSM1010878 Myers HudsonAlpha SL9547 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep1 K562 CEBPB V11 1 CEBPB_(SC-150) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002346 2346 GSM1010878 Myers HudsonAlpha SL8085 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep2 K562 CBX3 V11 2 CBX3_(SC-101004) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002383 2383 GSM1010732 Myers HudsonAlpha SL7568 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep2 None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CBX3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep1 K562 CBX3 V11 1 CBX3_(SC-101004) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002383 2383 GSM1010732 Myers HudsonAlpha SL7105 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep1 None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CBX3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep2 K562 BCLAF1 2 BCLAF1_(SC-101388) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001571 1571 GSM803515 Myers HudsonAlpha SL1512 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep2 None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 BCLAF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep1 K562 BCLAF1 1 BCLAF1_(SC-101388) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001571 1571 GSM803515 Myers HudsonAlpha SL1273 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep1 None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 BCLAF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Atf3V0416101PkRep2 K562 ATF3 V101 2 ATF3 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001662 1662 GSM803380 Myers HudsonAlpha SL3926 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Atf3V0416101PkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ATF3 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Atf3V0416101PkRep1 K562 ATF3 V101 1 ATF3 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001662 1662 GSM803380 Myers HudsonAlpha SL3184 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Atf3V0416101PkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ATF3 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep2 hESC YY1 V102 2 YY1_(SC-281) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001567 1567 GSM803513 Myers HudsonAlpha SL1967 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC YY1 281 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep1 hESC YY1 V102 1 YY1_(SC-281) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001567 1567 GSM803513 Myers HudsonAlpha SL1657 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC YY1 281 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep2 hESC USF1 PCR1 2 USF-1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001532 1532 GSM803426 Myers HudsonAlpha SL1319 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC USF-1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep1 hESC USF1 PCR1 1 USF-1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001532 1532 GSM803426 Myers HudsonAlpha SL1159 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC USF-1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep2 hESC TEAD4 V11 2 TEAD4_(SC-101184) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003214 3214 GSM1010845 Myers HudsonAlpha SL12417 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep1 hESC TEAD4 V11 1 TEAD4_(SC-101184) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003214 3214 GSM1010845 Myers HudsonAlpha SL10882 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep2 hESC TCF12 PCR1 2 TCF12 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001531 1531 GSM803427 Myers HudsonAlpha SL1315 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TCF12 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep1 hESC TCF12 PCR1 1 TCF12 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001531 1531 GSM803427 Myers HudsonAlpha SL1158 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TCF12 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf7sc101167V0416102PkRep2 hESC TAF7 V102 2 TAF7_(SC-101167) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-13 2011-09-13 wgEncodeEH001610 1610 GSM803501 Myers HudsonAlpha SL3062 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescTaf7sc101167V0416102PkRep2 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TAF7 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf7sc101167V0416102PkRep1 hESC TAF7 V102 1 TAF7_(SC-101167) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-13 2011-09-13 wgEncodeEH001610 1610 GSM803501 Myers HudsonAlpha SL2697 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescTaf7sc101167V0416102PkRep1 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TAF7 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf1V0416102PkRep2 hESC TAF1 V102 2 TAF1 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001500 1500 GSM803450 Myers HudsonAlpha SL964 v041610.2 2 exp wgEncodeHaibTfbsH1hescTaf1V0416102PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TAF1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf1V0416102PkRep1 hESC TAF1 V102 1 TAF1 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001500 1500 GSM803450 Myers HudsonAlpha SL853 v041610.2 1 exp wgEncodeHaibTfbsH1hescTaf1V0416102PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TAF1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSrfPcr1xPkRep2 hESC SRF PCR1 2 SRF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001533 1533 GSM803425 Myers HudsonAlpha SL1659 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescSrfPcr1xPkRep2 None Peaks Serum response transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SRF PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSrfPcr1xPkRep1 hESC SRF PCR1 1 SRF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001533 1533 GSM803425 Myers HudsonAlpha SL1483 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescSrfPcr1xPkRep1 None Peaks Serum response transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SRF PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp4v20V0422111PkRep2 hESC SP4 V11 2 SP4_(V-20) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002317 2317 GSM1010743 Myers HudsonAlpha SL8135 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescSp4v20V0422111PkRep2 None Peaks Binds to GT and GC boxes promoters elements. Probable transcriptional activator. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC SP4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp4v20V0422111PkRep1 hESC SP4 V11 1 SP4_(V-20) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002317 2317 GSM1010743 Myers HudsonAlpha SL7836 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescSp4v20V0422111PkRep1 None Peaks Binds to GT and GC boxes promoters elements. Probable transcriptional activator. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC SP4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp2V0422111PkRep2 hESC SP2 V11 2 SP2_(SC-643) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-07 2012-06-07 wgEncodeEH002302 2302 GSM1010776 Myers HudsonAlpha SL6005 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescSp2V0422111PkRep2 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC SP2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp2V0422111PkRep1 hESC SP2 V11 1 SP2_(SC-643) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-07 2012-06-07 wgEncodeEH002302 2302 GSM1010776 Myers HudsonAlpha SL5690 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescSp2V0422111PkRep1 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC SP2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp1Pcr1xPkRep2 hESC SP1 PCR1 2 SP1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001529 1529 GSM803377 Myers HudsonAlpha SL1318 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescSp1Pcr1xPkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SP1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp1Pcr1xPkRep1 hESC SP1 PCR1 1 SP1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001529 1529 GSM803377 Myers HudsonAlpha SL1166 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescSp1Pcr1xPkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SP1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSix5Pcr1xPkRep2 hESC SIX5 PCR1 2 SIX5 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001528 1528 GSM803405 Myers HudsonAlpha SL1317 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescSix5Pcr1xPkRep2 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SIX5 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSix5Pcr1xPkRep1 hESC SIX5 PCR1 1 SIX5 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001528 1528 GSM803405 Myers HudsonAlpha SL1162 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescSix5Pcr1xPkRep1 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SIX5 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSin3ak20Pcr1xPkRep2 hESC Sin3A PCR1 2 Sin3Ak-20 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001530 1530 GSM803428 Myers HudsonAlpha SL1313 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescSin3ak20Pcr1xPkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Sin3Ak-20 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSin3ak20Pcr1xPkRep1 hESC Sin3A PCR1 1 Sin3Ak-20 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001530 1530 GSM803428 Myers HudsonAlpha SL1157 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescSin3ak20Pcr1xPkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Sin3Ak-20 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxraV0416102PkRep2 hESC RXRA V102 2 RXRA H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-13 2011-06-13 wgEncodeEH001560 1560 GSM803506 Myers HudsonAlpha SL2346 v041610.2 2 exp wgEncodeHaibTfbsH1hescRxraV0416102PkRep2 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC RXRA v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxraV0416102PkRep1 hESC RXRA V102 1 RXRA H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-13 2011-06-13 wgEncodeEH001560 1560 GSM803506 Myers HudsonAlpha SL1163 v041610.2 1 exp wgEncodeHaibTfbsH1hescRxraV0416102PkRep1 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC RXRA v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRad21V0416102PkRep2 hESC RAD21 V102 2 Rad21 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001593 1593 GSM803466 Myers HudsonAlpha SL3066 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescRad21V0416102PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC RAD21 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRad21V0416102PkRep1 hESC RAD21 V102 1 Rad21 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001593 1593 GSM803466 Myers HudsonAlpha SL2689 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescRad21V0416102PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC RAD21 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102PkRep2 hESC POU5F1 2 POU5F1_(SC-9081) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001636 1636 GSM803438 Myers HudsonAlpha SL3453 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102PkRep2 None Peaks This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC POU5F1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102PkRep1 hESC POU5F1 1 POU5F1_(SC-9081) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001636 1636 GSM803438 Myers HudsonAlpha SL2548 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102PkRep1 None Peaks This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC POU5F1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol24h8V0416102PkRep2 hESC Pol2-4H8 V102 2 Pol2-4H8 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001514 1514 GSM803484 Myers HudsonAlpha SL1051 v041610.2 2 exp wgEncodeHaibTfbsH1hescPol24h8V0416102PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol24h8V0416102PkRep1 hESC Pol2-4H8 V102 1 Pol2-4H8 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001514 1514 GSM803484 Myers HudsonAlpha SL979 v041610.2 1 exp wgEncodeHaibTfbsH1hescPol24h8V0416102PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol2V0416102PkRep2 hESC Pol2 V102 2 Pol2 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001499 1499 GSM803366 Myers HudsonAlpha SL1052 v041610.2 2 exp wgEncodeHaibTfbsH1hescPol2V0416102PkRep2 None Peaks RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Pol2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol2V0416102PkRep1 hESC Pol2 V102 1 Pol2 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001499 1499 GSM803366 Myers HudsonAlpha SL980 v041610.2 1 exp wgEncodeHaibTfbsH1hescPol2V0416102PkRep1 None Peaks RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Pol2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescP300V0416102PkRep2 hESC p300 V102 2 p300 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001574 1574 GSM803542 Myers HudsonAlpha SL1883 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescP300V0416102PkRep2 None Peaks EP300(c-20) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC p300 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescP300V0416102PkRep1 hESC p300 V102 1 p300 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001574 1574 GSM803542 Myers HudsonAlpha SL2250 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescP300V0416102PkRep1 None Peaks EP300(c-20) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC p300 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNrsfV0416102PkRep2 hESC NRSF V102 2 NRSF H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001498 1498 GSM803365 Myers HudsonAlpha SL1053 v041610.2 2 exp wgEncodeHaibTfbsH1hescNrsfV0416102PkRep2 None Peaks Neuron-restrictive silencer transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC NRSF v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNrsfV0416102PkRep1 hESC NRSF V102 1 NRSF H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001498 1498 GSM803365 Myers HudsonAlpha SL978 v041610.2 1 exp wgEncodeHaibTfbsH1hescNrsfV0416102PkRep1 None Peaks Neuron-restrictive silencer transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC NRSF v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNanogsc33759V0416102PkRep2 hESC NANOG V102 2 NANOG_(SC-33759) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001635 1635 GSM803437 Myers HudsonAlpha SL3068 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescNanogsc33759V0416102PkRep2 None Peaks Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC NANOG v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNanogsc33759V0416102PkRep1 hESC NANOG V102 1 NANOG_(SC-33759) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001635 1635 GSM803437 Myers HudsonAlpha SL2687 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescNanogsc33759V0416102PkRep1 None Peaks Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC NANOG v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescMaxV0422111PkRep2 hESC Max V11 2 Max H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003225 3225 GSM1010898 Myers HudsonAlpha SL13302 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescMaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescMaxV0422111PkRep1 hESC Max V11 1 Max H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003225 3225 GSM1010898 Myers HudsonAlpha SL12411 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescMaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescJundV0416102PkRep2 hESC JunD V102 2 JunD H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH001579 1579 GSM803529 Myers HudsonAlpha SL3065 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescJundV0416102PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC JunD v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescJundV0416102PkRep1 hESC JunD V102 1 JunD H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH001579 1579 GSM803529 Myers HudsonAlpha SL2690 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescJundV0416102PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC JunD v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep2 hESC HDAC2 V102 2 HDAC2_(SC-6296) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2011-12-02 wgEncodeEH001659 1659 GSM803345 Myers HudsonAlpha SL3454 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep2 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC HDAC2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep1 hESC HDAC2 V102 1 HDAC2_(SC-6296) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2011-12-02 wgEncodeEH001659 1659 GSM803345 Myers HudsonAlpha SL3935 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep1 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC HDAC2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescGabpPcr1xPkRep2 hESC GABP PCR1 2 GABP H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-29 2011-01-29 wgEncodeEH001534 1534 GSM803424 Myers HudsonAlpha SL1660 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescGabpPcr1xPkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC GABP PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescGabpPcr1xPkRep1 hESC GABP PCR1 1 GABP H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-29 2011-01-29 wgEncodeEH001534 1534 GSM803424 Myers HudsonAlpha SL1518 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescGabpPcr1xPkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC GABP PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescFosl1sc183V0416102PkRep2 hESC FOSL1 V102 2 FOSL1_(SC-183) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001660 1660 GSM803382 Myers HudsonAlpha SL4211 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescFosl1sc183V0416102PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC FOSL1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescFosl1sc183V0416102PkRep1 hESC FOSL1 V102 1 FOSL1_(SC-183) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001660 1660 GSM803382 Myers HudsonAlpha SL2692 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescFosl1sc183V0416102PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC FOSL1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescEgr1V0416102PkRep2 hESC Egr-1 V102 2 Egr-1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-05-27 2011-02-27 wgEncodeEH001538 1538 GSM803430 Myers HudsonAlpha SL1885 hg19 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescEgr1V0416102PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Egr-1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescEgr1V0416102PkRep1 hESC Egr-1 V102 1 Egr-1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-05-27 2011-02-27 wgEncodeEH001538 1538 GSM803430 Myers HudsonAlpha SL1482 hg19 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescEgr1V0416102PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Egr-1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescE2f6V0422111PkRep2 hESC E2F6 V11 2 E2F6 H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003224 3224 GSM1010899 Myers HudsonAlpha SL13304 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescE2f6V0422111PkRep2 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC E2F6 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescE2f6V0422111PkRep1 hESC E2F6 V11 1 E2F6 H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003224 3224 GSM1010899 Myers HudsonAlpha SL12414 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescE2f6V0422111PkRep1 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC E2F6 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCtcfsc5916V0416102PkRep2 hESC CTCF V102 2 CTCF_(SC-5916) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001649 1649 GSM803419 Myers HudsonAlpha SL3067 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescCtcfsc5916V0416102PkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC CTCF 5916 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCtcfsc5916V0416102PkRep1 hESC CTCF V102 1 CTCF_(SC-5916) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001649 1649 GSM803419 Myers HudsonAlpha SL2688 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescCtcfsc5916V0416102PkRep1 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC CTCF 5916 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCreb1sc240V0422111PkRep2 hESC CREB1 V11 2 CREB1_(SC-240) H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003229 3229 GSM1010896 Myers HudsonAlpha SL13303 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescCreb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCreb1sc240V0422111PkRep1 hESC CREB1 V11 1 CREB1_(SC-240) H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003229 3229 GSM1010896 Myers HudsonAlpha SL12413 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescCreb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescBcl11aV0416102PkRep2 hESC BCL V102 2 BCL11A H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001625 1625 GSM803476 Myers HudsonAlpha SL3989 v041610.2 2 exp wgEncodeHaibTfbsH1hescBcl11aV0416102PkRep2 None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC BCL11A v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescBcl11aPcr1xPkRep1 hESC BCL PCR1 1 BCL11A H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2010-04-22 2011-01-22 wgEncodeEH001527 1527 GSM803396 Myers HudsonAlpha SL1314 PCR1x 1 exp wgEncodeHaibTfbsH1hescBcl11aPcr1xPkRep1 None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC BCL11A PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf3V0416102PkRep2 hESC ATF3 V102 2 ATF3 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001566 1566 GSM803512 Myers HudsonAlpha SL1968 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescAtf3V0416102PkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC ATF3 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf3V0416102PkRep1 hESC ATF3 V102 1 ATF3 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001566 1566 GSM803512 Myers HudsonAlpha SL1519 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescAtf3V0416102PkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC ATF3 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf2sc81188V0422111PkRep2 hESC ATF2 V11 2 ATF2_(SC-81188) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002316 2316 GSM1010742 Myers HudsonAlpha SL8136 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescAtf2sc81188V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC ATF2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf2sc81188V0422111PkRep1 hESC ATF2 V11 1 ATF2_(SC-81188) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002316 2316 GSM1010742 Myers HudsonAlpha SL7904 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescAtf2sc81188V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC ATF2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102PkRep2 GM78 ZEB1 V102 2 ZEB1_(SC-25388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001645 1645 GSM803411 Myers HudsonAlpha SL3254 v041610.2 2 exp MACS wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102PkRep2 None Peaks This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ZEB1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102PkRep1 GM78 ZEB1 V102 1 ZEB1_(SC-25388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001645 1645 GSM803411 Myers HudsonAlpha SL2957 v041610.2 1 exp MACS wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102PkRep1 None Peaks This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ZEB1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zbtb33Pcr1xPkRep2 GM78 ZBTB33 2 ZBTB33 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-30 2010-08-30 wgEncodeEH001488 1488 GSM803392 Myers HudsonAlpha SL923 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Zbtb33Pcr1xPkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ZBTB33 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zbtb33Pcr1xPkRep1 GM78 ZBTB33 1 ZBTB33 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-30 2010-08-30 wgEncodeEH001488 1488 GSM803392 Myers HudsonAlpha SL814 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Zbtb33Pcr1xPkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ZBTB33 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xPkRep2 GM78 YY1 PCR1 2 YY1_(SC-281) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-15 2011-11-15 wgEncodeEH001657 1657 GSM803406 Myers HudsonAlpha SL2129 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xPkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 YY1 281 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xPkRep1 GM78 YY1 PCR1 1 YY1_(SC-281) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-15 2011-11-15 wgEncodeEH001657 1657 GSM803406 Myers HudsonAlpha SL1475 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xPkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 YY1 281 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Usf1Pcr2xPkRep2 GM78 USF1 PCR2 2 USF-1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2009-07-02 2010-04-01 wgEncodeEH001468 1468 GSM803347 Myers HudsonAlpha SL483 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878Usf1Pcr2xPkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 USF-1 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Usf1Pcr2xPkRep1 GM78 USF1 PCR2 1 USF-1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2009-07-02 2010-04-01 wgEncodeEH001468 1468 GSM803347 Myers HudsonAlpha SL448 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878Usf1Pcr2xPkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 USF-1 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf3Pcr1xPkRep2 GM78 TCF3 PCR1 2 TCF3_(SC-349) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002315 2315 GSM1010745 Myers HudsonAlpha SL633 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Tcf3Pcr1xPkRep2 None Peaks Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TCF3 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf3Pcr1xPkRep1 GM78 TCF3 PCR1 1 TCF3_(SC-349) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002315 2315 GSM1010745 Myers HudsonAlpha SL480 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Tcf3Pcr1xPkRep1 None Peaks Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TCF3 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep2 GM78 TCF12 PCR1 2 TCF12 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-29 2010-07-29 wgEncodeEH001485 1485 GSM803389 Myers HudsonAlpha SL1019 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TCF12 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep1 GM78 TCF12 PCR1 1 TCF12 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-27 2010-07-27 wgEncodeEH001485 1485 GSM803389 Myers HudsonAlpha SL673 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TCF12 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep2 GM78 TAF1 PCR1 2 TAF1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2009-10-29 2010-07-29 wgEncodeEH001478 1478 GSM803537 Myers HudsonAlpha SL1062 PCR1x 2 exp wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TAF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep1 GM78 TAF1 PCR1 1 TAF1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2009-07-20 2010-04-20 wgEncodeEH001478 1478 GSM803537 Myers HudsonAlpha SL805 PCR1x 1 exp wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TAF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep2 GM78 STAT5A V11 2 STAT5A_(SC-74442) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002321 2321 GSM1010721 Myers HudsonAlpha SL8127 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 STAT5A v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep1 GM78 STAT5A V11 1 STAT5A_(SC-74442) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002321 2321 GSM1010721 Myers HudsonAlpha SL7897 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 STAT5A v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfV0416101PkRep2 GM78 SRF V101 2 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001624 1624 GSM803477 Myers HudsonAlpha SL3827 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878SrfV0416101PkRep2 None Peaks Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SRF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfV0416101PkRep1 GM78 SRF V101 1 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001624 1624 GSM803477 Myers HudsonAlpha SL3578 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878SrfV0416101PkRep1 None Peaks Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SRF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfPcr2xPkRep2 GM78 SRF PCR2 2 SRF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001464 1464 GSM803350 Myers HudsonAlpha SL292 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878SrfPcr2xPkRep2 None Peaks Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 SRF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfPcr2xPkRep1 GM78 SRF PCR2 1 SRF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001464 1464 GSM803350 Myers HudsonAlpha SL291 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878SrfPcr2xPkRep1 None Peaks Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 SRF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Sp1Pcr1xPkRep2 GM78 SP1 PCR1 2 SP1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-17 2010-09-16 wgEncodeEH001496 1496 GSM803363 Myers HudsonAlpha SL846 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Sp1Pcr1xPkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SP1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Sp1Pcr1xPkRep1 GM78 SP1 PCR1 1 SP1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-17 2010-09-16 wgEncodeEH001496 1496 GSM803363 Myers HudsonAlpha SL746 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Sp1Pcr1xPkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SP1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Six5Pcr1xPkRep2 GM78 SIX5 PCR1 2 SIX5 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH001542 1542 GSM803338 Myers HudsonAlpha SL1200 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Six5Pcr1xPkRep2 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SIX5 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Six5Pcr1xPkRep1 GM78 SIX5 PCR1 1 SIX5 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH001542 1542 GSM803338 Myers HudsonAlpha SL1061 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Six5Pcr1xPkRep1 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SIX5 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxraPcr1xPkRep2 GM78 RXRA PCR1 2 RXRA GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001541 1541 GSM803341 Myers HudsonAlpha SL1265 PCR1x 2 exp wgEncodeHaibTfbsGm12878RxraPcr1xPkRep2 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 RXRA PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxraPcr1xPkRep1 GM78 RXRA PCR1 1 RXRA GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001541 1541 GSM803341 Myers HudsonAlpha SL1063 PCR1x 1 exp wgEncodeHaibTfbsGm12878RxraPcr1xPkRep1 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 RXRA PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep2 GM78 RUNX3 V11 2 RUNX3_(SC-101553) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002330 2330 GSM1010893 Myers HudsonAlpha SL8128 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep2 None Peaks This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 RUNX3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep1 GM78 RUNX3 V11 1 RUNX3_(SC-101553) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002330 2330 GSM1010893 Myers HudsonAlpha SL7898 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep1 None Peaks This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 RUNX3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Rad21V0416101PkRep2 GM78 RAD21 V101 2 Rad21 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001640 1640 GSM803416 Myers HudsonAlpha SL3934 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Rad21V0416101PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 RAD21 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Rad21V0416101PkRep1 GM78 RAD21 V101 1 Rad21 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001640 1640 GSM803416 Myers HudsonAlpha SL3933 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Rad21V0416101PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 RAD21 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep3 GM78 PU.1 PCR1 3 PU.1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL963 PCR1x 3 exp MACS wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep3 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PU.1 PCR1x ChIP-seq Peaks Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep2 GM78 PU.1 PCR1 2 PU.1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL649 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep2 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PU.1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep1 GM78 PU.1 PCR1 1 PU.1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL612 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep1 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PU.1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep3 GM78 POU2F2 3 POU2F2 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL851 PCR1x 3 exp MACS wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep3 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 POU2F2 PCR1x ChIP-seq Peaks Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep2 GM78 POU2F2 2 POU2F2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL648 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep2 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 POU2F2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep1 GM78 POU2F2 1 POU2F2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL614 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep1 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 POU2F2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep2 GM78 Pol2-4H8 PCR1 2 Pol2-4H8 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-08 2010-10-08 wgEncodeEH001517 1517 GSM803485 Myers HudsonAlpha SL847 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 Pol2-4H8 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep1 GM78 Pol2-4H8 PCR1 1 Pol2-4H8 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-08 2010-10-08 wgEncodeEH001517 1517 GSM803485 Myers HudsonAlpha SL748 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 Pol2-4H8 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol2Pcr2xPkRep2 GM78 Pol2 PCR2 2 Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001463 1463 GSM803355 Myers HudsonAlpha SL209 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878Pol2Pcr2xPkRep2 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 Pol2 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol2Pcr2xPkRep1 GM78 Pol2 PCR2 1 Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001463 1463 GSM803355 Myers HudsonAlpha SL207 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878Pol2Pcr2xPkRep1 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 Pol2 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep2 GM78 PML V11 2 PML_(SC-71910) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002308 2308 GSM1010771 Myers HudsonAlpha SL7831 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 PML v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep1 GM78 PML V11 1 PML_(SC-71910) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002308 2308 GSM1010771 Myers HudsonAlpha SL7281 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 PML v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pbx3Pcr1xPkRep2 GM78 PBx3 PCR1 2 Pbx3 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001477 1477 GSM803532 Myers HudsonAlpha SL647 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pbx3Pcr1xPkRep2 None Peaks Pbx 3 (D-17) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PBx3 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pbx3Pcr1xPkRep1 GM78 PBx3 PCR1 1 Pbx3 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001477 1477 GSM803532 Myers HudsonAlpha SL615 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pbx3Pcr1xPkRep1 None Peaks Pbx 3 (D-17) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PBx3 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5n19Pcr1xPkRep2 GM78 PAX5 PCR1 2 PAX5-N19 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-17 2010-09-17 wgEncodeEH001495 1495 GSM803362 Myers HudsonAlpha SL848 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pax5n19Pcr1xPkRep2 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PAX5-N19 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5n19Pcr1xPkRep1 GM78 PAX5 PCR1 1 PAX5-N19 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-17 2010-09-17 wgEncodeEH001495 1495 GSM803362 Myers HudsonAlpha SL677 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pax5n19Pcr1xPkRep1 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PAX5-N19 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5c20Pcr1xPkRep2 GM78 PAX5 PCR1 2 PAX5-C20 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-04 2010-09-04 wgEncodeEH001489 1489 GSM803391 Myers HudsonAlpha SL735 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pax5c20Pcr1xPkRep2 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PAX5-C20 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5c20Pcr1xPkRep1 GM78 PAX5 PCR1 1 PAX5-C20 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-04 2010-09-04 wgEncodeEH001489 1489 GSM803391 Myers HudsonAlpha SL675 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pax5c20Pcr1xPkRep1 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PAX5-C20 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878P300Pcr1xPkRep2 GM78 p300 PCR1 2 p300 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-25 2010-08-25 wgEncodeEH001487 1487 GSM803387 Myers HudsonAlpha SL564 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878P300Pcr1xPkRep2 None Peaks EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 p300 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878P300Pcr1xPkRep1 GM78 p300 PCR1 1 p300 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-25 2010-08-25 wgEncodeEH001487 1487 GSM803387 Myers HudsonAlpha SL551 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878P300Pcr1xPkRep1 None Peaks EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 p300 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep2 GM78 NRSF PCR2 2 NRSF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-25 2009-08-25 wgEncodeEH001465 1465 GSM803349 Myers HudsonAlpha SL204 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep1 GM78 NRSF PCR2 1 NRSF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-08-06 2008-11-25 2011-05-06 wgEncodeEH001465 1465 GSM803349 Myers HudsonAlpha SL202 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr1xPkRep2 GM78 NRSF PCR1 2 NRSF GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002314 2314 GSM1010744 Myers HudsonAlpha SL7333 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878NrsfPcr1xPkRep2 None Peaks Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 NRSF PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr1xPkRep1 GM78 NRSF PCR1 1 NRSF GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002314 2314 GSM1010744 Myers HudsonAlpha SL852 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878NrsfPcr1xPkRep1 None Peaks Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 NRSF PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep2 GM78 NFIC V11 2 NFIC_(SC-81335) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002343 2343 GSM1010881 Myers HudsonAlpha SL8392 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep2 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 NFIC v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1 GM78 NFIC V11 1 NFIC_(SC-81335) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002343 2343 GSM1010881 Myers HudsonAlpha SL8083 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 NFIC v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep2 GM78 NFATC1 V11 2 NFATC1_(SC-17834) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002307 2307 GSM1010779 Myers HudsonAlpha SL7830 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep2 None Peaks The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Five transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 NFATC1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep1 GM78 NFATC1 V11 1 NFATC1_(SC-17834) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002307 2307 GSM1010779 Myers HudsonAlpha SL7280 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep1 None Peaks The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Five transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 NFATC1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep2 GM78 MTA3 V11 2 MTA3_(SC-81325) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002329 2329 GSM1010729 Myers HudsonAlpha SL8129 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep2 None Peaks Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 MTA3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep1 GM78 MTA3 V11 1 MTA3_(SC-81325) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002329 2329 GSM1010729 Myers HudsonAlpha SL7899 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep1 None Peaks Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 MTA3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep2 GM78 MEFC V101 2 MEF2C_(SC-13268) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001648 1648 GSM803420 Myers HudsonAlpha SL2127 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep2 None Peaks This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 MEF2C v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep1 GM78 MEFC V101 1 MEF2C_(SC-13268) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001648 1648 GSM803420 Myers HudsonAlpha SL1654 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep1 None Peaks This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 MEF2C v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep2 GM78 MEF2A PCR1 2 MEF2A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001565 1565 GSM803511 Myers HudsonAlpha SL1792 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep2 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 MEF2A PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep1 GM78 MEF2A PCR1 1 MEF2A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001565 1565 GSM803511 Myers HudsonAlpha SL1425 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep1 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 MEF2A PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep2 GM78 IRF4 PCR1 2 IRF4_(SC-6059) GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-29 2010-07-29 wgEncodeEH001484 1484 GSM803390 Myers HudsonAlpha SL951 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep2 None Peaks The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 IRF4 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep1 GM78 IRF4 PCR1 1 IRF4_(SC-6059) GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-27 2010-07-27 wgEncodeEH001484 1484 GSM803390 Myers HudsonAlpha SL838 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep1 None Peaks The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 IRF4 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878GabpPcr2xPkRep2 GM78 GABP PCR2 2 GABP GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001462 1462 GSM803356 Myers HudsonAlpha SL205 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878GabpPcr2xPkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 GABP PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878GabpPcr2xPkRep1 GM78 GABP PCR2 1 GABP GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001462 1462 GSM803356 Myers HudsonAlpha SL203 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878GabpPcr2xPkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 GABP PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep2 GM78 FOXM1 V11 2 FOXM1_(SC-502) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002529 2529 GSM1010731 Myers HudsonAlpha SL7834 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep2 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 FOXM1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep1 GM78 FOXM1 V11 1 FOXM1_(SC-502) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002529 2529 GSM1010731 Myers HudsonAlpha SL7551 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep1 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 FOXM1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep2V2 GM78 ETS1 PCR1 2 ETS1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH001564 1564 GSM803510 Myers HudsonAlpha SL1655 PCR1x 2 exp wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep2V2 None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ETS1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep1V2 GM78 ETS1 PCR1 1 ETS1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH001564 1564 GSM803510 Myers HudsonAlpha SL1507 PCR1x 1 exp wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep1V2 None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ETS1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep2 GM78 ELF1 V101 2 ELF1_(SC-631) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001617 1617 GSM803496 Myers HudsonAlpha SL3352 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ELF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep1 GM78 ELF1 V101 1 ELF1_(SC-631) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001617 1617 GSM803496 Myers HudsonAlpha SL2253 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ELF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1V0416101PkRep2 GM78 Egr-1 V101 2 Egr-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001632 1632 GSM803434 Myers HudsonAlpha SL3828 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Egr1V0416101PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 Egr-1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1V0416101PkRep1 GM78 Egr-1 V101 1 Egr-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001632 1632 GSM803434 Myers HudsonAlpha SL3579 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Egr1V0416101PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 Egr-1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1Pcr2xPkRep3 GM78 Egr-1 PCR2 3 Egr-1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002328 2328 GSM1010730 Myers HudsonAlpha SL482 PCR2x 3 exp MACS wgEncodeHaibTfbsGm12878Egr1Pcr2xPkRep3 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 Egr-1 PCR2x ChIP-seq Peaks Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep2 GM78 EBF1 PCR1 2 EBF1_(SC-137065) GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001480 1480 GSM803386 Myers HudsonAlpha SL988 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep2 None Peaks Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 EBF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep1 GM78 EBF1 PCR1 1 EBF1_(SC-137065) GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001480 1480 GSM803386 Myers HudsonAlpha SL745 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep1 None Peaks Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 EBF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep2 GM78 CREB1 V11 2 CREB1_(SC-240) GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003275 3275 GSM1010760 Myers HudsonAlpha SL16741 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep1 GM78 CREB1 V11 1 CREB1_(SC-240) GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003275 3275 GSM1010760 Myers HudsonAlpha SL12408 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep2 GM78 CEBPB V11 2 CEBPB_(SC-150) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003212 3212 GSM1010850 Myers HudsonAlpha SL9542 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep1 GM78 CEBPB V11 1 CEBPB_(SC-150) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003212 3212 GSM1010850 Myers HudsonAlpha SL8084 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep2 GM78 BCLAF1 2 BCLAF1_(SC-101388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001563 1563 GSM803509 Myers HudsonAlpha SL2128 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep2 None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCLAF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep1 GM78 BCLAF1 1 BCLAF1_(SC-101388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001563 1563 GSM803509 Myers HudsonAlpha SL1509 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep1 None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCLAF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep2 GM78 BCL3 V101 2 BCL3 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH001658 1658 GSM803342 Myers HudsonAlpha SL3931 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep2 None Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCL3 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep1 GM78 BCL3 V101 1 BCL3 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH001658 1658 GSM803342 Myers HudsonAlpha SL3728 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep1 None Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCL3 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep2 GM78 BCL PCR1 2 BCL11A GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-25 2010-08-25 wgEncodeEH001486 1486 GSM803388 Myers HudsonAlpha SL976 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep2 None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCL11A PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep1 GM78 BCL PCR1 1 BCL11A GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-25 2010-08-25 wgEncodeEH001486 1486 GSM803388 Myers HudsonAlpha SL650 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep1 None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCL11A PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878BatfPcr1xPkRep2 GM78 BATF PCR1 2 BATF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001479 1479 GSM803538 Myers HudsonAlpha SL985 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878BatfPcr1xPkRep2 None Peaks The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BATF PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878BatfPcr1xPkRep1 GM78 BATF PCR1 1 BATF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001479 1479 GSM803538 Myers HudsonAlpha SL839 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878BatfPcr1xPkRep1 None Peaks The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BATF PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep2 GM78 ATF3 PCR1 2 ATF3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001562 1562 GSM803508 Myers HudsonAlpha SL1508 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ATF3 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep1 GM78 ATF3 PCR1 1 ATF3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001562 1562 GSM803508 Myers HudsonAlpha SL1269 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ATF3 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep2 GM78 ATF2 V11 2 ATF2_(SC-81188) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002306 2306 GSM1010780 Myers HudsonAlpha SL7561 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 ATF2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep1 GM78 ATF2 V11 1 ATF2_(SC-81188) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002306 2306 GSM1010780 Myers HudsonAlpha SL7282 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 ATF2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeSunyAlbanyGeneSt SUNY RIP GeneST GSE31724 RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany Regulation Description This track is produced as part of the ENCODE Project. This track displays transcriptional fragments associated with RNA binding proteins in different cell lines using RIP-Chip (Ribonomic) profiling on Affymetrix GeneChip&reg; Human Gene 1.0 ST Arrays. These sutracks show the genomic location of transcripts associated with the array probes. Data for this track was produced as part of the Encyclopedia of DNA Elements (ENCODE) Project. In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Chip profiling. Display Conventions and Configuration This track has multiple subtracks that display individually in the browser. The subtracks within this track correspond to different antibodies/target proteins tested in different cell lines. These subtracks show the genomic location of the mRNA transcripts associated with RNA Binding Proteins as determined by the Affymetrix GeneChip&reg; Human Gene 1.0 ST Array probes. Items are shaded by p-value using the formula (maxPossibleScore-((maxPossibleScore/cutOffValue)*pValue)) so that items with more significant expression levels are shaded darker. The p-values are displayed in the browser convention as -log10(pValue). Methods RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols. Antibodies specific to the RNA Binding Protein (RBP) in question were first coated onto protein A/G containing magnetic beads and then used to immunoprecipitate the targeted, endogenously-formed mRNP complexes. Antibody-coated beads were incubated/tumbled with cell lysate overnight in the cold followed by extensive rinsing and subsequent purification of associated RNA using Phenol/Chloroform extraction and ethanol precipitation. The associated transcripts were identified using GeneChip&reg; Human Gene 1.0 ST Arrays. Arrays were analyzed using Agilent's GeneSpringGX software (version 11.0). Arrays were analyzed a group at a time by applying the Iterative PLIER16 algorithm using quantile normalization. Probesets whose normalized expression levels (signal value) fell within the 18 to 98 percentile in at least two of the three replicates were retained for further analysis. A TTest (T7-Tag and RIP-Input) or a one-way ANOVA (samples and controls) was applied to these probesets and a p-value cutoff of .05 was applied. The Benjamini-Hochberg false discovery rate algorithm was then applied to generate corrected p-values, also known as q-values. The RIP-Input was summarized first and selected probesets were retained for further analysis. Next, the arrays for T7Tag (background/negative control) RIPs were summarized with those retained RIP-input probesets. Probesets that fit the above criteria for either group (RIP-Input or T7Tag) were then filtered for those that showed a minimum 2 fold increase of expression in T7Tag versus RIP-Input. Finally, arrays for treatment RIP samples were summarized together with those for RIP-inputs and T7Tag RIPs. Probesets that fit the above criteria for any group (RIP-Input or T7Tag or samples) were then filtered for probesets that showed a minimum 2 fold increase of expression in treatment over total. A similar list was produced for probesets showing the same enrichment in the T7Tag RIP set. Probesets which appeared in both treatment and negative control at these cutoff stringencies were subtracted from the treatment results as background noise, yielding the final data track. Verification All experiments (including controls) were performed in and analyzed as triplicates. Release Notes Release 2 (September 2011) of this track corrects the scores and the calculated P and Q values. In this release, the calculated P and Q values are -log10(P) and -log10(Q), and the scores, and therefore the shading of items, reflect the p-values as described in the Display Conventions and Configuration section above. Credits These data were produced and analyzed by a collaboration between the Tenenbaum lab at the University at Albany-SUNY, College of Nanoscale Science and Engineering, the Luiz Penalva group at the Greehey Children's Cancer Research Institute, University of Texas Health Science Center and the Microarray Core Facility at the Center for Functional Genomics, Rensselaer, NY . Contact: Scott Tenenbaum References Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol. 2008;419:93-108. George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006;3(2):57-9. Epub 2006 Apr 1. Jain R, Devine T, George AD, Chittur SV, Baroni TE, Penalva LO, Tenenbaum SA. RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63 Jayaseelan S, Doyle F, Currenti S, Tenenbaum SA. RIP: An mRNA Localization Technique. Methods Mol Biol. 2011;714:407-422. Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell. 2002;9(6):1161-7. Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes. Methods Mol Biol. 2004;257:125-34. Tenenbaum SA, Carson CC, Lager PJ, Keene JD. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14085-90. Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods. 2002 Feb;26(2):191-8. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeRbpSuper ENC RNA Binding ENCODE RNA Binding Proteins Regulation Description In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs (mRNAs) have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins (RBPs) play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks can elucidate RNA processing by identifying RNA molecules that interact with specific RBPs. They were developed using assays that first purify mRNA-RBP complexes and then separate the complexes to identify the target mRNAs bound to specific RBPs. The mRNAs can be identified by methods including sequencing, microarrays, and SAGE. The tracks in this supertrack contain two forms of information: genes whose transcripts were bound by the given RBP (such as SUNY RIP GeneSt) and approximate location of the RBP binding site in the mRNA sequence (such SUNY RIP Tiling and SUNY RIP-seq). Please note: RIP input tracks (both array and sequencing based) were created for use in downstream informatic analysis to produce RBP specific RIP tracks. Low abundance RNA that is undetectable in the input samples may be proportionally enriched to the point of detection in the RIPs. This may be confusing to some users expecting to see RIP as a subset of input. Users seeking information on total RNA should examine the "expression" RNA-seq tracks produced by other ENCODE groups. Display Conventions and Configuration These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol. 2008;419:93-108. George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006 Apr;3(2):57-9. Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell. 2002 Jun;9(6):1161-7. Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes. Methods Mol Biol. 2004;257:125-34. Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods. 2002 Feb;26(2):191-8. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeSunyAlbanyGeneStHepg2RipinputRbpAssocRnaV2 HepG2 RIP-Input ripInput HepG2 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001221 1221 GSM787611 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStHepg2RipinputRbpAssocRnaV2 RbpAssocRna hepatocellular carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HepG2 RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHepg2T7tagRbpAssocRnaV2 HepG2 T7Tag T7Tag HepG2 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001232 1232 GSM787608 Tenenbaum SunyAlbany Nov_69522,Mil_AB3790 antibodies hg18 wgEncodeSunyAlbanyGeneStHepg2T7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) hepatocellular carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HepG2 T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHepg2Pabpc1RbpAssocRnaV2 HepG2 PABPC1 PABPC1 HepG2 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001231 1231 GSM787617 Tenenbaum SunyAlbany Sig_P6246 antibody hg18 wgEncodeSunyAlbanyGeneStHepg2Pabpc1RbpAssocRnaV2 RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). hepatocellular carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HepG2 PABPC1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHepg2Elavl1RbpAssocRnaV2 HepG2 ELAVL1 ELAVL1 HepG2 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001230 1230 GSM787614 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStHepg2Elavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) hepatocellular carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HepG2 ELAVL1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHelas3RipinputRbpAssocRnaV2 HeLa-S3 RIP-Input ripInput HeLa-S3 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001220 1220 GSM787599 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStHelas3RipinputRbpAssocRnaV2 RbpAssocRna cervical carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HeLa-S3 RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHelas3T7tagRbpAssocRnaV2 HeLa-S3 T7Tag T7Tag HeLa-S3 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001229 1229 GSM787596 Tenenbaum SunyAlbany Nov_69522,Mil_AB3790 antibodies hg18 wgEncodeSunyAlbanyGeneStHelas3T7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) cervical carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HeLa-S3 T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHelas3Pabpc1RbpAssocRnaV2 HeLa-S3  PABPC1 PABPC1 HeLa-S3 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001228 1228 GSM787605 Tenenbaum SunyAlbany Sig_P6246 antibody hg18 wgEncodeSunyAlbanyGeneStHelas3Pabpc1RbpAssocRnaV2 RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). cervical carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HeLa-S3 PABPC1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHelas3Elavl1RbpAssocRnaV2 HeLa-S3 ELAV1 ELAVL1 HeLa-S3 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001227 1227 GSM787602 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStHelas3Elavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) cervical carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HeLa-S3 ELAV1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562RipinputRbpAssocRnaV2 K562 RIP-Input ripInput K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001226 1226 GSM787561 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStK562RipinputRbpAssocRnaV2 RbpAssocRna leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562T7tagRbpAssocRnaV2 K562 T7Tag T7Tag K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001225 1225 GSM787558 Tenenbaum SunyAlbany Nov_69522 antibody hg18 wgEncodeSunyAlbanyGeneStK562T7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562SlbpRbpAssocRnaV2 K562 SLBP SLBP K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001224 1224 GSM787573 Tenenbaum SunyAlbany SC_26522,Mil_061376 antibodies hg18 wgEncodeSunyAlbanyGeneStK562SlbpRbpAssocRnaV2 RbpAssocRna Stem-loop binding protein (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 SLBP RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562Pabpc1RbpAssocRnaV2 K562 PABPC1 PABPC1 K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001223 1223 GSM787567 Tenenbaum SunyAlbany Sig_P6246  antibody hg18 wgEncodeSunyAlbanyGeneStK562Pabpc1RbpAssocRnaV2 RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 PABPC1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562Elavl1RbpAssocRnaV2 K562 ELAVL1 ELAVL1 K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001222 1222 GSM787564 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStK562Elavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 ELAVL1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562Celf1RbpAssocRnaV2 K562 CELF1 CELF1 K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001233 1233 GSM787570 Tenenbaum SunyAlbany Mil_05621 antibody hg18 wgEncodeSunyAlbanyGeneStK562Celf1RbpAssocRnaV2 RbpAssocRna Embryo deadenylation element-binding protein homolog (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 CELF1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStH1hescRipinputRbpAssocRnaV2 H1hESC RIP-Input ripInput H1-hESC RipGeneSt ENCODE Mar 2012 Freeze 2010-12-10 2011-09-10 wgEncodeEH001236 1236 GSM787623 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStH1hescRipinputRbpAssocRnaV2 RbpAssocRna embryonic stem cells RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA H1-hESC RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStH1hescT7tagRbpAssocRnaV2 H1hESC T7Tag T7Tag H1-hESC RipGeneSt ENCODE Mar 2012 Freeze 2010-12-10 2011-09-10 wgEncodeEH001235 1235 GSM787620 Tenenbaum SunyAlbany Nov_69522,Mil_AB3790 antibodies hg18 wgEncodeSunyAlbanyGeneStH1hescT7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) embryonic stem cells RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA H1-hESC T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStH1hescElavl1RbpAssocRnaV2 H1hESC ELAVL1 ELAVL1 H1-hESC RipGeneSt ENCODE Mar 2012 Freeze 2010-12-10 2011-09-10 wgEncodeEH001234 1234 GSM787626 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStH1hescElavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) embryonic stem cells RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA H1-hESC ELAV1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878RipinputRbpAssocRnaV2 GM12878 RIP-Input ripInput GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001219 1219 GSM787540 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStGm12878RipinputRbpAssocRnaV2 RbpAssocRna B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878T7tagRbpAssocRnaV2 GM12878 T7Tag T7Tag GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001218 1218 GSM787537 Tenenbaum SunyAlbany Nov_69522 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878T7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878SlbpRbpAssocRnaV2 GM12878 SLBP SLBP GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001217 1217 GSM787552 Tenenbaum SunyAlbany SC_26522 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878SlbpRbpAssocRnaV2 RbpAssocRna Stem-loop binding protein (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 SLBP RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878Pabpc1RbpAssocRnaV2 GM12878 PABPC1 PABPC1 GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001216 1216 GSM787546 Tenenbaum SunyAlbany Sig_P6246 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878Pabpc1RbpAssocRnaV2 RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 PABPC1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878Igf2bp1RbpAssocRnaV2 GM12878 IGF2BP1 IGF2BP1 GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001215 1215 GSM787555 Tenenbaum SunyAlbany SC_21027 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878Igf2bp1RbpAssocRnaV2 RbpAssocRna Insulin-like growth factor 2 mRNA binding protein 1 (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 IGF2BP1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878Elavl1RbpAssocRnaV2 GM12878 ELAVL1 ELAVL1 GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001214 1214 GSM787543 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878Elavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 ELAVL1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878Celf1RbpAssocRnaV2 GM12878 CELF1 CELF1 GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001213 1213 GSM787549 Tenenbaum SunyAlbany Mil_05621 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878Celf1RbpAssocRnaV2 RbpAssocRna Embryo deadenylation element-binding protein homolog (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 CELF1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTiling SUNY RIP Tiling GSE40691 RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany Regulation Description This track is produced as part of the ENCODE Project. This track displays transcriptional fragments associated with RNA binding proteins in different cell lines, using RIP-Chip (Ribonomic) profiling on Affymetrix GeneChip ENCODE 2.0R Tiling Arrays. The RBP Assoc RNA view shows the genomic location of transcripts associated with the array probes. Data for this track was produced as part of the Encyclopedia of DNA Elements (ENCODE) Project. In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Chip profiling. Display Conventions and Configuration This track is a multi-view composite track. For each view there are multiple subtracks that display individually in the browser. The subtracks within this track correspond to different antibodies/target proteins tested in different cell lines. This track is initially released with a single view: RBP Assoc RNA The RBP Assoc RNA view shows the genomic extent of the transcriptional segments associated with the Affymetrix Tiling Array probes. Instructions for configuring multi-view tracks are here. Methods RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols . The associated transcriptional fragments were identified using Affymetrix GeneChip ENCODE 2.0R Tiling Arrays. Arrays were analyzed using Affymetrix Tiling Analysis Software (TAS) version 1.1. Total Input and T7Tag (negative control) tracks were each developed by single sample analysis of their respective triplicate sets with quantile normalization and linear scaling applied. Probe signals were calculated using the Hodges-Lehmann estimator with a bandwidth of 100 bases. Resulting signal files were examined to develop percentiles. Interval analysis was performed using a minimum cut-off equal to the 95th percentile signal score, a minimum run of 21 (3 * platform resolution) and max gap of 63 (9 * platform resolution). Treatment RIP tracks (e.g., ELAVL1, PABC1) were developed by two sample analysis with T7Tag used as the control. Quantile normalization and scaling was applied to these sample groups individually. Probe signals were calculated with the Hodges-Lehmann estimator using signal log (log2) ratios and a bandwidth of 100 bases. Resulting signal files were examined to develop percentiles. Interval analysis was performed using a minimum cut-off equal to the 95th percentile signal ratio score, a minimum run of 21 (3 * platform resolution) and max gap of 63 (9 * platform resolution). For additional RIP methods detail, see Tenenbaum et al. 2002; Baroni et al. 2008; Penalva et al. 2004, below. Verification All experiments (including controls) performed in and analyzed as triplicates. Credits These data were produced and analyzed by a collaboration between the Tenenbaum lab at the University at Albany-SUNY, College of Nanoscale Science and Engineering, the Luiz Penalva group at the Greehey Children's Cancer Research Institute, University of Texas Health Science Center and the Microarray Core Facility at the Center for Functional Genomics, Rensselaer, NY . Contact: &#83;&#84;&#101;&#110;&#101;&#110;&#98;&#97;um&#64;&#117;&#97;m&#97;&#105;&#108;. &#97;&#108;&#98;&#97;ny. &#101;&#100;&#117; References Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods. 2002 Feb;26(2):191-8. Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol. 2008;419:93-108. Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes. Methods Mol Biol. 2004;257:125-34. Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell. 2002;9(6):1161-7. George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006;3(2):57-9. Epub 2006 Apr 1. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeSunyAlbanyTilingView SunyAlbanyTiling RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany Regulation 
wgEncodeSunyAlbanyTilingK562RipinputRbpAssocRna K562 Input ripInput K562 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001261 1261 GSM999236 Tenenbaum SunyAlbany Input wgEncodeSunyAlbanyTilingK562RipinputRbpAssocRna RbpAssocRna leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 Input RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingK562T7tagRbpAssocRna K562 T7Tag T7Tag K562 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001260 1260 GSM999237 Tenenbaum SunyAlbany Nov_69522,Mil_AB3790 antibodies wgEncodeSunyAlbanyTilingK562T7tagRbpAssocRna RbpAssocRna T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 T7Tag RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingK562Pabpc1RbpAssocRna K562 PABPC1 PABPC1 K562 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001259 1259 GSM999239 Tenenbaum SunyAlbany Sig_P6246 antibody wgEncodeSunyAlbanyTilingK562Pabpc1RbpAssocRna RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 PABPC1 RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingK562Elavl1RbpAssocRna K562 ELAVL1 ELAVL1 K562 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001258 1258 GSM999238 Tenenbaum SunyAlbany SC_5261 antibody wgEncodeSunyAlbanyTilingK562Elavl1RbpAssocRna RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 ELAVL1 RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingGm12878RipinputRbpAssocRna GM12878 Input ripInput GM12878 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001257 1257 GSM999240 Tenenbaum SunyAlbany Input wgEncodeSunyAlbanyTilingGm12878RipinputRbpAssocRna RbpAssocRna B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 Input RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingGm12878T7tagRbpAssocRna GM12878 T7Tag T7Tag GM12878 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001256 1256 GSM999241 Tenenbaum SunyAlbany Nov_69522 antibody wgEncodeSunyAlbanyTilingGm12878T7tagRbpAssocRna RbpAssocRna T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 T7Tag RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingGm12878Pabpc1RbpAssocRna GM12878 PABPC1 PABPC1 GM12878 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001255 1255 GSM999243 Tenenbaum SunyAlbany Sig_P6246 antibody wgEncodeSunyAlbanyTilingGm12878Pabpc1RbpAssocRna RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 PABPC1 RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingGm12878Elavl1RbpAssocRna GM12878 ELAVL1 ELAVL1 GM12878 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001254 1254 GSM999242 Tenenbaum SunyAlbany SC_5261 antibody wgEncodeSunyAlbanyTilingGm12878Elavl1RbpAssocRna RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 ELAVL1 RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeq SUNY RIP-seq GSE35585 RIP-seq from ENCODE/SUNY Albany Regulation Description The RNA binding protein (RBP) associated mRNA sequencing track (RIP-Seq) is produced as part of the Encyclopedia of DNA Elements (ENCODE) Project. This track displays transcriptional fragments associated with RBP in cell lines K562 and GM12878, using Ribonomic profiling via Illumina SBS. In eukaryotic organisms gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Seq profiling. Display Conventions and Configuration This track is a multi-view composite track. For each view there are multiple subtracks that display individually in the browser. The subtracks within this track correspond to different antibodies/target proteins tested in different cell lines. Peaks The Peaks view shows the genomic extent of the sequencing read peaks. Signal Density graph of signal enrichment based on a normalized aligned read density (Read Per Million, RPM). RPM is reported in the score field and is equal to the number of reads at that position divided by the total number of reads divided by one million. The Signal view is unflitered and displays dense, continuous data as a graph and the RPM measure assists in visualizing the relative amount of a given transcript across multiple samples. Alignments The Alignments view shows reads mapped to the genome. The alignment file follows the standard SAM format of Bowtie output. See the Bowtie Manual for more information about the SAM Bowtie output and the SAM Format Specification for more information on the SAM/BAM file format. Instructions for configuring multi-view tracks are here. Methods RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols . RNA samples were amplified and converted to cDNA with the Nugen Ovation&#169; RNA-Seq System and prepped for sequencing with the Illumina mRNA-Seq protocol. Approximately 30 million single end sequencing reads were obtained for each K562 and GM12878. RIP samples were analyzed for signal that was at or above the 60th percentile and statistically enriched compared to the negative control. Sequences were analyzed using TopHat (Trapnell et al., 2009) with Bowtie (Langmead et al., 2009). Peaks were called from the top 40&#37; of TopHat normalized reads, with a max gap, min run of (24:48). Unions of overlapping peak regions from total RNA replicates (RIP-Input) are presented with p-value from a one tailed t-test for average signal from replicates versus 0 (no cut-off was used for totals). Replicate overlap for positive RIP treatment peaks (ELAVL1 and PABPC1) are presented with a p-value from one tailed t-test versus signal for same the region in negative control replicates (T7-tag). RIP peaks were from sequences longer than 120 bp and p-value &lt; .05. For both totals (RIP-input) and RIPs, the peak scores are scaled relative p-values between treatment and control. Credits These data were produced and analyzed by a collaboration between the Tenenbaum lab at the University at Albany-SUNY, College of Nanoscale Science and Engineering,the Luiz Penalva group at the Greehey Children's Cancer Research Institute, University of Texas Health Science Center and the Microarray Core Facility at the Center for Functional Genomics, Rensselaer, NY. Contact: Scott Tenenbaum References Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling . Methods Mol Biol. 2008;419:93-108. George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements . RNA Biol. 2006;3(2):57-9. Epub 2006 Apr 1. Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons . Mol Cell. 2002;9(6):1161-7. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome . Genome Biology. 2009 Mar; 10:R25. Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes . Methods Mol Biol. 2004;257:125-34. Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays . Methods. 2002 Feb;26(2):191-8. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeSunyRipSeqViewSignal Signal RIP-seq from ENCODE/SUNY Albany Regulation 
wgEncodeSunyRipSeqK562RipinputSigRep2 K562 Input 2 ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000795 795 GSM944521 Tenenbaum SunyAlbany 2 wgEncodeSunyRipSeqK562RipinputSigRep2 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 RIP-Input RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562RipinputSigRep1 K562 Input 1 ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000795 795 GSM944521 Tenenbaum SunyAlbany 1 wgEncodeSunyRipSeqK562RipinputSigRep1 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 RIP-Input RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562T7tagSigRep2 K562 T7Tag 2 T7Tag K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000800 800 GSM944526 Tenenbaum SunyAlbany Nov_69522 antibody 2 wgEncodeSunyRipSeqK562T7tagSigRep2 Signal T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 T7Tag RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562T7tagSigRep1 K562 T7Tag 1 T7Tag K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000800 800 GSM944526 Tenenbaum SunyAlbany Nov_69522 antibody 1 wgEncodeSunyRipSeqK562T7tagSigRep1 Signal T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 T7Tag RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1SigRep2 K562 PABPC1 2 PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000794 794 GSM944522 Tenenbaum SunyAlbany Sig_P6246 antibody 2 wgEncodeSunyRipSeqK562Pabpc1SigRep2 Signal Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 PABPC1 RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1SigRep1 K562 PABPC1 1 PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000794 794 GSM944522 Tenenbaum SunyAlbany Sig_P6246 antibody 1 wgEncodeSunyRipSeqK562Pabpc1SigRep1 Signal Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 PABPC1 RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1SigRep2 K562 ELAVL1 2 ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000793 793 GSM944523 Tenenbaum SunyAlbany SC_5261 antibody 2 wgEncodeSunyRipSeqK562Elavl1SigRep2 Signal (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 ELAVL1 RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1SigRep1 K562 ELAVL1 1 ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000793 793 GSM944523 Tenenbaum SunyAlbany SC_5261 antibody 1 wgEncodeSunyRipSeqK562Elavl1SigRep1 Signal (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 ELAVL1 RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputSigRep2 GM12878 Input 2 ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000798 798 GSM944525 Tenenbaum SunyAlbany 2 wgEncodeSunyRipSeqGm12878RipinputSigRep2 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 RIP-Input RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputSigRep1 GM12878 Input 1 ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000798 798 GSM944525 Tenenbaum SunyAlbany 1 wgEncodeSunyRipSeqGm12878RipinputSigRep1 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 RIP-Input RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878T7tagSigRep2 GM12878 T7Tag 2 T7Tag GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000799 799 GSM944524 Tenenbaum SunyAlbany Nov_69522 antibody 2 wgEncodeSunyRipSeqGm12878T7tagSigRep2 Signal T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 T7Tag RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878T7tagSigRep1 GM12878 T7Tag 1 T7Tag GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000799 799 GSM944524 Tenenbaum SunyAlbany Nov_69522 antibody 1 wgEncodeSunyRipSeqGm12878T7tagSigRep1 Signal T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 T7Tag RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1SigRep2 GM12878 PABPC1 2 PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000797 797 GSM944519 Tenenbaum SunyAlbany Sig_P6246 antibody 2 wgEncodeSunyRipSeqGm12878Pabpc1SigRep2 Signal Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 PABPC1 RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1SigRep1 GM12878 PABPC1 1 PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000797 797 GSM944519 Tenenbaum SunyAlbany Sig_P6246 antibody 1 wgEncodeSunyRipSeqGm12878Pabpc1SigRep1 Signal Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 PABPC1 RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1SigRep2 GM12878 ELAVL1 2 ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000796 796 GSM944520 Tenenbaum SunyAlbany SC_5261 antibody 2 wgEncodeSunyRipSeqGm12878Elavl1SigRep2 Signal (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 ELAVL1 RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1SigRep1 GM12878 ELAVL1 1 ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000796 796 GSM944520 Tenenbaum SunyAlbany SC_5261 antibody 1 wgEncodeSunyRipSeqGm12878Elavl1SigRep1 Signal (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 ELAVL1 RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqViewPeaks Peaks RIP-seq from ENCODE/SUNY Albany Regulation 
wgEncodeSunyRipSeqK562RipinputPk K562 Input Pk ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000795 795 GSM944521 Tenenbaum SunyAlbany wgEncodeSunyRipSeqK562RipinputPk Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment K562 RIP-Input RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1Pk K562 PABPC1 Pk PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000794 794 GSM944522 Tenenbaum SunyAlbany Sig_P6246 antibody wgEncodeSunyRipSeqK562Pabpc1Pk Peaks Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment K562 PABPC1 RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1Pk K562 ELAVL1 Pk ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000793 793 GSM944523 Tenenbaum SunyAlbany SC_5261 antibody wgEncodeSunyRipSeqK562Elavl1Pk Peaks (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment K562 ELAVL1 RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputPk GM12878 Input Pk ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH000798 798 GSM944525 Tenenbaum SunyAlbany wgEncodeSunyRipSeqGm12878RipinputPk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment GM12878 RIP-Input RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1Pk GM12878 PABPC1 Pk PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH000797 797 GSM944519 Tenenbaum SunyAlbany Sig_P6246 antibody wgEncodeSunyRipSeqGm12878Pabpc1Pk Peaks Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment GM12878 PABPC1 RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1Pk GM12878 ELAVL1 Pk ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH000796 796 GSM944520 Tenenbaum SunyAlbany SC_5261 antibody wgEncodeSunyRipSeqGm12878Elavl1Pk Peaks (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment GM12878 ELAVL1 RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqViewAlignments Alignments RIP-seq from ENCODE/SUNY Albany Regulation 
wgEncodeSunyRipSeqK562RipinputAlnRep2 K562 Input 2 ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000795 795 Tenenbaum SunyAlbany 2 wgEncodeSunyRipSeqK562RipinputAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 RIP-Input RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562RipinputAlnRep1 K562 Input 1 ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000795 795 Tenenbaum SunyAlbany 1 wgEncodeSunyRipSeqK562RipinputAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 RIP-Input RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562T7tagAlnRep2 K562 T7Tag 2 T7Tag K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000800 800 Tenenbaum SunyAlbany Nov_69522 antibody 2 wgEncodeSunyRipSeqK562T7tagAlnRep2 Alignments T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 T7Tag RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562T7tagAlnRep1 K562 T7Tag 1 T7Tag K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000800 800 Tenenbaum SunyAlbany Nov_69522 antibody 1 wgEncodeSunyRipSeqK562T7tagAlnRep1 Alignments T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 T7Tag RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1AlnRep2 K562 PABPC1 2 PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000794 794 Tenenbaum SunyAlbany Sig_P6246 antibody 2 wgEncodeSunyRipSeqK562Pabpc1AlnRep2 Alignments Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 PABPC1 RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1AlnRep1 K562 PABPC1 1 PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000794 794 Tenenbaum SunyAlbany Sig_P6246 antibody 1 wgEncodeSunyRipSeqK562Pabpc1AlnRep1 Alignments Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 PABPC1 RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1AlnRep2 K562 ELAVL1 2 ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000793 793 Tenenbaum SunyAlbany SC_5261 antibody 2 wgEncodeSunyRipSeqK562Elavl1AlnRep2 Alignments (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 ELAVL1 RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1AlnRep1 K562 ELAVL1 1 ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000793 793 Tenenbaum SunyAlbany SC_5261 antibody 1 wgEncodeSunyRipSeqK562Elavl1AlnRep1 Alignments (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 ELAVL1 RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputAlnRep2 GM12878 Input 2 ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000798 798 Tenenbaum SunyAlbany 2 wgEncodeSunyRipSeqGm12878RipinputAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 RIP-Input RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputAlnRep1 GM12878 Input 1 ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000798 798 Tenenbaum SunyAlbany 1 wgEncodeSunyRipSeqGm12878RipinputAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 RIP-Input RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878T7tagAlnRep2 GM12878 T7Tag 2 T7Tag GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000799 799 Tenenbaum SunyAlbany Nov_69522 antibody 2 wgEncodeSunyRipSeqGm12878T7tagAlnRep2 Alignments T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 T7Tag RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878T7tagAlnRep1 GM12878 T7Tag 1 T7Tag GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000799 799 Tenenbaum SunyAlbany Nov_69522 antibody 1 wgEncodeSunyRipSeqGm12878T7tagAlnRep1 Alignments T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 T7Tag RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1AlnRep2 GM12878 PABPC1 2 PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000797 797 Tenenbaum SunyAlbany Sig_P6246 antibody 2 wgEncodeSunyRipSeqGm12878Pabpc1AlnRep2 Alignments Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 PABPC1 RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1AlnRep1 GM12878 PABPC1 1 PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000797 797 Tenenbaum SunyAlbany Sig_P6246 antibody 1 wgEncodeSunyRipSeqGm12878Pabpc1AlnRep1 Alignments Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 PABPC1 RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1AlnRep2 GM12878 ELAVL1 2 ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000796 796 Tenenbaum SunyAlbany SC_5261 antibody 2 wgEncodeSunyRipSeqGm12878Elavl1AlnRep2 Alignments (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 ELAVL1 RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1AlnRep1 GM12878 ELAVL1 1 ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000796 796 Tenenbaum SunyAlbany SC_5261 antibody 1 wgEncodeSunyRipSeqGm12878Elavl1AlnRep1 Alignments (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 ELAVL1 RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSydhHistone SYDH Histone GSE31755 Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation Description This track, produced as part of the ENCODE Project, displays maps of histone modifications genome-wide using ChIP-seq in different cell lines. The ChIP-seq method involves first using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA within cells. The cross-linked chromatin is subsequently extracted, sheared, and immunoprecipitated using specific antibodies. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. Chemical modifications (e.g. methylation or acetylation) of the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription factors. Shown for each experiment (defined as a particular antibody and a particular cell type) is a track of enrichment for the specifically modified histone (Signal), along with sites that have the greatest enrichment (Peaks). Also, included for each cell type is the input signal, which represents the control condition where no antibody targeting was performed. In general, the following chemical modifications have associated genetic phenotypes: H3K4me3 and H3K9ac are considered to be marks of active or potentially active promoter regions H3K4me1 and H3K27ac are considered to be marks of active or potentially active enhancer regions\ H3K36me3 and H3K79me2 are considered to be marks of transcriptional elongation H3K27me3 and H3K9me3 are considered to be marks of inactive regions. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: Peaks Regions of signal enrichment based on processed data (usually normalized data from pooled replicates). Signal Density graph (wiggle) of signal enrichment based on aligned read density. Peaks and signals displayed in this track are the results of pooled replicate sequence. Alignment files for each replicate are available for download. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Briefly, cells were cross-linked, chromatin was extracted and sonicated using a Bioruptor sonicator (Diagenode) to an average size of 300-500 bp, and individual ChIP assays were performed using antibodies to modified histones. For the K562, MCF-7, HCT-116, NTera-2 (NT2-D1), PANC-1 and PBMC histone ChIP-seq samples, immunoprecipitates were collected using protein G-coupled magnetic beads; a detailed ChIP and library protocol can be found at the Roadmap Epigenome Project. For the U2OS histone ChIP-seq samples, immunoprecipitates were collected using StaphA cells. detailed protocol can be found at the UCD Genome Center. --> Library DNA was quantitated using either a Nanodrop or a BioAnalyzer and sequenced on an Illumina GA2. The sequencing reads were mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length &#126;30 bps) that align uniquely to the human genome. From the mapped tags, a signal map of ChIP DNA fragments (average fragment length &#126; 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome. For each 1 Mb segment of each chromosome, a peak height threshold was determined by requiring a false discovery rate &lt;&#61; 0.05 when comparing the number of peaks above threshold as compared to the number obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value &lt;&#61; 0.05 are considered to be significantly enriched compared to the input DNA control. Release Notes This is Release 3 (June 2012) of this track, which adds 9 new experiments for the MCF-7, HCT-116 and PANC-1 cell lines. Credits These data were generated and analyzed by the labs of Peggy Farnham (USC/Norris Cancer Center; previously at UC Davis) and Michael Snyder at Stanford University. Contact: Peggy Farnham for questions concerning data collection and usage and Philip Cayting for data scoring and submission inquiries. References Blahnik KR, Dou L, Echupare L, Iyengar S, O&#39;Geen H, et al. Characterization of the Contradictory Chromatin Signatures at the 3&#39; Exons of Zinc Finger Genes. PLoS One. 2011;6(2):e17121. O&#39;Geen H, Echipare L, Farnham PJ Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol Biol. 2011;791;265-286. O&#39;Geen H, Frietze S, Farnham PJ Using ChIP-seq Technology to Identify Targets of Zinc Finger Transcription Factors. Methods Mol Biol. 2010;649:437-455. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeSydhHistoneViewSignal Signal Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation 
wgEncodeSydhHistoneU2osInputUcdSig U2OS Input Input U2OS UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-11 2011-03-11 wgEncodeEH000916 916 GSM788069 Snyder USC PeakSeq1.0 input wgEncodeSydhHistoneU2osInputUcdSig None Signal osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneU2osH3k36me3bUcdSig U2OS H3K36me3 H3K36me3B U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-11-02 2011-02-15 wgEncodeEH000920 920 GSM788076 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneU2osH3k36me3bUcdSig None Signal Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS H3K36me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneU2osH3k9me3UcdSig U2OS H3K9me3 H3K9me3 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-16 2011-05-16 wgEncodeEH000919 919 GSM788078 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneU2osH3k9me3UcdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS H3K9me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcInputUcdSig PBMC Input Input PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH001883 1883 GSM788070 Snyder USC PeakSeq1.0 input wgEncodeSydhHistonePbmcInputUcdSig None Signal peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k27me3bUcdSig PBMC H3K27me3 H3K27me3B PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001746 1746 GSM788073 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k27me3bUcdSig None Signal Histone H3 (tri-methyl K27) marks repressed chromatin regions peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC H3K27me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k9me3UcdSig PBMC H3K9me3 H3K9me3 PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001748 1748 GSM788079 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k9me3UcdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC H3K9me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k04me3bUcdSig PBMC H3K4me3 H3K4me3B PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH001882 1882 GSM788075 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k04me3bUcdSig None Signal Histone H3 (tri-methyl K4) marks promoters in chromatin regions peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC H3K4me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k4me1UcdSig PBMC H3K4me1 H3K4me1 PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001747 1747 GSM788084 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k4me1UcdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC H3K4me1 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1InputUcdSig PANC-1 Input Input PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002070 2070 GSM818828 Snyder USC PeakSeq1.0 input wgEncodeSydhHistonePanc1InputUcdSig None Signal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC-1 Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k27acUcdSig PANC-1 H3K27ac H3K27ac PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002080 2080 GSM818826 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k27acUcdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC-1 H3K27ac Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k04me3bUcdSig PANC-1 H3K4me3 H3K4me3B PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002876 2876 GSM945856 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k04me3bUcdSig None Signal Histone H3 (tri-methyl K4) marks promoters in chromatin regions pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC-1 H3K4me3 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k04me1bUcdSig PANC-1 H3K4me1 H3K4me1_(pAb-037-050) PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002081 2081 GSM818827 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k04me1bUcdSig None Signal Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution.Histone tails undergo numerous posttranslational modifications. This antibodies recognizes histone H3 monomethylated on lysine 4. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC-1 H3K4me1 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1InputUcdSig NT2-D1 Input Input NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000654 654 GSM788077 Snyder USC PeakSeq1.0 input wgEncodeSydhHistoneNt2d1InputUcdSig None Signal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k36me3bUcdSig NT2-D1 H3K36me3 H3K36me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000915 915 GSM788081 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k36me3bUcdSig None Signal Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K36me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k27me3bUcdSig NT2-D1 H3K27me3 H3K27me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000908 908 GSM788071 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k27me3bUcdSig None Signal Histone H3 (tri-methyl K27) marks repressed chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K27me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k9acbUcdSig NT2-D1 H3K9ac H3K9acB NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000910 910 GSM788086 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k9acbUcdSig None Signal Histone H3 (acetyl K9) marks promoters in chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K9ac Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k09me3UcdSig NT2-D1 H3K9me3 H3K9me3 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2010-06-22 2011-03-21 wgEncodeEH000918 918 GSM788080 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k09me3UcdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K9me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k4me3bUcdSig NT2-D1 H3K4me3 H3K4me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000909 909 GSM788072 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k4me3bUcdSig None Signal Histone H3 (tri-methyl K4) marks promoters in chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K4me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k4me1UcdSig NT2-D1 H3K4me1 H3K4me1 NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-21 wgEncodeEH000917 917 GSM788083 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k4me1UcdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K4me1 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116InputUcdSig HCT-116 Input Input HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH000627 627 GSM945855 Snyder USC PeakSeq1.0 input wgEncodeSydhHistoneHct116InputUcdSig None Signal colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 Input Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116H3k27acUcdSig HCT-116 H3K27ac H3K27ac HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002873 2873 GSM945853 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneHct116H3k27acUcdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 H3K27ac Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116H3k04me1UcdSig HCT-116 H3K4me1 H3K4me1 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002874 2874 GSM945858 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneHct116H3k04me1UcdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 H3K4me1 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7InputUcdSig MCF7 Inupt Input MCF-7 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000762 762 GSM945859 Snyder USC hg18 input wgEncodeSydhHistoneMcf7InputUcdSig None Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k36me3bUcdSig MCF-7 H3K36me3 H3K36me3B MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-07 2013-03-07 wgEncodeEH002923 2923 GSM970217 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k36me3bUcdSig None Signal Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 H3K36me3 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k27me3bUcdSig MCF-7 H3K27me3 H3K27me3B MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-07 2013-03-07 wgEncodeEH002922 2922 GSM970218 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k27me3bUcdSig None Signal Histone H3 (tri-methyl K27) marks repressed chromatin regions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 H3K27me3 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k27acUcdSig MCF-7 H3K27ac H3K27ac MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-01-22 2012-10-21 wgEncodeEH002872 2872 GSM945854 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k27acUcdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 H3K27ac Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k09me3UcdSig MCF-7 H3K9me3 H3K9me3 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002875 2875 GSM945857 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k09me3UcdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 H3K9me3 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562InputUcdSig K562 Input Input K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2009-06-11 2010-03-11 wgEncodeEH000672 672 GSM788074 Snyder USC hg18 input wgEncodeSydhHistoneK562InputUcdSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k27me3bUcdSig K562 H3K27me3 H3K27me3B K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000912 912 GSM788088 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k27me3bUcdSig None Signal Histone H3 (tri-methyl K27) marks repressed chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 H3K27me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k9acbUcdSig K562 H3K9ac H3K9acB K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000914 914 GSM788082 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k9acbUcdSig None Signal Histone H3 (acetyl K9) marks promoters in chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 H3K9ac Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k4me3bUcdSig K562 H3K4me3 H3K4me3B K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000913 913 GSM788087 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k4me3bUcdSig None Signal Histone H3 (tri-methyl K4) marks promoters in chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 H3K4me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k4me1UcdSig K562 H3K4me1 H3K4me1 K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH000911 911 GSM788085 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k4me1UcdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 H3K4me1 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation 
wgEncodeSydhHistoneU2osH3k36me3bUcdPk U2OS H3K36me3 H3K36me3B U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-11-02 2011-02-15 wgEncodeEH000920 920 GSM788076 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneU2osH3k36me3bUcdPk None Peaks Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment U2OS H3K36me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneU2osH3k9me3UcdPk U2OS H3K9me3 H3K9me3 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-16 2011-05-16 wgEncodeEH000919 919 GSM788078 Snyder USC PeakSeq1.0.  Submitted even though replicate peak overlap below threshold because data visually looks good, but calling peaks for H3K9me3 is very difficult due to the nature of the signal and not the quality of the data.  When we call peaks using our program that has been modified for histones, we get a ~60% overlap. That's about as good as it gets with H3K9me3 peak calling. exp wgEncodeSydhHistoneU2osH3k9me3UcdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment U2OS H3K9me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k27me3bUcdPk PBMC H3K27me3 H3K27me3B PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001746 1746 GSM788073 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k27me3bUcdPk None Peaks Histone H3 (tri-methyl K27) marks repressed chromatin regions peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBMC H3K27me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k9me3UcdPk PBMC H3K9me3 H3K9me3 PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001748 1748 GSM788079 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k9me3UcdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBMC H3K9me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k04me3bUcdPk PBMC H3K4me3 H3K4me3B PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH001882 1882 GSM788075 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k04me3bUcdPk None Peaks Histone H3 (tri-methyl K4) marks promoters in chromatin regions peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBMC H3K4me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k4me1UcdPk PBMC H3K4me1 H3K4me1 PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001747 1747 GSM788084 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k4me1UcdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBMC H3K4me1 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k27acUcdPk PANC-1 H3K27ac H3K27ac PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002080 2080 GSM818826 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k27acUcdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PANC-1 H3K27ac Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k04me3bUcdPk PANC-1 H3K4me3 H3K4me3B PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002876 2876 GSM945856 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k04me3bUcdPk None Peaks Histone H3 (tri-methyl K4) marks promoters in chromatin regions pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PANC-1 H3K4me3 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k04me1bUcdPk PANC-1 H3K4me1 H3K4me1_(pAb-037-050) PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002081 2081 GSM818827 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k04me1bUcdPk None Peaks Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution.Histone tails undergo numerous posttranslational modifications. This antibodies recognizes histone H3 monomethylated on lysine 4. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PANC-1 H3K4me1 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k36me3bUcdPk NT2-D1 H3K36me3 H3K36me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000915 915 GSM788081 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k36me3bUcdPk None Peaks Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K36me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k27me3bUcdPk NT2-D1 H3K27me3 H3K27me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000908 908 GSM788071 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k27me3bUcdPk None Peaks Histone H3 (tri-methyl K27) marks repressed chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K27me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k9acbUcdPk NT2-D1 H3K9ac H3K9acB NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000910 910 GSM788086 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k9acbUcdPk None Peaks Histone H3 (acetyl K9) marks promoters in chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K9ac Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k09me3UcdPk NT2-D1 H3K9me3 H3K9me3 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2010-06-22 2011-03-21 wgEncodeEH000918 918 GSM788080 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k09me3UcdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K9me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k4me3bUcdPk NT2-D1 H3K4me3 H3K4me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000909 909 GSM788072 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k4me3bUcdPk None Peaks Histone H3 (tri-methyl K4) marks promoters in chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K4me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k4me1UcdPk NT2-D1 H3K4me1 H3K4me1 NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-21 wgEncodeEH000917 917 GSM788083 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k4me1UcdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K4me1 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116H3k27acUcdPk HCT-116 H3K27ac H3K27ac HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002873 2873 GSM945853 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneHct116H3k27acUcdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 H3K27ac Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116H3k04me1UcdPk HCT-116 H3K4me1 H3K4me1 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002874 2874 GSM945858 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneHct116H3k04me1UcdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 H3K4me1 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k36me3bUcdPk MCF-7 H3K36me3 H3K36me3B MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-07 2013-03-07 wgEncodeEH002923 2923 GSM970217 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k36me3bUcdPk None Peaks Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 H3K36me3 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k27me3bUcdPk MCF-7 H3K27me3 H3K27me3B MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-07 2013-03-07 wgEncodeEH002922 2922 GSM970218 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k27me3bUcdPk None Peaks Histone H3 (tri-methyl K27) marks repressed chromatin regions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 H3K27me3 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k27acUcdPk MCF-7 H3K27ac H3K27ac MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-01-22 2012-10-21 wgEncodeEH002872 2872 GSM945854 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k27acUcdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 H3K27ac Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k09me3UcdPk MCF-7 H3K9me3 H3K9me3 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002875 2875 GSM945857 Snyder USC PeakSeq1.0. Spreading mark so standard peak calling does not work well.  Replicates appear to agree regardless. exp wgEncodeSydhHistoneMcf7H3k09me3UcdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 H3K9me3 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k27me3bUcdPk K562 H3K27me3 H3K27me3B K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000912 912 GSM788088 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k27me3bUcdPk None Peaks Histone H3 (tri-methyl K27) marks repressed chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 H3K27me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k9acbUcdPk K562 H3K9ac H3K9acB K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000914 914 GSM788082 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k9acbUcdPk None Peaks Histone H3 (acetyl K9) marks promoters in chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 H3K9ac Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k4me3bUcdPk K562 H3K4me3 H3K4me3B K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000913 913 GSM788087 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k4me3bUcdPk None Peaks Histone H3 (tri-methyl K4) marks promoters in chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 H3K4me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k4me1UcdPk K562 H3K4me1 H3K4me1 K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH000911 911 GSM788085 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k4me1UcdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 H3K4me1 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhRnaSeq SYDH RNA-seq GSE35587 RNA-seq from ENCODE/Stanford/Yale/USC/Harvard Expression Description The tracks show enrichment of RNA sequence tags generated by high throughput sequencing (RNA-seq) and mapped to the human genome. Double stranded cDNA was synthesized from polyadenylated RNA (polyA+) . PCR amplified, adapter ligated cDNA, 150-300nt long, was sequenced on an Illumina GA sequencer. Where designated, cell lines received specific treatments prior to RNA isolation. As indicated, K562 cells were treated with either interferon-a or interferon-g for 30 minutes or 6 hours. These experiments were carried out in conjunction with ChIP-Seq experiments on the transcription factors STAT1 and STAT2 in order to examine the effects that inducers of a specific transcriptional response might have on gene expression and on transcription factor binding site discovery. K562 cells were treated with a-amanitin in order to examine the effects of RNA polymerase II inhibition on RNA polymerase III-mediated transcription. This track shows expression data generated as confirmation of the SYDH TFBS tracks.--> SYDH TFBS tracks currently available on genome-preview. Display Conventions and Configuration This is a composite track that contains multiple data types (views). Instructions for configuring composite tracks are here. Raw SignalDensity graph (wiggle) of signal enrichment. Alignments The Alignments view shows reads mapped to the genome and indicates where bases may mismatch. The alignment file follows the standard SAM format of Bowtie output with the following additions: the custom tags X0 X1 XN XM XO XG XT XA XS XF XE are present. These tags are described by the BWA specifications. See the Bowtie Manual for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format. Methods Cells were grown according to the approved ENCODE cell culture protocols. Total RNA was extracted using TRIzol reagents (15596-018, Life Tech), following the manufacturer's protocol. For polyA+ samples, polyadenylated RNA was purified using the MicroPoly(A) Purist kit (AM1919, Life Tech) and fragmented using RNA Fragmentation Reagent (AM8740, Life Tech). Illumina adapters were ligated to double stranded cDNA which was synthesized using reagents from Life Tech (11917-010). PCR amplified adapter ligated cDNA (150-300 bp) was sequenced using Illumina GA. Sequence reads of 27-33nt long with 0-2 mismatches were mapped to the genome. The signal height corresponds to the number of overlapping fragments at each nucleotide position in the genome. Samples originally mapped to the hg18 version of the human genome were remapped to hg19 using the BWA aligner, version 0.5.7. Credits These data were generated and analyzed by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University; Peggy Farnham at USC; and Kevin Struhl at Harvard. &nbsp;&nbsp; Contact: Gerstein Lab. References Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 Jun 6;320(5881):1344-9. Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3639-44. Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S et al. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5254-9. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeSydhRnaSeqViewSignal Signal RNA-seq from ENCODE/Stanford/Yale/USC/Harvard Expression 
wgEncodeSydhRnaSeqK562Ifng6hPolyaRaw K562 pA+ Ng6h K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH000527 527 GSM922958 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifng6hPolyaRaw IFNg6h RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon gamma treatment - 6 hours (Snyder) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 polyA+ IFNg6h RNA-seq Raw Signal from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifng30PolyaRaw K562 pA+ Ng30 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH000526 526 GSM922957 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifng30PolyaRaw IFNg30 RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon gamma treatment - 30 minutes (Snyder) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 polyA+ IFNg30 RNA-seq Raw Signal from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifna6hPolyaRaw K562 pA+ Na6h K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH000525 525 GSM922956 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifna6hPolyaRaw IFNa6h RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon alpha treatment - 6 hours (Snyder) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 polyA+ IFNa6h RNA-seq Raw Signal from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifna30PolyaRaw K562 pA+ Na30 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH000524 524 GSM922955 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifna30PolyaRaw IFNa30 RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA 30 m of Interferon alpha (Snyder) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 polyA+ IFNa30 RNA-seq Raw Signal from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqViewAlignments Alignments RNA-seq from ENCODE/Stanford/Yale/USC/Harvard Expression 
wgEncodeSydhRnaSeqK562Ifng6hPolyaAln K562 pA+ Ng6h K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-23 2010-09-24 2010-06-24 wgEncodeEH000527 527 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifng6hPolyaAln IFNg6h Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon gamma treatment - 6 hours (Snyder) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polyA+ IFNg6h RNA-seq Alignments from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifng30PolyaAln K562 pA+ Ng30 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-23 2010-09-24 2010-06-24 wgEncodeEH000526 526 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifng30PolyaAln IFNg30 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon gamma treatment - 30 minutes (Snyder) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polyA+ IFNg30 RNA-seq Alignments from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifna6hPolyaAln K562 pA+ Na6h K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-23 2010-09-24 2010-06-24 wgEncodeEH000525 525 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifna6hPolyaAln IFNa6h Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon alpha treatment - 6 hours (Snyder) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polyA+ IFNa6h RNA-seq Alignments from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifna30PolyaAln K562 pA+ Na30 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-23 2010-09-24 2010-06-24 wgEncodeEH000524 524 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifna30PolyaAln IFNa30 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA 30 m of Interferon alpha (Snyder) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polyA+ IFNa30 RNA-seq Alignments from ENCODE/SYDH Expression 
wgEncodeSydhTfbs SYDH TFBS GSE31477 Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation Description This track shows probable binding sites of the specified transcription factors (TFs) in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq). Included for each cell type is the input signal, which represents the control condition where no antibody targeting was performed. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for TF binding (Signal), along with sites that have the greatest evidence of transcription factor binding (Peaks). The sequence reads, quality scores, and alignment coordinates from these experiments are available for download. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. ENCODE tracks typically contain one or more of the following views: Peaks Regions of signal enrichment based on processed data (normalized data from pooled replicates). ENCODE Peaks tables contain fields for statistical significance, including the minimum false discovery rate (FDR) threshold at which the test may be called significant (qValue). SignalDensity graph (wiggle) of signal enrichment based on processed data. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Further preparations were similar to those previously published (Euskirchen et al., 2007) with the exceptions that the cells were unstimulated and sodium orthovanadate was omitted from the buffers. For details on the chromatin immunoprecipitation protocol used, see (Euskirchen et al., 2007) and (Rozowsky et al., 2009). DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bp) that align uniquely to the human genome. From the mapped tags a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome. For each 1 Mb segment of each chromosome a peak height threshold was determined by requiring a false discovery rate less than or equal to 0.05 when comparing the number of peaks above threshold as compared the number obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value less than or equal to 0.05 are considered to be significantly enriched compared to the input DNA control. Release Notes This is Release 3 (August 2012). This release adds in 37 new experiments including 1 new cell line and 7 new antibodies. Credits These data were generated and analyzed by the labs of Michael Snyder at Stanford University; Mark Gerstein and Sherman Weissman at Yale University; Peggy Farnham at University of Southern California; and Kevin Struhl at Harvard. Contact: Philip Cayting. References Cao AR, Rabinovich R, Xu M, Xu X, Jin VX, Farnham PJ. Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome. J Biol Chem. 2011 Apr 8;286(14):11985-96. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M et al. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol. 2004 May;24(9):3804-14. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun;17(6):898-909. Iyengar S, Ivanov AV, Jin VX, Rauscher FJ 3rd, Farnham PJ. Functional analysis of KAP1 genomic recruitment. Mol Cell Biol. 2011 May;31(9):1833-47. Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M et al. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug;4(8):651-7. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009 Jan;27(1):66-75. Publications Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol. 2012 Jan;32(1):226-39. Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell. 2011 Nov 4;44(3):410-23. Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH. Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13641-6. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeSydhTfbsViewSignal Signal Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation 
wgEncodeSydhTfbsU2osInputUcdSig U2OS Inpt UCD Input U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH000916 916 GSM935288 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsU2osInputUcdSig None Signal osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsU2osSetdb1UcdSig U2OS STDB UCD SETDB1 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001762 1762 GSM935458 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsU2osSetdb1UcdSig None Signal SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS SETDB1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsU2osKap1UcdSig U2OS KAP1 UCD KAP1 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-05-31 wgEncodeEH001776 1776 GSM935587 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsU2osKap1UcdSig None Signal KRAB Associated Protein 1, helps regulate transcriptional repression. osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS KAP1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yInputUcdSig SHSY Inpt UCD Input SH-SY5Y UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-02-03 2011-11-03 wgEncodeEH001783 1783 GSM935321 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsShsy5yInputUcdSig None Signal neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal SH-SY5Y Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdSig SHSY GAT3 UCD GATA3_(SC-269) SH-SY5Y UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002031 2031 GSM935567 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdSig None Signal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal SH-SY5Y GATA3 SC269 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yGata2UcdSig SHSY GAT2 UCD GATA-2 SH-SY5Y UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001770 1770 GSM935589 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsShsy5yGata2UcdSig None Signal GATA binding protein 2 neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal SH-SY5Y GATA2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsRajiInputUcdSig Raji Inpt UCD Input Raji UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001760 1760 GSM935460 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsRajiInputUcdSig None Signal B lymphocyte, "The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal Raji Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsRajiPol2UcdSig Raji Pol2 UCD Pol2 Raji UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001761 1761 GSM935461 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsRajiPol2UcdSig None Signal RNA Polymerase II B lymphocyte, "The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal Raji Pol2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdefetalInputUcdSig PBDF Inpt UCD Input PBDEFetal UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001786 1786 GSM935334 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsPbdefetalInputUcdSig None Signal peripheral blood-derived erythroblasts from 16-19 week human fetal liver Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE-Fetal Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdefetalGata1UcdSig PBDF GAT1 UCD GATA-1 PBDEFetal UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001785 1785 GSM935333 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdefetalGata1UcdSig None Signal GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts from 16-19 week human fetal liver Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE-Fetal GATA1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdeInputUcdSig PBDE Inpt UCD Input PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH001778 1778 GSM935593 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsPbdeInputUcdSig None Signal peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdePol2UcdSig PBDE Pol2 UCD Pol2 PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001766 1766 GSM935462 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdePol2UcdSig None Signal RNA Polymerase II peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE Pol2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdeGata1UcdSig PBDE GAT1 UCD GATA-1 PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-09-23 2011-06-23 wgEncodeEH001765 1765 GSM935465 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdeGata1UcdSig None Signal GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE GATA1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPanc1InputUcdSig PANC Inpt UCD Input PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002070 2070 GSM935617 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsPanc1InputUcdSig None Signal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC1 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPanc1Tcf7l2UcdSig PANC TCF7L2 UCD TCF7L2 PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002071 2071 GSM816437 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPanc1Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC1 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1InputUcdSig NT2D Inpt UCD Input NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000654 654 GSM935421 Snyder USC hg18 input wgEncodeSydhTfbsNt2d1InputUcdSig None Signal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2-D1 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Znf274UcdSig NT2D Z274 UCD ZNF274 NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001775 1775 GSM935584 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNt2d1Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2-D1 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Yy1UcdSig NT2D YY1 UCD YY1 NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000653 653 GSM935424 Snyder USC hg18 exp wgEncodeSydhTfbsNt2d1Yy1UcdSig None Signal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2-D1 YY1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Suz12UcdSig NT2D SZ12 UCD SUZ12 NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000652 652 GSM935423 Snyder USC hg18 exp wgEncodeSydhTfbsNt2d1Suz12UcdSig None Signal Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2-D1 SUZ12 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4InputStdSig NB4 Inpt Std Input NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000617 617 GSM935359 Snyder Yale hg18 input wgEncodeSydhTfbsNb4InputStdSig None Signal acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal NB4 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4Pol2StdSig NB4 Pol2 Std Pol2 NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000618 618 GSM935354 Snyder Yale hg18 exp wgEncodeSydhTfbsNb4Pol2StdSig None Signal RNA Polymerase II acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal NB4 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4MaxStdSig NB4 Max Std Max NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-26 2011-05-26 wgEncodeEH001806 1806 GSM935644 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNb4MaxStdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal NB4 Max Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4CmycStdSig NB4 cMyc Std c-Myc NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-26 2011-05-26 wgEncodeEH001807 1807 GSM935643 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNb4CmycStdSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal NB4 c-Myc Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesInputStdSig MCF1 Inpt Std Input MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2011-02-03 2011-11-03 wgEncodeEH001782 1782 GSM935641 Snyder Harvard PeakSeq1.0 hg19 input wgEncodeSydhTfbsMcf10aesInputStdSig None Signal mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal MCF10A Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesInputEtoh01cStdSig MCF1 Et12 Inpt Sd Input MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-13 wgEncodeEH001869 1869 GSM935550 Snyder Harvard PeakSeq1.0 hg19 input wgEncodeSydhTfbsMcf10aesInputEtoh01cStdSig EtOH_0.01pct_12hr Signal mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 h with 0.01% Ethanol (Snyder) Signal MCF10A Input Standard EtOH .01% 36h 12h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesInputEtoh01bStdSig MCF1 Et4h Inpt Sd Input MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-13 wgEncodeEH001870 1870 GSM935418 Snyder Harvard PeakSeq1.0 hg19 input wgEncodeSydhTfbsMcf10aesInputEtoh01bStdSig EtOH_0.01pct_4hr Signal mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 h with 0.01% Ethanol (Snyder) Signal MCF10A Input Standard EtOH .01% 36h 4h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesInputHvdSig MCF1 Input Hvd Input MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Jul 2012 Freeze 2012-04-25 2013-01-25 wgEncodeEH002871 2871 GSM935605 Snyder Harvard PeakSeq1.0 input wgEncodeSydhTfbsMcf10aesInputHvdSig None Signal mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal MCF10A Input Harvard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3TamStdSig MCF1 TAM STA3 Std STAT3 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001769 1769 GSM935457 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesStat3TamStdSig 4OHTAM_1uM_36hr Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Signal MCF10A STAT3 Standard 4-hydroxytamoxifen 36hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3Etoh01StdSig MCF1 EtH STA3 Std STAT3 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001772 1772 GSM935591 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesStat3Etoh01StdSig EtOH_0.01pct Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Signal MCF10A STAT3 Standard EtOH .01% 36h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3Tam112hHvdSig MCF1 TAM 12h STA3 STAT3 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002836 2836 GSM935399 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesStat3Tam112hHvdSig 4OHTAM_1uM_12hr Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Signal MCF10A STAT3 Harvard 4-hydroxytamoxifen 12hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesPol2TamStdSig MCF1 TAM Pol2 Std Pol2 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001768 1768 GSM935456 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesPol2TamStdSig 4OHTAM_1uM_36hr Signal RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Signal MCF10A Pol2 Standard 4-hydroxytamoxifen 36hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesPol2Etoh01StdSig MCF1 EtH Pol2 Std Pol2 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001771 1771 GSM935588 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesPol2Etoh01StdSig EtOH_0.01pct Signal RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Signal MCF10A Pol2 Standard EtOH .01% 36h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesE2f4TamHvdSig MCF1 TAM E2F4 Hvd E2F4 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002835 2835 GSM935400 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesE2f4TamHvdSig 4OHTAM_1uM_36hr Signal mapping at the C-terminus of E2F4 of human origin mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Signal MCF10A E2F4 Harvard 4-hydroxytamoxifen 36hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCmycTam14hHvdSig MCF1 TAM 14h cMyc c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002840 2840 GSM935491 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCmycTam14hHvdSig 4OHTAM_1uM_4hr Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Signal MCF10A c-Myc Harvard 4-hydroxytamoxifen 14hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCmycEtoh01HvdSig MCF1 EtH cMyc Hvd c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002816 2816 GSM935441 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCmycEtoh01HvdSig EtOH_0.01pct Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Signal MCF10A c-Myc Harvard EtOH .01% 36h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTam14hHvdSig MCF1 TAM 14h cFOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002838 2838 GSM935397 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTam14hHvdSig 4OHTAM_1uM_4hr Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Signal MCF10A c-FOS Harvard 4-hydroxytamoxifen 14hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTam112hHvdSig MCF1 TAM 12h cFOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002837 2837 GSM935398 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTam112hHvdSig 4OHTAM_1uM_12hr Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Signal MCF10A c-FOS Harvard 4-hydroxytamoxifen 12hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTamHvdSig MCF1 TAM cFOS Hvd c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002839 2839 GSM935396 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTamHvdSig 4OHTAM_1uM_36hr Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Signal MCF10A c-FOS Harvard 4-hydroxytamoxifen 36hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosEtoh01HvdSig MCF1 EtH cFOS Hvd c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002815 2815 GSM935438 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosEtoh01HvdSig EtOH_0.01pct Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Signal MCF10A c-FOS Harvard EtOH .01% 36h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293tInputUcdSig HEKT Inpt UCD Input HEK293-T-REx UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-02-03 2011-11-03 wgEncodeEH001784 1784 GSM935327 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsHek293tInputUcdSig None Signal embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line, hypotriploid, XXX Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293-T-REx Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293tZnf263UcdSig HEKT Z263 UCD ZNF263 HEK293-T-REx UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-24 2011-10-24 wgEncodeEH001781 1781 GSM935577 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293tZnf263UcdSig None Signal ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line, hypotriploid, XXX Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293-T-REx ZNF263 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293InputUcdSig HEK2 Inpt UCD Input HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-13 wgEncodeEH001777 1777 GSM935586 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsHek293InputUcdSig None Signal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293InputStdSig HEK2 Inpt Std Input HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000631 631 GSM935533 Snyder Yale hg18 input wgEncodeSydhTfbsHek293InputStdSig None Signal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HEK293 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Tcf7l2UcdSig HEK2 TCF7L2 UCD TCF7L2 HEK293 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2012-03-22 wgEncodeEH002022 2022 GSM782124 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Pol2StdSig HEK2 Pol2 Std Pol2 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000632 632 GSM935534 Snyder Yale hg18 exp wgEncodeSydhTfbsHek293Pol2StdSig None Signal RNA Polymerase II embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HEK293 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Kap1UcdSig HEK2 KAP1 UCD KAP1 HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-05-31 wgEncodeEH001779 1779 GSM935592 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Kap1UcdSig None Signal KRAB Associated Protein 1, helps regulate transcriptional repression. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293 KAP1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Elk4UcdSig HEK2 ELK4 UCD ELK4 HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-05-31 wgEncodeEH001773 1773 GSM935590 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Elk4UcdSig None Signal This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293 ELK4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116InputUcdSig HCT Inpt UCD Input HCT-116 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000627 627 GSM817344 Snyder USC hg18 input wgEncodeSydhTfbsHct116InputUcdSig None Signal colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116Tcf7l2UcdSig HCT TCF7L2 UCD TCF7L2 HCT-116 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000629 629 GSM782123 Snyder USC hg18 exp wgEncodeSydhTfbsHct116Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116Pol2UcdSig HCT Pol2 UCD Pol2 HCT-116 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000651 651 GSM935426 Snyder USC hg18 exp wgEncodeSydhTfbsHct116Pol2UcdSig None Signal RNA Polymerase II colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 Pol2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193InputTnfaIggrabSig GM93 TNF Inpt IgR Input GM19193 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000779 779 GSM935454 Snyder Stanford hg18 input wgEncodeSydhTfbsGm19193InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM19193 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193InputIggmusSig GM93 Inpt IgM Input GM19193 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000742 742 GSM935324 Snyder Stanford hg18 input wgEncodeSydhTfbsGm19193InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM19193 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193Pol2IggmusSig GM93 Pol2 IgM Pol2 GM19193 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000743 743 GSM935325 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19193Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM19193 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193NfkbTnfaIggrabSig GM93 TNF NKB IgR NFKB GM19193 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000718 718 GSM935279 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19193NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM19193 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099InputTnfaIggrabSig GM99 TNF Inpt IgR Input GM19099 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000778 778 GSM935455 Snyder Stanford hg18 input wgEncodeSydhTfbsGm19099InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM19099 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099InputIggmusSig GM99 Inpt IgM Input GM19099 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000740 740 GSM935322 Snyder Stanford hg18 input wgEncodeSydhTfbsGm19099InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM19099 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099Pol2IggmusSig GM99 Pol2 IgM Pol2 GM19099 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000741 741 GSM935323 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19099Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM19099 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099NfkbTnfaIggrabSig GM99 TNF NKB IgR NFKB GM19099 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000717 717 GSM935273 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19099NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM19099 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951InputTnfaIggrabSig GM51 TNF Inpt IgR Input GM18951 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000777 777 GSM935448 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18951InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18951 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951InputIggmusSig GM51 Inpt IgM Input GM18951 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000737 737 GSM935528 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18951InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18951 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951Pol2IggmusSig GM51 Pol2 IgM Pol2 GM18951 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000739 739 GSM935530 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18951Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18951 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951NfkbTnfaIggrabSig GM51 TNF NKB IgR NFKB GM18951 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000738 738 GSM935531 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18951NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18951 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526InputTnfaIggrabSig GM26 TNF Inpt IgR Input GM18526 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000776 776 GSM935449 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18526InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18526 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526InputIggmusSig GM26 Inpt IgM Input GM18526 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000732 732 GSM935525 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18526InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18526 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526Pol2IggmusSig GM26 Pol2 IgM Pol2 GM18526 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000733 733 GSM935524 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18526Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18526 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526NfkbTnfaIggrabSig GM26 TNF NKB IgR NFKB GM18526 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000716 716 GSM935281 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18526NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18526 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505InputTnfaIggrabSig GM05 TNF Inpt IgR Input GM18505 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000775 775 GSM935446 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18505InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18505 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505InputIggmusSig GM05 Inpt IgM Input GM18505 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000730 730 GSM935523 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18505InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18505 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505Pol2IggmusSig GM05 Pol2 IgM Pol2 GM18505 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000731 731 GSM935522 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18505Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18505 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505NfkbTnfaIggrabSig GM05 TNF NKB IgR NFKB GM18505 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000715 715 GSM935282 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18505NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18505 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510InputTnfaIggrabSig GM10 TNF Inpt IgR Input GM15510 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000774 774 GSM935447 Snyder Stanford hg18 input wgEncodeSydhTfbsGm15510InputTnfaIggrabSig TNFa Signal lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM15510 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510InputIggmusSig GM10 Inpt IgM Input GM15510 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000713 713 GSM935284 Snyder Stanford hg18 input wgEncodeSydhTfbsGm15510InputIggmusSig None Signal lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM15510 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510Pol2IggmusSig GM10 Pol2 IgM Pol2 GM15510 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000714 714 GSM935291 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm15510Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM15510 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510NfkbTnfaIggrabSig GM10 TNF NKB IgR NFKB GM15510 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000736 736 GSM935529 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm15510NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM15510 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892InputTnfaIggrabSig GM92 TNF Inpt IgR Input GM12892 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000773 773 GSM935452 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12892InputTnfaIggrabSig TNFa Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12892 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892InputIggmusSig GM92 Inpt IgM Input GM12892 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000711 711 GSM935286 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12892InputIggmusSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12892 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892Pol2IggmusSig GM92 Pol2 IgM Pol2 GM12892 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000729 729 GSM935640 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12892Pol2IggmusSig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12892 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892NfkbTnfaIggrabSig GM92 TNF NKB IgR NFKB GM12892 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000712 712 GSM935285 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12892NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12892 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891InputTnfaIggrabSig GM91 TNF Inpt IgR Input GM12891 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000772 772 GSM935453 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12891InputTnfaIggrabSig TNFa Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12891 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891InputIggmusSig GM91 Inpt IgM Input GM12891 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000709 709 GSM935387 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12891InputIggmusSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12891 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891Pol2IggmusSig GM91 Pol2 IgM Pol2 GM12891 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000710 710 GSM935287 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12891Pol2IggmusSig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12891 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891NfkbTnfaIggrabSig GM91 TNF NKB IgR NFKB GM12891 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000735 735 GSM935526 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12891NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12891 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847InputTnfaIggrabSig GM47 TNF Inpt IgR Input GM10847 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000770 770 GSM935451 Snyder Stanford hg18 input wgEncodeSydhTfbsGm10847InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM10847 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847InputIggmusSig GM47 Inpt IgM Input GM10847 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000728 728 GSM935639 Snyder Stanford hg18 input wgEncodeSydhTfbsGm10847InputIggmusSig None Signal lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM10847 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847Pol2IggmusSig GM47 Pol2 IgM Pol2 GM10847 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000705 705 GSM935389 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm10847Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM10847 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847NfkbTnfaIggrabSig GM47 TNF NKB IgR NFKB GM10847 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000734 734 GSM935527 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm10847NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM10847 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm08714InputUcdSig GM14 Inpt UCD Input GM08714 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-04-19 2013-01-19 wgEncodeEH002870 2870 GSM935607 Snyder USC PeakSeq1.0 input wgEncodeSydhTfbsGm08714InputUcdSig None Signal lymphoblastoid cell line, Instability of heterochromatin of chromosomes 1, 9, and 16 with variable combined immunodeficiency; dysmorphic facial features, developmental delay, malabsorption, and recurrent infections; see GM08747 Fibroblast; donor subject is a compound heterozygote: one allele has a G&gt;A transition at nucleotide 1807 (1807G&gt;A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B; the second allele has a G&gt;A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G&gt;A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM08714 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm08714Znf274UcdSig GM14 Z274 UCD ZNF274 GM08714 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002866 2866 GSM935329 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsGm08714Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. lymphoblastoid cell line, Instability of heterochromatin of chromosomes 1, 9, and 16 with variable combined immunodeficiency; dysmorphic facial features, developmental delay, malabsorption, and recurrent infections; see GM08747 Fibroblast; donor subject is a compound heterozygote: one allele has a G&gt;A transition at nucleotide 1807 (1807G&gt;A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B; the second allele has a G&gt;A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G&gt;A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM08714 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshInputIggrabSig SKSH Inpt IgR Input SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-14 2013-05-14 wgEncodeEH003393 3393 GSM1003624 Snyder Stanford PeakSeq1.0 input wgEncodeSydhTfbsSknshInputIggrabSig None Signal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshSmc3IggrabSig SKSH SMC3 IgR SMC3_(ab9263) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003377 3377 GSM1003627 Snyder Stanford exp wgEncodeSydhTfbsSknshSmc3IggrabSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH SMC3 (ab9263) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshRfx5IggrabSig SKSH RFX5 IgR RFX5_(200-401-194) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003375 3375 GSM1003629 Snyder Stanford exp wgEncodeSydhTfbsSknshRfx5IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH RFX5 (200-401-194) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshRad21IggrabSig SKSH Rad21 IgR Rad21 SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003376 3376 GSM1003628 Snyder Stanford exp wgEncodeSydhTfbsSknshRad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshP300bIggrabSig SKSH p300 IgR p300_(SC-584) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003378 3378 GSM1003626 Snyder Stanford exp wgEncodeSydhTfbsSknshP300bIggrabSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH p300 (SC-584) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshNrf1IggrabSig SKSH Nrf1 IgR Nrf1 SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003374 3374 GSM1003630 Snyder Stanford exp wgEncodeSydhTfbsSknshNrf1IggrabSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH Nrf1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshMxi1IggrabSig SKSH Mxi1 IgR Mxi1_(AF4185) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003373 3373 GSM1003631 Snyder Stanford exp wgEncodeSydhTfbsSknshMxi1IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH Mxi1 (AF4185) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshJundIggrabSig SKSH JunD IgR JunD SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003372 3372 GSM1003632 Snyder Stanford exp wgEncodeSydhTfbsSknshJundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshCtcfbIggrabSig SKSH CTCF IgR CTCF_(SC-15914) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003371 3371 GSM1003633 Snyder Stanford exp wgEncodeSydhTfbsSknshCtcfbIggrabSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH CTCF (SC-15914) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7InputUcdSig MCF7 Inpt UCD Input MCF-7 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000762 762 GSM935485 Snyder USC hg18 input wgEncodeSydhTfbsMcf7InputUcdSig None Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Znf217UcdSig MCF7 Z217 UCD ZNF217 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-08-03 2012-05-03 wgEncodeEH002036 2036 GSM935563 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Znf217UcdSig None Signal ZNF217 is an important oncogene based on the high frequency of amplification and overexpression in many cancer types, but its molecular mode of gene regulation is poorly understood. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. ZNF217 contains seven C2H2 zinc finger domains and has been shown to bind to gene promoters mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 ZNF217 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Tcf7l2UcdSig MCF7 TCF7L2 UCD TCF7L2 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-20 2012-06-19 wgEncodeEH002072 2072 GSM816438 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Hae2f1UcdSig MCF7 HAE2 UCD HA-E2F1 MCF-7 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000693 693 GSM935477 Snyder USC hg18 exp wgEncodeSydhTfbsMcf7Hae2f1UcdSig None Signal The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 HA-E2F1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Gata3sc269UcdSig MCF7 GAT3 UCD GATA3_(SC-269) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002812 2812 GSM935445 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsMcf7Gata3sc269UcdSig None Signal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 GATA3 SC269 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Gata3UcdSig MCF7 GAT3 UCD GATA3_(SC-268) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-08-03 2012-05-03 wgEncodeEH002035 2035 GSM825711 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Gata3UcdSig None Signal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 GATA3 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90InputIggrabSig IMR90 Inpt IgR Input IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002808 2808 GSM935512 Snyder Stanford PeakSeq1.0 input wgEncodeSydhTfbsImr90InputIggrabSig None Signal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Rfx5IggrabSig IMR90 RFX5 IgR RFX5_(200-401-194) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003367 3367 GSM1003615 Snyder Stanford exp wgEncodeSydhTfbsImr90Rfx5IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 RFX5 (200-401-194) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Rad21IggrabSig IMR90 Rad2 IgR Rad21 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002810 2810 GSM935624 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Pol2IggrabSig IMR90 Pol2 IgR Pol2 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002809 2809 GSM935513 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90Pol2IggrabSig None Signal RNA Polymerase II fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 Pol2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Mxi1IggrabSig IMR90 Mxi1 IgR Mxi1_(AF4185) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003366 3366 GSM1003614 Snyder Stanford exp wgEncodeSydhTfbsImr90Mxi1IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 Mxi1 (AF4185) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Mazab85725IggrabSig IMR90 MAZ IgR MAZ_(ab85725) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003365 3365 GSM1003613 Snyder Stanford exp wgEncodeSydhTfbsImr90Mazab85725IggrabSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 MAZ (ab85725) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90MafkIggrabSig IMR90 MafK IgR MafK_(ab50322) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002832 2832 GSM935403 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90MafkIggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90CtcfbIggrabSig IMR90 CTCF IgR CTCF_(SC-15914) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002831 2831 GSM935404 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90CtcfbIggrabSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 CTCF IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Corestsc30189IggrabSig IMR90 COREST IgR COREST_(sc-30189) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003364 3364 GSM1003612 Snyder Stanford exp wgEncodeSydhTfbsImr90Corestsc30189IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 COREST (SC-30189) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Chd1nb10060411IggrabSig IMR90 CHD1 IgR CHD1_(NB100-60411) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003390 3390 GSM1003623 Snyder Stanford exp wgEncodeSydhTfbsImr90Chd1nb10060411IggrabSig None Signal ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 CHD1 (NB100-60411) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90CebpbIggrabSig IMR90 CBPB IgR CEBPB IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002807 2807 GSM935519 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecInputUcdSig HUVEC Inpt UCD Input HUVEC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001759 1759 GSM935346 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsHuvecInputUcdSig None Signal umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HUVEC Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecInputStdSig HUVEC Inpt Std Input HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000780 780 GSM935510 Snyder Yale hg18 input wgEncodeSydhTfbsHuvecInputStdSig None Signal umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HUVEC Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecPol2StdSig HUVEC Pol2 Std Pol2 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000702 702 GSM935393 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecPol2StdSig None Signal RNA Polymerase II umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HUVEC Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecMaxStdSig HUVEC Max Std Max HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000768 768 GSM935572 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecMaxStdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HUVEC Max Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecGata2UcdSig HUVEC GAT2 UCD GATA-2 HUVEC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001758 1758 GSM935347 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHuvecGata2UcdSig None Signal GATA binding protein 2 umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HUVEC GATA2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecCjunStdSig HUVEC cJun Std c-Jun HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000719 719 GSM935278 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecCjunStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HUVEC c-Jun Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecCfosUcdSig HUVEC cFOS UCD c-Fos HUVEC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001774 1774 GSM935585 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHuvecCfosUcdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HUVEC c-FOS UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputUcdSig HEPG Inpt UCD Input HepG2 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000674 674 GSM817343 Snyder USC hg18 input wgEncodeSydhTfbsHepg2InputUcdSig None Signal hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEPG2 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputPravastStdSig HEPG prav Inpt Sd Input HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000640 640 GSM935313 Snyder Yale hg18 input wgEncodeSydhTfbsHepg2InputPravastStdSig pravastatin Signal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Signal HEPG2 Input Standard pravastatin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputInslnStdSig HEPG isln Inpt Sd Input HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000756 756 GSM935443 Snyder Stanford hg18 input wgEncodeSydhTfbsHepg2InputInslnStdSig insulin Signal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder) Signal HEPG2 Input Standard insulin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputForsklnStdSig HEPG frsk Inpt Sd Input HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000755 755 GSM935444 Snyder Stanford hg18 input wgEncodeSydhTfbsHepg2InputForsklnStdSig forskolin Signal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 Input Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputIggrabSig HEPG Inpt IgR Input HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001791 1791 GSM935604 Snyder Stanford PeakSeq1.0 hg19 input wgEncodeSydhTfbsHepg2InputIggrabSig None Signal hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputIgggoatSig HEPG Inpt IgG Input HepG2 IgG-goat ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002803 2803 GSM935515 Snyder Stanford PeakSeq1.0 input wgEncodeSydhTfbsHepg2InputIgggoatSig None Signal hepatocellular carcinoma Input signal from Normal Goat IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Input IgG-goat ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Znf274UcdSig HEPG Z274 UCD ZNF274 HepG2 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001755 1755 GSM935350 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEPG2 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Usf2IggrabSig HEPG USF2 IgR USF2 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001804 1804 GSM935646 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Usf2IggrabSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 USF2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Tr4UcdSig HEPG TR4 UCD TR4 HepG2 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000675 675 GSM935596 Snyder USC hg18 exp wgEncodeSydhTfbsHepg2Tr4UcdSig None Signal (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEPG2 TR4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Tcf7l2UcdSig HEPG TCF7L2 UCD TCF7L2 HepG2 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2001-06-27 2011-01-19 2011-10-19 wgEncodeEH001780 1780 GSM782122 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEPG2 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2TbpIggrabSig HEPG TBP IgR TBP HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001793 1793 GSM935280 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2TbpIggrabSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 TBP IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp2PravastStdSig HEPG prav SBP2 Sd SREBP2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000643 643 GSM935314 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Srebp2PravastStdSig pravastatin Signal Sterol regulatory element binding transcription factor 2 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Signal HEPG2 SREBP2 Standard pravastatin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp1PravastStdSig HEPG prav SRBP Sd SREBP1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000642 642 GSM935315 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Srebp1PravastStdSig pravastatin Signal Sterol regulatory element binding transcription factor 1 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Signal HEPG2 SREBP1 Standard pravastatin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp1InslnStdSig HEPG isln SRBP Sd SREBP1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000759 759 GSM935627 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Srebp1InslnStdSig insulin Signal Sterol regulatory element binding transcription factor 1 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder) Signal HEPG2 SREBP1 Standard insulin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Smc3ab9263IggrabSig HEPG SMC3 IgR SMC3_(ab9263) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001861 1861 GSM935542 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Smc3ab9263IggrabSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 SMC3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Rfx5200401194IggrabSig HEPG RFX5 IgR RFX5_(200-401-194) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001843 1843 GSM935304 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Rfx5200401194IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 RFX5 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Rad21IggrabSig HEPG Rad2 IgR Rad21 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001803 1803 GSM935647 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2s2IggrabSig HEPG PolS IgR Pol2(phosphoS2) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001860 1860 GSM935543 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Pol2s2IggrabSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Pol2 S2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2PravastStdSig HEPG prav Pol2 Sd Pol2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000641 641 GSM935312 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Pol2PravastStdSig pravastatin Signal RNA Polymerase II hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Signal HEPG2 Pol2 Standard pravastatin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2ForsklnStdSig HEPG frsk Pol2 Sd Pol2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000758 758 GSM935628 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Pol2ForsklnStdSig forskolin Signal RNA Polymerase II hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 Pol2 Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2IggrabSig HEPG Pol2 IgR Pol2 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001792 1792 GSM935603 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Pol2IggrabSig None Signal RNA Polymerase II hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Pol2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pgc1aForsklnStdSig HEPG frsk PGC1 Sd PGC1A HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000757 757 GSM935623 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Pgc1aForsklnStdSig forskolin Signal The protein encoded by this gene is a transcriptional coactivator that regulates the genes involved in energy metabolism. This protein interacts with PPARgamma, which permits the interaction of this protein with multiple transcription factors. This protein can interact with, and regulate the activities of, cAMP response element binding protein (CREB) and nuclear respiratory factors (NRFs). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 PGC1A Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2P300sc582IggrabSig HEPG p300 IgR p300_(SC-584) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001862 1862 GSM935545 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2P300sc582IggrabSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 p300 SC584 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Nrf1IggrabSig HEPG Nrf1 IgR Nrf1 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001802 1802 GSM935648 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Nrf1IggrabSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Nrf1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mafksc477IggrabSig HEPG MafK IgR MafK_(SC-477) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001850 1850 GSM935610 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mafksc477IggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 MafK SC477 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mxi1StdSig HEPG Mxi1 Std Mxi1_(AF4185) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002029 2029 GSM935437 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mxi1StdSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Mxi1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mazab85725IggrabSig HEPG MAZ IgR MAZ_(ab85725) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002860 2860 GSM935335 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Mazab85725IggrabSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 MAZ IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2MaxIggrabSig HEPG Max IgR Max HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002796 2796 GSM935406 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2MaxIggrabSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Max IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mafkab50322IggrabSig HEPG MafK IgR MafK_(ab50322) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001842 1842 GSM935305 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mafkab50322IggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Maffm8194IggrabSig HEPG MafF IgR MafF_(M8194) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001841 1841 GSM935306 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Maffm8194IggrabSig None Signal The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 MafF IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2JundIggrabSig HEPG JunD IgR JunD HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001801 1801 GSM935649 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2JundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Irf3IggrabSig HEPG IRF3 IgR IRF3 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001800 1800 GSM935650 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Irf3IggrabSig None Signal Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 IRF3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Hsf1ForsklnStdSig HEPG frsk HSF1 Sd HSF1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000754 754 GSM935626 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Hsf1ForsklnStdSig forskolin Signal Epitope corresponding to amino acids 219-529 of heat shock transcription factor 1 (HSF1) of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 HSF1 Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Hnf4aForsklnStdSig HEPG frsk HNF4 Sd HNF4A HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000753 753 GSM935619 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Hnf4aForsklnStdSig forskolin Signal Epitope mapping at the C-terminus of Rab 11 of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 HNF4A Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Grp20ForsklnStdSig HEPG frsk GR20 Sd GRp20 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000752 752 GSM935620 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Grp20ForsklnStdSig forskolin Signal Epitope mapping at the C-terminus of GR alpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 GRp20 Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2ErraForsklnStdSig HEPG frsk ERRA Sd ERRA HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000751 751 GSM935621 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2ErraForsklnStdSig forskolin Signal Epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 ERRA Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Corestsc30189IggrabSig HEPG COREST IgR COREST_(sc-30189) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002845 2845 GSM935579 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Corestsc30189IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 COREST SC30189 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CjunIggrabSig HEPG cJun IgR c-Jun HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001794 1794 GSM935364 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2CjunIggrabSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 c-Jun IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Chd2ab68301IggrabSig HEPG CHD2 IgR CHD2_(AB68301) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001840 1840 GSM935307 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Chd2ab68301IggrabSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 CHD2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpzIggrabSig HEPG CEBPZ IgR CEBPZ HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002859 2859 GSM935274 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2CebpzIggrabSig None Signal Stimulates transcription from the HSP70 promoter. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 CEBPZ IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpbForsklnStdSig HEPG frsk CBPB Sd CEBPB HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000750 750 GSM935622 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2CebpbForsklnStdSig forskolin Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 CEBPB Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpbIggrabSig HEPG CBPB IgR CEBPB HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-04 2011-01-14 2011-10-13 wgEncodeEH001829 1829 GSM935493 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Brca1a300IggrabSig HEPG BRC1 IgR BRCA1_(A300-000A) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001859 1859 GSM935609 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Brca1a300IggrabSig None Signal Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 BRCA1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Bhlhe40cIggrabSig HEPG BHL4 IgR BHLHE40_(NB100-1800) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002032 2032 GSM935566 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Bhlhe40cIggrabSig None Signal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 BHLHE40 NB100 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Arid3anb100279IggrabSig HEPG ARI3 IgR ARID3A_(NB100-279) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002858 2858 GSM935275 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Arid3anb100279IggrabSig None Signal This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 ARID3A NB100279 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputUcdSig HeLa Inpt UCD Input HeLa-S3 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001754 1754 GSM818744 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsHelas3InputUcdSig None Signal cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputStdSig HeLa Inpt Std Input HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000612 612 GSM817342 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputStdSig None Signal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputIfng30StdSig HeLa IFg3 Inpt Sd Input HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000611 611 GSM935357 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputIfng30StdSig IFNg30 Signal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Signal HeLa-S3 Input Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputNakeddnaSig HeLa Inpt NDNA Input HeLa-S3 Naked_DNA ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000636 636 GSM935538 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputNakeddnaSig None Signal cervical carcinoma Control signal from Naked DNA. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input Naked DNA ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputMnaseSig HeLa Inpt MNas Input HeLa-S3 MNase ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000635 635 GSM935537 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputMnaseSig None Signal cervical carcinoma Input signal from MNase digested DNA. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input MNase ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputLargefragmentSig HeLa Inpt LFrg Input HeLa-S3 Large_Fragment ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000634 634 GSM935536 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputLargefragmentSig None Signal cervical carcinoma Control signal from sonication into large fragments of DNA (350-800 bp). Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input Large Fragment ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputIggrabSig HeLa Inpt IgR Input HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000744 744 GSM935339 Snyder Stanford hg18 input wgEncodeSydhTfbsHelas3InputIggrabSig None Signal cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputIggmusSig HeLa Inpt IgM Input HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000633 633 GSM935535 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputIggmusSig None Signal cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Zzz3StdSig HeLa ZZZ3 Std ZZZ3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001872 1872 GSM935416 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Zzz3StdSig None Signal ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 ZZZ3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Znf274UcdSig HeLa Z274 UCD ZNF274 HeLa-S3 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001763 1763 GSM935459 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Znf143IggrabSig HeLa Z143 IgR Znf143_(16618-1-AP) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002028 2028 GSM935436 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Znf143IggrabSig None Signal Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Znf143 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabSig HeLa ZKSCN1 IgR ZKSCAN1_(HPA006672) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002857 2857 GSM935362 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabSig None Signal The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 ZKSCAN1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Usf2IggmusSig HeLa USF2 IgM USF2 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001819 1819 GSM935561 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Usf2IggmusSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 USF2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tr4StdSig HeLa TR4 Std TR4 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000687 687 GSM935369 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Tr4StdSig None Signal (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 TR4 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tf3c110StdSig HeLa TF3C Std TFIIIC-110 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000747 747 GSM935342 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Tf3c110StdSig None Signal TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 TFIIIC-110 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdSig HeLa TCF7L2 UCD TCF7L2_C9B9_(2565) HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-12-19 2012-09-18 wgEncodeEH002813 2813 GSM935625 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 TCF7L2 C9B9 2565 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tcf7l2UcdSig HeLa TCF7L2 UCD TCF7L2 HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002069 2069 GSM816436 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3TbpIggrabSig HeLa TBP IgR TBP HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001790 1790 GSM935606 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3TbpIggrabSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 TBP IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Stat3IggrabSig HeLa STA3 IgR STAT3 HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001799 1799 GSM935276 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Stat3IggrabSig None Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 STAT3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Stat1Ifng30StdSig HeLa IFg3 STA1 Sd STAT1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000614 614 GSM935360 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Stat1Ifng30StdSig IFNg30 Signal transcription factor, activated by interferon signalling cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Signal HeLa-S3 STAT1 Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Spt20StdSig HeLa SPT Std SPT20 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001855 1855 GSM935615 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Spt20StdSig None Signal Also known as FAM48A or P38IP. It is a component of SAGA complex. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 SPT20 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Smc3ab9263IggrabSig HeLa SMC3 IgR SMC3_(ab9263) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001839 1839 GSM935384 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Smc3ab9263IggrabSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 SMC3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rpc155StdSig HeLa RPC1 Std RPC155 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000766 766 GSM935489 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Rpc155StdSig None Signal polymerase (RNA) III (DNA directed) polypeptide A, 155kDa cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 RPC155 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rfx5200401194IggrabSig HeLa RFX5 IgR RFX5_(200-401-194) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001818 1818 GSM935560 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Rfx5200401194IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 RFX5 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rad21IggrabSig HeLa Rad2 IgR Rad21 HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001789 1789 GSM935571 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Prdm19115IggrabSig HeLa PRDM IgR PRDM1_(9115) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001817 1817 GSM935555 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Prdm19115IggrabSig None Signal Transcriptional repressor that binds specifically to the PRDI element in the promoter of the beta-interferon gene. Drives the maturation of B-lymphocytes into Ig secreting cells. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 PRDM1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Pol2s2IggrabSig HeLa PolS IgR Pol2(phosphoS2) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001838 1838 GSM935383 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Pol2s2IggrabSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Pol2 S2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Pol2StdSig HeLa Pol2 Std Pol2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000613 613 GSM935395 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Pol2StdSig None Signal RNA Polymerase II cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3P300sc584sc584IggrabSig HeLa p300 IgR p300_(SC-584) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001820 1820 GSM935500 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3P300sc584sc584IggrabSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 p300 SC584 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Nrf1IggmusSig HeLa Nrf1 IgM Nrf1 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000723 723 GSM935636 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Nrf1IggmusSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Nrf1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3NfybIggrabSig HeLa NYB IgR NF-YB HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002067 2067 GSM935408 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3NfybIggrabSig None Signal NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 NF-YB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3NfyaIggrabSig HeLa NYA IgR NF-YA HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002066 2066 GSM935508 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3NfyaIggrabSig None Signal NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 NF-YA IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Mxi1af4185IggrabSig HeLa Mxi1 IgR Mxi1_(AF4185) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001826 1826 GSM935498 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Mxi1af4185IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Mxi1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Mazab85725IggrabSig HeLa MAZ IgR MAZ_(ab85725) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002855 2855 GSM935272 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Mazab85725IggrabSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 MAZ IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MaxStdSig HeLa Max Std Max HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000646 646 GSM935318 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3MaxStdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Max Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MaxIggrabSig HeLa Max IgR Max HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002830 2830 GSM935405 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3MaxIggrabSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Max IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MafkIggrabSig HeLa MafK IgR MafK_(ab50322) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002856 2856 GSM935290 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3MafkIggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3JundIggrabSig HeLa JunD IgR JunD HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000745 745 GSM935328 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3JundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Irf3IggrabSig HeLa IRF3 IgR IRF3 HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001788 1788 GSM935570 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Irf3IggrabSig None Signal Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 IRF3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ini1IggmusSig HeLa INI1 IgM Ini1 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000722 722 GSM935635 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Ini1IggmusSig None Signal Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 INI1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Hcfc1nb10068209IggrabSig HeLa-S3 HCFC1 IgR HCFC1_(NB100-68209) HeLa-S3 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003389 3389 GSM1003618 Snyder Stanford exp wgEncodeSydhTfbsHelas3Hcfc1nb10068209IggrabSig None Signal The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 HCFC1 (NB100-68209) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Hae2f1StdSig HeLa HAE2 Std HA-E2F1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000688 688 GSM935366 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Hae2f1StdSig None Signal The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 HA-E2F1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabSig HeLa GT2F IgR GTF2F1_(AB28179) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001816 1816 GSM935554 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabSig None Signal RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 GTF2F1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Gcn5StdSig HeLa GCN5 Std GCN5 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001849 1849 GSM935302 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Gcn5StdSig None Signal KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 GCN5 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Elk4UcdSig HeLa ELK4 UCD ELK4 HeLa-S3 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001753 1753 GSM935351 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Elk4UcdSig None Signal This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 ELK4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Elk112771IggrabSig HeLa ELK1 IgR ELK1_(1277-1) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH002864 2864 GSM935326 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Elk112771IggrabSig None Signal Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 ELK1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f6StdSig HeLa E2F6 Std E2F6 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000692 692 GSM935476 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f6StdSig None Signal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 E2F6 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f4StdSig HeLa E2F4 Std E2F4 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000689 689 GSM935365 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f4StdSig None Signal mapping at the C-terminus of E2F4 of human origin cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 E2F4 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f1StdSig HeLa E2F1 Std E2F1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000699 699 GSM935484 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f1StdSig None Signal E2F1, the original member of the E2F family of transcription factors, was identified as a cellular protein with DNA binding activity associated with the adenovirus E2 gene promoter. E2F1 is cell cycle regulated with very low levels in early G1, then increasing levels as cells move from G1 to S, and highest levels of protein at the G1/S boundary, which is consistent with its role in S-phase entry. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 E2F1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Corestsc30189IggrabSig HeLa COREST IgR COREST_(sc-30189) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002844 2844 GSM935578 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Corestsc30189IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 COREST SC30189 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CmycStdSig HeLa cMyc Std c-Myc HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000648 648 GSM935320 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3CmycStdSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 c-Myc Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CjunIggrabSig HeLa cJun IgR c-Jun HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000746 746 GSM935341 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3CjunIggrabSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 c-Jun IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Chd2IggrabSig HeLa CHD2 IgR CHD2_(AB68301) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002027 2027 GSM935432 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Chd2IggrabSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 CHD2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CfosStdSig HeLa cFOS Std c-Fos HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000647 647 GSM935317 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3CfosStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 c-FOS Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CebpbIggrabSig HeLa CBPB IgR CEBPB HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001815 1815 GSM935553 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brg1IggmusSig HeLa BRG1 IgM Brg1 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000781 781 GSM935511 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Brg1IggmusSig None Signal Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 BRG1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brf2StdSig HeLa BRF2 Std BRF2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000765 765 GSM935435 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Brf2StdSig None Signal Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 BRF2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brf1StdSig HeLa BRF1 Std BRF1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000764 764 GSM935582 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Brf1StdSig None Signal 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 BRF1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brca1a300IggrabSig HeLa BRC1 IgR BRCA1_(A300-000A) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001814 1814 GSM935552 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Brca1a300IggrabSig None Signal Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 BRCA1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Bdp1StdSig HeLa BDP1 Std BDP1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000763 763 GSM935486 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Bdp1StdSig None Signal 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 BDP1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Baf170IggmusSig HeLa BAF7 IgM BAF170 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000721 721 GSM935638 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Baf170IggmusSig None Signal BAF170 (SMARCC2, Brg1-Associated Factor, 170 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 BAF170 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Baf155IggmusSig HeLa BAF5 IgM BAF155 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000720 720 GSM935637 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Baf155IggmusSig None Signal BAF155 (SMARCC1, Brg1-Associated Factor, 155 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 BAF155 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ap2gammaStdSig HeLa AP2g Std AP-2gamma HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000686 686 GSM935370 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Ap2gammaStdSig None Signal Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5'-GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 AP-2g Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ap2alphaStdSig HeLa AP2a Std AP-2alpha HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000685 685 GSM935367 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Ap2alphaStdSig None Signal Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5' -GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. AP-2alpha is the only AP-2 protein required for early morphogenesis of the lens vesicle (by similarity). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 AP-2a Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549InputIggrabSig A549 Inpt IgR Input A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002819 2819 GSM935629 Snyder Stanford PeakSeq1.0 input wgEncodeSydhTfbsA549InputIggrabSig None Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Rad21IggrabSig A549 Rad2 IgR Rad21 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002822 2822 GSM935300 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Pol2s2IggrabSig A549 PolS IgR Pol2(phosphoS2) A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002821 2821 GSM935299 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Pol2s2IggrabSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 Pol2 S2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549MaxIggrabSig A549 Max IgR Max A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002820 2820 GSM935298 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549MaxIggrabSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 Max IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CtcfbIggrabSig A549 CTCF IgR CTCF_(SC-15914) A549 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003384 3384 GSM1003606 Snyder Stanford exp wgEncodeSydhTfbsA549CtcfbIggrabSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 CTCF (SC-15914) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CmycIggrabSig A549 c-Myc IgR c-Myc A549 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003385 3385 GSM1003607 Snyder Stanford exp wgEncodeSydhTfbsA549CmycIggrabSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 c-Myc IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CebpbIggrabSig A549 CBPB IgR CEBPB A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002818 2818 GSM935630 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Bhlhe40IggrabSig A549 BHL4 IgR BHLHE40 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002817 2817 GSM935440 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Bhlhe40IggrabSig None Signal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 BHLHE40 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputUcdSig K562 Inpt UCD Input K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000672 672 GSM935601 Snyder USC hg18 input wgEncodeSydhTfbsK562InputUcdSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputStdSig K562 Inpt Std Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000615 615 GSM935363 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputStdSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIfng6hStdSig K562 IFg6 Inpt Sd Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000658 658 GSM935427 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputIfng6hStdSig IFNg6h Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Signal K562 Input Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIfng30StdSig K562 IFg3 Inpt Sd Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000657 657 GSM935420 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputIfng30StdSig IFNg30 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 Input Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIfna6hStdSig K562 IFa6 Inpt Sd Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000656 656 GSM935419 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputIfna6hStdSig IFNa6h Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 Input Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIfna30StdSig K562 IFa3 Inpt Sd Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000655 655 GSM935422 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputIfna30StdSig IFNa30 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 Input Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIggrabSig K562 Inpt IgR Input K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001795 1795 GSM935618 Snyder Stanford PeakSeq1.0 hg19 input wgEncodeSydhTfbsK562InputIggrabSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIggmusSig K562 Inpt IgM Input K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000726 726 GSM935631 Snyder Stanford hg18 input wgEncodeSydhTfbsK562InputIggmusSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znfmizdcp1ab65767IggrabSig K562 ZNF-MIZD IgR ZNF-MIZD-CP1_(ab65767) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003381 3381 GSM1003611 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Znfmizdcp1ab65767IggrabSig None Signal Zinc finger MIZ domain-containing protein 1 that increases ligand-dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ZNF-MIZD-CP1 (ab65767) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf384hpa004051IggrabSig K562 ZNF384 IgR ZNF384_(HPA004051) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003382 3382 GSM1003621 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Znf384hpa004051IggrabSig None Signal This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ZNF384 (HPA004051) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf274m01UcdSig K562 Z274M UCD ZNF274_(M01) K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002068 2068 GSM935503 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Znf274m01UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 ZNF274 (M01) UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf274UcdSig K562 Z274 UCD ZNF274 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000696 696 GSM935479 Snyder USC hg18 exp wgEncodeSydhTfbsK562Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf263UcdSig K562 Z263 UCD ZNF263 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000630 630 GSM935532 Snyder USC hg18 exp wgEncodeSydhTfbsK562Znf263UcdSig None Signal ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 ZNF263 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf143IggrabSig K562 Z143 IgR Znf143_(16618-1-AP) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002030 2030 GSM935568 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Znf143IggrabSig None Signal Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Znf143 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabSig K562 ZC3H11A IgR ZC3H11A_(NB100-74650) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003380 3380 GSM1003610 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabSig None Signal ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ZC3H11A (NB100-74650) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Yy1UcdSig K562 YY1 UCD YY1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000684 684 GSM935368 Snyder USC hg18 exp wgEncodeSydhTfbsK562Yy1UcdSig None Signal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 YY1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Xrcc4StdSig K562 XRCC Std XRCC4 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000650 650 GSM935425 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Xrcc4StdSig None Signal Recognizes the XRCC4 protein (X ray cross complementation protein). XRCC4 is a ubiquitous protein reported to have a role in DNA double-stranded break repair and in V(D)J recombination. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 XRCC4 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Usf2IggrabSig K562 USF2 IgR USF2 K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001797 1797 GSM935356 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Usf2IggrabSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 USF2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ubtfsab1404509IggmusSig K562 UBTF IgM UBTF_(SAB1404509) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002850 2850 GSM935642 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Ubtfsab1404509IggmusSig None Signal Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 UBTF IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ubfsc13125IggmusSig K562 UBF IgM UBF_(sc-13125) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002863 2863 GSM935338 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Ubfsc13125IggmusSig None Signal Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 UBF IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tr4UcdSig K562 TR4 UCD TR4 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000682 682 GSM935374 Snyder USC hg18 exp wgEncodeSydhTfbsK562Tr4UcdSig None Signal (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 TR4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tf3c110StdSig K562 TF3C Std TFIIIC-110 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000748 748 GSM935343 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Tf3c110StdSig None Signal TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 TFIIIC-110 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562TbpIggmusSig K562 TBP IgM TBP K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001825 1825 GSM935495 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562TbpIggmusSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 TBP IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tblr1nb600270IggrabSig K562 TBLR1 IgR TBLR1_(NB600-270) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002848 2848 GSM935574 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Tblr1nb600270IggrabSig None Signal F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 TBLR1 NB600270 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tblr1ab24550IggrabSig K562 TBLR1 IgR TBLR1_(ab24550) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002849 2849 GSM935575 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Tblr1ab24550IggrabSig None Signal F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 TBLR1 AB24550 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tal1sc12984IggmusSig K562 TAL1 IgM TAL1_(SC-12984) K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001824 1824 GSM935496 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Tal1sc12984IggmusSig None Signal TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 TAL1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat2Ifna6hStdSig K562 IFa6 STA2 Sd STAT2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000666 666 GSM935469 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat2Ifna6hStdSig IFNa6h Signal peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 STAT2 Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat2Ifna30StdSig K562 IFa3 STA2 Sd STAT2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000665 665 GSM935470 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat2Ifna30StdSig IFNa30 Signal peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 STAT2 Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifng6hStdSig K562 IFg6 STA1 Sd STAT1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000761 761 GSM935488 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Stat1Ifng6hStdSig IFNg6h Signal transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Signal K562 STAT1 Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifng30StdSig K562 IFg3 STA1 Sd STAT1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000760 760 GSM935487 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Stat1Ifng30StdSig IFNg30 Signal transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 STAT1 Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifna6hStdSig K562 IFa6 STA1 Sd STAT1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000664 664 GSM935471 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat1Ifna6hStdSig IFNa6h Signal transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 STAT1 Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifna30StdSig K562 IFa3 STA1 Sd STAT1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000663 663 GSM935472 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat1Ifna30StdSig IFNa30 Signal transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 STAT1 Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Smc3ab9263IggrabSig K562 SMC3 IgR SMC3_(ab9263) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001845 1845 GSM935310 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Smc3ab9263IggrabSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 SMC3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Sirt6StdSig K562 SIRT Std SIRT6 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000681 681 GSM935371 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Sirt6StdSig None Signal A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 SIRT6 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Setdb1UcdSig K562 STDB UCD SETDB1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000677 677 GSM935598 Snyder USC hg18 exp wgEncodeSydhTfbsK562Setdb1UcdSig None Signal SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 SETDB1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Setdb1MnasedUcdSig K562 MNas STDB UC SETDB1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000769 769 GSM935573 Snyder USC hg18 exp wgEncodeSydhTfbsK562Setdb1MnasedUcdSig MNaseD Signal SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Fragmented using micrococcal nuclease digestion Signal K562 SETDB1 UC Davis MNaseD ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rpc155StdSig K562 RPC1 Std RPC155 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000680 680 GSM935372 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Rpc155StdSig None Signal polymerase (RNA) III (DNA directed) polypeptide A, 155kDa leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 RPC155 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rfx5IggrabSig K562 RFX5 IgR RFX5_(200-401-194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002033 2033 GSM935565 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Rfx5IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 RFX5 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rad21StdSig K562 Rad2 Std Rad21 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000649 649 GSM935319 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Rad21StdSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 Rad21 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol3StdSig K562 Pol3 Std Pol3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000694 694 GSM935481 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol3StdSig None Signal RNA Polymerase III leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 POL3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2s2StdSig K562 PolS Std Pol2(phosphoS2) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-12 2011-04-12 wgEncodeEH001805 1805 GSM935645 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Pol2s2StdSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Pol2 S2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2s2IggrabSig K562 PolS IgR Pol2(phosphoS2) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002833 2833 GSM935402 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Pol2s2IggrabSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Pol2 S2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2StdSig K562 Pol2 Std Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000616 616 GSM935358 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2StdSig None Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifng6hStdSig K562 IFg6 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000662 662 GSM935473 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifng6hStdSig IFNg6h Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Signal K562 Pol2 Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifng30StdSig K562 IFg3 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000704 704 GSM935388 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol2Ifng30StdSig IFNg30 Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 Pol2 Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifna6hStdSig K562 IFa6 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000661 661 GSM935474 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifna6hStdSig IFNa6h Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 Pol2 Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifna30StdSig K562 IFa3 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000660 660 GSM935475 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifna30StdSig IFNa30 Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 Pol2 Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2IggmusSig K562 Pol2 IgM Pol2 K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000727 727 GSM935632 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol2IggmusSig None Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562P300sc584sc48343IggrabSig K562 p300 IgR p300_(SC-48343) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001828 1828 GSM935494 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562P300sc584sc48343IggrabSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 p300 SC48343 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562P300IggrabSig K562 p300 IgR p300 K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002834 2834 GSM935401 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562P300IggrabSig None Signal EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 p300 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Nrf1IggrabSig K562 Nrf1 IgR Nrf1 K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001796 1796 GSM935361 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Nrf1IggrabSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Nrf1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NfybStdSig K562 NYB Std NF-YB K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002024 2024 GSM935429 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562NfybStdSig None Signal NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 NF-YB Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NfyaStdSig K562 NYA Std NF-YA K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2012-03-22 wgEncodeEH002021 2021 GSM935433 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562NfyaStdSig None Signal NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 NF-YA Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Nfe2StdSig K562 NFE2 Std NF-E2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000624 624 GSM935414 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Nfe2StdSig None Signal Nuclear factor, erythroid-derived 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 NF-E2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NelfeStdSig K562 NELF Std NELFe K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000701 701 GSM935392 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562NelfeStdSig None Signal NELF-E (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 NELFe Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mxi1af4185IggrabSig K562 Mxi1 IgR Mxi1_(AF4185) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001827 1827 GSM935497 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Mxi1af4185IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Mxi1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mazab85725IggrabSig K562 MAZ IgR MAZ_(ab85725) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002862 2862 GSM935337 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Mazab85725IggrabSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 MAZ IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaxStdSig K562 Max Std Max K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000637 637 GSM935539 Snyder Yale hg18 exp wgEncodeSydhTfbsK562MaxStdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 Max Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaxIggrabSig K562 Max IgR Max K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002869 2869 GSM935344 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562MaxIggrabSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Max IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mafkab50322IggrabSig K562 MafK IgR MafK_(ab50322) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001844 1844 GSM935311 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Mafkab50322IggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaffIggrabSig K562 MafF IgR MafF_(M8194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002804 2804 GSM935520 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562MaffIggrabSig None Signal The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 MafF IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Kap1UcdSig K562 KAP1 UCD KAP1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-23 2011-05-23 wgEncodeEH001764 1764 GSM935464 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Kap1UcdSig None Signal KRAB Associated Protein 1, helps regulate transcriptional repression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 KAP1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562JundIggrabSig K562 JunD IgR JunD K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002164 2164 GSM935569 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562JundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifng6hStdSig K562 IFg6 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001866 1866 GSM935549 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Irf1Ifng6hStdSig IFNg6h Signal Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Signal K562 IRF1 Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifng30StdSig K562 IFg3 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002799 2799 GSM935505 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Irf1Ifng30StdSig IFNg30 Signal Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 IRF1 Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifna6hStdSig K562 IFa6 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002798 2798 GSM935504 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Irf1Ifna6hStdSig IFNa6h Signal Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon alpha treatment - 6 hours (Snyder) Signal K562 IRF1 Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifna30StdSig K562 IFa3 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001865 1865 GSM935546 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Irf1Ifna30StdSig IFNa30 Signal Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University 30 m of Interferon alpha (Snyder) Signal K562 IRF1 Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ini1IggmusSig K562 INI1 IgM Ini1 K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000725 725 GSM935634 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Ini1IggmusSig None Signal Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 INI1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Hmgn3StdSig K562 HMGN Std HMGN3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001863 1863 GSM935544 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Hmgn3StdSig None Signal HMGN3 is a high-mobility group protein. These proteins are small, 8 to 11 kDa, ubiquitous proteins believed to play a role in chromatin structure. HMGNs bind to nucleosomes between the histone core and DNA and reduce chromatin compaction. As a result HMGNs, HMGN3 included, are believed to increase access to DNA for DNA replication, repair and transcription. HMGN3 has specifically been implicated in the action of Thyroid horomone receptors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 HMGN3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabSig K562 HCFC1 IgR HCFC1_(NB100-68209) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003392 3392 GSM1003625 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabSig None Signal The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 HCFC1 (NB100-68209) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabSig K562 GT2F IgR GTF2F1_(AB28179) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001823 1823 GSM935501 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabSig None Signal RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 GTF2F1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gtf2bStdSig K562 GT2B Std GTF2B K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-06-14 2010-12-06 2011-09-06 wgEncodeEH000703 703 GSM935394 Snyder Harvard PeakSeq1.0 hg18 exp wgEncodeSydhTfbsK562Gtf2bStdSig None Signal DNA- binding general transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 GTF2B Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata2UcdSig K562 GAT2 UCD GATA-2 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000683 683 GSM935373 Snyder USC hg18 exp wgEncodeSydhTfbsK562Gata2UcdSig None Signal GATA binding protein 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 GATA2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata1bIggmusSig K562 GATA1 IgM GATA1_(SC-266) K562 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003368 3368 GSM1003608 Snyder Stanford exp wgEncodeSydhTfbsK562Gata1bIggmusSig None Signal GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 GATA1 (SC-266) IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata1UcdSig K562 GAT1 UCD GATA-1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000638 638 GSM935540 Snyder USC hg18 exp wgEncodeSydhTfbsK562Gata1UcdSig None Signal GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 GATA1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Elk112771IggrabSig K562 ELK1 IgR ELK1_(1277-1) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH003356 3356 GSM1003620 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Elk112771IggrabSig None Signal Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ELK1 (1277-1) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562E2f6UcdSig K562 E2F6 UCD E2F6 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000676 676 GSM935597 Snyder USC hg18 exp wgEncodeSydhTfbsK562E2f6UcdSig None Signal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 E2F6 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562E2f4UcdSig K562 E2F4 UCD E2F4 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000671 671 GSM935600 Snyder USC hg18 exp wgEncodeSydhTfbsK562E2f4UcdSig None Signal mapping at the C-terminus of E2F4 of human origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 E2F4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CtcfbIggrabSig K562 CTCF IgR CTCF_(SC-15914) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002797 2797 GSM935407 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CtcfbIggrabSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 CTCF IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Corestsc30189IggrabSig K562 COREST IgR COREST_(sc-30189) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-01-22 2012-10-21 wgEncodeEH002814 2814 GSM935439 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Corestsc30189IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 COREST SC30189 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Corestab24166IggrabSig K562 COREST IgR COREST_(ab24166) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002847 2847 GSM935385 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Corestab24166IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 COREST AB24166 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycStdSig K562 cMyc Std c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000621 621 GSM935410 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycStdSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 c-Myc Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfng6hStdSig K562 IFg6 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000670 670 GSM935599 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfng6hStdSig IFNg6h Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Signal K562 c-Myc Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfng30StdSig K562 IFg3 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001867 1867 GSM935548 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562CmycIfng30StdSig IFNg30 Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 c-Myc Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfna6hStdSig K562 IFa6 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000669 669 GSM935466 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfna6hStdSig IFNa6h Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 c-Myc Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfna30StdSig K562 IFa3 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000659 659 GSM935428 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfna30StdSig IFNa30 Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 c-Myc Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIggrabSig K562 cMyc IgR c-Myc K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002800 2800 GSM935516 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CmycIggrabSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 c-Myc IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunStdSig K562 cJun Std c-Jun K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000620 620 GSM935411 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 c-Jun Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfng6hStdSig K562 IFg6 cJun Sd c-Jun K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000668 668 GSM935467 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfng6hStdSig IFNg6h Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Signal K562 c-Jun Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfng30StdSig K562 IFg3 cJun Sd c-Jun K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000673 673 GSM935602 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfng30StdSig IFNg30 Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 c-Jun Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfna6hStdSig K562 IFa6 cJun Sd c-Jun K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000667 667 GSM935468 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfna6hStdSig IFNa6h Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 c-Jun Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfna30StdSig K562 IFa3 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002805 2805 GSM935521 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CjunIfna30StdSig IFNa30 Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University 30 m of Interferon alpha (Snyder) Signal K562 c-Jun Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIggrabSig K562 c-Jun IgR c-Jun K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003369 3369 GSM1003609 Snyder Stanford exp wgEncodeSydhTfbsK562CjunIggrabSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 c-Jun IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Chd2ab68301IggrabSig K562 CHD2 IgR CHD2_(AB68301) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001822 1822 GSM935502 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Chd2ab68301IggrabSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 CHD2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CfosStdSig K562 cFOS Std c-Fos K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000619 619 GSM935355 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CfosStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 c-FOS Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CebpbIggrabSig K562 CBPB IgR CEBPB K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001821 1821 GSM935499 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Cdpsc6327IggrabSig K562 CDP IgR CDP_(sc-6327) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003391 3391 GSM1003622 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Cdpsc6327IggrabSig None Signal CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 CDP (SC-6327) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ccnt2StdSig K562 CNT2 Std CCNT2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001864 1864 GSM935547 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Ccnt2StdSig None Signal CycT2 is one of three cyclins that can form a heterodimer with cyclin-dependent kinase 9 (CDK9). The heterodimer is known as positive elongation factor b (P-TEFb) and is responsible for the phosphophorylation of Ser2 of the heptad repeat in the C-terminal domain of RNA polymerase II as well as the negative elongation factors DSIF (hSpt4/hSpt5) and NELF. Phosphorylation of RNA polymerase II and the negative elongation factors by P-TEFb promotes elongation. CycT2 contains a leucine rich domain capable of binding to the C-terminal domain of RNA polymerase II. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 CCNT2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brg1IggmusSig K562 BRG1 IgM Brg1 K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000724 724 GSM935633 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Brg1IggmusSig None Signal Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 BRG1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brf2StdSig K562 BRF2 Std BRF2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000767 767 GSM935490 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Brf2StdSig None Signal Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 BRF2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brf1StdSig K562 BRF1 Std BRF1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000679 679 GSM935595 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Brf1StdSig None Signal 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 BRF1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bhlhe40nb100IggrabSig K562 BHL4 IgR BHLHE40_(NB100-1800) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEH001857 1857 GSM935616 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Bhlhe40nb100IggrabSig None Signal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 BHLHE40 NB100 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bdp1StdSig K562 BDP1 Std BDP1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000678 678 GSM935594 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Bdp1StdSig None Signal 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 BDP1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bach1sc14700IggrabSig K562 Bach1 IgR Bach1_(sc-14700) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002846 2846 GSM935576 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Bach1sc14700IggrabSig None Signal This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Bach1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Atf3StdSig K562 ATF3 Std ATF3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000700 700 GSM935391 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Atf3StdSig None Signal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 ATF3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Atf106325StdSig K562 ATF1 Std ATF1_(06-325) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH002865 2865 GSM935340 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsK562Atf106325StdSig None Signal ATF1 is a bZip transcription factor from the CREB family. ATF1 binds to both cAMP response elements (TGACGTCA). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 ATF1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Arid3asc8821IggrabSig K562 ARI3 IgR ARID3A_(sc-8821) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002861 2861 GSM935336 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Arid3asc8821IggrabSig None Signal This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ARID3A SC8821 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescInputUcdSig H1ES Inpt UCD Input H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001751 1751 GSM935353 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsH1hescInputUcdSig None Signal embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescInputIggrabSig H1ES Inpt IgR Input H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001834 1834 GSM935381 Snyder Stanford PeakSeq1.0 hg19 input wgEncodeSydhTfbsH1hescInputIggrabSig None Signal embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescZnf274m01UcdSig H1ES ZNF274 UCD ZNF274_(M01) H1-hESC UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-06 2013-03-05 wgEncodeEH003357 3357 GSM1003619 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsH1hescZnf274m01UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC ZNF274 (M01) UC Davis ChIP-seq Signal from ENCODE/USC Regulation 
wgEncodeSydhTfbsH1hescZnf143IggrabSig H1ES Z143 IgR Znf143_(16618-1-AP) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002802 2802 GSM935514 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescZnf143IggrabSig None Signal Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Znf143 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescUsf2IggrabSig H1ES USF2 IgR USF2 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001837 1837 GSM935380 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescUsf2IggrabSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC USF2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescTbpIggrabSig H1ES TBP IgR TBP H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001848 1848 GSM935303 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescTbpIggrabSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC TBP IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescSuz12UcdSig H1ES SZ12 UCD SUZ12 H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001752 1752 GSM935352 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescSuz12UcdSig None Signal Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC SUZ12 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescSin3anb6001263IggrabSig H1ES SIN3A IgR SIN3A_(NB600-1263) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002854 2854 GSM935289 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescSin3anb6001263IggrabSig None Signal Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC SIN3A IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescRfx5200401194IggrabSig H1ES RFX5 IgR RFX5_(200-401-194) H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001835 1835 GSM935382 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescRfx5200401194IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC RFX5 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescRad21IggrabSig H1ES Rad2 IgR Rad21 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001836 1836 GSM935379 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescRad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescNrf1IggrabSig H1ES Nrf1 IgR Nrf1 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001847 1847 GSM935308 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescNrf1IggrabSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Nrf1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMxi1IggrabSig H1ES Mxi1 IgR Mxi1_(AF4185) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002829 2829 GSM935293 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescMxi1IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Mxi1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMaxUcdSig H1ES Max UCD Max H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001757 1757 GSM935348 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescMaxUcdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC Max UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMafkIggrabSig H1ES MafK IgR MafK_(ab50322) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002828 2828 GSM935292 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescMafkIggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescJundIggrabSig H1ES JunD IgR JunD H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002023 2023 GSM935434 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescJundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescGtf2f1IggrabSig H1ES GT2F IgR GTF2F1_(AB28179) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002843 2843 GSM935581 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescGtf2f1IggrabSig None Signal RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC GTF2F1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCtbp2UcdSig H1ES CBP2 UCD CtBP2 H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001767 1767 GSM935463 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescCtbp2UcdSig None Signal C-terminal binding protein 2 embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC CtBP2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCmycIggrabSig H1ES cMyc IgR c-Myc H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002795 2795 GSM935509 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescCmycIggrabSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC c-Myc IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCjunIggrabSig H1ES cJun IgR c-Jun H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-19 wgEncodeEH001854 1854 GSM935614 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescCjunIggrabSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC c-Jun IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescChd2IggrabSig H1ES CHD2 IgR CHD2_(AB68301) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002827 2827 GSM935297 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescChd2IggrabSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC CHD2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescChd1a301218aIggrabSig H1ES CHD1 IgR CHD1_(A301-218A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002826 2826 GSM935296 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescChd1a301218aIggrabSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC CHD1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCebpbIggrabSig H1ES CBPB IgR CEBPB H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002825 2825 GSM935295 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescCebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescBrca1IggrabSig H1ES BRC1 IgR BRCA1_(A300-000A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002801 2801 GSM935517 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescBrca1IggrabSig None Signal Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC BRCA1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescBach1sc14700IggrabSig H1ES Bach1 IgR Bach1_(sc-14700) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002842 2842 GSM935580 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescBach1sc14700IggrabSig None Signal This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Bach1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878InputStdSig GM78 Inpt Std Input GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000625 625 GSM935413 Snyder Yale hg18 input wgEncodeSydhTfbsGm12878InputStdSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878InputIggrabSig GM78 Inpt IgR Input GM12878 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-07-27 2012-04-27 wgEncodeEH000771 771 GSM935450 Snyder Stanford PeakSeq1.0 hg18 input wgEncodeSydhTfbsGm12878InputIggrabSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878InputTnfaIggrabSig GM78 TNF Inpt IgR Input GM12878 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH002034 2034 GSM935564 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12878InputTnfaIggrabSig TNFa Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12878 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878InputIggmusSig GM78 Inpt IgM Input GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000706 706 GSM935390 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12878InputIggmusSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Zzz3StdSig GM78 ZZZ3 Std ZZZ3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000698 698 GSM935483 Snyder Harvard hg18 exp wgEncodeSydhTfbsGm12878Zzz3StdSig None Signal ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 ZZZ3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusSig GM78 ZNF384 IgM ZNF384_(HPA004051) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003388 3388 GSM1003602 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusSig None Signal This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 ZNF384 (HPA004051) IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf274StdSig GM78 Z274 Std ZNF274 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001756 1756 GSM935349 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Znf274StdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM12878 ZNF274 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf143166181apStdSig GM78 Z143 Std Znf143_(16618-1-AP) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001853 1853 GSM935613 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Znf143166181apStdSig None Signal Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Znf143 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Yy1StdSig GM78 YY1 Std YY1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000695 695 GSM935482 Snyder USC hg18 exp wgEncodeSydhTfbsGm12878Yy1StdSig None Signal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM12878 YY1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878WhipIggmusSig GM78 WHIP IgM WHIP GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2010-04-26 2011-01-26 wgEncodeEH001787 1787 GSM935492 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878WhipIggmusSig None Signal Interacts with the N-terminal portion of Werner protein containing the exonuclease domain, shows homology to replication factor C family proteins, and is conserved from E. coli to human. Studies in yeast suggest that this gene may influence the aging process. Functions as a modulator for initiation or reinitiation events during DNA polymerase delta-mediated DNA synthesis. Has an intrinsic ATPase activity that functions as a sensor of DNA damage or of arrested replication forks and regulates the extent of DNA synthesis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 WHIP IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Usf2IggmusSig GM78 USF2 IgM USF2 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001812 1812 GSM935558 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Usf2IggmusSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 USF2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Tr4StdSig GM78 TR4 Std TR4 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000697 697 GSM935480 Snyder USC hg18 exp wgEncodeSydhTfbsGm12878Tr4StdSig None Signal (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM12878 TR4 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878TbpIggmusSig GM78 TBP IgM TBP GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001798 1798 GSM935277 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878TbpIggmusSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 TBP IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusSig GM78 TBLR1 IgM TBLR1_(ab24550) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002853 2853 GSM935653 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusSig None Signal F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 TBLR1 AB24550 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Stat3IggmusSig GM78 STA3 IgM STAT3 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001811 1811 GSM935557 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Stat3IggmusSig None Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 STAT3 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Stat1StdSig GM78 STA1 Std STAT1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001852 1852 GSM935612 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Stat1StdSig None Signal transcription factor, activated by interferon signalling B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 STAT1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Srebp2IggrabSig GM78 SREBP2 IgR SREBP2 GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003363 3363 GSM1003603 Snyder Stanford exp wgEncodeSydhTfbsGm12878Srebp2IggrabSig None Signal Sterol regulatory element binding transcription factor 2 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 SREBP2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Srebp1IggrabSig GM78 SREBP1 IgR SREBP1 GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003362 3362 GSM1003617 Snyder Stanford exp wgEncodeSydhTfbsGm12878Srebp1IggrabSig None Signal Sterol regulatory element binding transcription factor 1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 SREBP1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Spt20StdSig GM78 SPT Std SPT20 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001873 1873 GSM935417 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Spt20StdSig None Signal Also known as FAM48A or P38IP. It is a component of SAGA complex. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 SPT20 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Smc3ab9263IggmusSig GM78 SMC3 IgM SMC3_(ab9263) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001833 1833 GSM935376 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Smc3ab9263IggmusSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 SMC3 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusSig GM78 SIN3A IgM SIN3A_(NB600-1263) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002868 2868 GSM935331 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusSig None Signal Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 SIN3A IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Rfx5200401194IggmusSig GM78 RFX5 IgM RFX5_(200-401-194) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001810 1810 GSM935556 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Rfx5200401194IggmusSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 RFX5 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Rad21IggrabSig GM78 Rad2 IgR Rad21 GM12878 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000749 749 GSM935332 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol3StdSig GM78 Pol3 Std Pol3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000645 645 GSM935316 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878Pol3StdSig None Signal RNA Polymerase III B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 POL3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2s2IggmusSig GM78 PolS IgM Pol2(phosphoS2) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001858 1858 GSM935608 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Pol2s2IggmusSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Pol2 S2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2StdSig GM78 Pol2 Std Pol2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000626 626 GSM935412 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878Pol2StdSig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2IggmusSig GM78 Pol2 IgM Pol2 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000708 708 GSM935386 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878Pol2IggmusSig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300bStdSig GM78 p300 Std p300_(SC-584) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002037 2037 GSM935562 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878P300bStdSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 p300 SC584 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300sc584IggmusSig GM78 p300 IgM p300_(SC-584) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001813 1813 GSM935559 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878P300sc584IggmusSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 p300 SC584 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300IggmusSig GM78 p300 IgM p300 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002824 2824 GSM935294 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878P300IggmusSig None Signal EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 p300 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Nrf1IggmusSig GM78 Nrf1 IgM Nrf1 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001846 1846 GSM935309 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Nrf1IggmusSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Nrf1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfybIggmusSig GM78 NYB IgM NF-YB GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002065 2065 GSM935507 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878NfybIggmusSig None Signal NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 NF-YB IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfyaIggmusSig GM78 NYA IgM NF-YA GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002064 2064 GSM935506 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878NfyaIggmusSig None Signal NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 NF-YA IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfkbTnfaIggrabSig GM78 TNF NKB IgR NFKB GM12878 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000690 690 GSM935478 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12878 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Nfe2sc22827StdSig GM78 NFE2 Std NF-E2_(SC-22827) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-09-03 2011-06-03 wgEncodeEH001808 1808 GSM935652 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Nfe2sc22827StdSig None Signal Transcription factor NFE2 45 kDa subunit is a component of the NFE2 complex and essential for regulating erythroid and megakaryocytic maturation and differentiation. Binds to the hypersensitive site 2 (HS2) of the beta-globin control region (LCR). This subunit (NFE2)recognizes the TCAT/C sequence of the AP-1-like core palindrome present in a number of erythroid and megakaryocytic gene promoters. Requires MAFK or other small MAF proteins for binding to the NFE2 motif. May play a role in all aspects of hemoglobin production from globin and heme synthesis to procurement of iron. NFE2 has been shown to interact with CREB binding protein. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 NF-E2 SC22827 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Mxi1IggmusSig GM78 Mxi1 IgM Mxi1_(AF4185) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002026 2026 GSM935431 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Mxi1IggmusSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Mxi1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Mazab85725IggmusSig GM78 MAZ IgM MAZ_(ab85725) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002852 2852 GSM935283 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Mazab85725IggmusSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 MAZ IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878MaxIggmusSig GM78 Max IgM Max GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002806 2806 GSM935518 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878MaxIggmusSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Max IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878MafkIggmusSig GM78 MafK IgM MafK_(ab50322) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003361 3361 GSM1003616 Snyder Stanford exp wgEncodeSydhTfbsGm12878MafkIggmusSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 MafK (ab50322) IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878JundStdSig GM78 JunD Std JunD GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000639 639 GSM935541 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878JundStdSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 JunD Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878JundIggrabSig GM78 JunD IgR JunD GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003370 3370 GSM1003634 Snyder Stanford exp wgEncodeSydhTfbsGm12878JundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Irf3IggmusSig GM78 IRF3 IgM IRF3 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001809 1809 GSM935651 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Irf3IggmusSig None Signal Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 IRF3 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdSig GM78 IKZF1 Std IKZF1_(IkN)_(UCLA) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002811 2811 GSM935442 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdSig None Signal IKAROS family zinc finger 1 (Ikaros or IKZF1) is a C2H2 zinc finger transcription factor that is associated with various chromatin-modifying complexes and is suggested to play a role in the development of lymphocytes, B- and T-cells. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM12878 IKZF1 IKN UCLA Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Gcn5StdSig GM78 GCN5 Std GCN5 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-20 wgEncodeEH001874 1874 GSM935415 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Gcn5StdSig None Signal KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 GCN5 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878ErraIggrabSig GM78 ERRA IgR ERRA GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003387 3387 GSM1003605 Snyder Stanford exp wgEncodeSydhTfbsGm12878ErraIggrabSig None Signal Epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 ERRA IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Elk112771IggmusSig GM78 ELK1 IgM ELK1_(1277-1) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002851 2851 GSM935345 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Elk112771IggmusSig None Signal Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 ELK1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ebf1sc137065StdSig GM78 EBF1 Std EBF1_(SC-137065) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001832 1832 GSM935375 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Ebf1sc137065StdSig None Signal Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 EBF1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878E2f4IggmusSig GM78 E2F4 IgM E2F4 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002867 2867 GSM935330 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878E2f4IggmusSig None Signal mapping at the C-terminus of E2F4 of human origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 E2F4 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdSig GM78 CTCF Std CTCF_(SC-15914) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-19 wgEncodeEH001851 1851 GSM935611 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 CTCF Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Corestsc30189IggmusSig GM78 COREST IgM COREST_(sc-30189) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002841 2841 GSM935583 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Corestsc30189IggmusSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 COREST SC30189 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Chd2ab68301IggmusSig GM78 CHD2 IgM CHD2_(AB68301) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001831 1831 GSM935378 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Chd2ab68301IggmusSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 CHD2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Chd1a301218aIggmusSig GM78 CHD1 IgM CHD1_(A301-218A) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002823 2823 GSM935301 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Chd1a301218aIggmusSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 CHD1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878CfosStdSig GM78 cFOS Std c-Fos GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000622 622 GSM935409 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878CfosStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 c-FOS Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Cdpsc6327IggmusSig GM78 CDP IgM CDP_(sc-6327) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003386 3386 GSM1003604 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Cdpsc6327IggmusSig None Signal CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 CDP (SC-6327) IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Brca1a300IggmusSig GM78 BRC1 IgM BRCA1_(A300-000A) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001830 1830 GSM935377 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Brca1a300IggmusSig None Signal Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 BRCA1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Bhlhe40cIggmusSig GM78 BHL4 IgM BHLHE40_(NB100-1800) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002025 2025 GSM935430 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Bhlhe40cIggmusSig None Signal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 BHLHE40 NB100 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsViewPeaks Peaks Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation 
wgEncodeSydhTfbsU2osSetdb1UcdPk U2OS STDB UCD SETDB1 U2OS UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001762 1762 GSM935458 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsU2osSetdb1UcdPk None Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment U2OS SETDB1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsU2osKap1UcdPk U2OS KAP1 UCD KAP1 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-05-31 wgEncodeEH001776 1776 GSM935587 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsU2osKap1UcdPk None Peaks KRAB Associated Protein 1, helps regulate transcriptional repression. osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment U2OS KAP1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdPk SHSY GAT3 UCD GATA3_(SC-269) SH-SY5Y UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002031 2031 GSM935567 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdPk None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment SH-SY5Y GATA3 SC269 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yGata2UcdPk SHSY GAT2 UCD GATA-2 SH-SY5Y UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001770 1770 GSM935589 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsShsy5yGata2UcdPk None Peaks GATA binding protein 2 neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment SH-SY5Y GATA2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsRajiPol2UcdPk Raji Pol2 UCD Pol2 Raji UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001761 1761 GSM935461 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsRajiPol2UcdPk None Peaks RNA Polymerase II B lymphocyte, "The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment Raji Pol2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdefetalGata1UcdPk PBDF GAT1 UCD GATA-1 PBDEFetal UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001785 1785 GSM935333 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdefetalGata1UcdPk None Peaks GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts from 16-19 week human fetal liver Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBDE-Fetal GATA1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdePol2UcdPk PBDE Pol2 UCD Pol2 PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001766 1766 GSM935462 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdePol2UcdPk None Peaks RNA Polymerase II peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBDE Pol2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdeGata1UcdPk PBDE GAT1 UCD GATA-1 PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-09-23 2011-06-23 wgEncodeEH001765 1765 GSM935465 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdeGata1UcdPk None Peaks GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBDE GATA1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPanc1Tcf7l2UcdPk PANC TCF7L2 UCD TCF7L2 PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002071 2071 GSM816437 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPanc1Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PANC1 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Znf274UcdPk NT2D Z274 UCD ZNF274 NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001775 1775 GSM935584 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNt2d1Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2-D1 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Yy1UcdPk NT2D YY1 UCD YY1 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000653 653 GSM935424 Snyder USC hg18 exp wgEncodeSydhTfbsNt2d1Yy1UcdPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2-D1 YY1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Suz12UcdPk NT2D SZ12 UCD SUZ12 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000652 652 GSM935423 Snyder USC hg18 exp wgEncodeSydhTfbsNt2d1Suz12UcdPk None Peaks Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2-D1 SUZ12 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4Pol2StdPk NB4 Pol2 Std Pol2 NB4 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000618 618 GSM935354 Snyder Yale hg18 exp wgEncodeSydhTfbsNb4Pol2StdPk None Peaks RNA Polymerase II acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment NB4 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4MaxStdPk NB4 Max Std Max NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-26 2011-05-26 wgEncodeEH001806 1806 GSM935644 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNb4MaxStdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment NB4 Max Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4CmycStdPk NB4 cMyc Std c-Myc NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-26 2011-05-26 wgEncodeEH001807 1807 GSM935643 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNb4CmycStdPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment NB4 c-Myc Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3TamStdPk MCF1 TAM STA3 Std STAT3 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001769 1769 GSM935457 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesStat3TamStdPk 4OHTAM_1uM_36hr Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A STAT3 Standard 4-hydroxytamoxifen 36hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3Etoh01StdPk MCF1 EtH STA3 Std STAT3 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001772 1772 GSM935591 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesStat3Etoh01StdPk EtOH_0.01pct Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A STAT3 Standard EtOH .01% 36h ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3Tam112hHvdPk MCF1 TAM 12h STA3 STAT3 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002836 2836 GSM935399 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesStat3Tam112hHvdPk 4OHTAM_1uM_12hr Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A STAT3 Harvard 4-hydroxytamoxifen 12hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesPol2TamStdPk MCF1 TAM Pol2 Std Pol2 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001768 1768 GSM935456 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesPol2TamStdPk 4OHTAM_1uM_36hr Peaks RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A Pol2 Standard 4-hydroxytamoxifen 36hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesPol2Etoh01StdPk MCF1 EtH Pol2 Std Pol2 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001771 1771 GSM935588 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesPol2Etoh01StdPk EtOH_0.01pct Peaks RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A Pol2 Standard EtOH .01% 36h ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesE2f4TamHvdPk MCF1 TAM E2F4 Hvd E2F4 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002835 2835 GSM935400 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesE2f4TamHvdPk 4OHTAM_1uM_36hr Peaks mapping at the C-terminus of E2F4 of human origin mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A E2F4 Harvard 4-hydroxytamoxifen 36hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCmycTam14hHvdPk MCF1 TAM 14h cMyc c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002840 2840 GSM935491 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCmycTam14hHvdPk 4OHTAM_1uM_4hr Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A c-Myc Harvard 4-hydroxytamoxifen 14hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCmycEtoh01HvdPk MCF1 EtH cMyc Hvd c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002816 2816 GSM935441 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCmycEtoh01HvdPk EtOH_0.01pct Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A c-Myc Harvard EtOH .01% 36h ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTam14hHvdPk MCF1 TAM 14h cFOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002838 2838 GSM935397 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTam14hHvdPk 4OHTAM_1uM_4hr Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A c-FOS Harvard 4-hydroxytamoxifen 14hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTam112hHvdPk MCF1 TAM 12h cFOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002837 2837 GSM935398 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTam112hHvdPk 4OHTAM_1uM_12hr Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A c-FOS Harvard 4-hydroxytamoxifen 12hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTamHvdPk MCF1 TAM cFOS Hvd c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002839 2839 GSM935396 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTamHvdPk 4OHTAM_1uM_36hr Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A c-FOS Harvard 4-hydroxytamoxifen 36hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosEtoh01HvdPk MCF1 EtH cFOS Hvd c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002815 2815 GSM935438 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosEtoh01HvdPk EtOH_0.01pct Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A c-FOS Harvard EtOH .01% 36h ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293tZnf263UcdPk HEKT Z263 UCD ZNF263 HEK293-T-REx UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-24 2011-10-24 wgEncodeEH001781 1781 GSM935577 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293tZnf263UcdPk None Peaks ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line, hypotriploid, XXX Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEK293-T-REx ZNF263 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Tcf7l2UcdPk HEK2 TCF7L2 UCD TCF7L2 HEK293 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2012-03-22 wgEncodeEH002022 2022 GSM782124 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEK293 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Pol2StdPk HEK2 Pol2 Std Pol2 HEK293 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000632 632 GSM935534 Snyder Yale hg18 exp wgEncodeSydhTfbsHek293Pol2StdPk None Peaks RNA Polymerase II embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HEK293 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Kap1UcdPk HEK2 KAP1 UCD KAP1 HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-05-31 wgEncodeEH001779 1779 GSM935592 Snyder USC PeakSeq1.0. KAP1 colocalizes with H3K9me3 marks and peak analysis should be performed using programs modified for spreading histone marks such as H3K9me3 and H3K27me3. hg19 exp wgEncodeSydhTfbsHek293Kap1UcdPk None Peaks KRAB Associated Protein 1, helps regulate transcriptional repression. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEK293 KAP1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Elk4UcdPk HEK2 ELK4 UCD ELK4 HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-05-31 wgEncodeEH001773 1773 GSM935590 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Elk4UcdPk None Peaks This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEK293 ELK4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116Tcf7l2UcdPk HCT TCF7L2 UCD TCF7L2 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000629 629 GSM782123 Snyder USC hg18 exp wgEncodeSydhTfbsHct116Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116Pol2UcdPk HCT Pol2 UCD Pol2 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000651 651 GSM935426 Snyder USC hg18 exp wgEncodeSydhTfbsHct116Pol2UcdPk None Peaks RNA Polymerase II colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 Pol2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193Pol2IggmusPk GM93 Pol2 IgM Pol2 GM19193 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000743 743 GSM935325 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19193Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM19193 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193NfkbTnfaIggrabPk GM93 TNF NKB IgR NFKB GM19193 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000718 718 GSM935279 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19193NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM19193 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099Pol2IggmusPk GM99 Pol2 IgM Pol2 GM19099 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000741 741 GSM935323 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19099Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM19099 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099NfkbTnfaIggrabPk GM99 TNF NKB IgR NFKB GM19099 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000717 717 GSM935273 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19099NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM19099 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951Pol2IggmusPk GM51 Pol2 IgM Pol2 GM18951 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000739 739 GSM935530 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18951Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM18951 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951NfkbTnfaIggrabPk GM51 TNF NKB IgR NFKB GM18951 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000738 738 GSM935531 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18951NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM18951 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526Pol2IggmusPk GM26 Pol2 IgM Pol2 GM18526 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000733 733 GSM935524 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18526Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM18526 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526NfkbTnfaIggrabPk GM26 TNF NKB IgR NFKB GM18526 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000716 716 GSM935281 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18526NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM18526 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505Pol2IggmusPk GM05 Pol2 IgM Pol2 GM18505 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH000731 731 GSM935522 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18505Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM18505 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505NfkbTnfaIggrabPk GM05 TNF NKB IgR NFKB GM18505 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000715 715 GSM935282 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18505NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM18505 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510Pol2IggmusPk GM10 Pol2 IgM Pol2 GM15510 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000714 714 GSM935291 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm15510Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM15510 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510NfkbTnfaIggrabPk GM10 TNF NKB IgR NFKB GM15510 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000736 736 GSM935529 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm15510NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM15510 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892Pol2IggmusPk GM92 Pol2 IgM Pol2 GM12892 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000729 729 GSM935640 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12892Pol2IggmusPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12892 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892NfkbTnfaIggrabPk GM92 TNF NKB IgR NFKB GM12892 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000712 712 GSM935285 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12892NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM12892 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891Pol2IggmusPk GM91 Pol2 IgM Pol2 GM12891 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000710 710 GSM935287 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12891Pol2IggmusPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12891 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891NfkbTnfaIggrabPk GM91 TNF NKB IgR NFKB GM12891 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000735 735 GSM935526 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12891NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM12891 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847Pol2IggmusPk GM47 Pol2 IgM Pol2 GM10847 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH000705 705 GSM935389 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm10847Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM10847 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847NfkbTnfaIggrabPk GM47 TNF NKB IgR NFKB GM10847 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000734 734 GSM935527 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm10847NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM10847 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm08714Znf274UcdPk GM14 Z274 UCD ZNF274 GM08714 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002866 2866 GSM935329 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsGm08714Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. lymphoblastoid cell line, Instability of heterochromatin of chromosomes 1, 9, and 16 with variable combined immunodeficiency; dysmorphic facial features, developmental delay, malabsorption, and recurrent infections; see GM08747 Fibroblast; donor subject is a compound heterozygote: one allele has a G&gt;A transition at nucleotide 1807 (1807G&gt;A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B; the second allele has a G&gt;A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G&gt;A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM08714 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshSmc3IggrabPk SKSH SMC3 IgR SMC3_(ab9263) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003377 3377 GSM1003627 Snyder Stanford exp wgEncodeSydhTfbsSknshSmc3IggrabPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH SMC3 (ab9263) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshRfx5IggrabPk SKSH RFX5 IgR RFX5_(200-401-194) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003375 3375 GSM1003629 Snyder Stanford exp wgEncodeSydhTfbsSknshRfx5IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH RFX5 (200-401-194) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshRad21IggrabPk SKSH Rad21 IgR Rad21 SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003376 3376 GSM1003628 Snyder Stanford exp wgEncodeSydhTfbsSknshRad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshP300bIggrabPk SKSH p300 IgR p300_(SC-584) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003378 3378 GSM1003626 Snyder Stanford exp wgEncodeSydhTfbsSknshP300bIggrabPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH p300 (SC-584) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshNrf1IggrabPk SKSH Nrf1 IgR Nrf1 SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003374 3374 GSM1003630 Snyder Stanford exp wgEncodeSydhTfbsSknshNrf1IggrabPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH Nrf1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshMxi1IggrabPk SKSH Mxi1 IgR Mxi1_(AF4185) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003373 3373 GSM1003631 Snyder Stanford exp wgEncodeSydhTfbsSknshMxi1IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH Mxi1 (AF4185) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshJundIggrabPk SKSH JunD IgR JunD SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003372 3372 GSM1003632 Snyder Stanford exp wgEncodeSydhTfbsSknshJundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshCtcfbIggrabPk SKSH CTCF IgR CTCF_(SC-15914) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003371 3371 GSM1003633 Snyder Stanford exp wgEncodeSydhTfbsSknshCtcfbIggrabPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH CTCF (SC-15914) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Znf217UcdPk MCF7 Z217 UCD ZNF217 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-08-03 2012-05-03 wgEncodeEH002036 2036 GSM935563 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Znf217UcdPk None Peaks ZNF217 is an important oncogene based on the high frequency of amplification and overexpression in many cancer types, but its molecular mode of gene regulation is poorly understood. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. ZNF217 contains seven C2H2 zinc finger domains and has been shown to bind to gene promoters mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 ZNF217 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Tcf7l2UcdPk MCF7 TCF7L2 UCD TCF7L2 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-20 2012-06-19 wgEncodeEH002072 2072 GSM816438 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Hae2f1UcdPk MCF7 HAE2 UCD HA-E2F1 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000693 693 GSM935477 Snyder USC hg18 exp wgEncodeSydhTfbsMcf7Hae2f1UcdPk None Peaks The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 HA-E2F1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Gata3sc269UcdPk MCF7 GAT3 UCD GATA3_(SC-269) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002812 2812 GSM935445 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsMcf7Gata3sc269UcdPk None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 GATA3 SC269 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Gata3UcdPk MCF7 GAT3 UCD GATA3_(SC-268) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-08-03 2012-05-03 wgEncodeEH002035 2035 GSM825711 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Gata3UcdPk None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 GATA3 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Rfx5IggrabPk IMR90 RFX5 IgR RFX5_(200-401-194) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003367 3367 GSM1003615 Snyder Stanford exp wgEncodeSydhTfbsImr90Rfx5IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 RFX5 (200-401-194) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Rad21IggrabPk IMR90 Rad2 IgR Rad21 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002810 2810 GSM935624 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Pol2IggrabPk IMR90 Pol2 IgR Pol2 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002809 2809 GSM935513 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90Pol2IggrabPk None Peaks RNA Polymerase II fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 Pol2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Mxi1IggrabPk IMR90 Mxi1 IgR Mxi1_(AF4185) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003366 3366 GSM1003614 Snyder Stanford exp wgEncodeSydhTfbsImr90Mxi1IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 Mxi1 (AF4185) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Mazab85725IggrabPk IMR90 MAZ IgR MAZ_(ab85725) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003365 3365 GSM1003613 Snyder Stanford exp wgEncodeSydhTfbsImr90Mazab85725IggrabPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 MAZ (ab85725) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90MafkIggrabPk IMR90 MafK IgR MafK_(ab50322) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002832 2832 GSM935403 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90MafkIggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90CtcfbIggrabPk IMR90 CTCF IgR CTCF_(SC-15914) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002831 2831 GSM935404 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90CtcfbIggrabPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 CTCF IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Corestsc30189IggrabPk IMR90 COREST IgR COREST_(sc-30189) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003364 3364 GSM1003612 Snyder Stanford exp wgEncodeSydhTfbsImr90Corestsc30189IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 COREST (SC-30189) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Chd1nb10060411IggrabPk IMR90 CHD1 IgR CHD1_(NB100-60411) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003390 3390 GSM1003623 Snyder Stanford exp wgEncodeSydhTfbsImr90Chd1nb10060411IggrabPk None Peaks ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 CHD1 (NB100-60411) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90CebpbIggrabPk IMR90 CBPB IgR CEBPB IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002807 2807 GSM935519 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecPol2StdPk HUVEC Pol2 Std Pol2 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000702 702 GSM935393 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecPol2StdPk None Peaks RNA Polymerase II umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HUVEC Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecMaxStdPk HUVEC Max Std Max HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000768 768 GSM935572 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecMaxStdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HUVEC Max Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecGata2UcdPk HUVEC GAT2 UCD GATA-2 HUVEC UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001758 1758 GSM935347 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHuvecGata2UcdPk None Peaks GATA binding protein 2 umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HUVEC GATA2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecCjunStdPk HUVEC cJun Std c-Jun HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000719 719 GSM935278 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecCjunStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HUVEC c-Jun Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecCfosUcdPk HUVEC cFOS UCD c-Fos HUVEC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001774 1774 GSM935585 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHuvecCfosUcdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HUVEC c-FOS UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Znf274UcdPk HEPG Z274 UCD ZNF274 HepG2 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-10 2011-02-10 wgEncodeEH001755 1755 GSM935350 Snyder USC PeakSeq1.0.  Replicate overlap below cutoff, but submitted because there are very few biologically real targets and all the targets are in heterochromatic regions. hg19 exp wgEncodeSydhTfbsHepg2Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEPG2 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Usf2IggrabPk HEPG USF2 IgR USF2 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001804 1804 GSM935646 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Usf2IggrabPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 USF2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Tr4UcdPk HEPG TR4 UCD TR4 HepG2 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000675 675 GSM935596 Snyder USC hg18 exp wgEncodeSydhTfbsHepg2Tr4UcdPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEPG2 TR4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Tcf7l2UcdPk HEPG TCF7L2 UCD TCF7L2 HepG2 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2001-06-27 2011-01-19 2011-10-19 wgEncodeEH001780 1780 GSM782122 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEPG2 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2TbpIggrabPk HEPG TBP IgR TBP HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001793 1793 GSM935280 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2TbpIggrabPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 TBP IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp2PravastStdPk HEPG prav SBP2 Sd SREBP2 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000643 643 GSM935314 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Srebp2PravastStdPk pravastatin Peaks Sterol regulatory element binding transcription factor 2 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Regions of enriched signal in experiment HEPG2 SREBP2 Standard pravastatin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp1PravastStdPk HEPG prav SRBP Sd SREBP1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000642 642 GSM935315 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Srebp1PravastStdPk pravastatin Peaks Sterol regulatory element binding transcription factor 1 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Regions of enriched signal in experiment HEPG2 SREBP1 Standard pravastatin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp1InslnStdPk HEPG isln SRBP Sd SREBP1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000759 759 GSM935627 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Srebp1InslnStdPk insulin Peaks Sterol regulatory element binding transcription factor 1 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder) Regions of enriched signal in experiment HEPG2 SREBP1 Standard insulin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Smc3ab9263IggrabPk HEPG SMC3 IgR SMC3_(ab9263) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001861 1861 GSM935542 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Smc3ab9263IggrabPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 SMC3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Rfx5200401194IggrabPk HEPG RFX5 IgR RFX5_(200-401-194) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001843 1843 GSM935304 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Rfx5200401194IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 RFX5 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Rad21IggrabPk HEPG Rad2 IgR Rad21 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001803 1803 GSM935647 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2s2IggrabPk HEPG PolS IgR Pol2(phosphoS2) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001860 1860 GSM935543 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Pol2s2IggrabPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Pol2 S2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2PravastStdPk HEPG prav Pol2 Sd Pol2 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000641 641 GSM935312 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Pol2PravastStdPk pravastatin Peaks RNA Polymerase II hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Regions of enriched signal in experiment HEPG2 Pol2 Standard pravastatin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2ForsklnStdPk HEPG frsk Pol2 Sd Pol2 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000758 758 GSM935628 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Pol2ForsklnStdPk forskolin Peaks RNA Polymerase II hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 Pol2 Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2IggrabPk HEPG Pol2 IgR Pol2 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001792 1792 GSM935603 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Pol2IggrabPk None Peaks RNA Polymerase II hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Pol2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pgc1aForsklnStdPk HEPG frsk PGC1 Sd PGC1A HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000757 757 GSM935623 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Pgc1aForsklnStdPk forskolin Peaks The protein encoded by this gene is a transcriptional coactivator that regulates the genes involved in energy metabolism. This protein interacts with PPARgamma, which permits the interaction of this protein with multiple transcription factors. This protein can interact with, and regulate the activities of, cAMP response element binding protein (CREB) and nuclear respiratory factors (NRFs). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 PGC1A Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2P300sc582IggrabPk HEPG p300 IgR p300_(SC-584) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001862 1862 GSM935545 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2P300sc582IggrabPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 p300 SC584 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Nrf1IggrabPk HEPG Nrf1 IgR Nrf1 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001802 1802 GSM935648 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Nrf1IggrabPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Nrf1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mafksc477IggrabPk HEPG MafK IgR MafK_(SC-477) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001850 1850 GSM935610 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mafksc477IggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 MafK SC477 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mxi1StdPk HEPG Mxi1 Std Mxi1_(AF4185) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002029 2029 GSM935437 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mxi1StdPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Mxi1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mazab85725IggrabPk HEPG MAZ IgR MAZ_(ab85725) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002860 2860 GSM935335 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Mazab85725IggrabPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 MAZ IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2MaxIggrabPk HEPG Max IgR Max HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002796 2796 GSM935406 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2MaxIggrabPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Max IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mafkab50322IggrabPk HEPG MafK IgR MafK_(ab50322) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001842 1842 GSM935305 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mafkab50322IggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Maffm8194IggrabPk HEPG MafF IgR MafF_(M8194) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001841 1841 GSM935306 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Maffm8194IggrabPk None Peaks The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 MafF IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2JundIggrabPk HEPG JunD IgR JunD HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001801 1801 GSM935649 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2JundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Irf3IggrabPk HEPG IRF3 IgR IRF3 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001800 1800 GSM935650 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Irf3IggrabPk None Peaks Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 IRF3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Hsf1ForsklnStdPk HEPG frsk HSF1 Sd HSF1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000754 754 GSM935626 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Hsf1ForsklnStdPk forskolin Peaks Epitope corresponding to amino acids 219-529 of heat shock transcription factor 1 (HSF1) of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 HSF1 Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Hnf4aForsklnStdPk HEPG frsk HNF4 Sd HNF4A HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000753 753 GSM935619 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Hnf4aForsklnStdPk forskolin Peaks Epitope mapping at the C-terminus of Rab 11 of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 HNF4A Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Grp20ForsklnStdPk HEPG frsk GR20 Sd GRp20 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000752 752 GSM935620 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Grp20ForsklnStdPk forskolin Peaks Epitope mapping at the C-terminus of GR alpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 GRp20 Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2ErraForsklnStdPk HEPG frsk ERRA Sd ERRA HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000751 751 GSM935621 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2ErraForsklnStdPk forskolin Peaks Epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 ERRA Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Corestsc30189IggrabPk HEPG COREST IgR COREST_(sc-30189) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002845 2845 GSM935579 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Corestsc30189IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 COREST SC30189 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CjunIggrabPk HEPG cJun IgR c-Jun HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001794 1794 GSM935364 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2CjunIggrabPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 c-Jun IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Chd2ab68301IggrabPk HEPG CHD2 IgR CHD2_(AB68301) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001840 1840 GSM935307 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Chd2ab68301IggrabPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 CHD2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpzIggrabPk HEPG CEBPZ IgR CEBPZ HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002859 2859 GSM935274 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2CebpzIggrabPk None Peaks Stimulates transcription from the HSP70 promoter. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 CEBPZ IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpbForsklnStdPk HEPG frsk CBPB Sd CEBPB HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000750 750 GSM935622 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2CebpbForsklnStdPk forskolin Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 CEBPB Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpbIggrabPk HEPG CBPB IgR CEBPB HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-04 2011-01-14 2011-10-13 wgEncodeEH001829 1829 GSM935493 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Brca1a300IggrabPk HEPG BRC1 IgR BRCA1_(A300-000A) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001859 1859 GSM935609 Snyder Stanford PeakSeq1.0.  Although this dataset narrowly misses the ENCODE standard for peak concordance, we submit this data because we feel it is of good quality and will be particularly valuable for comparison to BRCA1 datasets in other cell lines. hg19 exp wgEncodeSydhTfbsHepg2Brca1a300IggrabPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 BRCA1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Bhlhe40cIggrabPk HEPG BHL4 IgR BHLHE40_(NB100-1800) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002032 2032 GSM935566 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Bhlhe40cIggrabPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 BHLHE40 NB100 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Arid3anb100279IggrabPk HEPG ARI3 IgR ARID3A_(NB100-279) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002858 2858 GSM935275 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Arid3anb100279IggrabPk None Peaks This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 ARID3A NB100279 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Zzz3StdPk HeLa ZZZ3 Std ZZZ3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001872 1872 GSM935416 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Zzz3StdPk None Peaks ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 ZZZ3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Znf274UcdPk HeLa Z274 UCD ZNF274 HeLa-S3 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001763 1763 GSM935459 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Znf143IggrabPk HeLa Z143 IgR Znf143_(16618-1-AP) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002028 2028 GSM935436 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Znf143IggrabPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Znf143 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabPk HeLa ZKSCN1 IgR ZKSCAN1_(HPA006672) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002857 2857 GSM935362 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabPk None Peaks The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 ZKSCAN1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Usf2IggmusPk HeLa USF2 IgM USF2 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001819 1819 GSM935561 Snyder Stanford PeakSeq1.0: We submit this dataset because of its high signal quality, although it narrowly missed the cut-off for replicate peak concordance hg19 exp wgEncodeSydhTfbsHelas3Usf2IggmusPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 USF2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tr4StdPk HeLa TR4 Std TR4 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000687 687 GSM935369 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Tr4StdPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TR4 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tf3c110StdPk HeLa TF3C Std TFIIIC-110 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000747 747 GSM935342 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Tf3c110StdPk None Peaks TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFIIIC-110 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdPk HeLa TCF7L2 UCD TCF7L2_C9B9_(2565) HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-12-19 2012-09-18 wgEncodeEH002813 2813 GSM935625 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TCF7L2 C9B9 2565 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tcf7l2UcdPk HeLa TCF7L2 UCD TCF7L2 HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002069 2069 GSM816436 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3TbpIggrabPk HeLa TBP IgR TBP HeLa-S3 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001790 1790 GSM935606 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3TbpIggrabPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TBP IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Stat3IggrabPk HeLa STA3 IgR STAT3 HeLa-S3 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001799 1799 GSM935276 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Stat3IggrabPk None Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 STAT3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Stat1Ifng30StdPk HeLa IFg3 STA1 Sd STAT1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000614 614 GSM935360 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Stat1Ifng30StdPk IFNg30 Peaks transcription factor, activated by interferon signalling cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment HeLa-S3 STAT1 Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Spt20StdPk HeLa SPT Std SPT20 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001855 1855 GSM935615 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Spt20StdPk None Peaks Also known as FAM48A or P38IP. It is a component of SAGA complex. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 SPT20 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Smc3ab9263IggrabPk HeLa SMC3 IgR SMC3_(ab9263) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001839 1839 GSM935384 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Smc3ab9263IggrabPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 SMC3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rpc155StdPk HeLa RPC1 Std RPC155 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000766 766 GSM935489 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Rpc155StdPk None Peaks polymerase (RNA) III (DNA directed) polypeptide A, 155kDa cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 RPC155 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rfx5200401194IggrabPk HeLa RFX5 IgR RFX5_(200-401-194) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001818 1818 GSM935560 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Rfx5200401194IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 RFX5 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rad21IggrabPk HeLa Rad2 IgR Rad21 HeLa-S3 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001789 1789 GSM935571 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Prdm19115IggrabPk HeLa PRDM IgR PRDM1_(9115) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001817 1817 GSM935555 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Prdm19115IggrabPk None Peaks Transcriptional repressor that binds specifically to the PRDI element in the promoter of the beta-interferon gene. Drives the maturation of B-lymphocytes into Ig secreting cells. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 PRDM1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Pol2s2IggrabPk HeLa PolS IgR Pol2(phosphoS2) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001838 1838 GSM935383 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Pol2s2IggrabPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Pol2 S2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Pol2StdPk HeLa Pol2 Std Pol2 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000613 613 GSM935395 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Pol2StdPk None Peaks RNA Polymerase II cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3P300sc584sc584IggrabPk HeLa p300 IgR p300_(SC-584) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001820 1820 GSM935500 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3P300sc584sc584IggrabPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 p300 SC584 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Nrf1IggmusPk HeLa Nrf1 IgM Nrf1 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000723 723 GSM935636 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Nrf1IggmusPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Nrf1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3NfybIggrabPk HeLa NYB IgR NF-YB HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002067 2067 GSM935408 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3NfybIggrabPk None Peaks NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 NF-YB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3NfyaIggrabPk HeLa NYA IgR NF-YA HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002066 2066 GSM935508 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3NfyaIggrabPk None Peaks NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 NF-YA IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Mxi1af4185IggrabPk HeLa Mxi1 IgR Mxi1_(AF4185) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001826 1826 GSM935498 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Mxi1af4185IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Mxi1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Mazab85725IggrabPk HeLa MAZ IgR MAZ_(ab85725) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002855 2855 GSM935272 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Mazab85725IggrabPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 MAZ IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MaxStdPk HeLa Max Std Max HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000646 646 GSM935318 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3MaxStdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 Max Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MaxIggrabPk HeLa Max IgR Max HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002830 2830 GSM935405 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3MaxIggrabPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Max IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MafkIggrabPk HeLa MafK IgR MafK_(ab50322) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002856 2856 GSM935290 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3MafkIggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3JundIggrabPk HeLa JunD IgR JunD HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000745 745 GSM935328 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3JundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Irf3IggrabPk HeLa IRF3 IgR IRF3 HeLa-S3 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001788 1788 GSM935570 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Irf3IggrabPk None Peaks Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 IRF3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ini1IggmusPk HeLa INI1 IgM Ini1 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000722 722 GSM935635 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Ini1IggmusPk None Peaks Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 INI1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Hcfc1nb10068209IggrabPk HeLa-S3 HCFC1 IgR HCFC1_(NB100-68209) HeLa-S3 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003389 3389 GSM1003618 Snyder Stanford exp wgEncodeSydhTfbsHelas3Hcfc1nb10068209IggrabPk None Peaks The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 HCFC1 (NB100-68209) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Hae2f1StdPk HeLa HAE2 Std HA-E2F1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000688 688 GSM935366 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Hae2f1StdPk None Peaks The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 HA-E2F1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabPk HeLa GT2F IgR GTF2F1_(AB28179) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001816 1816 GSM935554 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabPk None Peaks RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 GTF2F1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Gcn5StdPk HeLa GCN5 Std GCN5 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001849 1849 GSM935302 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Gcn5StdPk None Peaks KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 GCN5 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Elk4UcdPk HeLa ELK4 UCD ELK4 HeLa-S3 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001753 1753 GSM935351 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Elk4UcdPk None Peaks This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 ELK4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Elk112771IggrabPk HeLa ELK1 IgR ELK1_(1277-1) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH002864 2864 GSM935326 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Elk112771IggrabPk None Peaks Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 ELK1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f6StdPk HeLa E2F6 Std E2F6 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000692 692 GSM935476 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f6StdPk None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 E2F6 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f4StdPk HeLa E2F4 Std E2F4 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000689 689 GSM935365 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f4StdPk None Peaks mapping at the C-terminus of E2F4 of human origin cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 E2F4 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f1StdPk HeLa E2F1 Std E2F1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000699 699 GSM935484 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f1StdPk None Peaks E2F1, the original member of the E2F family of transcription factors, was identified as a cellular protein with DNA binding activity associated with the adenovirus E2 gene promoter. E2F1 is cell cycle regulated with very low levels in early G1, then increasing levels as cells move from G1 to S, and highest levels of protein at the G1/S boundary, which is consistent with its role in S-phase entry. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 E2F1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Corestsc30189IggrabPk HeLa COREST IgR COREST_(sc-30189) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002844 2844 GSM935578 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Corestsc30189IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 COREST SC30189 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CmycStdPk HeLa cMyc Std c-Myc HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000648 648 GSM935320 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3CmycStdPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 c-Myc Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CjunIggrabPk HeLa cJun IgR c-Jun HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000746 746 GSM935341 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3CjunIggrabPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 c-Jun IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Chd2IggrabPk HeLa CHD2 IgR CHD2_(AB68301) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002027 2027 GSM935432 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Chd2IggrabPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 CHD2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CfosStdPk HeLa cFOS Std c-Fos HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000647 647 GSM935317 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3CfosStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 c-FOS Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CebpbIggrabPk HeLa CBPB IgR CEBPB HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001815 1815 GSM935553 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brg1IggmusPk HeLa BRG1 IgM Brg1 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000781 781 GSM935511 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Brg1IggmusPk None Peaks Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 BRG1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brf2StdPk HeLa BRF2 Std BRF2 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000765 765 GSM935435 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Brf2StdPk None Peaks Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 BRF2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brf1StdPk HeLa BRF1 Std BRF1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000764 764 GSM935582 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Brf1StdPk None Peaks 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 BRF1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brca1a300IggrabPk HeLa BRC1 IgR BRCA1_(A300-000A) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001814 1814 GSM935552 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Brca1a300IggrabPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 BRCA1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Bdp1StdPk HeLa BDP1 Std BDP1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000763 763 GSM935486 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Bdp1StdPk None Peaks 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 BDP1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Baf170IggmusPk HeLa BAF7 IgM BAF170 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000721 721 GSM935638 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Baf170IggmusPk None Peaks BAF170 (SMARCC2, Brg1-Associated Factor, 170 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 BAF170 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Baf155IggmusPk HeLa BAF5 IgM BAF155 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000720 720 GSM935637 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Baf155IggmusPk None Peaks BAF155 (SMARCC1, Brg1-Associated Factor, 155 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 BAF155 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ap2gammaStdPk HeLa AP2g Std AP-2gamma HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000686 686 GSM935370 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Ap2gammaStdPk None Peaks Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5'-GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 AP-2g Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ap2alphaStdPk HeLa AP2a Std AP-2alpha HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000685 685 GSM935367 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Ap2alphaStdPk None Peaks Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5' -GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. AP-2alpha is the only AP-2 protein required for early morphogenesis of the lens vesicle (by similarity). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 AP-2a Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Rad21IggrabPk A549 Rad2 IgR Rad21 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002822 2822 GSM935300 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Pol2s2IggrabPk A549 PolS IgR Pol2(phosphoS2) A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002821 2821 GSM935299 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Pol2s2IggrabPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 Pol2 S2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549MaxIggrabPk A549 Max IgR Max A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002820 2820 GSM935298 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549MaxIggrabPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 Max IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CtcfbIggrabPk A549 CTCF IgR CTCF_(SC-15914) A549 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003384 3384 GSM1003606 Snyder Stanford exp wgEncodeSydhTfbsA549CtcfbIggrabPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 CTCF (SC-15914) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CmycIggrabPk A549 c-Myc IgR c-Myc A549 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003385 3385 GSM1003607 Snyder Stanford exp wgEncodeSydhTfbsA549CmycIggrabPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 c-Myc IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CebpbIggrabPk A549 CBPB IgR CEBPB A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002818 2818 GSM935630 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Bhlhe40IggrabPk A549 BHL4 IgR BHLHE40 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002817 2817 GSM935440 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Bhlhe40IggrabPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 BHLHE40 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znfmizdcp1ab65767IggrabPk K562 ZNF-MIZD IgR ZNF-MIZD-CP1_(ab65767) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003381 3381 GSM1003611 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Znfmizdcp1ab65767IggrabPk None Peaks Zinc finger MIZ domain-containing protein 1 that increases ligand-dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ZNF-MIZD-CP1 (ab65767) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf384hpa004051IggrabPk K562 ZNF384 IgR ZNF384_(HPA004051) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003382 3382 GSM1003621 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Znf384hpa004051IggrabPk None Peaks This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ZNF384 (HPA004051) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf274m01UcdPk K562 Z274M UCD ZNF274_(M01) K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002068 2068 GSM935503 Snyder USC PeakSeq1.0. This factor has a limited number of highly enriched target sites and for factors with so few binding sites, we believe that in order to get a good overlap between replicate datasets one must have fewer reads.  We are confident with the overlap of the highly enriched binding sites for this dataset regardless of the poor replicate overlap. hg19 exp wgEncodeSydhTfbsK562Znf274m01UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 ZNF274 (M01) UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf274UcdPk K562 Z274 UCD ZNF274 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000696 696 GSM935479 Snyder USC hg18 exp wgEncodeSydhTfbsK562Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf263UcdPk K562 Z263 UCD ZNF263 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000630 630 GSM935532 Snyder USC hg18 exp wgEncodeSydhTfbsK562Znf263UcdPk None Peaks ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 ZNF263 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf143IggrabPk K562 Z143 IgR Znf143_(16618-1-AP) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002030 2030 GSM935568 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Znf143IggrabPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Znf143 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabPk K562 ZC3H11A IgR ZC3H11A_(NB100-74650) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003380 3380 GSM1003610 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabPk None Peaks ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ZC3H11A (NB100-74650) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Yy1UcdPk K562 YY1 UCD YY1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000684 684 GSM935368 Snyder USC hg18 exp wgEncodeSydhTfbsK562Yy1UcdPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 YY1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Xrcc4StdPk K562 XRCC Std XRCC4 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000650 650 GSM935425 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Xrcc4StdPk None Peaks Recognizes the XRCC4 protein (X ray cross complementation protein). XRCC4 is a ubiquitous protein reported to have a role in DNA double-stranded break repair and in V(D)J recombination. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 XRCC4 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Usf2IggrabPk K562 USF2 IgR USF2 K562 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001797 1797 GSM935356 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Usf2IggrabPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 USF2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ubtfsab1404509IggmusPk K562 UBTF IgM UBTF_(SAB1404509) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002850 2850 GSM935642 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Ubtfsab1404509IggmusPk None Peaks Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 UBTF IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ubfsc13125IggmusPk K562 UBF IgM UBF_(sc-13125) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002863 2863 GSM935338 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Ubfsc13125IggmusPk None Peaks Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 UBF IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tr4UcdPk K562 TR4 UCD TR4 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000682 682 GSM935374 Snyder USC hg18 exp wgEncodeSydhTfbsK562Tr4UcdPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 TR4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tf3c110StdPk K562 TF3C Std TFIIIC-110 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000748 748 GSM935343 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Tf3c110StdPk None Peaks TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 TFIIIC-110 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562TbpIggmusPk K562 TBP IgM TBP K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001825 1825 GSM935495 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562TbpIggmusPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 TBP IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tblr1nb600270IggrabPk K562 TBLR1 IgR TBLR1_(NB600-270) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002848 2848 GSM935574 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Tblr1nb600270IggrabPk None Peaks F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 TBLR1 NB600270 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tblr1ab24550IggrabPk K562 TBLR1 IgR TBLR1_(ab24550) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002849 2849 GSM935575 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Tblr1ab24550IggrabPk None Peaks F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 TBLR1 AB24550 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tal1sc12984IggmusPk K562 TAL1 IgM TAL1_(SC-12984) K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001824 1824 GSM935496 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Tal1sc12984IggmusPk None Peaks TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 TAL1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat2Ifna6hStdPk K562 IFa6 STA2 Sd STAT2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000666 666 GSM935469 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat2Ifna6hStdPk IFNa6h Peaks peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 STAT2 Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat2Ifna30StdPk K562 IFa3 STA2 Sd STAT2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000665 665 GSM935470 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat2Ifna30StdPk IFNa30 Peaks peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 STAT2 Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifng6hStdPk K562 IFg6 STA1 Sd STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000761 761 GSM935488 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Stat1Ifng6hStdPk IFNg6h Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 STAT1 Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifng30StdPk K562 IFg3 STA1 Sd STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000760 760 GSM935487 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Stat1Ifng30StdPk IFNg30 Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 STAT1 Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifna6hStdPk K562 IFa6 STA1 Sd STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000664 664 GSM935471 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat1Ifna6hStdPk IFNa6h Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 STAT1 Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifna30StdPk K562 IFa3 STA1 Sd STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000663 663 GSM935472 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat1Ifna30StdPk IFNa30 Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 STAT1 Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Smc3ab9263IggrabPk K562 SMC3 IgR SMC3_(ab9263) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001845 1845 GSM935310 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Smc3ab9263IggrabPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 SMC3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Sirt6StdPk K562 SIRT Std SIRT6 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000681 681 GSM935371 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Sirt6StdPk None Peaks A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 SIRT6 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Setdb1UcdPk K562 STDB UCD SETDB1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000677 677 GSM935598 Snyder USC hg18 exp wgEncodeSydhTfbsK562Setdb1UcdPk None Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 SETDB1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Setdb1MnasedUcdPk K562 MNas STDB UC SETDB1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000769 769 GSM935573 Snyder USC hg18 exp wgEncodeSydhTfbsK562Setdb1MnasedUcdPk MNaseD Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Fragmented using micrococcal nuclease digestion Regions of enriched signal in experiment K562 SETDB1 UC Davis MNaseD ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rpc155StdPk K562 RPC1 Std RPC155 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000680 680 GSM935372 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Rpc155StdPk None Peaks polymerase (RNA) III (DNA directed) polypeptide A, 155kDa leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 RPC155 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rfx5IggrabPk K562 RFX5 IgR RFX5_(200-401-194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002033 2033 GSM935565 Snyder Stanford PeakSeq1.0.  Although this dataset narrowly misses the ENCODE cut-off for peak agreement between replicates, the exceptionally strong signals observed at the HLA loci on chromosome 6 indicate that this is a high-quality dataset. hg19 exp wgEncodeSydhTfbsK562Rfx5IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 RFX5 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rad21StdPk K562 Rad2 Std Rad21 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000649 649 GSM935319 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Rad21StdPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 Rad21 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol3StdPk K562 Pol3 Std Pol3 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000694 694 GSM935481 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol3StdPk None Peaks RNA Polymerase III leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 POL3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2s2StdPk K562 PolS Std Pol2(phosphoS2) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-12 2011-04-12 wgEncodeEH001805 1805 GSM935645 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Pol2s2StdPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Pol2 S2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2s2IggrabPk K562 PolS IgR Pol2(phosphoS2) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002833 2833 GSM935402 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Pol2s2IggrabPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Pol2 S2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2StdPk K562 Pol2 Std Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000616 616 GSM935358 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2StdPk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifng6hStdPk K562 IFg6 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000662 662 GSM935473 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifng6hStdPk IFNg6h Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 Pol2 Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifng30StdPk K562 IFg3 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000704 704 GSM935388 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol2Ifng30StdPk IFNg30 Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 Pol2 Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifna6hStdPk K562 IFa6 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000661 661 GSM935474 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifna6hStdPk IFNa6h Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 Pol2 Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifna30StdPk K562 IFa3 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000660 660 GSM935475 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifna30StdPk IFNa30 Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 Pol2 Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2IggmusPk K562 Pol2 IgM Pol2 K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000727 727 GSM935632 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol2IggmusPk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562P300sc584sc48343IggrabPk K562 p300 IgR p300_(SC-48343) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001828 1828 GSM935494 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562P300sc584sc48343IggrabPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 p300 SC48343 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562P300IggrabPk K562 p300 IgR p300 K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002834 2834 GSM935401 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562P300IggrabPk None Peaks EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 p300 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Nrf1IggrabPk K562 Nrf1 IgR Nrf1 K562 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001796 1796 GSM935361 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Nrf1IggrabPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Nrf1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NfybStdPk K562 NYB Std NF-YB K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002024 2024 GSM935429 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562NfybStdPk None Peaks NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 NF-YB Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NfyaStdPk K562 NYA Std NF-YA K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2012-03-22 wgEncodeEH002021 2021 GSM935433 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562NfyaStdPk None Peaks NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 NF-YA Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Nfe2StdPk K562 NFE2 Std NF-E2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000624 624 GSM935414 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Nfe2StdPk None Peaks Nuclear factor, erythroid-derived 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 NF-E2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NelfeStdPk K562 NELF Std NELFe K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000701 701 GSM935392 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562NelfeStdPk None Peaks NELF-E (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 NELFe Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mxi1af4185IggrabPk K562 Mxi1 IgR Mxi1_(AF4185) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001827 1827 GSM935497 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Mxi1af4185IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Mxi1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mazab85725IggrabPk K562 MAZ IgR MAZ_(ab85725) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002862 2862 GSM935337 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Mazab85725IggrabPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 MAZ IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaxStdPk K562 Max Std Max K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000637 637 GSM935539 Snyder Yale hg18 exp wgEncodeSydhTfbsK562MaxStdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 Max Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaxIggrabPk K562 Max IgR Max K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002869 2869 GSM935344 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562MaxIggrabPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Max IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mafkab50322IggrabPk K562 MafK IgR MafK_(ab50322) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001844 1844 GSM935311 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Mafkab50322IggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaffIggrabPk K562 MafF IgR MafF_(M8194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002804 2804 GSM935520 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562MaffIggrabPk None Peaks The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 MafF IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Kap1UcdPk K562 KAP1 UCD KAP1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-23 2011-05-23 wgEncodeEH001764 1764 GSM935464 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Kap1UcdPk None Peaks KRAB Associated Protein 1, helps regulate transcriptional repression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 KAP1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562JundIggrabPk K562 JunD IgR JunD K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002164 2164 GSM935569 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562JundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifng6hStdPk K562 IFg6 IRF1 Sd IRF1 K562 std ChipSeq ENCODE June 2010 Freeze 2010-04-29 2011-01-29 wgEncodeEH001866 1866 GSM935549 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Irf1Ifng6hStdPk IFNg6h Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 IRF1 Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifng30StdPk K562 IFg3 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002799 2799 GSM935505 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Irf1Ifng30StdPk IFNg30 Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 IRF1 Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifna6hStdPk K562 IFa6 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002798 2798 GSM935504 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Irf1Ifna6hStdPk IFNa6h Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 IRF1 Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifna30StdPk K562 IFa3 IRF1 Sd IRF1 K562 std ChipSeq ENCODE June 2010 Freeze 2010-04-29 2011-01-29 wgEncodeEH001865 1865 GSM935546 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Irf1Ifna30StdPk IFNa30 Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 IRF1 Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ini1IggmusPk K562 INI1 IgM Ini1 K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000725 725 GSM935634 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Ini1IggmusPk None Peaks Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 INI1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Hmgn3StdPk K562 HMGN Std HMGN3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001863 1863 GSM935544 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Hmgn3StdPk None Peaks HMGN3 is a high-mobility group protein. These proteins are small, 8 to 11 kDa, ubiquitous proteins believed to play a role in chromatin structure. HMGNs bind to nucleosomes between the histone core and DNA and reduce chromatin compaction. As a result HMGNs, HMGN3 included, are believed to increase access to DNA for DNA replication, repair and transcription. HMGN3 has specifically been implicated in the action of Thyroid horomone receptors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 HMGN3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabPk K562 HCFC1 IgR HCFC1_(NB100-68209) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003392 3392 GSM1003625 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabPk None Peaks The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 HCFC1 (NB100-68209) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabPk K562 GT2F IgR GTF2F1_(AB28179) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001823 1823 GSM935501 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabPk None Peaks RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 GTF2F1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gtf2bStdPk K562 GT2B Std GTF2B K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-01-11 2010-10-11 wgEncodeEH000703 703 GSM935394 Snyder Harvard PeakSeq1.0 hg18 exp wgEncodeSydhTfbsK562Gtf2bStdPk None Peaks DNA- binding general transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 GTF2B Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata2UcdPk K562 GAT2 UCD GATA-2 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000683 683 GSM935373 Snyder USC hg18 exp wgEncodeSydhTfbsK562Gata2UcdPk None Peaks GATA binding protein 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 GATA2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata1bIggmusPk K562 GATA1 IgM GATA1_(SC-266) K562 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003368 3368 GSM1003608 Snyder Stanford exp wgEncodeSydhTfbsK562Gata1bIggmusPk None Peaks GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 GATA1 (SC-266) IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata1UcdPk K562 GAT1 UCD GATA-1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000638 638 GSM935540 Snyder USC hg18 exp wgEncodeSydhTfbsK562Gata1UcdPk None Peaks GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 GATA1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Elk112771IggrabPk K562 ELK1 IgR ELK1_(1277-1) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH003356 3356 GSM1003620 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Elk112771IggrabPk None Peaks Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ELK1 (1277-1) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562E2f6UcdPk K562 E2F6 UCD E2F6 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000676 676 GSM935597 Snyder USC hg18 exp wgEncodeSydhTfbsK562E2f6UcdPk None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 E2F6 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562E2f4UcdPk K562 E2F4 UCD E2F4 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000671 671 GSM935600 Snyder USC hg18 exp wgEncodeSydhTfbsK562E2f4UcdPk None Peaks mapping at the C-terminus of E2F4 of human origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 E2F4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CtcfbIggrabPk K562 CTCF IgR CTCF_(SC-15914) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002797 2797 GSM935407 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CtcfbIggrabPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 CTCF IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Corestsc30189IggrabPk K562 COREST IgR COREST_(sc-30189) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-01-22 2012-10-21 wgEncodeEH002814 2814 GSM935439 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Corestsc30189IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 COREST SC30189 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Corestab24166IggrabPk K562 COREST IgR COREST_(ab24166) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002847 2847 GSM935385 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Corestab24166IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 COREST AB24166 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycStdPk K562 cMyc Std c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000621 621 GSM935410 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycStdPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 c-Myc Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfng6hStdPk K562 IFg6 cMyc Sd c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000670 670 GSM935599 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfng6hStdPk IFNg6h Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 c-Myc Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfng30StdPk K562 IFg3 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001867 1867 GSM935548 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562CmycIfng30StdPk IFNg30 Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 c-Myc Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfna6hStdPk K562 IFa6 cMyc Sd c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000669 669 GSM935466 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfna6hStdPk IFNa6h Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 c-Myc Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfna30StdPk K562 IFa3 cMyc Sd c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000659 659 GSM935428 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfna30StdPk IFNa30 Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 c-Myc Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIggrabPk K562 cMyc IgR c-Myc K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002800 2800 GSM935516 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CmycIggrabPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 c-Myc IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunStdPk K562 cJun Std c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000620 620 GSM935411 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 c-Jun Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfng6hStdPk K562 IFg6 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000668 668 GSM935467 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfng6hStdPk IFNg6h Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 c-Jun Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfng30StdPk K562 IFg3 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000673 673 GSM935602 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfng30StdPk IFNg30 Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 c-Jun Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfna6hStdPk K562 IFa6 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000667 667 GSM935468 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfna6hStdPk IFNa6h Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 c-Jun Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfna30StdPk K562 IFa3 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002805 2805 GSM935521 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CjunIfna30StdPk IFNa30 Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 c-Jun Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIggrabPk K562 c-Jun IgR c-Jun K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003369 3369 GSM1003609 Snyder Stanford exp wgEncodeSydhTfbsK562CjunIggrabPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 c-Jun IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Chd2ab68301IggrabPk K562 CHD2 IgR CHD2_(AB68301) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001822 1822 GSM935502 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Chd2ab68301IggrabPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 CHD2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CfosStdPk K562 cFOS Std c-Fos K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH000619 619 GSM935355 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CfosStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 c-FOS Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CebpbIggrabPk K562 CBPB IgR CEBPB K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001821 1821 GSM935499 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Cdpsc6327IggrabPk K562 CDP IgR CDP_(sc-6327) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003391 3391 GSM1003622 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Cdpsc6327IggrabPk None Peaks CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 CDP (SC-6327) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ccnt2StdPk K562 CNT2 Std CCNT2 K562 std ChipSeq ENCODE June 2010 Freeze 2010-04-28 2011-01-28 wgEncodeEH001864 1864 GSM935547 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Ccnt2StdPk None Peaks CycT2 is one of three cyclins that can form a heterodimer with cyclin-dependent kinase 9 (CDK9). The heterodimer is known as positive elongation factor b (P-TEFb) and is responsible for the phosphophorylation of Ser2 of the heptad repeat in the C-terminal domain of RNA polymerase II as well as the negative elongation factors DSIF (hSpt4/hSpt5) and NELF. Phosphorylation of RNA polymerase II and the negative elongation factors by P-TEFb promotes elongation. CycT2 contains a leucine rich domain capable of binding to the C-terminal domain of RNA polymerase II. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 CCNT2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brg1IggmusPk K562 BRG1 IgM Brg1 K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000724 724 GSM935633 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Brg1IggmusPk None Peaks Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 BRG1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brf2StdPk K562 BRF2 Std BRF2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000767 767 GSM935490 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Brf2StdPk None Peaks Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 BRF2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brf1StdPk K562 BRF1 Std BRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000679 679 GSM935595 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Brf1StdPk None Peaks 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 BRF1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bhlhe40nb100IggrabPk K562 BHL4 IgR BHLHE40_(NB100-1800) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEH001857 1857 GSM935616 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Bhlhe40nb100IggrabPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 BHLHE40 NB100 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bdp1StdPk K562 BDP1 Std BDP1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000678 678 GSM935594 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Bdp1StdPk None Peaks 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 BDP1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bach1sc14700IggrabPk K562 Bach1 IgR Bach1_(sc-14700) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002846 2846 GSM935576 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Bach1sc14700IggrabPk None Peaks This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Bach1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Atf3StdPk K562 ATF3 Std ATF3 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000700 700 GSM935391 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Atf3StdPk None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 ATF3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Atf106325StdPk K562 ATF1 Std ATF1_(06-325) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH002865 2865 GSM935340 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsK562Atf106325StdPk None Peaks ATF1 is a bZip transcription factor from the CREB family. ATF1 binds to both cAMP response elements (TGACGTCA). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 ATF1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Arid3asc8821IggrabPk K562 ARI3 IgR ARID3A_(sc-8821) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002861 2861 GSM935336 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Arid3asc8821IggrabPk None Peaks This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ARID3A SC8821 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescZnf274m01UcdPk H1ES ZNF274 UCD ZNF274_(M01) H1-hESC UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-06 2013-03-05 wgEncodeEH003357 3357 GSM1003619 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsH1hescZnf274m01UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC ZNF274 (M01) UC Davis ChIP-seq Peaks from ENCODE/USC Regulation 
wgEncodeSydhTfbsH1hescZnf143IggrabPk H1ES Z143 IgR Znf143_(16618-1-AP) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002802 2802 GSM935514 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescZnf143IggrabPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Znf143 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescUsf2IggrabPk H1ES USF2 IgR USF2 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001837 1837 GSM935380 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescUsf2IggrabPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC USF2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescTbpIggrabPk H1ES TBP IgR TBP H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001848 1848 GSM935303 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescTbpIggrabPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TBP IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescSuz12UcdPk H1ES SZ12 UCD SUZ12 H1-hESC UCDavis ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001752 1752 GSM935352 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescSuz12UcdPk None Peaks Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC SUZ12 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescSin3anb6001263IggrabPk H1ES SIN3A IgR SIN3A_(NB600-1263) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002854 2854 GSM935289 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescSin3anb6001263IggrabPk None Peaks Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC SIN3A IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescRfx5200401194IggrabPk H1ES RFX5 IgR RFX5_(200-401-194) H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001835 1835 GSM935382 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescRfx5200401194IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC RFX5 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescRad21IggrabPk H1ES Rad2 IgR Rad21 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001836 1836 GSM935379 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescRad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescNrf1IggrabPk H1ES Nrf1 IgR Nrf1 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001847 1847 GSM935308 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescNrf1IggrabPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Nrf1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMxi1IggrabPk H1ES Mxi1 IgR Mxi1_(AF4185) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002829 2829 GSM935293 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescMxi1IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Mxi1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMaxUcdPk H1ES Max UCD Max H1-hESC UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001757 1757 GSM935348 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescMaxUcdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC Max UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMafkIggrabPk H1ES MafK IgR MafK_(ab50322) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002828 2828 GSM935292 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescMafkIggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescJundIggrabPk H1ES JunD IgR JunD H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002023 2023 GSM935434 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescJundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescGtf2f1IggrabPk H1ES GT2F IgR GTF2F1_(AB28179) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002843 2843 GSM935581 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescGtf2f1IggrabPk None Peaks RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC GTF2F1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCtbp2UcdPk H1ES CBP2 UCD CtBP2 H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001767 1767 GSM935463 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescCtbp2UcdPk None Peaks C-terminal binding protein 2 embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC CtBP2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCmycIggrabPk H1ES cMyc IgR c-Myc H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002795 2795 GSM935509 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescCmycIggrabPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC c-Myc IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCjunIggrabPk H1ES cJun IgR c-Jun H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-19 wgEncodeEH001854 1854 GSM935614 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescCjunIggrabPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC c-Jun IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescChd2IggrabPk H1ES CHD2 IgR CHD2_(AB68301) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002827 2827 GSM935297 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescChd2IggrabPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC CHD2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescChd1a301218aIggrabPk H1ES CHD1 IgR CHD1_(A301-218A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002826 2826 GSM935296 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescChd1a301218aIggrabPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC CHD1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCebpbIggrabPk H1ES CBPB IgR CEBPB H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002825 2825 GSM935295 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescCebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescBrca1IggrabPk H1ES BRC1 IgR BRCA1_(A300-000A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002801 2801 GSM935517 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescBrca1IggrabPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC BRCA1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescBach1sc14700IggrabPk H1ES Bach1 IgR Bach1_(sc-14700) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002842 2842 GSM935580 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescBach1sc14700IggrabPk None Peaks This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Bach1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Zzz3StdPk GM78 ZZZ3 Std ZZZ3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000698 698 GSM935483 Snyder Harvard hg18 exp wgEncodeSydhTfbsGm12878Zzz3StdPk None Peaks ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 ZZZ3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusPk GM78 ZNF384 IgM ZNF384_(HPA004051) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003388 3388 GSM1003602 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusPk None Peaks This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 ZNF384 (HPA004051) IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf274StdPk GM78 Z274 Std ZNF274 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001756 1756 GSM935349 Snyder USC PeakSeq1.0.  Replicate overlap below cutoff, but submitted because there are very few biologically real targets and all the targets are in heterochromatic regions. hg19 exp wgEncodeSydhTfbsGm12878Znf274StdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM12878 ZNF274 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf143166181apStdPk GM78 Z143 Std Znf143_(16618-1-AP) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001853 1853 GSM935613 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Znf143166181apStdPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Znf143 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Yy1StdPk GM78 YY1 Std YY1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000695 695 GSM935482 Snyder USC hg18 exp wgEncodeSydhTfbsGm12878Yy1StdPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM12878 YY1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878WhipIggmusPk GM78 WHIP IgM WHIP GM12878 IgG-mus ChipSeq ENCODE June 2010 Freeze 2010-04-26 2011-01-26 wgEncodeEH001787 1787 GSM935492 Snyder Stanford PeakSeq1.0. Although this dataset barely misses the establish ENCODE standard for data agreement with 77% agreement between replicates instead of 80%, we have submitted it because it appears to be of high quality and because it is from the GM12878 cell line where we and others have generally observed weaker ChIP signal. hg19 exp wgEncodeSydhTfbsGm12878WhipIggmusPk None Peaks Interacts with the N-terminal portion of Werner protein containing the exonuclease domain, shows homology to replication factor C family proteins, and is conserved from E. coli to human. Studies in yeast suggest that this gene may influence the aging process. Functions as a modulator for initiation or reinitiation events during DNA polymerase delta-mediated DNA synthesis. Has an intrinsic ATPase activity that functions as a sensor of DNA damage or of arrested replication forks and regulates the extent of DNA synthesis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 WHIP IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Usf2IggmusPk GM78 USF2 IgM USF2 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001812 1812 GSM935558 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Usf2IggmusPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 USF2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Tr4StdPk GM78 TR4 Std TR4 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000697 697 GSM935480 Snyder USC hg18 exp wgEncodeSydhTfbsGm12878Tr4StdPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM12878 TR4 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878TbpIggmusPk GM78 TBP IgM TBP GM12878 IgG-mus ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001798 1798 GSM935277 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878TbpIggmusPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 TBP IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusPk GM78 TBLR1 IgM TBLR1_(ab24550) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002853 2853 GSM935653 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusPk None Peaks F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 TBLR1 AB24550 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Stat3IggmusPk GM78 STA3 IgM STAT3 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001811 1811 GSM935557 Snyder Stanford PeakSeq1.0.  Because of the common difficulty in achieving good signal strength with the GM12878 cell line, we submit this dataset although it narrowly missed the peak concordance standard. hg19 exp wgEncodeSydhTfbsGm12878Stat3IggmusPk None Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 STAT3 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Stat1StdPk GM78 STA1 Std STAT1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001852 1852 GSM935612 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Stat1StdPk None Peaks transcription factor, activated by interferon signalling B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 STAT1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Srebp2IggrabPk GM78 SREBP2 IgR SREBP2 GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003363 3363 GSM1003603 Snyder Stanford exp wgEncodeSydhTfbsGm12878Srebp2IggrabPk None Peaks Sterol regulatory element binding transcription factor 2 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 SREBP2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Srebp1IggrabPk GM78 SREBP1 IgR SREBP1 GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003362 3362 GSM1003617 Snyder Stanford exp wgEncodeSydhTfbsGm12878Srebp1IggrabPk None Peaks Sterol regulatory element binding transcription factor 1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 SREBP1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Spt20StdPk GM78 SPT Std SPT20 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001873 1873 GSM935417 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Spt20StdPk None Peaks Also known as FAM48A or P38IP. It is a component of SAGA complex. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 SPT20 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Smc3ab9263IggmusPk GM78 SMC3 IgM SMC3_(ab9263) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001833 1833 GSM935376 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Smc3ab9263IggmusPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 SMC3 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusPk GM78 SIN3A IgM SIN3A_(NB600-1263) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002868 2868 GSM935331 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusPk None Peaks Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 SIN3A IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Rfx5200401194IggmusPk GM78 RFX5 IgM RFX5_(200-401-194) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001810 1810 GSM935556 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Rfx5200401194IggmusPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 RFX5 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Rad21IggrabPk GM78 Rad2 IgR Rad21 GM12878 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000749 749 GSM935332 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol3StdPk GM78 Pol3 Std Pol3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000645 645 GSM935316 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878Pol3StdPk None Peaks RNA Polymerase III B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment GM12878 POL3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2s2IggmusPk GM78 PolS IgM Pol2(phosphoS2) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001858 1858 GSM935608 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Pol2s2IggmusPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Pol2 S2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2StdPk GM78 Pol2 Std Pol2 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000626 626 GSM935412 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878Pol2StdPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment GM12878 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2IggmusPk GM78 Pol2 IgM Pol2 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000708 708 GSM935386 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878Pol2IggmusPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300bStdPk GM78 p300 Std p300_(SC-584) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002037 2037 GSM935562 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878P300bStdPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 p300 SC584 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300sc584IggmusPk GM78 p300 IgM p300_(SC-584) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001813 1813 GSM935559 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878P300sc584IggmusPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 p300 SC584 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300IggmusPk GM78 p300 IgM p300 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002824 2824 GSM935294 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878P300IggmusPk None Peaks EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 p300 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Nrf1IggmusPk GM78 Nrf1 IgM Nrf1 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001846 1846 GSM935309 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Nrf1IggmusPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Nrf1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfybIggmusPk GM78 NYB IgM NF-YB GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002065 2065 GSM935507 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878NfybIggmusPk None Peaks NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 NF-YB IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfyaIggmusPk GM78 NYA IgM NF-YA GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002064 2064 GSM935506 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878NfyaIggmusPk None Peaks NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 NF-YA IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfkbTnfaIggrabPk GM78 TNF NKB IgR NFKB GM12878 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000690 690 GSM935478 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM12878 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Nfe2sc22827StdPk GM78 NFE2 Std NF-E2_(SC-22827) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-09-03 2011-06-03 wgEncodeEH001808 1808 GSM935652 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Nfe2sc22827StdPk None Peaks Transcription factor NFE2 45 kDa subunit is a component of the NFE2 complex and essential for regulating erythroid and megakaryocytic maturation and differentiation. Binds to the hypersensitive site 2 (HS2) of the beta-globin control region (LCR). This subunit (NFE2)recognizes the TCAT/C sequence of the AP-1-like core palindrome present in a number of erythroid and megakaryocytic gene promoters. Requires MAFK or other small MAF proteins for binding to the NFE2 motif. May play a role in all aspects of hemoglobin production from globin and heme synthesis to procurement of iron. NFE2 has been shown to interact with CREB binding protein. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 NF-E2 SC22827 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Mxi1IggmusPk GM78 Mxi1 IgM Mxi1_(AF4185) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002026 2026 GSM935431 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Mxi1IggmusPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Mxi1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Mazab85725IggmusPk GM78 MAZ IgM MAZ_(ab85725) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002852 2852 GSM935283 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Mazab85725IggmusPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 MAZ IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878MaxIggmusPk GM78 Max IgM Max GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002806 2806 GSM935518 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878MaxIggmusPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Max IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878MafkIggmusPk GM78 MafK IgM MafK_(ab50322) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003361 3361 GSM1003616 Snyder Stanford exp wgEncodeSydhTfbsGm12878MafkIggmusPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 MafK (ab50322) IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878JundStdPk GM78 JunD Std JunD GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000639 639 GSM935541 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878JundStdPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment GM12878 JunD Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878JundIggrabPk GM78 JunD IgR JunD GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003370 3370 GSM1003634 Snyder Stanford exp wgEncodeSydhTfbsGm12878JundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Irf3IggmusPk GM78 IRF3 IgM IRF3 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001809 1809 GSM935651 Snyder Stanford PeakSeq1.0.  Because of the common difficulty in achieving strong signal with the GM12878 cell line, we submit this dataset, although it narrowly misses the peak concordance standard. hg19 exp wgEncodeSydhTfbsGm12878Irf3IggmusPk None Peaks Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 IRF3 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdPk GM78 IKZF1 Std IKZF1_(IkN)_(UCLA) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002811 2811 GSM935442 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdPk None Peaks IKAROS family zinc finger 1 (Ikaros or IKZF1) is a C2H2 zinc finger transcription factor that is associated with various chromatin-modifying complexes and is suggested to play a role in the development of lymphocytes, B- and T-cells. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM12878 IKZF1 IKN UCLA Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Gcn5StdPk GM78 GCN5 Std GCN5 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-20 wgEncodeEH001874 1874 GSM935415 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Gcn5StdPk None Peaks KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 GCN5 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878ErraIggrabPk GM78 ERRA IgR ERRA GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003387 3387 GSM1003605 Snyder Stanford exp wgEncodeSydhTfbsGm12878ErraIggrabPk None Peaks Epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 ERRA IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Elk112771IggmusPk GM78 ELK1 IgM ELK1_(1277-1) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002851 2851 GSM935345 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Elk112771IggmusPk None Peaks Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 ELK1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ebf1sc137065StdPk GM78 EBF1 Std EBF1_(SC-137065) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001832 1832 GSM935375 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Ebf1sc137065StdPk None Peaks Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 EBF1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878E2f4IggmusPk GM78 E2F4 IgM E2F4 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002867 2867 GSM935330 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878E2f4IggmusPk None Peaks mapping at the C-terminus of E2F4 of human origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 E2F4 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdPk GM78 CTCF Std CTCF_(SC-15914) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-19 wgEncodeEH001851 1851 GSM935611 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 CTCF Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Corestsc30189IggmusPk GM78 COREST IgM COREST_(sc-30189) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002841 2841 GSM935583 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Corestsc30189IggmusPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 COREST SC30189 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Chd2ab68301IggmusPk GM78 CHD2 IgM CHD2_(AB68301) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001831 1831 GSM935378 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Chd2ab68301IggmusPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 CHD2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Chd1a301218aIggmusPk GM78 CHD1 IgM CHD1_(A301-218A) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002823 2823 GSM935301 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Chd1a301218aIggmusPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 CHD1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878CfosStdPk GM78 cFOS Std c-Fos GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000622 622 GSM935409 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878CfosStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment GM12878 c-FOS Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Cdpsc6327IggmusPk GM78 CDP IgM CDP_(sc-6327) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003386 3386 GSM1003604 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Cdpsc6327IggmusPk None Peaks CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 CDP (SC-6327) IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Brca1a300IggmusPk GM78 BRC1 IgM BRCA1_(A300-000A) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001830 1830 GSM935377 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Brca1a300IggmusPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 BRCA1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Bhlhe40cIggmusPk GM78 BHL4 IgM BHLHE40_(NB100-1800) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002025 2025 GSM935430 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Bhlhe40cIggmusPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 BHLHE40 NB100 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeUchicagoTfbs UChicago TFBS GSE31363 Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago Regulation Description This track maps genome-wide human transcription factor binding sites using second-generation massively parallel sequencing. This mapping uses expressed transcription factors as GFP-tagged fusion proteins after bacterial artificial chromosome (BAC) recombineering (recombination-mediated genetic engineering). The University of Chicago and Max Planck Institute (Dresden) pipeline generates recombineered BACs for the production of cell lines or animals that express fusion proteins from epitope-tagged transgenes. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: Peaks Regions of signal enrichment based on processed data (usually normalized data from pooled replicates). Signal Density graph (wiggle) of signal enrichment based on aligned read density. Peaks and signals displayed in this track are the results of pooled replicate sequence. Alignment files for each replicate are available for download. Methods Cells were grown according to the approved ENCODE cell culture protocols. Recombineering Strategy To facilitate high-throughput production of the transgenic constructs, the program BACFinder (Crowe et al., 2002) automatically selects the most suitable BAC clone for any given human gene and generates the sets of PCR primers required for tagging and verification (Poser et al., 2008). Recombineering is used for tagging cassettes at either the N or C terminus of the protein. The N-terminal cassette has a dual eukaryotic-prokaryotic promoter (PGK-gb2) driving a neomycin-kanamycin resistance gene within an artificial intron inside the tag coding sequence. The selection cassette is flanked by two loxP sites and can be permanently removed by Cre Recombinase-mediated excision. The C-terminal cassette contains the sequence encoding the tag followed by an internal ribosome entry site (IRES) in front of the neomycin resistance gene. In addition, a short bacterial promoter (Gb3) drives the expression of the neomycin-kanamycin resistance gene in E. coli. The tagging cassettes, containing 50 nucleotides of PCR-introduced homology arms, were inserted into the BAC by recombineering, either behind the start codon (for the N-terminal tag) or in front of the stop codon (for the C-terminal tag) of the gene. E. coli cells that had successfully recombined the cassette were selected for kanamycin resistance in liquid culture. Each saturated culture from a specific recombineering reaction derived 10-200 independent recombination events. Two independent clones were checked for each PCR through the tag insertion point and 97% (85/88) yielded a PCR product of the expected size. Most of the clones that failed to grow were missing the targeted genomic region. An estimated 10% of the BACs used were chimeric, rearranged or wrongly mapped. Thus, initial results indicated that the necessary recombineering steps could be carried out with high fidelity. The White lab produced all epitope tagged transcription and chromatin factor BACs, as well as the genome-wide ChIP data and analysis. An application of this approach to the analysis of closely related paralogs (RARa and RARg) yielded transcription factors, chromatin factors, cell lines, ChIP-chip data and ChIP-seq data (Hua et al., 2009). Such paralogous transcription factors often cannot otherwise be distinguished by antibodies. Sample Preparation ChIP DNA from samples were sheared to approximately 800 bp using a nebulizer. The ends of the DNA were polished and two unique adapters were ligated to the fragments. Ligated fragments of 150-200 bp were isolated by gel extraction and amplified using limited cycles of PCR. Sequencing System Illumina GAIIx and HySeq next-generation sequencing were used to produce all ChIP-seq data. Processing and Analysis Software Raw sequencing reads were aligned using Bowtie 0.12.5 (Langmead et al., 2009). The &quot;-m 1&quot; parameter was applied to suppress alignments mapping more than once in the genome. Reads were aligned to the UCSC hg19 assembly. Wiggle format signal files were generated with SPP 2.7.1 (Kharchenko et al., 2008) for R 2.7.1. MACS 1.3.7 was used to call peaks. The MACS parameters used varied by experiment. The White lab used goat anti-GFP antibody to perform ChIP in untagged K562 cells as a background control. The test IP was performed in the same manner as the background control. Results were expressed as values of the test normalized to the background. Credits These data and annotations were created by a collaboration of University of Chicago and Argonne National Laboratory: Kevin White (Principal Investigator at University of Chicago) Subhradip Karmakar (Project Lead at University of Chicago) Nick Bild (Data Analyst at University of Chicago) Alina Choudhury (Laboratory Technician at University of Chicago) Marc Domanus (Sequencing Technician at Argonne National Lab) References Crowe ML, Rana D, Fraser F, Bancroft I, Trick M. BACFinder: genomic localisation of large insert genomic clones based on restriction fingerprinting. Nucleic Acids Res. 2002 Nov 1;30(21):e118. Hua S, Kittler R, White KP. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell. 2009 Jun 26;137(7):1259-71. Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec;26(12):1351-9. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Poser I, Sarov M, Hutchins JR, H&#233;rich&#233; JK, Toyoda Y, Pozniakovsky A, Weigl D, Nitzsche A, Hegemann B, Bird AW et al. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods. 2008 May;5(5):409-15. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUchicagoTfbsViewSignal Signal Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Enr4a1ControlSig K562 NR4A1/GFP Sg eGFP-NR4A1 K562 Control_eGFP-NR4A1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001212 1212 GSM777637 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Enr4a1ControlSig Signal NR4A1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-NR4A1 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 NR4A1 GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EjundControlSig K562 JunD/GFP Sg eGFP-JunD K562 Control_eGFP-JunD ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001211 1211 GSM777639 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EjundControlSig Signal JUND leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JUND Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 JunD GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EjunbControlSig K562 JunB/GFP Sg eGFP-JunB K562 Control_eGFP-JunB ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001210 1210 GSM777638 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EjunbControlSig Signal JUNB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JunB Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 JunB GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Ehdac8ControlSig K562 HDAC8/GFP Sg eGFP-HDAC8 K562 Control_eGFP-HDAC8 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001209 1209 GSM777640 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Ehdac8ControlSig Signal HDAC8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-HDAC8 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 HDAC8 GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Egata2ControlSig K562 GATA2/GFP Sg eGFP-GATA2 K562 Control_eGFP-GATA2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001208 1208 GSM777641 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Egata2ControlSig Signal GATA2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-GATA2 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 GATA2 GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EfosControlSig K562 FOS/GFP Sg eGFP-FOS K562 Control_eGFP-FOS ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001207 1207 GSM777644 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EfosControlSig Signal FOS leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-FOS Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 FOS GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsPeaks Peaks Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Enr4a1ControlPk K562 NR4A1/GFP Pk eGFP-NR4A1 K562 Control_eGFP-NR4A1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001212 1212 GSM777637 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Enr4a1ControlPk Peaks NR4A1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-NR4A1 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 NR4A1 GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EjundControlPk K562 JunD/GFP Pk eGFP-JunD K562 Control_eGFP-JunD ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001211 1211 GSM777639 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EjundControlPk Peaks JUND leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JUND Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 JunD GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EjunbControlPk K562 JunB/GFP Pk eGFP-JunB K562 Control_eGFP-JunB ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001210 1210 GSM777638 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EjunbControlPk Peaks JUNB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JunB Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 JunB GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Ehdac8ControlPk K562 HDAC8/GFP Pk eGFP-HDAC8 K562 Control_eGFP-HDAC8 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001209 1209 GSM777640 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Ehdac8ControlPk Peaks HDAC8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-HDAC8 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 HDAC8 GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Egata2ControlPk K562 GATA2/GFP Pk eGFP-GATA2 K562 Control_eGFP-GATA2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001208 1208 GSM777641 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Egata2ControlPk Peaks GATA2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-GATA2 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 GATA2 GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EfosControlPk K562 FOS/GFP Pk eGFP-FOS K562 Control_eGFP-FOS ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001207 1207 GSM777644 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EfosControlPk Peaks FOS leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-FOS Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 FOS GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUmassDekker5C UMass 5C GSE39510 Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. Regulation Description This track contains chromatin interaction data generated using the 5C (Chromatin Conformation Capture Carbon Copy) method by the ENCODE group (Dekker Lab) located at the University of Massachusetts, Worcester, MA. This track shows the significant looping interactions between transcriptional start sites (TSS) and distal regulatory elements in the context of the 44 ENCODE pilot regions spanning 1% of the human genome. Although the DNA is a linear sequence, the chromatin, which is packed and organized inside the nucleus, does not function linearly. This is most clearly illustrated by the fact that genes are often regulated by elements that are located hundreds of kilobases away in the linear genome. Imaging techniques have shown that regulatory elements can act over large genomic distances by engaging in direct physical interactions with target genes, resulting in the formation of chromatin loops. Based on these observations, we have envisaged that the spatial organization of the genome resembles a three-dimensional network that is driven by physical associations between genes and regulatory elements, both in cis (within the same chromosome) and in trans (between different chromosomes) (Dekker, 2006). Apart from imaging technology which is labor intensive and low-throughput, long-range chromatin looping interactions can be detected using the Chromosome Conformation Capture (3C) technology (Dekker et al., 2002). The 3C method employs formaldehyde cross-linking to covalently link interacting chromatin segments in intact cells. Cells are subsequently lysed and chromatin is digested with a restriction enzyme of choice. The digested fragments are then ligated under dilute conditions to facilitate intramolecular ligation. The result is a genome-wide interaction library of ligation products corresponding to all possible chromatin interactions. Specific ligation products can then be detected by PCR using specific primer pairs. The 5C method was developed to dramatically increase 3C throughput (Dostie et al., 2006; Dostie and Dekker, 2007). The 5C method greatly increases the scale of chromatin interaction detection by replacing the PCR detection step of 3C with ligation-mediated amplification (LMA). LMA is advantageous due to a much higher level of multiplexing by using thousands of primers in a single reaction to detect millions of chromatin interactions (ligation junctions) in parallel. The LMA step effectively "copies" 3C ligation products into much smaller 5C ligation products that precisely correspond to ligation junctions formed during the 3C procedure. The products of the multiplexed LMA reaction constitute the 5C library. The composition of the 5C library is determined using high-throughput DNA sequencing. Display Conventions and Configuration In the graphical display, the significant looping interactions in cis (i.e., from the same ENCODE pilot regions) are represented by blocks and connected by a horizontal line. Users can opt to filter the significant looping interactions according to their respective z-score (scaled to 0-1000) by using the built-in genome browser display score threshold. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. File Conventions The following types of data are available for download: Matrix Interaction files are in a matrix format indicating interaction strength with "reverse primer name | genome version | reverse HindIII fragment coordinates" in the top row and "forward primer name | genome version | forward primer fragment coordinates" in the first column. The number of sequences mapped to each interaction fills the matrix. In order to understand the Matrix data, you must download the associated primer data file. Primer Primer data files include the sequences of the primers used in the experiments. These files are available for download in the supplemental materials. Raw Data Sequencing files provided in fastQ format. Methods The aim of the pilot study was to generate a "connectivity map" between transcription start sites (TSS) and distal regulatory elements within the 44 ENCODE PILOT regions. In the current scheme, 5C primers were designed for all HindIII restriction fragments. Reverse primers were designed on fragments containing the TSS of annotated genes. Forward primers were designed on all other fragments. This design allowed for the interrogation of all TSS with all other restriction fragments, thus generating an interaction map between TSS and regulatory elements. For gene desert ENCODE pilot regions (for example ENr313), an altered scheme of forward and reverse primers was designed. Primers were selected for relative uniqueness using a custom 15-mer frequency table and BLAST. A custom hexamer barcode was added to each primer to ensure the sequence was unique relative to the primer pool being used. Primers were also selected for the appropriate melting temperature and GC-content and a universal tail sequence for amplification. The 44 ENCODE regions were analyzed in two groups using two separate 5C primer pools. The first group (ENm) contained the manually-picked ENCODE regions, ENm001-014 and ENr313. The second group (ENr) contained the 30 randomly-picked ENCODE regions. The two 5C primer pools were made by pooling 5C primers for interrogating long-range interactions in the two groups of ENCODE regions. The primer pool for the ENm group contained a total of 3,150 primers (476 reverse 5C primers and 2674 forward 5C primers). This primer pool allowed interrogation of a total of 1,272,824 interactions. Of these, 83,427 interactions were between fragments that were both located in the same ENCODE region. This primer pool for the ENr group contained a total of 3,152 primers (505 reverse 5C primers and 2647 forward 5C primers). This primer pool allowed interrogation of a total of 1,336,735 interactions. Of these, 34,859 interactions were between fragments that were both located in the same ENCODE region. In total, 981 reverse primers and 5,321 forward primers were designed (corresponding to ~77.1% (6,302/8,174) of all HindIII fragments in the 44 ENCODE regions). Currently, data for two biological replicates have been generated for ENCODE Tier I (GM12878 and K562), Tier II (HeLa-S3), and H1 human embryonic stem cells (H1-hESC), spanning 14 ENCODE manual regions along with one random region (ENr313) as well as 30 random regions separately using high-throughput paired-end sequencing in the Illumina GA2 platform. The looping interactions, which are detected in both the biological replicates, are considered significant. Release Notes This is Release 2 (July 2012). There is no new data for this release all new data has the version number appended to the name (e.g., V2). Peak files have been reanalyzed and more complete Raw Data files have been submitted. Credits All provided data were produced by the Dekker Lab at UMass Medical School, Worcester, MA. The following personnel contributed to the project (contacts): Wet Lab: Amartya Sanyal Dry Lab: Bryan R. Lajoie, Gaurav Jain Principal Investigator: Job Dekker Additional information and/or vizualization tools can be found on the Dekker Lab website. References Ba&#249; D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. The three-dimensional folding of the &#945;-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol. 2011 Jan;18(1):107-14. Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat. Methods. 2006;3(1):17-21. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15;295(5558):1306-11. Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nature Protocols. 2007;2(4):988-1002. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct;16(10):1299-309. Lajoie BR, van Berkum NL, Sanyal A, Dekker J. My5C: web tools for chromosome conformation capture studies. Nat. Methods. 2009;6(1):690-91. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUmassDekker5CHelas3PkV2 HeLa-S3 Pk HeLa-S3 5C ENCODE Jul 2012 Freeze 2012-06-05 2011-01-25 2011-10-25 wgEncodeEH001667 1667 GSM970497 Dekker UMass-Dekker wgEncodeUmassDekker5CHelas3PkV2 Peaks cervical carcinoma 5C Chromatin Interactions Dekker Dekker - University of Massachusettes Regions of enriched signal in experiment HeLa-S3 5C Peaks from ENCODE/UMass-Dekker Regulation 
wgEncodeUmassDekker5CK562PkV2 K562 Pk K562 5C ENCODE Jul 2012 Freeze 2012-06-05 2011-01-25 2011-10-25 wgEncodeEH001668 1668 GSM970500 Dekker UMass-Dekker wgEncodeUmassDekker5CK562PkV2 Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC 5C Chromatin Interactions Dekker Dekker - University of Massachusettes Regions of enriched signal in experiment K562 5C Peaks from ENCODE/UMass-Dekker Regulation 
wgEncodeUmassDekker5CH1hescPkV2 H1-hESC Pk H1-hESC 5C ENCODE Jul 2012 Freeze 2012-06-05 2011-01-25 2011-10-25 wgEncodeEH001666 1666 GSM970498 Dekker UMass-Dekker wgEncodeUmassDekker5CH1hescPkV2 Peaks embryonic stem cells 5C Chromatin Interactions Dekker Dekker - University of Massachusettes Regions of enriched signal in experiment H1-hESC 5C Peaks from ENCODE/UMass-Dekker Regulation 
wgEncodeUmassDekker5CGm12878PkV2 GM12878 Pk GM12878 5C ENCODE Jul 2012 Freeze 2012-06-05 2011-01-25 2011-10-25 wgEncodeEH001665 1665 GSM970499 Dekker UMass-Dekker wgEncodeUmassDekker5CGm12878PkV2 Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus 5C Chromatin Interactions Dekker Dekker - University of Massachusettes Regions of enriched signal in experiment GM12878 5C Peaks from ENCODE/UMass-Dekker Regulation 
wgEncodeUncBsuProtGenc UNC/BSU ProtGenc Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression Description The ENCODE project has revealed the functional elements of segments of the human genome in unprecedented detail. However, the ability to distinguish between transcripts designated for translation into protein and those that serve purely regulatory roles remains elusive. A standard means to determine if translation is occurring is to measure protein produced by transcripts via mass spectrometry-based proteogenomic mapping. In this process, proteins were digested to peptides using a protease such as trypsin and these petides were chromatographically fractionated and fed into a tandem mass spectrometer (MS/MS). This process creates a signature series of fragment masses which can be scanned against the theoretical translation and proteolytic digest of an entire genome to identify the genomic origins of sample proteins (Giddings et al., 2003). This proteogenomic track displays mass spectrometry data that have been matched to genomic sequences for selected cell lines, using a workflow and software specifically designed for this purpose. The track can be used to identify which parts of the genome are translated into proteins, to verify which transcripts discovered by other ENCODE experiments are protein-coding, to reveal new genes and/or splice variants and proteins with post-translational modifications (PTM). Of particular interest is the possibility of uncovering the translation of small open reading frames (ORFs), antisense transcripts, or protein-coding regions that have been annotated as introns previously. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types and compartments. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. This track shows peptide mappings as contiguous rectangular items rendered in grayscale according to their score, with darker items representing higher-confidence peptide mappings. The name of each item is the amino acid sequence of the peptide where a period (.) at the end of a name signifies a stop codon. Peptide Genome and GENCODE Mapping(Filtered) Peptide mapping results based on hg19 and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered for a false discovery rate (FDR) better than 5%. Specific field descriptions can be found below. Modified Peptide Genome and GENCODE Mapping(Filtered) Modified peptide mapping results based on hg19 and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered for a false discovery rate (FDR) better than 5%. Unfiltered views are available on the Downloads page. Fields specific to Proteogenomic tracks include: The Item names the peptide sequence and is appended with a number for proteins with post-translational modifications (PTM) representing the integer portion of the PTM mass. The peptide sequence appears as a short label beside the main Genome Browser display window depending on the view configuration. The Score is used to render shade to displayed rectangular items and is derived from the rawScore (see below) given by the proteomics peptide mapping software Peppy. It is computed as [(rawScore - rawScore at 10% FDR cutoff) / (rawScore at near 0% FDR cutoff - rawScore at 10% FDR cutoff)] * 1000, and is then converted to an integer. Raw scores above the 0% FDR threshold have a score of 1000 (best), while those below the 10% FDR threshold have a score of 0 (worst). The rawScore is given by Peppy and is expressed as the negative log 10 of the p-value, which reflects the confidence of the mapping between the peptides and the spectrums. On the item details pages, rawScore is labeled: Raw score for a peptide/spectrum match. The spectrumId is an identifier of the spectrum associated with the peptide mapping and can be used to track the original spectrum. On the item details pages, spectrumId is labeled: An identifier of the spectrum associated with the peptide mapping. The peptideRank is a rank of the peptide/spectrum match used for a spectrum matching to different peptides. A spectrum can be chimeric (containing more than one peptide) and the spectrum can be mapped to two or more distinct peptides. Here, only the top-scoring match is reported. If more than one peptide "tied" for the top score, then all peptides were included and all matches have a peptideRank of 1. On the item details pages, peptideRank is labeled: Rank of the peptide/spectrum match, for spectrum matching to different peptides. The peptideRepeatCount indicates the number of places in the genome where the peptide is encoded for a peptide/spectrum match. It reflects the prevalence or uniqueness of the peptide mapping in the genome. Those peptides mapped to only a few genomic locations will have a low peptideRepeatCount, whereas those peptides mapped to highly duplicated regions will have a high peptideRepeatCount. Peptides with a peptideRepeatCount greater than 10 times in the genome were deleted from the track (this field is for regular peptides only). On the item details pages, peptideRepeatCount is labeled: Indicates the number of places in the genome where the peptide is encoded for a peptide/spectrum match. The modificationMass reflects the additional molecular weight for each modified peptide matched to a spectrum (this field is for PTM peptides only). On the item details pages, modificationMass is labeled: Reflects the additional molecular weight for each modified peptide matched to a spectrum. Methods ENCODE cell lines K562, GM12878, H1-hESC and H1-neurons were used for this large scale proteomic analysis. Cell lines were cultured according to standard ENCODE cell culture protocols and tryptic peptides were prepared using In-gel digestion (Shevchenko et al., 2007), FASP (Wiseniewski et al., 2009; Manza et al., 2005) or MudPIT (Washburn et al., 2001) protocols as indicated for each sample. Tandem mass spectrometry (RPLC-MS/MS) analysis was then performed on an Eksigent Ultra-LTQ Orbitrap system or a Q Exactive system (Thermo Scientific) as indicated.* The number of arginine or lysine sites missed by the trypsin enzyme is indicated by the metadata parameter miscleavages. We performed proteogenomic mapping (Jaffe et al., 2004) on an in silico translation and proteolytic digestion of the whole human genome (UCSC Hg19), and the GENCODE translation of protein-coding transcripts database with up to one missed cleavage using Peppy software. The GENCODE version for H1-hESC (FASP protocol), K562, and GM12878 is V11 and it is V10 for H1-hESC (MudPIT protocol) and H1-neurons datasets. GENCODE V11 was initially used for database search and it was later found that GENCODE V10 is the preferred version and was subsequently used to replace GENCODE V11 for the analyses of the later datasets. Peppy's embedded algorithm matches the MS/MS spectra to peptides and outputs a matching score, and the peptides are then mapped back to their corresponding genomic sequences. The peptide/spectrum matches (PSMs) found from Hg19 genome and GENCODE searches were compared and the PSMs of higher score from either matches were reported. If the scores from both matches are equal, both of them were reported. Additional peptides matches were found by GENCODE search that were not found in Hg19 genome search, some of which span slice junctions. Overall, a cross-comparison and inclusion of results from both database searches resulted in a greater coverage. For both the Hg19 genome and GENCODE database searches, a blind search for post-translational modifications (PTMs) was performed using Peppy software. In a blind PTM search, when Peppy matches a MS/MS spectrum to a peptide, if the matching score is increased after the addition of the molecular weight (MW) of a potential PTM, the peptide is determined as having a PTM. In the output of both the Hg19 genome and GENCODE searches, some spectra were output as matched with peptides of PTMs and others were output as matched with regular peptides, i.e., peptides without PTMs. Once the best-ranking PSMs were identified from either search, the regular peptides and peptides with PTMs were displayed in separate tracks. For each data set, a reverse database search was also performed using all spectra to calculate the false discovery rate (FDR) (Elias et al., 2007). Only those matches with a FDR rate below 5% were included in this track. The unfiltered results of those peptides matches with an FDR rate below 10% are available for download. *H1-hESC (FASP protocol), K562 and GM12878 samples were analyzed on the Eksigent Ultra LTQ Orbitrap system (Thermo Scientific) whereas H1-hESC (MudPIT protocol), H1-neurons sample were analyzed on the Q Exactive system (Thermo Scientific). Release Notes This is Release 1 of this track (Sept 2012). Unlike other ENCODE data, these data are not archived at GEO but at Proteome Commons. The first 32 digits of the Tranche Hash for each data set is stored as the labExpId. Credits Proteogenomic mapping: Dr. John Wrobel, Dr. Jainab Khatun, Mr. Brian Risk, and Mr. David Thomas (Giddings Lab). Proteomic analysis: Dr. Yanbao Yu, Dr. Harsha Gunawardena, Dr. Ling Xie and Ms. Li Wang (Chen Lab). Main Contact: John Wrobel References Giddings MC, Shah AA, Gesteland R, Moore B. Genome-based peptide fingerprint scanning. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):20-5. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc. 2006;1(6):2856-60. Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods. 2009 May;6(5):359-62. Manza LL, Stamer SL, Ham AJ, Codreanu SG, Liebler DC. Sample preparation and digestion for proteomic analyses using spin filters. Proteomics. 2005 May;5(7):1742-5. Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 2001 Mar;19(3):242-7. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan;4(1):59-77. Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007 Mar;4(3):207-14. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column above. The full data release policy for ENCODE is available here. 
wgEncodeProtGenoSuper ENC ProtGeno ENCODE Proteogenomics Expression Description This super track shows proteogenomic mappings of peptides from ENCODE cell types mapped to the human genome which represent fragments of translated proteins from the respective cell lines. Proteogenomic methods differ from conventional mass-spec proteomic methods. Conventional mass-spec proteomic methods identify peptides by comparing them to peptides produced from known proteins. In contrast, proteogenomic methods compare the peptides to all peptides that might theoretically be produced by the six possible translation frames of the genome (three on the forward strand plus three on the reverse strand) to identify the genomic region from which the peptides were produced. Study of proteogenomic data offers insights on numerous regulatory mechanisms, including: translation, pre-mRNA splicing and transcript diversity, nonsense-mediated decay, and transcription of novel protein-coding genes. Two tracks UNC/BSU ProtGenc and UNC/BSU ProtGeno that differ in database search scheme are presented here. UNC/BSU ProtGenc are the combined results from searching against Hg19 and GENCODE of peptides of both regular and post-translational modifications. UNC/BSU ProtGeno only contains the database search results of Hg19 of regular peptides. Display Conventions and Configuration Most ENCODE tracks contain multiple subtracks corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Giddings MC, Shah AA, Gesteland R, Moore B. Genome-based peptide fingerprint scanning. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):20-5. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan;4(1):59-77. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeUncBsuProtGencViewpepMapGcFt pepMapping Gc Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression 
wgEncodeUncBsuProtGencK562CellIngelpepMapGcFt K562 Ce K562 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003041 3041 Giddings UNC/BSU xcl9urKnTHhc0qEOIR+zbkKc4hlktYQx enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell In-gel wgEncodeUncBsuProtGencK562CellIngelpepMapGcFt pepMapGcFt leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell In-gel digestion proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. K562 In-gel ProtG GENCODE11 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1neuronsCellMudpitpepMapGcFt H1-neurons Ce H1-neurons Proteogenomics ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003043 3043 Giddings UNC/BSU AmpuUJeecTjp8adhqKVDfzos/0Q694X4 enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=50ppm cell MudPIT wgEncodeUncBsuProtGencH1neuronsCellMudpitpepMapGcFt pepMapGcFt neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Multidimensional Protein Identification Technology (MudPIT) proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-neurons MudPIT ProtG GENCODE10 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1hescCellMudpitpepMapGcFt H1-hESC Ce M H1-hESC Proteogenomics ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003042 3042 Giddings UNC/BSU Qe8pClnCCX+8LPbKv7RuRfN/rXkxbq5G enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=50ppm cell MudPIT wgEncodeUncBsuProtGencH1hescCellMudpitpepMapGcFt pepMapGcFt embryonic stem cells Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Multidimensional Protein Identification Technology (MudPIT) proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-hESC MudPIT ProtG GENCODE10 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1hescCellFasppepMapGcFt H1-hESC Ce F H1-hESC Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003040 3040 Giddings UNC/BSU YvRPXIoQz2jxniZvFp68FrcHhobcfvAk enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell FASP wgEncodeUncBsuProtGencH1hescCellFasppepMapGcFt pepMapGcFt embryonic stem cells Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Filter-Assisted Sample Preparation (FASP) proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-hESC FASP ProtG GENCODE11 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencGm12878CytosolIngelpepMapGcFt GM12878 Cyt GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003039 3039 Giddings UNC/BSU g9xv8oYkcWO3eKO5h58XMTgCfe/5JTg8 enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cytosol In-gel wgEncodeUncBsuProtGencGm12878CytosolIngelpepMapGcFt pepMapGcFt B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University The fluid between the cells outer membrane and the nucleus In-gel digestion proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. GM12878 Cytosol InGel ProtG GENCODE11 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencGm12878CellIngelpepMapGcFt GM12878 Ce GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003038 3038 Giddings UNC/BSU mmsilk35SUJQSp8Cls/3c42WCVEPxAcE enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell In-gel wgEncodeUncBsuProtGencGm12878CellIngelpepMapGcFt pepMapGcFt B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell In-gel digestion proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. GM12878 In-gel ProtG GENCODE11 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencViewmPepMapGcFt modPepMapping Gc Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression 
wgEncodeUncBsuProtGencK562CellIngelmPepMapGcFt K562 Ce PTM K562 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003041 3041 Giddings UNC/BSU xcl9urKnTHhc0qEOIR+zbkKc4hlktYQx enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell In-gel wgEncodeUncBsuProtGencK562CellIngelmPepMapGcFt mPepMapGcFt leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell In-gel digestion proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. K562 In-gel ProtG GENCODE11 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1neuronsCellMudpitmPepMapGcFt H1-neurons Ce PTM H1-neurons Proteogenomics ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003043 3043 Giddings UNC/BSU AmpuUJeecTjp8adhqKVDfzos/0Q694X4 enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=50ppm cell MudPIT wgEncodeUncBsuProtGencH1neuronsCellMudpitmPepMapGcFt mPepMapGcFt neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Multidimensional Protein Identification Technology (MudPIT) proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-neurons MudPIT ProtG GENCODE10 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1hescCellMudpitmPepMapGcFt H1-hESC Ce M PTM H1-hESC Proteogenomics ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003042 3042 Giddings UNC/BSU Qe8pClnCCX+8LPbKv7RuRfN/rXkxbq5G enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=50ppm cell MudPIT wgEncodeUncBsuProtGencH1hescCellMudpitmPepMapGcFt mPepMapGcFt embryonic stem cells Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Multidimensional Protein Identification Technology (MudPIT) proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-hESC MudPIT ProtG GENCODE10 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1hescCellFaspmPepMapGcFt H1-hESC Ce PTM H1-hESC Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003040 3040 Giddings UNC/BSU YvRPXIoQz2jxniZvFp68FrcHhobcfvAk enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell FASP wgEncodeUncBsuProtGencH1hescCellFaspmPepMapGcFt mPepMapGcFt embryonic stem cells Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Filter-Assisted Sample Preparation (FASP) proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-hESC FASP ProtG GENCODE11 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencGm12878CytosolIngelmPepMapGcFt GM12878 Cyt PTM GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003039 3039 Giddings UNC/BSU g9xv8oYkcWO3eKO5h58XMTgCfe/5JTg8 enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cytosol In-gel wgEncodeUncBsuProtGencGm12878CytosolIngelmPepMapGcFt mPepMapGcFt B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University The fluid between the cells outer membrane and the nucleus In-gel digestion proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. GM12878 Cytosol InGel ProtG GENCODE11 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencGm12878CellIngelmPepMapGcFt GM12878 Ce PTM GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003038 3038 Giddings UNC/BSU mmsilk35SUJQSp8Cls/3c42WCVEPxAcE enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell In-gel wgEncodeUncBsuProtGencGm12878CellIngelmPepMapGcFt mPepMapGcFt B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell In-gel digestion proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. GM12878 In-gel ProtG GENCODE11 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProt UNC/BSU ProtGeno Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression Description The ENCODE project has revealed the functional elements of segments of the human genome in unprecedented detail. However, the ability to clearly distinguish transcripts designated for translation into protein versus those that serve purely regulatory roles remains elusive. The standard means for doing this is to measure the proteins, if any, that are produced by transcripts via mass spectrometry-based proteogenomic mapping. In this process, chromatographically fractionated peptides are fed into a tandem mass spectrometer (MS/MS). The series of fragment masses produced in MS/MS create a signature that can then be used to identify the peptide from a protein or DNA sequence database. For proteogenomic mapping, this identifying spectrum is mapped directly back to its most likely encoding locus on a genome sequence (Giddings, et al. 2003). This allows the direct verification of protein-encoding transcripts. The proteogenomic track displays mass spectrometry data that have been matched to the genomic sequence for selected cell lines, using a workflow and software specifically designed for this purpose. The proteogenomic tracks can be used to identify which parts of the genome are translated into proteins, to verify which transcripts discovered by ENCODE are protein-encoding, and can also reveal new genes and/or splice variants of genes. Of particular interest may be its ability to reveal the translation of small open reading frames (ORFs), antisense transcripts, or sites annotated as introns that encode proteins. Display Conventions and Configuration The display for this track shows peptide mappings as contiguous, rectangular items. These items are rendered in grayscale according to the score, with darker items representing higher-confidence peptide mappings. The name of each item is the amino acid sequence of the peptide. If a period (.) appears at the end of a name, it signifies a stop codon. In addition to the displayed genomic coordinates, several additional fields are available for each track item. The Raw Score reflects the strength of the peptide mapping, in contrast to the Score field which reflects the confidence of the mapping. The Score field is computed as -100&times;log10(E-Value) for the peptide mapping, and scores of 200 or greater have an estimated 5% false discovery rate (FDR) while scores of 230 or greater have an estimated 1% FDR. The Raw Score offers an additional level of confidence: raw scores of 300 or greater have an estimated 5% false discovery rate. Note that Raw Score is not normalized for the length of the peptide mapping, while Score is. Consequently, short mappings might have a strong Raw Score but a weaker Score. The Spectrum ID is a semi-unique identifier of the spectrum associated with the peptide mapping, and can be used to track the origins of the mapping. The Peptide Rank indicates the rank of each peptide/spectrum mapping. A spectrum can be chimeric, containing more than one peptide, and the spectrum can be mapped with confidence to two or more distinct peptides. Peptides with ranks greater than 3 are deleted from the track. The Peptide Repeat Count indicates the number of places in the genome that match the peptide sequence. This reflects the uniqueness of the peptide mapping in the genome. Any mappings to highly-duplicated regions will have a high Peptide Repeat Count and peptides which were repeated more than 10 times in the genome were deleted from the track. Methods ENCODE cell lines K562 and GM12878 were used for large scale proteomic analysis. Cell lines were cultured according to standard ENCODE cell culture protocols and in-gel digestion was completed according to the standard protocol (Shevchenko, et al. 2007). The proteolytic enzyme trypsin was used to digest the proteins in order to produce short, MS/MS analyzable peptides. Trypsin is a common protease that typically cleaves proteins after Arginine or Lysine. The metadata parameter enzyme specifies the restriction enzyme used for digestion. Tandem mass spectrometry (RPLC-MS/MS) analysis was then performed on an Eksigent Ultra-LTQ Orbitrap system. However, due to enzyme inefficiency, it does not always cleave at Arginine or Lysine, so there may be peptides that include an uncleaved Arg/Lys site. The number of such missed cleavages allowed in the search is described by the metadata parameter miscleavages. We performed proteogenomic mapping (Jaffe, et al., 2004) with two missed cleavages allowed and using the whole human genomic sequence (UCSC hg19) via the genome fingerprint scanning (GFS) program (Giddings, et al. 2003) and newly developed Peppy (http://www.peppyresearch.com/). We used HMM_Score (Khatun, et al. 2008) to accurately match MS/MS spectra to their corresponding genome sequences. E-values are calculated, which estimate the number of results at the given score level which would be expected by random chance. We then empirically derived the false discovery rate for a given E-Value using a decoy database search and only those matches falling within the specified 5% FDR rate (E-Value &lt;0.01) are included in the track. The results with 10% FDR (E-Value &lt;0.05) are available under the Downloads page as Raw Signal. Release Notes This is Release 2 (July 2012). It contains a total of seven Proteogenomics experiments with the addition of one experiment available by download only. Unlike other ENCODE data, these data are not archived at GEO but at Proteome Commons. The first 32 digits of the Tranche Hash for each data set is stored as the labExpId. Credits Proteogenomic mapping: Dr. Jainab Khatun, Brian Risk, Mustaque Ahamed, Christopher Maier, Dr. John Wrobel and Dennis Crenshaw (Giddings Lab). Proteomic analysis: Drs. Yanbao Yu and Ling Xie (Chen Lab). Main Contact: Jainab Khatun References Giddings MC, Shah AA, Gesteland R, Moore B. Genome-based peptide fingerprint scanning. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):20-5. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan;4(1):59-77. Khatun J, Hamlett E, Giddings MC. Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification. Bioinformatics. 2008 Mar 1;24(5):674-81. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc. 2006;1(6):2856-60. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeUncBsuProtViewSignal Signal Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression 
wgEncodeUncBsuProtK562NucleusSig K562 nucleus K562 Proteogenomics ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH001739 1739 Giddings UNC/BSU IIAwZ45L+6NW1WpXsldQPngd7uSYeRyG enzyme=trypsin,miscleavages=2,precursorMassTolerance=.1Da,msMsMassTolerance=0.5Da nucleus In-gel wgEncodeUncBsuProtK562NucleusSig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA In-gel digestion proteomics protocol (Giddings) Signal K562 Nucleus Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtK562MitoSig K562 mitochondria K562 Proteogenomics ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH001738 1738 Giddings UNC/BSU Jpyz/zLWVrm2PiRJ9/xclTu3hL/xFr0A enzyme=trypsin,miscleavages=2,precursorMassTolerance=.1Da,msMsMassTolerance=0.5Da mitochondria In-gel wgEncodeUncBsuProtK562MitoSig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Mitochondria In-gel digestion proteomics protocol (Giddings) Signal K562 Mitochondria Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtK562MembranefractionSig K562 membrane K562 Proteogenomics ENCODE Mar 2012 Freeze 2011-01-05 2012-10-05 wgEncodeEH001200 1200 Giddings UNC/BSU hdaLa/989p1R+esS5JtrPWNam6J6QDyK enzyme=trypsin,miscleavages=2,precursorMassTolerance=.1Da,msMsMassTolerance=0.5Da membraneFraction In-gel wgEncodeUncBsuProtK562MembranefractionSig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University That fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes. In-gel digestion proteomics protocol (Giddings) Signal K562 Membrane Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtK562CytosolSig K562 cytosol K562 Proteogenomics ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH001737 1737 Giddings UNC/BSU Q8FP+m7/Ep+JBw6Sf0Y1ffd0L+rycBiQ enzyme=trypsin,miscleavages=2,precursorMassTolerance=.1Da,msMsMassTolerance=0.5Da cytosol In-gel wgEncodeUncBsuProtK562CytosolSig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University The fluid between the cells outer membrane and the nucleus In-gel digestion proteomics protocol (Giddings) Signal K562 Cytosol Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGm12878NucleusSig GM12878 nucleus GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2011-01-05 2012-10-05 wgEncodeEH001199 1199 Giddings UNC/BSU V7YeoLFnPQLw3zGfK3PthRQUsPlna6Nj enzyme=trypsin,miscleavages=2,precursorMassTolerance=0.2Da,msMsMassTolerance=0.5Da nucleus In-gel wgEncodeUncBsuProtGm12878NucleusSig Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA In-gel digestion proteomics protocol (Giddings) Signal GM12878 Nucleus Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGm12878MitoSig GM12878 mito GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEH002074 2074 Giddings UNC/BSU ZOTAcOHHzELqE03RkiDdf8c+/4aLhjII enzyme=trypsin,miscleavages=2,precursorMassTolerance=0.1Da,msMsMassTolerance=0.5Da mitochondria In-gel wgEncodeUncBsuProtGm12878MitoSig Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Mitochondria In-gel digestion proteomics protocol (Giddings) Signal GM12878 Mitochondria Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGm12878MembranefractionSig GM12878 membrane GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEH002073 2073 Giddings UNC/BSU OgqVm65vZlAv8IguaucWsujQnNWYC3vO enzyme=trypsin,miscleavages=2,precursorMassTolerance=0.1Da,msMsMassTolerance=0.5Da membraneFraction In-gel wgEncodeUncBsuProtGm12878MembranefractionSig Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University That fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes. In-gel digestion proteomics protocol (Giddings) Signal GM12878 Membrane Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeOpenChromChip UTA TFBS GSE33213 None Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) Regulation Description These tracks display chromatin immunoprecipitation (ChIP-seq) evidence as part of the four Open Chromatin track sets (see below). ChIP-seq is a method to identify the specific location of proteins that are directly or indirectly bound to genomic DNA. By identifying the binding location of sequence-specific transcription factors, general transcription machinery components, and chromatin factors, ChIP can help in the functional annotation of the open chromatin regions identified by DNaseI HS mapping and FAIRE. Together with DNaseI HS and FAIRE experiments, these tracks display the locations of active regulatory elements identified as open chromatin in multiple cell types from the Duke, UNC-Chapel Hill, UT-Austin, and EBI ENCODE group. Within this project, open chromatin was identified using two independent and complementary methods: DNaseI hypersensitivity (HS) and Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE), combined with these ChIP-seq assays for select regulatory factors. DNaseI HS and FAIRE provide assay cross-validation with commonly identified regions delineating the highest confidence areas of open chromatin. These ChIP assays provide functional validation and preliminary annotation of a subset of open chromatin sites. Each method employed Illumina (formerly Solexa) sequencing by synthesis as the detection platform. The Tier 1 and Tier 2 cell types were additionally verified by a second platform, high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen. As a background control experiment, the input genomic DNA sample that was used for ChIP was sequenced. Crosslinked chromatin was sheared and the crosslinks were reversed without carrying out the immunoprecipitation step. This sample was otherwise processed in a manner identical to the ChIP sample as described below. The input track is useful in revealing potential artifacts arising from the sequence alignment process such as copy number differences between the reference genome and the sequenced samples, as well as regions of poor sequence alignability. For cell lines for which there is no input experiment available, the peaks were generated using the control of generic_male or generic_female, as an attempt to create a general background based on input data from several cell types. These files are in &quot;iff&quot; format, which is used when calling peaks with F-seq software, and can be downloaded from the production lab directly from under the section titled &quot;Copy number / karyotype correction.&quot; Other Open Chromatin track sets: Data for the DNaseI HS experiments can be found in Duke DNaseI HS. Data for the FAIRE experiments can be found in UNC FAIRE. A synthesis of all the open chromatin assays for select cell lines can be found in Open Chrom Synth. Display Conventions and Configuration This track is a multi-view composite track that contains a single data type with multiple levels of annotation (views). For each view, there are multiple subtracks representing different cell types that display individually on the browser. Instructions for configuring multi-view tracks are here. ChIP data displayed here represents a continuum of signal intensities. The Iyer lab recommends setting the &quot;Data view scaling: auto-scale&quot; option when viewing signal data in full mode to see the full dynamic range of the data. Note that in regions that do not have open chromatin sites, autoscale will rescale the data and inflate the background signal, making the regions appear noisy. Changing back to fixed scale will alleviate this issue. In general, for each experiment in each of the cell types, the UTA TFBS tracks contain the following views: Peaks Regions of enriched signal in ChIP experiments. Peaks were called based on signals created using F-Seq, a software program developed at Duke (Boyle et al., 2008b). Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. The solid vertical line in the peak represents the point with highest signal. F-Seq Density Signal Density graph (wiggle) of signal enrichment calculated using F-Seq for the combined set of sequences from all replicates. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). This method does not look at fixed-length windows but rather weights contributions of nearby sequences in proportion to their distance from that base. It only considers sequences aligned 4 or less times in the genome and uses an alignability background model to try to correct for regions where sequences cannot be aligned. For each cell type, especially important for those with an abnormal karyotype, a model to try to correct for amplifications and deletions that is based on control input data was also used. Base Overlap Signal An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Peaks and signals displayed in this track are the results of pooled replicates. The raw sequence and alignment files for each replicate are available for download. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. To perform ChIP, proteins were cross-linked to DNA in vivo using 1&#37; formaldehyde solution (Bhinge et al., 2007; ENCODE Project Consortium, 2007). Cross-linked chromatin was sheared by sonication and immunoprecipitated using a specific antibody against the protein of interest. After reversal of the cross-links, the immunoprecipitated DNA was used to identify the genomic location of transcription factor binding. This was accomplished by sequencing of the ends of the immunoprecipitated DNA (ChIP-seq) using the Illumina (Solexa) sequencing system. ChIP data for Tier 1 and Tier 2 cell lines were verified by comparing multiple independent growths (replicates) and determining the reproducibility of the data. For some cell types, additional verification was performed using the same immunoprecipitated DNA by labeling and hybridizing to NimbleGen Human ENCODE tiling arrays (1&#37; of the genome) along with the input DNA as reference (ChIP-chip). A more detailed protocol is available here. DNA fragments isolated by ChIP are 100-200 bp in length, with the average length being 134 bp. Sequences from each experiment were aligned to the genome using Burrows-Wheeler Aligner (Li et al., 2010) for the GRCh37 (hg19) assembly. The command used for these alignments was: &gt; bwa aln -t 8 genome.fa s_1.sequence.txt.bfq &gt; s_1.sequence.txt.sai Where genome.fa is the whole genome sequence and s_1.sequence.txt.bfq is one lane of sequences converted into the required bfq format. Sequences from multiple lanes are combined for a single replicate using the bwa samse command, and converted in the sam/bam format using SAMtools. Only those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes - see supplemental materials). The mappings of these short reads to the genome are available for download. The resulting digital signal was converted to a continuous wiggle track using F-Seq that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Input data has been generated for several cell lines. These are used directly to create a control/background model used for F-Seq when generating signal annotations for these cell lines. These models are meant to correct for sequencing biases, alignment artifacts, and copy number changes in these cell lines. Input data is not being generated directly for other cell lines. Instead, a general background model was derived from the available input data sets. This should provide corrections for sequencing biases and alignment artifacts, but will not correct for cell type specific copy number changes. The exact command used for this step is: CTCF: &gt; fseq -l 300 -v -b &lt;bff files&gt; -p &lt;iff files&gt; aligments.bed c-Myc: &gt; fseq -l 600 -v -b &lt;bff files&gt; -p &lt;iff files&gt; aligments.bed PolII: &gt; fseq -l 800 -v -b &lt;bff files&gt; -p &lt;iff files&gt; aligments.bed Where the (bff files) are the background files based on alignability, the (iff files) are the background files based on the input experiments, and alignments.bed are a bed file of filtered sequence alignments. Discrete ChIP sites (peaks) were identified from ChIP-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. Data from the high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen were normalized using the Tukey biweight normalization, and peaks were called using ChIPOTle (Buck, et al., 2005) at multiple levels of significance. Regions matched on size to these peaks that were devoid of any significant signal were also created as a null model. These data were used for additional verification of Tier 1 and Tier 2 cell lines by ROC analysis. Files labeled Validation view containing this data are available for download. Release Notes Release 2 (August 2011) of this track adds 34 new experiments including 17 new cell lines. Enhancer and Insulator Functional assays: A subset of DNase and FAIRE regions were cloned into functional tissue culture reporter assays to test for enhancer and insulator activity. Coordinates and results from these experiments can be found here. Credits These data and annotations were created by a collaboration of multiple institutions (contact: Terry Furey) Duke University's Institute for Genome Sciences & Policy (IGSP): Alan Boyle, Lingyun Song, and Greg Crawford University of North Carolina at Chapel Hill: Paul Giresi, Jason Lieb and Terry Furey University of Texas at Austin: Zheng Liu, Ryan McDaniell, Bum-Kyu Lee, and Vishy Iyer European Bioinformatics Insitute: Paul Flicek, Damian Keefe, and Ewan Birney University of Cambridge, Department of Oncology and CR-UK Cambridge Research Institute (CRI) : Stefan Graf We thank NHGRI for ENCODE funding support. References Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res. 2007 Jun;17(6):910-6. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008 Jan 25;132(2):311-22. Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8. Buck MJ, Nobel AB, Lieb JD. ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 2005;6(11):R97. Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods. 2006 Jul;3(7):503-9. Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123-31. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guig&#243; R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007 Jun;17(6):877-85. Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods. 2009 Jul;48(3):233-9. Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS et al. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res. 2012 Jan;22(1):9-24. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Nov;18(11):1851-8. Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384. Publications Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS et al. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res. 2012 Jan;22(1):9-24. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeOpenChromChipViewPeaks Peaks Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) Regulation 
wgEncodeOpenChromChipSpleenocCtcfPkRep1 Spleen CTCF Pk CTCF Spleen_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003464 3464 GSM1006883 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipSpleenocCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen spleen tissue from NICHD donor IDs 1863 (Rep B1) and 4548 (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Spleen OC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibPol2PkRep1 ProgFib Pol2 Pk Pol2 ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-10 2010-10-10 wgEncodeEH000606 606 GSM822282 Crawford UT-A privacy-noSequence p-value cutoff: 0.05 hg18 1 exp wgEncodeOpenChromChipProgfibPol2PkRep1 None Peaks RNA Polymerase II fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment ProgFib Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibCtcfPkRep1 ProgFib CTCF Pk CTCF ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-02 2010-10-02 wgEncodeEH000600 600 GSM822272 Crawford UT-A privacy-noSequence p-value cutoff: 0.05 hg18 1 exp wgEncodeOpenChromChipProgfibCtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment ProgFib CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipPancreasocCtcfPkRep1 Pancreas CTCF Pk CTCF Pancreas_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003463 3463 GSM1006881 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipPancreasocCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Pancreas OC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipNhekCtcfPk NHEK CTCF Pk CTCF NHEK ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000559 559 GSM822271 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipNhekCtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment NHEK CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMedulloCtcfPkRep1 Medullo CTCF Pk CTCF Medullo ChipSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003440 3440 GSM1006893 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMedulloCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Medullo CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLungocCtcfPkRep1 Lung CTCF Pk CTCF Lung_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003462 3462 GSM1006882 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipLungocCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen lung tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase) and CF Center donor IDs DD006I (Rep B1 FAIRE) and DD007I (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Lung OC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfAndroPkRep1 LNCaP CTCF Pk CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003460 3460 GSM1006887 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipLncapCtcfAndroPkRep1 androgen Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Regions of enriched signal in experiment LNCaP androgen CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfPkRep1 LNCaP CTCF Pk CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003459 3459 GSM1006874 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipLncapCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment LNCaP CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipKidneyocCtcfPkRep1 Kidney CTCF Pk CTCF Kidney_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003461 3461 GSM1006886 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipKidneyocCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Kidney OC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm20000CtcfPkRep1 GM20000 CTCF Pk CTCF GM20000 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003458 3458 GSM1006873 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm20000CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM20000 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19240CtcfPk GM19240 CTCF Pk CTCF GM19240 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-06 2010-07-06 wgEncodeEH000572 572 GSM822276 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm19240CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM19240 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19239CtcfPk GM19239 CTCF Pk CTCF GM19239 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000571 571 GSM822277 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm19239CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM19239 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19238CtcfPk GM19238 CTCF Pk CTCF GM19238 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000570 570 GSM822278 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm19238CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM19238 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13977CtcfPkRep1 GM13977 CTCF Pk CTCF GM13977 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003456 3456 GSM1006869 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm13977CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM13977 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13976CtcfPkRep1 GM13976 CTCF Pk CTCF GM13976 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003448 3448 GSM1006885 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm13976CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM13976 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12892CtcfPk GM12892 CTCF Pk CTCF GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-02 2010-07-02 wgEncodeEH000562 562 GSM822299 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm12892CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12892 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12891CtcfPk GM12891 CTCF Pk CTCF GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000569 569 GSM822294 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm12891CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12891 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10266CtcfPkRep1 GM10266 CTCF Pk CTCF GM10266 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003457 3457 GSM1006870 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm10266CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM10266 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10248CtcfPkRep1 GM10248 CTCF Pk CTCF GM10248 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003446 3446 GSM1006891 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm10248CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM10248 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaPol2PkRep1 Gliobla Pol2 Pk Pol2 Gliobla ChipSeq ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001136 1136 GSM822302 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipGlioblaPol2PkRep1 None Peaks RNA Polymerase II glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Gliobla Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaCtcfPkRep1 Gliobla CTCF Pk CTCF Gliobla ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001135 1135 GSM822303 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipGlioblaCtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Gliobla CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipFibroblCtcfPkRep1 Fibrobl CTCF Pk CTCF Fibrobl ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001127 1127 GSM822281 Crawford UT-A privacy-noSequence p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipFibroblCtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. child fibroblast Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Fibrobl CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstimPkRep1 MCF-7 Pol2 stm Pk Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003435 3435 GSM1006876 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7Pol2SerumstimPkRep1 serum_stimulated_media Peaks RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Regions of enriched signal in experiment MCF-7 serum stim Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstvdPkRep1 MCF-7 Pol2 stv Pk Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003438 3438 GSM1006865 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7Pol2SerumstvdPkRep1 serum_starved_media Peaks RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Regions of enriched signal in experiment MCF-7 serum starved Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2PkRep1 MCF-7 Pol2 Pk Pol2 MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001130 1130 GSM822295 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipMcf7Pol2PkRep1 None Peaks RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment MCF-7 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfVehPkRep1 MCF-7 veh CTCF Pk CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001132 1132 GSM822308 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipMcf7CtcfVehPkRep1 vehicle Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Regions of enriched signal in experiment MCF-7 vehicle CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstimPkRep1 MCF-7 CTCF stm Pk CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003434 3434 GSM1006875 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7CtcfSerumstimPkRep1 serum_stimulated_media Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Regions of enriched signal in experiment MCF-7 serum stim CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstvdPkRep1 MCF-7 CTCF stv Pk CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003437 3437 GSM1006878 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7CtcfSerumstvdPkRep1 serum_starved_media Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Regions of enriched signal in experiment MCF-7 serum starved CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfEstroPkRep1 MCF-7 est CTCF Pk CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001131 1131 GSM822309 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipMcf7CtcfEstroPkRep1 estrogen Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Regions of enriched signal in experiment MCF-7 estrogen CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfPk MCF-7 CTCF Pk CTCF MCF-7 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-28 2010-09-28 wgEncodeEH000598 598 GSM822305 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipMcf7CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment MCF-7 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycVehPkRep1 MCF-7 veh cMyc Pk c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001133 1133 GSM822301 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipMcf7CmycVehPkRep1 vehicle Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Regions of enriched signal in experiment MCF-7 vehicle cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstimPkRep1 MCF-7 cMyc stm Pk c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003436 3436 GSM1006877 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7CmycSerumstimPkRep1 serum_stimulated_media Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Regions of enriched signal in experiment MCF-7 serum stim cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstvdPkRep1 MCF-7 cMyc stv Pk c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH003439 3439 GSM1006866 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7CmycSerumstvdPkRep1 serum_starved_media Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Regions of enriched signal in experiment MCF-7 serum starved cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycEstroPkRep1 MCF-7 est cMyc Pk c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001134 1134 GSM822304 Crawford UT-A p-value cutoff: 0.05 hg19 1 exp wgEncodeOpenChromChipMcf7CmycEstroPkRep1 estrogen Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Regions of enriched signal in experiment MCF-7 estrogen cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecPol2Pk HUVEC Pol2 Pk Pol2 HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-28 2010-06-28 wgEncodeEH000552 552 GSM822306 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHuvecPol2Pk None Peaks RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HUVEC Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCtcfPk HUVEC CTCF Pk CTCF HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-25 2010-06-25 wgEncodeEH000551 551 GSM822279 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHuvecCtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HUVEC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCmycPk HUVEC cMyc Pk c-Myc HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-01 2010-07-01 wgEncodeEH000561 561 GSM822298 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipHuvecCmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HUVEC cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2Pol2Pk HepG2 Pol2 Pk Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-29 2010-06-29 wgEncodeEH000554 554 GSM822284 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHepg2Pol2Pk None Peaks RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HepG2 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CtcfPk HepG2 CTCF Pk CTCF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000543 543 GSM822287 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHepg2CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HepG2 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CmycPk HepG2 cMyc Pk c-Myc HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-22 2009-12-22 wgEncodeEH000545 545 GSM822291 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipHepg2CmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HepG2 cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3Pol2Pk HeLa-S3 Pol2 Pk Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-28 wgEncodeEH000597 597 GSM822273 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHelas3Pol2Pk None Peaks RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HeLa-S3 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CtcfPk HeLa-S3 CTCF Pk CTCF HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000541 541 GSM822285 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHelas3CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HeLa-S3 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CmycPk HeLa-S3 cMyc Pk c-Myc HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000542 542 GSM822286 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipHelas3CmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HeLa-S3 cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549Pol2PkRep1 A549 Pol2 Pk Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002079 2079 GSM822288 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipA549Pol2PkRep1 None Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment A549 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549CtcfPkRep1 A549 CTCF Pk CTCF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002078 2078 GSM822289 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipA549CtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment A549 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562Pol2Pk K562 Pol2 Pk Pol2 K562 ChipSeq ENCODE June 2010 Freeze 2011-01-12 2009-09-29 2010-06-29 wgEncodeEH000555 555 GSM822275 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipK562Pol2Pk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment K562 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CtcfPk K562 CTCF Pk CTCF K562 ChipSeq ENCODE June 2010 Freeze 2011-01-12 2009-03-20 2009-12-20 wgEncodeEH000535 535 GSM822311 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipK562CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment K562 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CmycPk K562 cMyc Pk c-Myc K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-03-20 2009-12-20 wgEncodeEH000536 536 GSM822310 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipK562CmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment K562 cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescPol2Pk H1-hESC Pol2 Pk Pol2 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-10-02 2010-07-02 wgEncodeEH000563 563 GSM822300 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipH1hescPol2Pk None Peaks RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment H1-hESC Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCtcfPk H1-hESC CTCF Pk CTCF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-01 2010-07-01 wgEncodeEH000560 560 GSM822297 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipH1hescCtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment H1-hESC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCmycPk H1-hESC cMyc Pk c-Myc H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-27 wgEncodeEH000596 596 GSM822274 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipH1hescCmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment H1-hESC cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878Pol2Pk GM12878 Pol2 Pk Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-12-23 2010-09-22 wgEncodeEH000592 592 GSM822270 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm12878Pol2Pk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12878 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CtcfPkRep1 GM12878 CTCF Pk CTCF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000532 532 GSM822312 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm12878CtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12878 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CmycPk GM12878 cMyc Pk c-Myc GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-02 2009-09-08 2010-06-08 wgEncodeEH000547 547 GSM822290 Crawford UT-A p-value cutoff: 0.001 hg18 exp wgEncodeOpenChromChipGm12878CmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12878 cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipViewSignal ChIP F-Seq DS Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) Regulation 
wgEncodeOpenChromChipSpleenocInputSig Spleen Input DS Input Spleen_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003455 3455 GSM1006872 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipSpleenocInputSig Signal Primary frozen spleen tissue from NICHD donor IDs 1863 (Rep B1) and 4548 (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Spleen OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipSpleenocCtcfSigRep1 Spleen CTCF DS CTCF Spleen_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003464 3464 GSM1006883 Crawford UT-A fseq v 1.84, iff_Spleen 1 exp wgEncodeOpenChromChipSpleenocCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen spleen tissue from NICHD donor IDs 1863 (Rep B1) and 4548 (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Spleen OC CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibInputSig ProgFib Input DS Input ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-23 2010-09-22 wgEncodeEH000593 593 GSM822269 Crawford UT-A privacy-noSequence fseq v 1.84 hg18 input wgEncodeOpenChromChipProgfibInputSig None Signal fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal ProgFib Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibPol2Sig ProgFib Pol2 DS Pol2 ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-10 2010-10-10 wgEncodeEH000606 606 GSM822282 Crawford UT-A privacy-noSequence fseq v 1.84, iff_FB0167P hg18 exp wgEncodeOpenChromChipProgfibPol2Sig None Signal RNA Polymerase II fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal ProgFib Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibCtcfSig ProgFib CTCF DS CTCF ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-02 2010-10-02 wgEncodeEH000600 600 GSM822272 Crawford UT-A privacy-noSequence fseq v 1.84, iff_FB0167P hg18 exp wgEncodeOpenChromChipProgfibCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal ProgFib CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipPancreasocInputSig Pancreas Input DS Input Pancreas_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003454 3454 GSM1006871 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipPancreasocInputSig Signal Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Pancreas OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipPancreasocCtcfSigRep1 Pancreas CTCF DS CTCF Pancreas_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003463 3463 GSM1006881 Crawford UT-A fseq v 1.84, iff_Pancreas 1 exp wgEncodeOpenChromChipPancreasocCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Pancreas OC CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipNhekCtcfSig NHEK CTCF DS CTCF NHEK ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000559 559 GSM822271 Crawford UT-A fseq v 1.84, iff_generic_female hg18 exp wgEncodeOpenChromChipNhekCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal NHEK CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMedulloInputSig Medullo Input DS Input Medullo ChipSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003441 3441 GSM1006892 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipMedulloInputSig Signal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Medullo Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMedulloCtcfSig Medullo CTCF DS CTCF Medullo ChipSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003440 3440 GSM1006893 Crawford UT-A fseq v 1.84, iff_D721 exp wgEncodeOpenChromChipMedulloCtcfSig Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Medullo CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLungocInputSig Lung Input DS Input Lung_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003453 3453 GSM1006880 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipLungocInputSig Signal Primary frozen lung tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase) and CF Center donor IDs DD006I (Rep B1 FAIRE) and DD007I (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Lung OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLungocCtcfSigRep1 Lung CTCF DS CTCF Lung_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003462 3462 GSM1006882 Crawford UT-A fseq v 1.84, iff_Lung 1 exp wgEncodeOpenChromChipLungocCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen lung tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase) and CF Center donor IDs DD006I (Rep B1 FAIRE) and DD007I (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Lung OC CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapInputSig LNCaP Input DS Input LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003452 3452 GSM1006879 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipLncapInputSig Signal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal LNCaP Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfAndroSigRep1 LNCaP CTCF DS CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003460 3460 GSM1006887 Crawford UT-A fseq v 1.84, iff_LnCAP 1 exp wgEncodeOpenChromChipLncapCtcfAndroSigRep1 androgen Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Signal LNCaP androgen CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfSigRep1 LNCaP CTCF DS CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003459 3459 GSM1006874 Crawford UT-A fseq v 1.84, iff_LnCAP 1 exp wgEncodeOpenChromChipLncapCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal LNCaP CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipKidneyocInputSig Kidney Input DS Input Kidney_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003451 3451 GSM1006868 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipKidneyocInputSig Signal Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Kidney OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipKidneyocCtcfSigRep1 Kidney CTCF DS CTCF Kidney_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003461 3461 GSM1006886 Crawford UT-A fseq v 1.84, iff_Kidney 1 exp wgEncodeOpenChromChipKidneyocCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Kidney OC CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHeartocInputSig Heart Input DS Input Heart_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003450 3450 GSM1006867 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipHeartocInputSig Signal Primary frozen heart tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B1 FAIRE), 4548 (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Heart OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm20000InputSig GM20000 Input DS Input GM20000 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003449 3449 GSM1006884 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm20000InputSig Signal lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM20000 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm20000CtcfSigRep1 GM20000 CTCF DS CTCF GM20000 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003458 3458 GSM1006873 Crawford UT-A fseq v 1.84, iff_20000 1 exp wgEncodeOpenChromChipGm20000CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM20000 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19240CtcfSig GM19240 CTCF DS CTCF GM19240 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-06 2010-07-06 wgEncodeEH000572 572 GSM822276 Crawford UT-A fseq v 1.84, iff_generic_female hg18 exp wgEncodeOpenChromChipGm19240CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM19240 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19239CtcfSig GM19239 CTCF DS CTCF GM19239 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000571 571 GSM822277 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipGm19239CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM19239 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19238CtcfSig GM19238 CTCF DS CTCF GM19238 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000570 570 GSM822278 Crawford UT-A fseq v 1.84, iff_generic_female hg18 exp wgEncodeOpenChromChipGm19238CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM19238 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13977InputSig GM13977 Input DS Input GM13977 ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003444 3444 GSM1006889 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm13977InputSig Signal lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM13977 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13977CtcfSigRep1 GM13977 CTCF DS CTCF GM13977 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003456 3456 GSM1006869 Crawford UT-A fseq v 1.84, iff_GM13977 1 exp wgEncodeOpenChromChipGm13977CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM13977 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13976InputSig GM13976 Input DS Input GM13976 ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003443 3443 GSM1006894 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm13976InputSig Signal lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM13976 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13976CtcfSigRep1 GM13976 CTCF DS CTCF GM13976 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003448 3448 GSM1006885 Crawford UT-A fseq v 1.84, iff_GM13976 1 exp wgEncodeOpenChromChipGm13976CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM13976 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12892CtcfSig GM12892 CTCF DS CTCF GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-02 2010-07-02 wgEncodeEH000562 562 GSM822299 Crawford UT-A fseq v 1.84, iff_generic_female hg18 exp wgEncodeOpenChromChipGm12892CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12892 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12891CtcfSig GM12891 CTCF DS CTCF GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000569 569 GSM822294 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipGm12891CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12891 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10266InputSig GM10266 Input DS Input GM10266 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003447 3447 GSM1006890 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm10266InputSig Signal lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM10266 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10266CtcfSigRep1 GM10266 CTCF DS CTCF GM10266 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003457 3457 GSM1006870 Crawford UT-A fseq v 1.84, iff_GM10266 1 exp wgEncodeOpenChromChipGm10266CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM10266 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10248InputSig GM10248 Input DS Input GM10248 ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003442 3442 GSM1006895 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm10248InputSig Signal lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM10248 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10248CtcfSigRep1 GM10248 CTCF DS CTCF GM10248 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003446 3446 GSM1006891 Crawford UT-A fseq v 1.84, iff_GM10248 1 exp wgEncodeOpenChromChipGm10248CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM10248 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaInputSig Gliobla Input DS Input Gliobla ChipSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001129 1129 GSM822268 Crawford UT-A fseq v 1.84 hg19 input wgEncodeOpenChromChipGlioblaInputSig None Signal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Gliobla Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaPol2Sig Gliobla Pol2 DS Pol2 Gliobla ChipSeq ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001136 1136 GSM822302 Crawford UT-A fseq v 1.84, iff_H54 hg19 exp wgEncodeOpenChromChipGlioblaPol2Sig None Signal RNA Polymerase II glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Gliobla Pol2 TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaCtcfSig Gliobla CTCF DS CTCF Gliobla ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001135 1135 GSM822303 Crawford UT-A fseq v 1.84, iff_H54 hg19 exp wgEncodeOpenChromChipGlioblaCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Gliobla CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipFibroblInputSig Fibrobl Input DS Input Fibrobl ChipSeq ENCODE Jan 2011 Freeze 2010-10-14 2011-07-14 wgEncodeEH001128 1128 GSM822267 Crawford UT-A privacy-noSequence fseq v 1.84 hg19 input wgEncodeOpenChromChipFibroblInputSig None Signal child fibroblast Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Fibrobl Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipFibroblCtcfSig Fibrobl CTCF DS CTCF Fibrobl ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001127 1127 GSM822281 Crawford UT-A privacy-noSequence fseq v 1.84, iff_FB8470 hg19 exp wgEncodeOpenChromChipFibroblCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. child fibroblast Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Fibrobl CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipColonocInputSig Colon Input DS Input Colon_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003445 3445 GSM1006888 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipColonocInputSig Signal Primary frozen colon tissue from NCTC donor IDs 10-0005A (Rep B1) and 10-0170A (Rep B2), African American and caucasian Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Colon OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMonocd14ro1746InputSig Mono-CD14+ Inp DS Input Monocytes-CD14+_RO01746 ChipSeq ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001137 1137 GSM822296 Crawford UT-A fseq v 1.84 hg19 input wgEncodeOpenChromChipMonocd14ro1746InputSig None Signal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Monocytes-CD14+ Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7InputSig MCF-7 Input DS Input MCF-7 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-22 2010-09-22 wgEncodeEH000589 589 GSM822283 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipMcf7InputSig None Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal MCF-7 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstimSig MCF-7 Pol2 stm DS Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003435 3435 GSM1006876 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7Pol2SerumstimSig serum_stimulated_media Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Signal MCF-7 serum stim Pol2 TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstvdSig MCF-7 Pol2 stv DS Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003438 3438 GSM1006865 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7Pol2SerumstvdSig serum_starved_media Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Signal MCF-7 serum starved Pol2 TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2Sig MCF-7 Pol2 DS Pol2 MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001130 1130 GSM822295 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7Pol2Sig None Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal MCF-7 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfVehSig MCF-7 veh CTCF DS CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001132 1132 GSM822308 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7CtcfVehSig vehicle Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Signal MCF-7 vehicle CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstimSig MCF-7 CTCF stm DS CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003434 3434 GSM1006875 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7CtcfSerumstimSig serum_stimulated_media Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Signal MCF-7 serum stim CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstvdSig MCF-7 CTCF stv DS CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003437 3437 GSM1006878 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7CtcfSerumstvdSig serum_starved_media Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Signal MCF-7 serum starved CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfEstroSig MCF-7 est CTCF DS CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001131 1131 GSM822309 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7CtcfEstroSig estrogen Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Signal MCF-7 estrogen CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSig MCF-7 CTCF DS CTCF MCF-7 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-28 2010-09-28 wgEncodeEH000598 598 GSM822305 Crawford UT-A fseq v 1.84, iff_MCF7 hg18 exp wgEncodeOpenChromChipMcf7CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal MCF-7 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycVehSig MCF-7 veh cMyc DS c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001133 1133 GSM822301 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7CmycVehSig vehicle Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Signal MCF-7 vehicle cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstimSig MCF-7 cMyc stm DS c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003436 3436 GSM1006877 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7CmycSerumstimSig serum_stimulated_media Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Signal MCF-7 serum stim cMyc TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstvdSig MCF-7 cMyc stv DS c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH003439 3439 GSM1006866 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7CmycSerumstvdSig serum_starved_media Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Signal MCF-7 serum starved cMyc TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycEstroSig MCF-7 est cMyc DS c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001134 1134 GSM822304 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7CmycEstroSig estrogen Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Signal MCF-7 estrogen cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecInputSig HUVEC Input DS Input HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-18 2009-09-24 2010-06-24 wgEncodeEH000550 550 GSM822280 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipHuvecInputSig None Signal umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HUVEC Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecPol2Sig HUVEC Pol2 DS Pol2 HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-28 2010-06-28 wgEncodeEH000552 552 GSM822306 Crawford UT-A fseq v 1.84, iff_HUVEC hg18 exp wgEncodeOpenChromChipHuvecPol2Sig None Signal RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HUVEC Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCtcfSig HUVEC CTCF DS CTCF HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-25 2010-06-25 wgEncodeEH000551 551 GSM822279 Crawford UT-A fseq v 1.84, iff_HUVEC hg18 exp wgEncodeOpenChromChipHuvecCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HUVEC CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCmycSig HUVEC cMyc DS c-Myc HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-01 2010-07-01 wgEncodeEH000561 561 GSM822298 Crawford UT-A fseq v 1.84, iff_HUVEC hg18 exp wgEncodeOpenChromChipHuvecCmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HUVEC cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2InputSig HepG2 Input DS Input HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-18 2009-03-13 2009-12-13 wgEncodeEH000538 538 GSM822314 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipHepg2InputSig None Signal hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HepG2 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2Pol2Sig HepG2 Pol2 DS Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-29 2010-06-29 wgEncodeEH000554 554 GSM822284 Crawford UT-A fseq v 1.84, iff_HepG2 hg18 exp wgEncodeOpenChromChipHepg2Pol2Sig None Signal RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HepG2 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CtcfSig HepG2 CTCF DS CTCF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000543 543 GSM822287 Crawford UT-A fseq v 1.84, iff_HepG2 hg18 exp wgEncodeOpenChromChipHepg2CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HepG2 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CmycSig HepG2 cMyc DS c-Myc HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-22 2009-12-22 wgEncodeEH000545 545 GSM822291 Crawford UT-A fseq v 1.84, iff_HepG2 hg18 exp wgEncodeOpenChromChipHepg2CmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HepG2 cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3InputSig HeLa-S3 Input DS Input HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-18 2009-03-16 2009-12-16 wgEncodeEH000539 539 GSM822313 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipHelas3InputSig None Signal cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HeLa-S3 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3Pol2Sig HeLa-S3 Pol2 DS Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-28 wgEncodeEH000597 597 GSM822273 Crawford UT-A fseq v 1.84, iff_HelaS3 hg18 exp wgEncodeOpenChromChipHelas3Pol2Sig None Signal RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HeLa-S3 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CtcfSig HeLa-S3 CTCF DS CTCF HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000541 541 GSM822285 Crawford UT-A fseq v 1.84, iff_HelaS3 hg18 exp wgEncodeOpenChromChipHelas3CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HeLa-S3 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CmycSig HeLa-S3 cMyc DS c-Myc HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000542 542 GSM822286 Crawford UT-A fseq v 1.84, iff_HelaS3 hg18 exp wgEncodeOpenChromChipHelas3CmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HeLa-S3 cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549InputSig A549 Input DS Input A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002077 2077 GSM822307 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipA549InputSig None Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal A549 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549Pol2Sig A549 Pol2 DS Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002079 2079 GSM822288 Crawford UT-A fseq v 1.84, iff_A549 exp wgEncodeOpenChromChipA549Pol2Sig None Signal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal A549 Pol2 TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549CtcfSig A549 CTCF DS CTCF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002078 2078 GSM822289 Crawford UT-A fseq v 1.84, iff_A549 exp wgEncodeOpenChromChipA549CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal A549 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562InputSig K562 Input DS Input K562 ChipSeq ENCODE June 2010 Freeze 2010-06-18 2008-12-05 2009-08-05 wgEncodeEH000529 529 GSM822293 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipK562InputSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal K562 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562Pol2Sig K562 Pol2 DS Pol2 K562 ChipSeq ENCODE June 2010 Freeze 2011-01-12 2009-09-29 2010-06-29 wgEncodeEH000555 555 GSM822275 Crawford UT-A fseq v 1.84, iff_K562 hg18 exp wgEncodeOpenChromChipK562Pol2Sig None Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal K562 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CtcfSig K562 CTCF DS CTCF K562 ChipSeq ENCODE June 2010 Freeze 2011-01-12 2009-02-27 2009-11-27 wgEncodeEH000535 535 GSM822311 Crawford UT-A fseq v 1.84, iff_K562 hg18 exp wgEncodeOpenChromChipK562CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal K562 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CmycSig K562 cMyc DS c-Myc K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-02-27 2009-11-27 wgEncodeEH000536 536 GSM822310 Crawford UT-A fseq v 1.84, iff_K562 hg18 exp wgEncodeOpenChromChipK562CmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal K562 cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescPol2Sig H1-hESC Pol2 DS Pol2 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-10-02 2010-07-02 wgEncodeEH000563 563 GSM822300 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipH1hescPol2Sig None Signal RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal H1-hESC Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCtcfSig H1-hESC CTCF DS CTCF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-01 2010-07-01 wgEncodeEH000560 560 GSM822297 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipH1hescCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal H1-hESC CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCmycSig H1-hESC cMyc DS c-Myc H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-27 wgEncodeEH000596 596 GSM822274 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipH1hescCmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal H1-hESC cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878InputSig GM12878 Input DS Input GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2008-11-07 2009-07-07 wgEncodeEH000528 528 GSM822292 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipGm12878InputSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12878 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878Pol2Sig GM12878 Pol2 DS Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-12-23 2010-09-22 wgEncodeEH000592 592 GSM822270 Crawford UT-A fseq v 1.84, iff_GM12878 hg18 exp wgEncodeOpenChromChipGm12878Pol2Sig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12878 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CtcfSig GM12878 CTCF DS CTCF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000532 532 GSM822312 Crawford UT-A fseq v 1.84, iff_GM12878 hg18 exp wgEncodeOpenChromChipGm12878CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12878 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CmycSig GM12878 cMyc DS c-Myc GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-02 2009-09-08 2010-06-08 wgEncodeEH000547 547 GSM822290 Crawford UT-A fseq v 1.84, iff_GM12878 hg18 exp wgEncodeOpenChromChipGm12878CmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12878 cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipViewSigBo Base OS Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) Regulation 
wgEncodeOpenChromChipSpleenocCtcfBaseOverlapSignalRep1 Spleen CTCF OS CTCF Spleen_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003464 3464 GSM1006883 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipSpleenocCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen spleen tissue from NICHD donor IDs 1863 (Rep B1) and 4548 (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Spleen OC CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibPol2BaseOverlapSignal ProgFib Pol2 OS Pol2 ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-10 2010-10-10 wgEncodeEH000606 606 GSM822282 Crawford UT-A privacy-noSequence baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipProgfibPol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. ProgFib Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibCtcfBaseOverlapSignal ProgFib CTCF OS CTCF ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-02 2010-10-02 wgEncodeEH000600 600 GSM822272 Crawford UT-A privacy-noSequence baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipProgfibCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. ProgFib CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipPancreasocCtcfBaseOverlapSignalRep1 Pancreas CTCF OS CTCF Pancreas_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003463 3463 GSM1006881 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipPancreasocCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Pancreas OC CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipNhekCtcfBaseOverlapSignal NHEK CTCF OS CTCF NHEK ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000559 559 GSM822271 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipNhekCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. NHEK CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMedulloCtcfBaseOverlapSignal Medullo CTCF OS CTCF Medullo ChipSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003440 3440 GSM1006893 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMedulloCtcfBaseOverlapSignal Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Medullo CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLungocCtcfBaseOverlapSignalRep1 Lung CTCF OS CTCF Lung_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003462 3462 GSM1006882 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipLungocCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen lung tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase) and CF Center donor IDs DD006I (Rep B1 FAIRE) and DD007I (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Lung OC CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfAndroBaseOverlapSignalRep1 LNCaP CTCF OS CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003460 3460 GSM1006887 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipLncapCtcfAndroBaseOverlapSignalRep1 androgen Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. LNCaP androgen CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfBaseOverlapSignalRep1 LNCaP CTCF OS CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003459 3459 GSM1006874 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipLncapCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. LNCaP CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipKidneyocCtcfBaseOverlapSignalRep1 Kidney CTCF OS CTCF Kidney_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003461 3461 GSM1006886 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipKidneyocCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Kidney OC CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm20000CtcfBaseOverlapSignalRep1 GM20000 CTCF OS CTCF GM20000 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003458 3458 GSM1006873 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm20000CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM20000 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19240CtcfBaseOverlapSignal GM19240 CTCF OS CTCF GM19240 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-06 2010-07-06 wgEncodeEH000572 572 GSM822276 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm19240CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19240 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19239CtcfBaseOverlapSignal GM19239 CTCF OS CTCF GM19239 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000571 571 GSM822277 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm19239CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19239 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19238CtcfBaseOverlapSignal GM19238 CTCF OS CTCF GM19238 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000570 570 GSM822278 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm19238CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19238 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13977CtcfBaseOverlapSignalRep1 GM13977 CTCF OS CTCF GM13977 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003456 3456 GSM1006869 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm13977CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM13977 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13976CtcfBaseOverlapSignalRep1 GM13976 CTCF OS CTCF GM13976 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003448 3448 GSM1006885 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm13976CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM13976 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12892CtcfBaseOverlapSignal GM12892 CTCF OS CTCF GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-02 2010-07-02 wgEncodeEH000562 562 GSM822299 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12892CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12892 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12891CtcfBaseOverlapSignal GM12891 CTCF OS CTCF GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000569 569 GSM822294 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12891CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12891 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10266CtcfBaseOverlapSignalRep1 GM10266 CTCF OS CTCF GM10266 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003457 3457 GSM1006870 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm10266CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM10266 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10248CtcfBaseOverlapSignalRep1 GM10248 CTCF OS CTCF GM10248 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003446 3446 GSM1006891 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm10248CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM10248 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaPol2BaseOverlapSignal Gliobla Pol2 OS Pol2 Gliobla ChipSeq ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001136 1136 GSM822302 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipGlioblaPol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Gliobla Pol2 TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaCtcfBaseOverlapSignal Gliobla CTCF OS CTCF Gliobla ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001135 1135 GSM822303 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipGlioblaCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Gliobla CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal Fibrobl CTCF OS CTCF Fibrobl ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001127 1127 GSM822281 Crawford UT-A privacy-noSequence baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. child fibroblast Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Fibrobl CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstimBaseOverlapSignal MCF-7 Pol2 stm OS Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003435 3435 GSM1006876 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7Pol2SerumstimBaseOverlapSignal serum_stimulated_media Base_Overlap_Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum stim Pol2 TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstvdBaseOverlapSignal MCF-7 Pol2 stv OS Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003438 3438 GSM1006865 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7Pol2SerumstvdBaseOverlapSignal serum_starved_media Base_Overlap_Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum starved Pol2 TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2BaseOverlapSignal MCF-7 Pol2 OS Pol2 MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001130 1130 GSM822295 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfVehBaseOverlapSignal MCF-7 veh CTCF OS CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001132 1132 GSM822308 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7CtcfVehBaseOverlapSignal vehicle Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 vehicle CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstimBaseOverlapSignal MCF-7 CTCF stm OS CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003434 3434 GSM1006875 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7CtcfSerumstimBaseOverlapSignal serum_stimulated_media Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum stim CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstvdBaseOverlapSignal MCF-7 CTCF stv OS CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003437 3437 GSM1006878 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7CtcfSerumstvdBaseOverlapSignal serum_starved_media Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum starved CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfEstroBaseOverlapSignal MCF-7 est CTCF OS CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001131 1131 GSM822309 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7CtcfEstroBaseOverlapSignal estrogen Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 estrogen CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfBaseOverlapSignal MCF-7 CTCF OS CTCF MCF-7 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-28 2010-09-28 wgEncodeEH000598 598 GSM822305 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipMcf7CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycVehBaseOverlapSignal MCF-7 veh cMyc OS c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001133 1133 GSM822301 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7CmycVehBaseOverlapSignal vehicle Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 vehicle cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstimBaseOverlapSignal MCF-7 cMyc stm OS c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003436 3436 GSM1006877 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7CmycSerumstimBaseOverlapSignal serum_stimulated_media Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum stim cMyc TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstvdBaseOverlapSignal MCF-7 cMyc stv OS c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH003439 3439 GSM1006866 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7CmycSerumstvdBaseOverlapSignal serum_starved_media Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum starved cMyc TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycEstroBaseOverlapSignal MCF-7 est cMyc OS c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001134 1134 GSM822304 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7CmycEstroBaseOverlapSignal estrogen Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 estrogen cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecPol2BaseOverlapSignal HUVEC Pol2 OS Pol2 HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-28 2010-06-28 wgEncodeEH000552 552 GSM822306 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHuvecPol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HUVEC Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCtcfBaseOverlapSignal HUVEC CTCF OS CTCF HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-25 2010-06-25 wgEncodeEH000551 551 GSM822279 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHuvecCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HUVEC CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCmycBaseOverlapSignal HUVEC cMyc OS c-Myc HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-01 2010-07-01 wgEncodeEH000561 561 GSM822298 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHuvecCmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HUVEC cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2Pol2BaseOverlapSignal HepG2 Pol2 OS Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-29 2010-06-29 wgEncodeEH000554 554 GSM822284 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHepg2Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HepG2 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CtcfBaseOverlapSignal HepG2 CTCF OS CTCF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000543 543 GSM822287 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHepg2CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HepG2 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CmycBaseOverlapSignal HepG2 cMyc OS c-Myc HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-22 2009-12-22 wgEncodeEH000545 545 GSM822291 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHepg2CmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HepG2 cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3Pol2BaseOverlapSignal HeLa-S3 Pol2 OS Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-28 wgEncodeEH000597 597 GSM822273 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHelas3Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CtcfBaseOverlapSignal HeLa-S3 CTCF OS CTCF HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000541 541 GSM822285 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHelas3CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CmycBaseOverlapSignal HeLa-S3 cMyc OS c-Myc HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000542 542 GSM822286 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHelas3CmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549Pol2BaseOverlapSignal A549 Pol2 OS Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002079 2079 GSM822288 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipA549Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. A549 Pol2 TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549CtcfBaseOverlapSignal A549 CTCF OS CTCF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002078 2078 GSM822289 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipA549CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. A549 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562Pol2BaseOverlapSignal K562 Pol2 OS Pol2 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-29 2010-06-29 wgEncodeEH000555 555 GSM822275 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipK562Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CtcfBaseOverlapSignal K562 CTCF OS CTCF K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-02-27 2009-11-27 wgEncodeEH000535 535 GSM822311 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipK562CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CmycBaseOverlapSignal K562 cMyc OS c-Myc K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-02-27 2009-11-27 wgEncodeEH000536 536 GSM822310 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipK562CmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescPol2BaseOverlapSignal H1-hESC Pol2 OS Pol2 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-10-02 2010-07-02 wgEncodeEH000563 563 GSM822300 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipH1hescPol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H1-hESC Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCtcfBaseOverlapSignal H1-hESC CTCF OS CTCF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-01 2010-07-01 wgEncodeEH000560 560 GSM822297 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipH1hescCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H1-hESC CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCmycBaseOverlapSignal H1-hESC cMyc OS c-Myc H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-27 wgEncodeEH000596 596 GSM822274 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipH1hescCmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H1-hESC cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878Pol2BaseOverlapSignal GM12878 Pol2 OS Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-12-23 2010-09-22 wgEncodeEH000592 592 GSM822270 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12878Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12878 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CtcfBaseOverlapSignal GM12878 CTCF OS CTCF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000532 532 GSM822312 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12878CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12878 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CmycBaseOverlapSignal GM12878 cMyc OS c-Myc GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-02 2009-09-08 2010-06-08 wgEncodeEH000547 547 GSM822290 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12878CmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12878 cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeUwAffyExonArray UW Affy Exon GSE19090 Affymetrix Exon Array from ENCODE/University of Washington Expression Description This track displays human tissue microarray data using Affymetrix Human Exon 1.0 GeneChip and was produced as part of the ENCODE Project. This track in the hg19 assembly is a continuation of the work displayed in the hg18 assembly with additional cell lines. Display Conventions and Configuration The display for this track shows probe location and signal value as grayscale-colored items where higher signal values correspond to darker-colored blocks. Items with score of 1000 are in the highest 10% quantile for signal value of that particular cell type. Similarly, items scoring 900 are the next 10% quantile and at the bottom of scale, items scoring 100 are in the lowest 10% quantile for signal value. The subtracks within this composite annotation track correspond to data from different cell types and tissues. The configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For information regarding specific microarray probes, look under the &quot;Expression&quot; track group and turn on the Affy Exon Array track. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. A subset of the cells were stored frozen in RNAlater. For the WI-38 Tamoxifen-treated (4OHTAM_20nM_72hr) cell type, cells at 50-80% confluency were treated for 72 hours with 20 nM 4-hydroxytamoxifen in growth medium (from a 1000X working stock in absolute ethanol). At harvest, greater than 95% of DNA synthesis was inhibited and the cells had an induced fusiform/round morphology with greater than 95% showing dramatic senescence-associated heterochromatic foci. Total RNA was labeled and hybridized to Affymetrix Human Exon 1.0 ST V2 arrays using hg19 probesets. Exon and gene level expression analysis were carried out using Affymetrix ExACT 1.2.1 and Affymetrix Expression Console 1.1 software tools. Samples were quantile normalized for background correction and Probe Logarithmic Intensity Error summarized. More detailed methods are here. Release Notes This is release 4 (Jul 2012) of this track. A patch update has removed previously released K562 zinc-finger experiments due to a data merging issue. This update adds in H7-hESC cells that have been differentiated with different time courses. Verification Data were verified by sequencing biological replicates displaying correlation coefficient of 0.9 or greater. Credits These data were generated by the University of Washington ENCODE group. Contact: Richard Sandstrom References Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwAffyExonArrayWi38OhtamSimpleSignalRep2 WI-38 tam 2 WI-38 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000830 830 GSM651583 Stam UW 2 wgEncodeUwAffyExonArrayWi38OhtamSimpleSignalRep2 4OHTAM_20nM_72hr SimpleSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Simple Signal WI-38 (tamoxifen) Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayWi38SimpleSignalRep2 WI-38 2 WI-38 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000829 829 GSM651581 Stam UW 2 wgEncodeUwAffyExonArrayWi38SimpleSignalRep2 SimpleSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal WI-38 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayWi38OhtamSimpleSignalRep1 WI-38 tam 1 WI-38 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000830 830 GSM651582 Stam UW 1 wgEncodeUwAffyExonArrayWi38OhtamSimpleSignalRep1 4OHTAM_20nM_72hr SimpleSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Simple Signal WI-38 (tamoxifen) Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayWi38SimpleSignalRep1 WI-38 1 WI-38 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000829 829 GSM651580 Stam UW 1 wgEncodeUwAffyExonArrayWi38SimpleSignalRep1 SimpleSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal WI-38 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayWerirb1SimpleSignalRep1 WERI-Rb-1 1 WERI-Rb-1 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002163 2163 GSM824870 Stam UW RS17575 1 wgEncodeUwAffyExonArrayWerirb1SimpleSignalRep1 SimpleSignal retinoblastoma (PMID: 844036) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal WERI-Rb-1 Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayTh1SimpleSignalRep1 Th1 1 Th1 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000364 364 GSM472914 Stam UW hg18 1 wgEncodeUwAffyExonArrayTh1SimpleSignalRep1 SimpleSignal primary Th1 T cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Th1 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySknshraSimpleSignalRep2 SK-N-SH_RA 2 SK-N-SH_RA AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000358 358 GSM472912 Stam UW hg18 2 wgEncodeUwAffyExonArraySknshraSimpleSignalRep2 SimpleSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SK-N-SH_RA Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySknshraSimpleSignalRep1 SK-N-SH_RA 1 SK-N-SH_RA AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000358 358 GSM472913 Stam UW hg18 1 wgEncodeUwAffyExonArraySknshraSimpleSignalRep1 SimpleSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SK-N-SH_RA Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySknmcSimpleSignalRep2 SK-N-MC 2 SK-N-MC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002162 2162 GSM824869 Stam UW RS17574 2 wgEncodeUwAffyExonArraySknmcSimpleSignalRep2 SimpleSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SK-N-MC Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySknmcSimpleSignalRep1 SK-N-MC 1 SK-N-MC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002162 2162 GSM824868 Stam UW RS17573 1 wgEncodeUwAffyExonArraySknmcSimpleSignalRep1 SimpleSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SK-N-MC Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySkmcSimpleSignalRep2 SKMC 2 SKMC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000363 363 GSM472911 Stam UW hg18 2 wgEncodeUwAffyExonArraySkmcSimpleSignalRep2 SimpleSignal skeletal muscle cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SKMC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySkmcSimpleSignalRep1 SKMC 1 SKMC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000363 363 GSM510509 Stam UW hg18 1 wgEncodeUwAffyExonArraySkmcSimpleSignalRep1 SimpleSignal skeletal muscle cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SKMC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySaecSimpleSignalRep2 SAEC 2 SAEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000374 374 GSM472922 Stam UW hg18 2 wgEncodeUwAffyExonArraySaecSimpleSignalRep2 SimpleSignal small airway epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SAEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySaecSimpleSignalRep1 SAEC 1 SAEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000374 374 GSM472923 Stam UW hg18 1 wgEncodeUwAffyExonArraySaecSimpleSignalRep1 SimpleSignal small airway epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SAEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayRptecSimpleSignalRep2 RPTEC 2 RPTEC AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000828 828 GSM651566 Stam UW 2 wgEncodeUwAffyExonArrayRptecSimpleSignalRep2 SimpleSignal renal proximal tubule epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal RPTEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayRptecSimpleSignalRep1 RPTEC 1 RPTEC AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000828 828 GSM651565 Stam UW 1 wgEncodeUwAffyExonArrayRptecSimpleSignalRep1 SimpleSignal renal proximal tubule epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal RPTEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayPrecSimpleSignalRep2 PrEC 2 PrEC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002161 2161 GSM824858 Stam UW RS19008 2 wgEncodeUwAffyExonArrayPrecSimpleSignalRep2 SimpleSignal prostate epithelial cell line Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal PrEC Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayPrecSimpleSignalRep1 PrEC 1 PrEC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002161 2161 GSM824857 Stam UW RS19007 1 wgEncodeUwAffyExonArrayPrecSimpleSignalRep1 SimpleSignal prostate epithelial cell line Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal PrEC Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayPanc1SimpleSignalRep2 PANC-1 2 PANC-1 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000373 373 GSM472938 Stam UW hg18 2 wgEncodeUwAffyExonArrayPanc1SimpleSignalRep2 SimpleSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal PANC-1 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayPanc1SimpleSignalRep1 PANC-1 1 PANC-1 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000373 373 GSM472939 Stam UW hg18 1 wgEncodeUwAffyExonArrayPanc1SimpleSignalRep1 SimpleSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal PANC-1 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNt2d1SimpleSignalRep2 NT2-D1 2 NT2-D1 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002160 2160 GSM824856 Stam UW RS19006 2 wgEncodeUwAffyExonArrayNt2d1SimpleSignalRep2 SimpleSignal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NT2-D1 Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNt2d1SimpleSignalRep1 NT2-D1 1 NT2-D1 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002160 2160 GSM824855 Stam UW RS19005 1 wgEncodeUwAffyExonArrayNt2d1SimpleSignalRep1 SimpleSignal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NT2-D1 Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhlfSimpleSignalRep2 NHLF 2 NHLF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000391 391 GSM510579 Stam UW hg18 2 wgEncodeUwAffyExonArrayNhlfSimpleSignalRep2 SimpleSignal lung fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHLF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhlfSimpleSignalRep1 NHLF 1 NHLF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000391 391 GSM510577 Stam UW hg18 1 wgEncodeUwAffyExonArrayNhlfSimpleSignalRep1 SimpleSignal lung fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHLF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhekSimpleSignalRep1 NHEK 1 NHEK AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000372 372 GSM472937 Stam UW hg18 1 wgEncodeUwAffyExonArrayNhekSimpleSignalRep1 SimpleSignal epidermal keratinocytes Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHEK Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhdfneoSimpleSignalRep2 NHDF-neo 2 NHDF-neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000390 390 GSM510557 Stam UW hg18 2 wgEncodeUwAffyExonArrayNhdfneoSimpleSignalRep2 SimpleSignal neonatal dermal fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHDF-neo Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhdfneoSimpleSignalRep1 NHDF-neo 1 NHDF-neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000390 390 GSM510554 Stam UW hg18 1 wgEncodeUwAffyExonArrayNhdfneoSimpleSignalRep1 SimpleSignal neonatal dermal fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHDF-neo Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhdfadSimpleSignalRep2 NHDF-Ad 2 NHDF-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000822 822 GSM580018 Stam UW 2 wgEncodeUwAffyExonArrayNhdfadSimpleSignalRep2 SimpleSignal adult dermal fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHDF-Ad Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhdfadSimpleSignalRep1 NHDF-Ad 1 NHDF-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000822 822 GSM580017 Stam UW 1 wgEncodeUwAffyExonArrayNhdfadSimpleSignalRep1 SimpleSignal adult dermal fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHDF-Ad Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhbeSimpleSignalRep2 NHBE 2 NHBE AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002159 2159 GSM824854 Stam UW RS19004 2 wgEncodeUwAffyExonArrayNhbeSimpleSignalRep2 SimpleSignal bronchial epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHBE Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhbeSimpleSignalRep1 NHBE 1 NHBE AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002159 2159 GSM824853 Stam UW RS19003 1 wgEncodeUwAffyExonArrayNhbeSimpleSignalRep1 SimpleSignal bronchial epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHBE Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhaSimpleSignalRep2 NH-A 2 NH-A AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000821 821 GSM580044 Stam UW 2 wgEncodeUwAffyExonArrayNhaSimpleSignalRep2 SimpleSignal astrocytes (also called Astrocy) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NH-A Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhaSimpleSignalRep1 NH-A 1 NH-A AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000821 821 GSM580043 Stam UW 1 wgEncodeUwAffyExonArrayNhaSimpleSignalRep1 SimpleSignal astrocytes (also called Astrocy) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NH-A Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNb4SimpleSignalRep2 NB4 2 NB4 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000371 371 GSM510513 Stam UW hg18 2 wgEncodeUwAffyExonArrayNb4SimpleSignalRep2 SimpleSignal acute promyelocytic leukemia cell line. (PMID: 1995093) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NB4 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNb4SimpleSignalRep1 NB4 1 NB4 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000371 371 GSM510512 Stam UW hg18 1 wgEncodeUwAffyExonArrayNb4SimpleSignalRep1 SimpleSignal acute promyelocytic leukemia cell line. (PMID: 1995093) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NB4 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayLncapSimpleSignalRep2 LNCaP 2 LNCaP AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000827 827 GSM651579 Stam UW 2 wgEncodeUwAffyExonArrayLncapSimpleSignalRep2 SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal LNCaP Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayLncapSimpleSignalRep1 LNCaP 1 LNCaP AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000827 827 GSM651578 Stam UW 1 wgEncodeUwAffyExonArrayLncapSimpleSignalRep1 SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal LNCaP Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayJurkatSimpleSignalRep2 Jurkat 2 Jurkat AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000369 369 GSM510511 Stam UW hg18 2 wgEncodeUwAffyExonArrayJurkatSimpleSignalRep2 SimpleSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Jurkat Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayJurkatSimpleSignalRep1 Jurkat 1 Jurkat AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000369 369 GSM472928 Stam UW hg18 1 wgEncodeUwAffyExonArrayJurkatSimpleSignalRep1 SimpleSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Jurkat Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHvmfSimpleSignalRep2 HVMF 2 HVMF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000820 820 GSM580038 Stam UW 2 wgEncodeUwAffyExonArrayHvmfSimpleSignalRep2 SimpleSignal villous mesenchymal fibroblast cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HVMF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHvmfSimpleSignalRep1 HVMF 1 HVMF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000820 820 GSM580037 Stam UW 1 wgEncodeUwAffyExonArrayHvmfSimpleSignalRep1 SimpleSignal villous mesenchymal fibroblast cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HVMF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHsmmtSimpleSignalRep2 HSMMtube 2 HSMMtube AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH000826 826 GSM824861 Stam UW RS17572 2 wgEncodeUwAffyExonArrayHsmmtSimpleSignalRep2 SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HSMMtube Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHsmmtSimpleSignalRep1 HSMMtube 1 HSMMtube AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000826 826 GSM651576 Stam UW 1 wgEncodeUwAffyExonArrayHsmmtSimpleSignalRep1 SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HSMMtube Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHsmmSimpleSignalRep2 HSMM 2 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000833 833 GSM651575 Stam UW 2 wgEncodeUwAffyExonArrayHsmmSimpleSignalRep2 SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HSMM Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHsmmSimpleSignalRep1 HSMM 1 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000833 833 GSM651574 Stam UW 1 wgEncodeUwAffyExonArrayHsmmSimpleSignalRep1 SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HSMM Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrpeSimpleSignalRep2 HRPEpiC 2 HRPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000389 389 GSM510515 Stam UW hg18 2 wgEncodeUwAffyExonArrayHrpeSimpleSignalRep2 SimpleSignal retinal pigment epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRPEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrpeSimpleSignalRep1 HRPEpiC 1 HRPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000389 389 GSM510514 Stam UW hg18 1 wgEncodeUwAffyExonArrayHrpeSimpleSignalRep1 SimpleSignal retinal pigment epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRPEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrgecSimpleSignalRep2 HRGEC 2 HRGEC AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000832 832 GSM651573 Stam UW 2 wgEncodeUwAffyExonArrayHrgecSimpleSignalRep2 SimpleSignal renal glomerular endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRGEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrgecSimpleSignalRep1 HRGEC 1 HRGEC AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000832 832 GSM651572 Stam UW 1 wgEncodeUwAffyExonArrayHrgecSimpleSignalRep1 SimpleSignal renal glomerular endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRGEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHreSimpleSignalRep2 HRE 2 HRE AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000356 356 GSM472918 Stam UW hg18 2 wgEncodeUwAffyExonArrayHreSimpleSignalRep2 SimpleSignal renal epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRE Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHreSimpleSignalRep1 HRE 1 HRE AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000356 356 GSM472919 Stam UW hg18 1 wgEncodeUwAffyExonArrayHreSimpleSignalRep1 SimpleSignal renal epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRE Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrceSimpleSignalRep2 HRCEpiC 2 HRCEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000355 355 GSM472921 Stam UW hg18 2 wgEncodeUwAffyExonArrayHrceSimpleSignalRep2 SimpleSignal renal cortical epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRCEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrceSimpleSignalRep1 HRCEpiC 1 HRCEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000355 355 GSM472920 Stam UW hg18 1 wgEncodeUwAffyExonArrayHrceSimpleSignalRep1 SimpleSignal renal cortical epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRCEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpfSimpleSignalRep2 HPF 2 HPF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000818 818 GSM580036 Stam UW 2 wgEncodeUwAffyExonArrayHpfSimpleSignalRep2 SimpleSignal pulmonary fibroblasts isolated from lung tissue Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpfSimpleSignalRep1 HPF 1 HPF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000818 818 GSM580035 Stam UW 1 wgEncodeUwAffyExonArrayHpfSimpleSignalRep1 SimpleSignal pulmonary fibroblasts isolated from lung tissue Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpdlfSimpleSignalRep2 HPdLF 2 HPdLF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000819 819 GSM580026 Stam UW 2 wgEncodeUwAffyExonArrayHpdlfSimpleSignalRep2 SimpleSignal periodontal ligament fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPdLF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpdlfSimpleSignalRep1 HPdLF 1 HPdLF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000819 819 GSM580025 Stam UW 1 wgEncodeUwAffyExonArrayHpdlfSimpleSignalRep1 SimpleSignal periodontal ligament fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPdLF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpafSimpleSignalRep2 HPAF 2 HPAF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000817 817 GSM580034 Stam UW 2 wgEncodeUwAffyExonArrayHpafSimpleSignalRep2 SimpleSignal pulmonary artery fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPAF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpafSimpleSignalRep1 HPAF 1 HPAF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000817 817 GSM580033 Stam UW 1 wgEncodeUwAffyExonArrayHpafSimpleSignalRep1 SimpleSignal pulmonary artery fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPAF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpaecSimpleSignalRep1 HPAEC 1 HPAEC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002158 2158 GSM824860 Stam UW RS19002 1 wgEncodeUwAffyExonArrayHpaecSimpleSignalRep1 SimpleSignal pulmonary artery endothelial cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPAEC Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHnpceSimpleSignalRep2 HNPCEpiC 2 HNPCEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000388 388 GSM510564 Stam UW hg18 2 wgEncodeUwAffyExonArrayHnpceSimpleSignalRep2 SimpleSignal non-pigment ciliary epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HNPCEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHnpceSimpleSignalRep1 HNPCEpiC 1 HNPCEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000388 388 GSM510560 Stam UW hg18 1 wgEncodeUwAffyExonArrayHnpceSimpleSignalRep1 SimpleSignal non-pigment ciliary epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HNPCEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecllySimpleSignalRep2 HMVEC-LLy 2 HMVEC-LLy AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000811 811 GSM580010 Stam UW 2 wgEncodeUwAffyExonArrayHmvecllySimpleSignalRep2 SimpleSignal lymphatic microvascular endothelial cells, lung-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-LLy Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecllySimpleSignalRep1 HMVEC-LLy 1 HMVEC-LLy AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000811 811 GSM580009 Stam UW 1 wgEncodeUwAffyExonArrayHmvecllySimpleSignalRep1 SimpleSignal lymphatic microvascular endothelial cells, lung-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-LLy Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmveclblSimpleSignalRep2 HMVEC-LBl 2 HMVEC-LBl AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000810 810 GSM580020 Stam UW 2 wgEncodeUwAffyExonArrayHmveclblSimpleSignalRep2 SimpleSignal blood microvascular endothelial cells, lung-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-LBl Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmveclblSimpleSignalRep1 HMVEC-LBl 1 HMVEC-LBl AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000810 810 GSM580019 Stam UW 1 wgEncodeUwAffyExonArrayHmveclblSimpleSignalRep1 SimpleSignal blood microvascular endothelial cells, lung-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-LBl Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdneoSimpleSignalRep2 HMVEC-dNeo 2 HMVEC-dNeo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000816 816 GSM580016 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdneoSimpleSignalRep2 SimpleSignal neonatal microvascular endothelial cells (single donor), dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dNeo Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdneoSimpleSignalRep1 HMVEC-dNeo 1 HMVEC-dNeo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000816 816 GSM580015 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdneoSimpleSignalRep1 SimpleSignal neonatal microvascular endothelial cells (single donor), dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dNeo Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdlyneoSimpleSignalRep2 HMVEC-dLy-Neo 2 HMVEC-dLy-Neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000815 815 GSM580012 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdlyneoSimpleSignalRep2 SimpleSignal neonatal lymphatic microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dLy-Neo Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdlyneoSimpleSignalRep1 HMVEC-dLy-Neo 1 HMVEC-dLy-Neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000815 815 GSM580011 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdlyneoSimpleSignalRep1 SimpleSignal neonatal lymphatic microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dLy-Neo Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdlyadSimpleSignalRep2 HMVEC-dLy-Ad 2 HMVEC-dLy-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000814 814 GSM580013 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdlyadSimpleSignalRep2 SimpleSignal adult lymphatic microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dLy-Ad Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdlyadSimpleSignalRep1 HMVEC-dLy-Ad 1 HMVEC-dLy-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000814 814 GSM580014 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdlyadSimpleSignalRep1 SimpleSignal adult lymphatic microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dLy-Ad Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdblneoSimpleSignalRep2 HMVEC-dBl-Neo 2 HMVEC-dBl-Neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000813 813 GSM580024 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdblneoSimpleSignalRep2 SimpleSignal neonatal blood microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dBl-Neo Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdblneoSimpleSignalRep1 HMVEC-dBl-Neo 1 HMVEC-dBl-Neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000813 813 GSM580023 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdblneoSimpleSignalRep1 SimpleSignal neonatal blood microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dBl-Neo Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdbladSimpleSignalRep2 HMVEC-dBl-Ad 2 HMVEC-dBl-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000812 812 GSM580022 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdbladSimpleSignalRep2 SimpleSignal adult blood microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dBl-Ad Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdbladSimpleSignalRep1 HMVEC-dBl-Ad 1 HMVEC-dBl-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000812 812 GSM580021 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdbladSimpleSignalRep1 SimpleSignal adult blood microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dBl-Ad Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdadSimpleSignalRep2 HMVEC-dAd 2 HMVEC-dAd AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002157 2157 GSM824852 Stam UW RS19001 2 wgEncodeUwAffyExonArrayHmvecdadSimpleSignalRep2 SimpleSignal adult dermal microvascular endothelial cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dAd Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdadSimpleSignalRep1 HMVEC-dAd 1 HMVEC-dAd AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002157 2157 GSM824851 Stam UW RS19000 1 wgEncodeUwAffyExonArrayHmvecdadSimpleSignalRep1 SimpleSignal adult dermal microvascular endothelial cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dAd Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmfSimpleSignalRep2 HMF 2 HMF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000809 809 GSM580042 Stam UW 2 wgEncodeUwAffyExonArrayHmfSimpleSignalRep2 SimpleSignal mammary fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmfSimpleSignalRep1 HMF 1 HMF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000809 809 GSM580041 Stam UW 1 wgEncodeUwAffyExonArrayHmfSimpleSignalRep1 SimpleSignal mammary fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmecSimpleSignalRep2 HMEC 2 HMEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000367 367 GSM580006 Stam UW 2 wgEncodeUwAffyExonArrayHmecSimpleSignalRep2 SimpleSignal mammary epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmecSimpleSignalRep1 HMEC 1 HMEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000367 367 GSM472934 Stam UW hg18 1 wgEncodeUwAffyExonArrayHmecSimpleSignalRep1 SimpleSignal mammary epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHl60SimpleSignalRep2 HL-60 2 HL-60 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000808 808 GSM472942 Stam UW hg18 2 wgEncodeUwAffyExonArrayHl60SimpleSignalRep2 SimpleSignal promyelocytic leukemia cells, (PMID: 276884) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HL-60 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHl60SimpleSignalRep1 HL-60 1 HL-60 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000808 808 GSM472908 Stam UW hg18 1 wgEncodeUwAffyExonArrayHl60SimpleSignalRep1 SimpleSignal promyelocytic leukemia cells, (PMID: 276884) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HL-60 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHipeSimpleSignalRep2 HIPEpiC 2 HIPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000387 387 GSM510519 Stam UW hg18 2 wgEncodeUwAffyExonArrayHipeSimpleSignalRep2 SimpleSignal iris pigment epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HIPEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHipeSimpleSignalRep1 HIPEpiC 1 HIPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000387 387 GSM510518 Stam UW hg18 1 wgEncodeUwAffyExonArrayHipeSimpleSignalRep1 SimpleSignal iris pigment epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HIPEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHgfSimpleSignalRep2 HGF 2 HGF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000807 807 GSM472941 Stam UW hg18 2 wgEncodeUwAffyExonArrayHgfSimpleSignalRep2 SimpleSignal gingival fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HGF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHgfSimpleSignalRep1 HGF 1 HGF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000807 807 GSM472940 Stam UW hg18 1 wgEncodeUwAffyExonArrayHgfSimpleSignalRep1 SimpleSignal gingival fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HGF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHffmycSimpleSignalRep2 HFF-Myc 2 HFF-Myc AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002156 2156 GSM824867 Stam UW RS17570 2 wgEncodeUwAffyExonArrayHffmycSimpleSignalRep2 SimpleSignal foreskin fibroblast cells expressing canine cMyc Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HFF-Myc Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHffmycSimpleSignalRep1 HFF-Myc 1 HFF-Myc AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002156 2156 GSM824866 Stam UW RS17569 1 wgEncodeUwAffyExonArrayHffmycSimpleSignalRep1 SimpleSignal foreskin fibroblast cells expressing canine cMyc Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HFF-Myc Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHffSimpleSignalRep2 HFF 2 HFF AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002155 2155 GSM824865 Stam UW RS17568 2 wgEncodeUwAffyExonArrayHffSimpleSignalRep2 SimpleSignal foreskin fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HFF Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHffSimpleSignalRep1 HFF 1 HFF AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002155 2155 GSM824864 Stam UW RS17567 1 wgEncodeUwAffyExonArrayHffSimpleSignalRep1 SimpleSignal foreskin fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HFF Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHek293SimpleSignalRep2 HEK293 2 HEK293 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000806 806 GSM580028 Stam UW 2 wgEncodeUwAffyExonArrayHek293SimpleSignalRep2 SimpleSignal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HEK293 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHek293SimpleSignalRep1 HEK293 1 HEK293 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000806 806 GSM580027 Stam UW 1 wgEncodeUwAffyExonArrayHek293SimpleSignalRep1 SimpleSignal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HEK293 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHeeSimpleSignalRep2 HEEpiC 2 HEEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000386 386 GSM510574 Stam UW hg18 2 wgEncodeUwAffyExonArrayHeeSimpleSignalRep2 SimpleSignal esophageal epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HEEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHeeSimpleSignalRep1 HEEpiC 1 HEEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000386 386 GSM510571 Stam UW hg18 1 wgEncodeUwAffyExonArrayHeeSimpleSignalRep1 SimpleSignal esophageal epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HEEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHct116SimpleSignalRep2 HCT-116 2 HCT-116 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000804 804 GSM580040 Stam UW 2 wgEncodeUwAffyExonArrayHct116SimpleSignalRep2 SimpleSignal colorectal carcinoma (PMID: 7214343) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCT-116 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHct116SimpleSignalRep1 HCT-116 1 HCT-116 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000804 804 GSM580039 Stam UW 1 wgEncodeUwAffyExonArrayHct116SimpleSignalRep1 SimpleSignal colorectal carcinoma (PMID: 7214343) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCT-116 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcpeSimpleSignalRep2 HCPEpiC 2 HCPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000385 385 GSM510551 Stam UW hg18 2 wgEncodeUwAffyExonArrayHcpeSimpleSignalRep2 SimpleSignal choroid plexus epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCPEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcpeSimpleSignalRep1 HCPEpiC 1 HCPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000385 385 GSM510547 Stam UW hg18 1 wgEncodeUwAffyExonArrayHcpeSimpleSignalRep1 SimpleSignal choroid plexus epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCPEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHconfSimpleSignalRep2 HConF 2 HConF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000805 805 GSM580008 Stam UW 2 wgEncodeUwAffyExonArrayHconfSimpleSignalRep2 SimpleSignal conjunctival fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HConF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHconfSimpleSignalRep1 HConF 1 HConF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000805 805 GSM580007 Stam UW 1 wgEncodeUwAffyExonArrayHconfSimpleSignalRep1 SimpleSignal conjunctival fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HConF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcmSimpleSignalRep2 HCM 2 HCM AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000384 384 GSM510569 Stam UW hg18 2 wgEncodeUwAffyExonArrayHcmSimpleSignalRep2 SimpleSignal cardiac myocytes Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCM Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcmSimpleSignalRep1 HCM 1 HCM AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000384 384 GSM510566 Stam UW hg18 1 wgEncodeUwAffyExonArrayHcmSimpleSignalRep1 SimpleSignal cardiac myocytes Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCM Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcfaaSimpleSignalRep2 HCFaa 2 HCFaa AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000803 803 GSM580032 Stam UW 2 wgEncodeUwAffyExonArrayHcfaaSimpleSignalRep2 SimpleSignal cardiac fibroblasts- adult atrial Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCFaa Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcfaaSimpleSignalRep1 HCFaa 1 HCFaa AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000803 803 GSM580031 Stam UW 1 wgEncodeUwAffyExonArrayHcfaaSimpleSignalRep1 SimpleSignal cardiac fibroblasts- adult atrial Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCFaa Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcfSimpleSignalRep2 HCF 2 HCF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000383 383 GSM510545 Stam UW hg18 2 wgEncodeUwAffyExonArrayHcfSimpleSignalRep2 SimpleSignal cardiac fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcfSimpleSignalRep1 HCF 1 HCF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000383 383 GSM510542 Stam UW hg18 1 wgEncodeUwAffyExonArrayHcfSimpleSignalRep1 SimpleSignal cardiac fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbvsmcSimpleSignalRep2 HBVSMC 2 HBVSMC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002154 2154 GSM824850 Stam UW RS18999 2 wgEncodeUwAffyExonArrayHbvsmcSimpleSignalRep2 SimpleSignal brain vascular smooth muscle cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBVSMC Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbvsmcSimpleSignalRep1 HBVSMC 1 HBVSMC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002154 2154 GSM824849 Stam UW RS18998 1 wgEncodeUwAffyExonArrayHbvsmcSimpleSignalRep1 SimpleSignal brain vascular smooth muscle cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBVSMC Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbvpSimpleSignalRep1 HBVP 1 HBVP AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002153 2153 GSM824859 Stam UW RS18997 1 wgEncodeUwAffyExonArrayHbvpSimpleSignalRep1 SimpleSignal brain vascular pericytes Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBVP Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbmecSimpleSignalRep2 HBMEC 2 HBMEC AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000802 802 GSM651564 Stam UW 2 wgEncodeUwAffyExonArrayHbmecSimpleSignalRep2 SimpleSignal brain microvascular endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBMEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbmecSimpleSignalRep1 HBMEC 1 HBMEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000802 802 GSM580045 Stam UW 1 wgEncodeUwAffyExonArrayHbmecSimpleSignalRep1 SimpleSignal brain microvascular endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBMEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHaspSimpleSignalRep2 HA-sp 2 HA-sp AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000825 825 GSM651563 Stam UW 2 wgEncodeUwAffyExonArrayHaspSimpleSignalRep2 SimpleSignal astrocytes spinal cord Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HA-sp Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHaspSimpleSignalRep1 HA-sp 1 HA-sp AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000825 825 GSM651562 Stam UW 1 wgEncodeUwAffyExonArrayHaspSimpleSignalRep1 SimpleSignal astrocytes spinal cord Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HA-sp Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHahSimpleSignalRep2 HA-h 2 HA-h AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002152 2152 GSM824863 Stam UW RS17566 2 wgEncodeUwAffyExonArrayHahSimpleSignalRep2 SimpleSignal astrocytes-hippocampal Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HA-h Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHahSimpleSignalRep1 HA-h 1 HA-h AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002152 2152 GSM824862 Stam UW RS17565 1 wgEncodeUwAffyExonArrayHahSimpleSignalRep1 SimpleSignal astrocytes-hippocampal Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HA-h Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHaeSimpleSignalRep2 HAEpiC 2 HAEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000382 382 GSM510517 Stam UW hg18 2 wgEncodeUwAffyExonArrayHaeSimpleSignalRep2 SimpleSignal amniotic epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HAEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHaeSimpleSignalRep1 HAEpiC 1 HAEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000382 382 GSM510516 Stam UW hg18 1 wgEncodeUwAffyExonArrayHaeSimpleSignalRep1 SimpleSignal amniotic epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HAEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHacSimpleSignalRep2 HAc 2 HAc AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000831 831 GSM651570 Stam UW 2 wgEncodeUwAffyExonArrayHacSimpleSignalRep2 SimpleSignal astrocytes-cerebellar Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HAc Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHacSimpleSignalRep1 HAc 1 HAc AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000831 831 GSM651569 Stam UW 1 wgEncodeUwAffyExonArrayHacSimpleSignalRep1 SimpleSignal astrocytes-cerebellar Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HAc Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa9dSimpleSignalRep2 H7-hESC 9d 2 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003051 3051 GSM1033349 Stam UW RS16722 2 wgEncodeUwAffyExonArrayH7esDiffa9dSimpleSignalRep2 diffProtA_9d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Simple Signal H7-hESC differentiated 9 d Exon Array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa5dSimpleSignalRep2 H7-hESC 5d 2 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003050 3050 GSM1033347 Stam UW RS16721 2 wgEncodeUwAffyExonArrayH7esDiffa5dSimpleSignalRep2 diffProtA_5d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Simple Signal H7-hESC differentiated 5 d Exon Array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa2dSimpleSignalRep2 H7-hESC 2d 2 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003049 3049 GSM1033352 Stam UW RS16720 2 wgEncodeUwAffyExonArrayH7esDiffa2dSimpleSignalRep2 diffProtA_2d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Simple Signal H7-hESC differentiated 2 d Exon Array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esSimpleSignalRep2 H7-hESC 2 H7-hESC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000381 381 GSM580005 Stam UW 2 wgEncodeUwAffyExonArrayH7esSimpleSignalRep2 SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal H7-hESC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa14dSimpleSignalRep2 H7-hESC 14d 2 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003048 3048 GSM1033350 Stam UW RS16723 2 wgEncodeUwAffyExonArrayH7esDiffa14dSimpleSignalRep2 diffProtA_14d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Simple Signal H7-hESC differentiated 14 d Exon Array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa9dSimpleSignalRep1 H7-hESC 9d 1 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003051 3051 GSM1033348 Stam UW DS15445 1 wgEncodeUwAffyExonArrayH7esDiffa9dSimpleSignalRep1 diffProtA_9d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Simple Signal H7-hESC differentiated 9 d Exon Array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa5dSimpleSignalRep1 H7-hESC 5d 1 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003050 3050 GSM1033346 Stam UW DS15444 1 wgEncodeUwAffyExonArrayH7esDiffa5dSimpleSignalRep1 diffProtA_5d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Simple Signal H7-hESC differentiated 5 d Exon Array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa2dSimpleSignalRep1 H7-hESC 2d 1 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003049 3049 GSM1033353 Stam UW DS15447 1 wgEncodeUwAffyExonArrayH7esDiffa2dSimpleSignalRep1 diffProtA_2d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Simple Signal H7-hESC differentiated 2 d Exon Array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa14dSimpleSignalRep1 H7-hESC 14d 1 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003048 3048 GSM1033351 Stam UW DS15446 1 wgEncodeUwAffyExonArrayH7esDiffa14dSimpleSignalRep1 diffProtA_14d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Simple Signal H7-hESC differentiated 14 d Exon Array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esSimpleSignalRep1 H7-hESC 1 H7-hESC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000381 381 GSM510581 Stam UW hg18 1 wgEncodeUwAffyExonArrayH7esSimpleSignalRep1 SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal H7-hESC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm12865SimpleSignalRep2 GM12865 2 GM12865 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002151 2151 GSM824874 Stam UW DS12442 2 wgEncodeUwAffyExonArrayGm12865SimpleSignalRep2 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM12865 Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm12865SimpleSignalRep1 GM12865 1 GM12865 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002151 2151 GSM824873 Stam UW DS12436 1 wgEncodeUwAffyExonArrayGm12865SimpleSignalRep1 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM12865 Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm12864SimpleSignalRep1 GM12864 1 GM12864 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002150 2150 GSM824872 Stam UW DS12431 1 wgEncodeUwAffyExonArrayGm12864SimpleSignalRep1 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM12864 Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm06990SimpleSignalRep2 GM06990 2 GM06990 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000360 360 GSM472904 Stam UW hg18 2 wgEncodeUwAffyExonArrayGm06990SimpleSignalRep2 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM06990 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm06990SimpleSignalRep1 GM06990 1 GM06990 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000360 360 GSM472903 Stam UW hg18 1 wgEncodeUwAffyExonArrayGm06990SimpleSignalRep1 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM06990 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayCmkSimpleSignalRep1 CMK 1 CMK AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000380 380 GSM510583 Stam UW hg18 1 wgEncodeUwAffyExonArrayCmkSimpleSignalRep1 SimpleSignal acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal CMK Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayCaco2SimpleSignalRep2 Caco-2 2 Caco-2 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000359 359 GSM472933 Stam UW hg18 2 wgEncodeUwAffyExonArrayCaco2SimpleSignalRep2 SimpleSignal colorectal adenocarcinoma. (PMID: 1939345) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Caco-2 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayCaco2SimpleSignalRep1 Caco-2 1 Caco-2 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000359 359 GSM472900 Stam UW hg18 1 wgEncodeUwAffyExonArrayCaco2SimpleSignalRep1 SimpleSignal colorectal adenocarcinoma. (PMID: 1939345) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Caco-2 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayBjSimpleSignalRep2 BJ 2 BJ AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000365 365 GSM472925 Stam UW hg18 2 wgEncodeUwAffyExonArrayBjSimpleSignalRep2 SimpleSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal BJ Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayBjSimpleSignalRep1 BJ 1 BJ AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000365 365 GSM472924 Stam UW hg18 1 wgEncodeUwAffyExonArrayBjSimpleSignalRep1 SimpleSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal BJ Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayBe2cSimpleSignalRep2 BE2_C 2 BE2_C AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000824 824 GSM651568 Stam UW 2 wgEncodeUwAffyExonArrayBe2cSimpleSignalRep2 SimpleSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal BE2_C Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayBe2cSimpleSignalRep1 BE2_C 1 BE2_C AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000824 824 GSM651567 Stam UW 1 wgEncodeUwAffyExonArrayBe2cSimpleSignalRep1 SimpleSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal BE2_C Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAoafSimpleSignalRep2 AoAF 2 AoAF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000801 801 GSM580030 Stam UW 2 wgEncodeUwAffyExonArrayAoafSimpleSignalRep2 SimpleSignal aortic adventitial fibroblast cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AoAF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAoafSimpleSignalRep1 AoAF 1 AoAF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000801 801 GSM580029 Stam UW 1 wgEncodeUwAffyExonArrayAoafSimpleSignalRep1 SimpleSignal aortic adventitial fibroblast cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AoAF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg10803SimpleSignalRep2 AG10803 2 AG10803 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000379 379 GSM510521 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg10803SimpleSignalRep2 SimpleSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG10803 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg10803SimpleSignalRep1 AG10803 1 AG10803 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000379 379 GSM510520 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg10803SimpleSignalRep1 SimpleSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG10803 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg09319SimpleSignalRep2 AG09319 2 AG09319 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000378 378 GSM510538 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg09319SimpleSignalRep2 SimpleSignal gum tissue fibroblasts from apparently heathly 24 year old Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG09319 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg09319SimpleSignalRep1 AG09319 1 AG09319 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000378 378 GSM510536 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg09319SimpleSignalRep1 SimpleSignal gum tissue fibroblasts from apparently heathly 24 year old Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG09319 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg09309SimpleSignalRep2 AG09309 2 AG09309 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000377 377 GSM510525 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg09309SimpleSignalRep2 SimpleSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG09309 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg09309SimpleSignalRep1 AG09309 1 AG09309 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000377 377 GSM510522 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg09309SimpleSignalRep1 SimpleSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG09309 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg04450SimpleSignalRep2 AG04450 2 AG04450 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000376 376 GSM510534 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg04450SimpleSignalRep2 SimpleSignal fetal lung fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG04450 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg04450SimpleSignalRep1 AG04450 1 AG04450 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000376 376 GSM510532 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg04450SimpleSignalRep1 SimpleSignal fetal lung fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG04450 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg04449SimpleSignalRep2 AG04449 2 AG04449 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000375 375 GSM510530 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg04449SimpleSignalRep2 SimpleSignal fetal buttock/thigh fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG04449 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg04449SimpleSignalRep1 AG04449 1 AG04449 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000375 375 GSM510528 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg04449SimpleSignalRep1 SimpleSignal fetal buttock/thigh fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG04449 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayMcf7SimpleSignalRep2 MCF-7 2 MCF-7 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000370 370 GSM510510 Stam UW hg18 2 wgEncodeUwAffyExonArrayMcf7SimpleSignalRep2 SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal MCF-7 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayMcf7SimpleSignalRep1 MCF-7 1 MCF-7 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000370 370 GSM472936 Stam UW hg18 1 wgEncodeUwAffyExonArrayMcf7SimpleSignalRep1 SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal MCF-7 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHuvecSimpleSignalRep2 HUVEC 2 HUVEC AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000368 368 GSM651577 Stam UW 2 wgEncodeUwAffyExonArrayHuvecSimpleSignalRep2 SimpleSignal umbilical vein endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HUVEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHuvecSimpleSignalRep1 HUVEC 1 HUVEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000368 368 GSM472935 Stam UW hg18 1 wgEncodeUwAffyExonArrayHuvecSimpleSignalRep1 SimpleSignal umbilical vein endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HUVEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHepg2SimpleSignalRep2 HepG2 2 HepG2 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000361 361 GSM472907 Stam UW hg18 2 wgEncodeUwAffyExonArrayHepg2SimpleSignalRep2 SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HepG2 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHepg2SimpleSignalRep1 HepG2 1 HepG2 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000361 361 GSM472906 Stam UW hg18 1 wgEncodeUwAffyExonArrayHepg2SimpleSignalRep1 SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HepG2 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHelas3SimpleSignalRep2 HeLa-S3 2 HeLa-S3 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000357 357 GSM472932 Stam UW hg18 2 wgEncodeUwAffyExonArrayHelas3SimpleSignalRep2 SimpleSignal cervical carcinoma Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HeLa-S3 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHelas3SimpleSignalRep1 HeLa-S3 1 HeLa-S3 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000357 357 GSM472916 Stam UW hg18 1 wgEncodeUwAffyExonArrayHelas3SimpleSignalRep1 SimpleSignal cervical carcinoma Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HeLa-S3 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayA549SimpleSignalRep2 A549 2 A549 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000823 823 GSM651561 Stam UW 2 wgEncodeUwAffyExonArrayA549SimpleSignalRep2 SimpleSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal A549 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayA549SimpleSignalRep1 A549 1 A549 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000823 823 GSM651560 Stam UW 1 wgEncodeUwAffyExonArrayA549SimpleSignalRep1 SimpleSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal A549 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayK562SimpleSignalRep2 K562 2 K562 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000362 362 GSM472927 Stam UW hg18 2 wgEncodeUwAffyExonArrayK562SimpleSignalRep2 SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal K562 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayK562SimpleSignalRep1 K562 1 K562 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000362 362 GSM472926 Stam UW hg18 1 wgEncodeUwAffyExonArrayK562SimpleSignalRep1 SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal K562 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm12878SimpleSignalRep1 GM12878 1 GM12878 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000366 366 GSM472931 Stam UW hg18 1 wgEncodeUwAffyExonArrayGm12878SimpleSignalRep1 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM12878 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwTfbs UW CTCF Binding GSE30263 None CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington Regulation Description This track was produced as part of the ENCODE Project. This track displays maps of genome-wide binding of the CTCF transcription factor in different cell lines using ChIP-seq high-throughput sequencing. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: HotSpots ChIP-seq affinity zones identified using the HotSpot algorithm. Peaks ChIP-seq affinity sites identified as signal peaks within affinity zones (FDR 1.0%). Raw Signal The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Cells were crosslinked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 &deg;C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross linking in immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. A quantity of 20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and a Solexa library was made for sequencing. ChIP-seq affinity was directly measured through raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). ChIP-seq affinity zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004); 1.0% false discovery rate thresholds (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. ChIP-seq affinities (Peaks) were identified as signal peaks within affinity zones (FDR 1.0%) using a peak-finding algorithm. All tracks have a False Discovery Rate of 1% (FDR 1.0%). Verification Data were verified by sequencing biological replicates displaying correlation coefficients &gt; 0.9. Release Notes Release 3 (February 2012) contains 3 new experiments. Credits These data were generated by the UW ENCODE group. Contact: Richard Sandstrom References Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwTfbsViewRawSig Raw Signal CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwTfbsWi38InputOhtamStdRawRep1 WI-38 In TAM Sg 1 Input WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002048 2048 GSM1022655 Stam UW DS18351 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsWi38InputOhtamStdRawRep1 4OHTAM_20nM_72hr RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 Input OH-tamoxifen 20 nM TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38InputStdRawRep1 WI-38 In Sg 1 Input WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001903 1903 GSM1022647 Stam UW DS18346 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsWi38InputStdRawRep1 None RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38CtcfStdRawRep2 WI-38 CTCF Sg 2 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022634 Stam UW DS18348 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsWi38CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38CtcfStdRawRep1 WI-38 CTCF Sg 1 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022637 Stam UW DS18347 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsWi38CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1InputStdRawRep1 WERI In Sg 1 Input WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000475 475 GSM749766 Stam UW DS11888 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsWerirb1InputStdRawRep1 None RawSignal retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdRawRep2 WERI CTCF Sg 2 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749679 Stam UW DS10408 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsWerirb1CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdRawRep1 WERI CTCF Sg 1 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749768 Stam UW DS10701 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsWerirb1CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraInputStdRawRep1 SKRA In Sg 1 Input SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000474 474 GSM749700 Stam UW DS11605 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsSknshraInputStdRawRep1 None RawSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdRawRep2 SKRA CTCF Sg 2 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000439 439 GSM749667 Stam UW DS12400 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsSknshraCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdRawRep1 SKRA CTCF Sg 1 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000439 439 GSM749693 Stam UW DS12399 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsSknshraCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknmcInputStdRawRep1 SKNMC In Sg 1 Input SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001901 1901 GSM1022638 Stam UW DS18341 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsSknmcInputStdRawRep1 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSkmcInputStdRawRep1 SKMC In Sg 1 Input SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002173 2173 GSM1022646 Stam UW DS16208 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsSkmcInputStdRawRep1 None RawSignal skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SKMC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecInputStdRawRep1 SAEC In Sg 1 Input SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000473 473 GSM749682 Stam UW DS11550 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsSaecInputStdRawRep1 None RawSignal small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdRawRep2 SAEC CTCF Sg 2 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749779 Stam UW DS12397 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsSaecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdRawRep1 SAEC CTCF Sg 1 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749684 Stam UW DS12398 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsSaecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecInputStdRawRep1 RPTC In Sg 1 Input RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002045 2045 GSM1022642 Stam UW DS18336 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsRptecInputStdRawRep1 None RawSignal renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdRawRep2 RPTC CTCF Sg 2 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022666 Stam UW DS18337 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsRptecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdRawRep1 RPTC CTCF Sg 1 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022667 Stam UW DS18338 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsRptecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsPanc1InputStdRawRep1 PANC In Sg 1 Input PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001900 1900 GSM1022632 Stam UW DS18331 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsPanc1InputStdRawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhlfInputStdRawRep1 NHLF In Sg 1 Input NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001899 1899 GSM1022641 Stam UW DS16347 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsNhlfInputStdRawRep1 None RawSignal lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhlfCtcfStdRawRep1 NHLF CTCF Sg 1 CTCF NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002548 2548 GSM1022626 Stam UW DS16349 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsNhlfCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekInputStdRawRep1 NHEK In Sg 1 Input NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000472 472 GSM749744 Stam UW DS11542 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsNhekInputStdRawRep1 None RawSignal epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdRawRep2 NHEK CTCF Sg 2 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000406 406 GSM749747 Stam UW DS11556 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsNhekCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdRawRep1 NHEK CTCF Sg 1 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000406 406 GSM749707 Stam UW DS12396 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsNhekCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoInputStdRawRep1 NHDF In Sg 1 Input NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000972 972 GSM749722 Stam UW DS16203 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsNhdfneoInputStdRawRep1 None RawSignal neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdRawRep2 NHDF CTCF Sg 2 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022676 Stam UW DS16205 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsNhdfneoCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdRawRep1 NHDF CTCF Sg 1 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022675 Stam UW DS16204 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsNhdfneoCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNb4InputStdRawRep1 NB4 In Sg 1 Input NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000970 970 GSM749716 Stam UW DS16344 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsNb4InputStdRawRep1 None RawSignal acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNb4CtcfStdRawRep1 NB4 CTCF Sg 1 CTCF NB4 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001898 1898 GSM1022643 Stam UW DS16345 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsNb4CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsLncapInputStdRawRep1 LNCP In Sg 1 Input LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001897 1897 GSM1022672 Stam UW DS18326 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsLncapInputStdRawRep1 None RawSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsJurkatInputStdRawRep1 Jurk In Sg 1 Input Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000966 966 GSM749672 Stam UW DS16193 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsJurkatInputStdRawRep1 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfInputStdRawRep1 HVMF In Sg 1 Input HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000964 964 GSM749703 Stam UW DS16190 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHvmfInputStdRawRep1 None RawSignal villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdRawRep2 HVMF CTCF Sg 2 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022628 Stam UW DS18572 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHvmfCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdRawRep1 HVMF CTCF Sg 1 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022630 Stam UW DS18571 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHvmfCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeInputStdRawRep1 HRpC In Sg 1 Input HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000962 962 GSM749771 Stam UW DS16014 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHrpeInputStdRawRep1 None RawSignal retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdRawRep2 HRpC CTCF Sg 2 CTCF HRPEpiC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000988 988 GSM1022665 Stam UW DS18570 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHrpeCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdRawRep1 HRpC CTCF Sg 1 CTCF HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000988 988 GSM749673 Stam UW DS16187 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHrpeCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreInputStdRawRep1 HRE In Sg 1 Input HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000467 467 GSM749778 Stam UW DS11549 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHreInputStdRawRep1 None RawSignal renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdRawRep2 HRE CTCF Sg 2 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000405 405 GSM749737 Stam UW DS11574 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHreCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdRawRep1 HRE CTCF Sg 1 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000405 405 GSM749727 Stam UW DS11572 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHreCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfInputStdRawRep1 HPF In Sg 1 Input HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000960 960 GSM749773 Stam UW DS16180 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHpfInputStdRawRep1 None RawSignal pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdRawRep2 HPF CTCF Sg 2 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749717 Stam UW DS16182 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHpfCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdRawRep1 HPF CTCF Sg 1 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749699 Stam UW DS16181 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHpfCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafInputStdRawRep1 HPAF In Sg 1 Input HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000958 958 GSM749709 Stam UW DS16177 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHpafInputStdRawRep1 None RawSignal pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdRawRep2 HPAF CTCF Sg 2 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749751 Stam UW DS16178 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHpafCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdRawRep1 HPAF CTCF Sg 1 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749681 Stam UW DS16179 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHpafCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfInputStdRawRep1 HMF In Sg 1 Input HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000956 956 GSM749763 Stam UW DS16174 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHmfInputStdRawRep1 None RawSignal mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdRawRep2 HMF CTCF Sg 2 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749675 Stam UW DS16175 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHmfCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdRawRep1 HMF CTCF Sg 1 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749665 Stam UW DS16176 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHmfCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecInputStdRawRep1 HMEC In Sg 1 Input HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000466 466 GSM749755 Stam UW DS13600 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHmecInputStdRawRep1 None RawSignal mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdRawRep2 HMEC CTCF Sg 2 CTCF HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000419 419 GSM1022631 Stam UW DS18569 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHmecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdRawRep1 HMEC CTCF Sg 1 CTCF HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000419 419 GSM749753 Stam UW DS11255 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHmecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHl60InputStdRawRep1 HL60 In Sg 1 Input HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000465 465 GSM749775 Stam UW DS13664 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHl60InputStdRawRep1 None RawSignal promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHl60CtcfStdRawRep1 HL60 CTCF Sg 1 CTCF HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000397 397 GSM749688 Stam UW DS9413 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHl60CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycInputStdRawRep1 HFMyc In Sg 1 Input HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001896 1896 GSM1022654 Stam UW DS18321 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHffmycInputStdRawRep1 None RawSignal foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF-Myc Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdRawRep2 HFMyc CTCF Sg 2 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022669 Stam UW DS18323 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHffmycCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF-Myc CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdRawRep1 HFMyc CTCF Sg 1 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022671 Stam UW DS18322 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHffmycCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF-Myc CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffInputStdRawRep1 HFF In Sg 1 Input HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002043 2043 GSM1022627 Stam UW DS18316 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHffInputStdRawRep1 None RawSignal foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffCtcfStdRawRep1 HFF CTCF Sg 1 CTCF HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002547 2547 GSM1022644 Stam UW DS18318 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHffCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293InputStdRawRep1 H293 In Sg 1 Input HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000464 464 GSM749767 Stam UW DS13603 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHek293InputStdRawRep1 None RawSignal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdRawRep2 H293 CTCF Sg 2 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000396 396 GSM749687 Stam UW DS10410 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHek293CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdRawRep1 H293 CTCF Sg 1 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000396 396 GSM749668 Stam UW DS10699 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHek293CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeInputStdRawRep1 HEpC In Sg 1 Input HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000952 952 GSM749698 Stam UW DS16057 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHeeInputStdRawRep1 None RawSignal esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdRawRep2 HEpC CTCF Sg 2 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749726 Stam UW DS16058 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHeeCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdRawRep1 HEpC CTCF Sg 1 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749712 Stam UW DS16059 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHeeCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116InputStdRawRep1 HCT16 In Sg 1 Input HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000950 950 GSM749774 Stam UW DS16013 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHct116InputStdRawRep1 None RawSignal colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdRawRep2 HCT16 CTCF Sg 2 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022651 Stam UW DS18568 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHct116CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdRawRep1 HCT16 CTCF Sg 1 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022652 Stam UW DS18710 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHct116CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeInputStdRawRep1 HCpC In Sg 1 Input HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000948 948 GSM749776 Stam UW DS15917 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHcpeInputStdRawRep1 None RawSignal choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpIC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdRawRep2 HCpC CTCF Sg 2 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749745 Stam UW DS16052 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHcpeCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpIC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdRawRep1 HCpC CTCF Sg 1 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749735 Stam UW DS16051 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHcpeCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpIC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmInputStdRawRep1 HCM In Sg 1 Input HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000946 946 GSM749738 Stam UW DS15916 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHcmInputStdRawRep1 None RawSignal cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdRawRep2 HCM CTCF Sg 2 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001894 1894 GSM1022677 Stam UW DS18567 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHcmCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdRawRep1 HCM CTCF Sg 1 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001894 1894 GSM1022657 Stam UW DS18566 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHcmCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfaaInputStdRawRep1 HCFa In Sg 1 Input HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000944 944 GSM749761 Stam UW DS15915 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHcfaaInputStdRawRep1 None RawSignal cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfaaCtcfStdRawRep1 HCFa CTCF Sg 1 CTCF HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000982 982 GSM749732 Stam UW DS16048 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHcfaaCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfInputStdRawRep1 HCF In Sg 1 Input HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000942 942 GSM749713 Stam UW DS15914 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHcfInputStdRawRep1 None RawSignal cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecInputStdRawRep1 HBMEC In Sg 1 Input HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000940 940 GSM749746 Stam UW DS15913 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHbmecInputStdRawRep1 None RawSignal brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdRawRep2 HBMEC CTCF Sg 2 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749710 Stam UW DS16047 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHbmecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdRawRep1 HBMEC CTCF Sg 1 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749743 Stam UW DS16046 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHbmecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspInputStdRawRep1 HAsp In Sg 1 Input HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000974 974 GSM749720 Stam UW DS16041 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHaspInputStdRawRep1 None RawSignal astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdRawRep2 HAsp CTCF Sg 2 CTCF HA-sp std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000989 989 GSM1022668 Stam UW DS18987 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHaspCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdRawRep1 HAsp CTCF Sg 1 CTCF HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000989 989 GSM749696 Stam UW DS16042 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHaspCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacInputStdRawRep1 HAc In Sg 1 Input HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002165 2165 GSM1022673 Stam UW DS18311 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHacInputStdRawRep1 None RawSignal astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdRawRep2 HAc CTCF Sg 2 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001893 1893 GSM1022662 Stam UW DS18312 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHacCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdRawRep1 HAc CTCF Sg 1 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001893 1893 GSM1022661 Stam UW DS18313 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHacCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsH7esInputStdRawRep1 H7 In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002532 2532 GSM1022649 Stam UW DS14111 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsH7esInputStdRawRep1 diffProtA_14d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-HESC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsH7esInputStdDiffa9dRawRep1 H7 In 9d Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002545 2545 GSM1022660 Stam UW DS15393 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsH7esInputStdDiffa9dRawRep1 diffProtA_9d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-HESC Input diffProtA 9d TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsH7esInputStdDiffa5dRawRep1 H7 In 5d Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002544 2544 GSM1022656 Stam UW DS14110 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsH7esInputStdDiffa5dRawRep1 diffProtA_5d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-HESC Input diffProtA 5d TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsH7esInputStdDiffa2dRawRep1 H7 In 2d Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002543 2543 GSM1022670 Stam UW DS15392 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsH7esInputStdDiffa2dRawRep1 diffProtA_2d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-HESC Input diffProtA 2d TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875InputStdRawRep1 GM75 In Sg 1 Input GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-16 2011-03-15 wgEncodeEH000462 462 GSM749724 Stam UW DS13589 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12875InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdRawRep2 GM75 CTCF Sg 2 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749670 Stam UW DS11899 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12875CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdRawRep1 GM75 CTCF Sg 1 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749764 Stam UW DS10993 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12875CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874InputStdRawRep1 GM74 In Sg 1 Input GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000461 461 GSM749742 Stam UW DS13588 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12874InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12874 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdRawRep2 GM74 CTCF Sg 2 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749741 Stam UW DS10992 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12874CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12874 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdRawRep1 GM74 CTCF Sg 1 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749757 Stam UW DS11503 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12874CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12874 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873InputStdRawRep1 GM73 In Sg 1 Input GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000460 460 GSM749685 Stam UW DS13586 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12873InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12873 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdRawRep3 GM73 CTCF Sg 3 CTCF GM12873 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000450 450 GSM1022629 Stam UW DS14433 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwTfbsGm12873CtcfStdRawRep3 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12873 CTCF TFBS ChIP-seq Raw Signal 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdRawRep2 GM73 CTCF Sg 2 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749686 Stam UW DS11501 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12873CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12873 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdRawRep1 GM73 CTCF Sg 1 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749730 Stam UW DS10990 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12873CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12873 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872InputStdRawRep1 GM72 In Sg 1 Input GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000459 459 GSM749765 Stam UW DS13585 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12872InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12872 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdRawRep3 GM72 CTCF Sg 3 CTCF GM12872 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000449 449 GSM1022633 Stam UW DS14432 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwTfbsGm12872CtcfStdRawRep3 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12872 CTCF TFBS ChIP-seq Raw Signal 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdRawRep2 GM72 CTCF Sg 2 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749692 Stam UW DS11500 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12872CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12872 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdRawRep1 GM72 CTCF Sg 1 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749694 Stam UW DS10989 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12872CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12872 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865InputStdRawRep1 GM65 In Sg 1 Input GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000458 458 GSM749777 Stam UW DS13590 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12865InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdRawRep3 GM65 CTCF Sg 3 CTCF GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000448 448 GSM1022636 Stam UW DS13756 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwTfbsGm12865CtcfStdRawRep3 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 CTCF TFBS ChIP-seq Raw Signal 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdRawRep2 GM65 CTCF Sg 2 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749725 Stam UW DS10991 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12865CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdRawRep1 GM65 CTCF Sg 1 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749740 Stam UW DS11502 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12865CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864InputStdRawRep1 GM64 In Sg 1 Input GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000457 457 GSM749754 Stam UW DS13587 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12864InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdRawRep3 GM64 CTCF Sg 3 CTCF GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000447 447 GSM1022664 Stam UW DS14431 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwTfbsGm12864CtcfStdRawRep3 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 CTCF TFBS ChIP-seq Raw Signal 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdRawRep2 GM64 CTCF Sg 2 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749762 Stam UW DS11499 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12864CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdRawRep1 GM64 CTCF Sg 1 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749676 Stam UW DS10988 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12864CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12801InputStdRawRep1 GM01 In Sg 1 Input GM12801 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000456 456 GSM749701 Stam UW DS13665 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12801InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12801 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12801CtcfStdRawRep1 GM01 CTCF Sg 1 CTCF GM12801 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000393 393 GSM749711 Stam UW DS8755 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12801CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12801 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990InputStdRawRep1 GM90 In Sg 1 Input GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000455 455 GSM749731 Stam UW DS11497 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm06990InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdRawRep2 GM90 CTCF Sg 2 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-21 2010-06-20 wgEncodeEH000392 392 GSM749705 Stam UW DS11520 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm06990CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdRawRep1 GM90 CTCF Sg 1 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-29 2010-03-29 wgEncodeEH000392 392 GSM749708 Stam UW DS11518 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm06990CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2InputStdRawRep1 Caco2 In Sg 1 Input Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000454 454 GSM749691 Stam UW DS13597 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsCaco2InputStdRawRep1 None RawSignal colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdRawRep2 Caco2 CTCF Sg 2 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749689 Stam UW DS11674 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsCaco2CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdRawRep1 Caco2 CTCF Sg 1 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749748 Stam UW DS11675 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsCaco2CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjInputStdRawRep1 BJ In Sg 1 Input BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000453 453 GSM749770 Stam UW DS11544 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsBjInputStdRawRep1 None RawSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdRawRep2 BJ CTCF Sg 2 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-19 wgEncodeEH000403 403 GSM749752 Stam UW DS11562 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsBjCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdRawRep1 BJ CTCF Sg 1 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-20 wgEncodeEH000403 403 GSM749677 Stam UW DS11560 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsBjCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cInputStdRawRep1 BE2c In Sg 1 Input BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001892 1892 GSM1022648 Stam UW DS18306 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsBe2cInputStdRawRep1 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2c Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdRawRep2 BE2c CTCF Sg 2 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022650 Stam UW DS18308 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsBe2cCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2c CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdRawRep1 BE2c CTCF Sg 1 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022653 Stam UW DS18307 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsBe2cCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2c CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafInputStdRawRep1 AoAF In Sg 1 Input AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000938 938 GSM749772 Stam UW DS15912 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAoafInputStdRawRep1 None RawSignal aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdRawRep2 AoAF CTCF Sg 2 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749736 Stam UW DS16039 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAoafCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdRawRep1 AoAF CTCF Sg 1 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749666 Stam UW DS16040 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAoafCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803InputStdRawRep1 AG03 In Sg 1 Input AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000936 936 GSM749734 Stam UW DS15911 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg10803InputStdRawRep1 None RawSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdRawRep2 AG03 CTCF Sg 2 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749759 Stam UW DS16038 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg10803CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdRawRep1 AG03 CTCF Sg 1 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749714 Stam UW DS16037 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg10803CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319InputStdRawRep1 AG19 In Sg 1 Input AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000934 934 GSM749671 Stam UW DS15910 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg09319InputStdRawRep1 None RawSignal gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdRawRep2 AG19 CTCF Sg 2 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749723 Stam UW DS16036 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg09319CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdRawRep1 AG19 CTCF Sg 1 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749728 Stam UW DS16035 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg09319CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309InputStdRawRep1 AG09 In Sg 1 Input AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000932 932 GSM749718 Stam UW DS16030 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg09309InputStdRawRep1 None RawSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdRawRep2 AG09 CTCF Sg 2 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749680 Stam UW DS16031 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg09309CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdRawRep1 AG09 CTCF Sg 1 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749750 Stam UW DS16032 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg09309CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450InputStdRawRep1 AG50 In Sg 1 Input AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000930 930 GSM749697 Stam UW DS15909 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg04450InputStdRawRep1 None RawSignal fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdRawRep2 AG50 CTCF Sg 2 CTCF AG04450 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH000976 976 GSM1022635 Stam UW DS18603 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg04450CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdRawRep1 AG50 CTCF Sg 1 CTCF AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000976 976 GSM749769 Stam UW DS16029 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg04450CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449InputStdRawRep1 AG49 In Sg 1 Input AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000928 928 GSM749702 Stam UW DS15908 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg04449InputStdRawRep1 None RawSignal fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdRawRep2 AG49 CTCF Sg 2 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749678 Stam UW DS15736 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg04449CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdRawRep1 AG49 CTCF Sg 1 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749695 Stam UW DS15738 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg04449CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMonocd14ro1746InputStdRawRep1 CD14+ In Sg 1 Input Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002169 2169 GSM1022659 Stam UW DS18980 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsMonocd14ro1746InputStdRawRep1 None RawSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Monocytes-CD14+ RO1746 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7InputStdRawRep1 MCF7 In Sg 1 Input MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000968 968 GSM749760 Stam UW DS16198 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsMcf7InputStdRawRep1 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdRawRep2 MCF7 CTCF Sg 2 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022663 Stam UW DS16199 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsMcf7CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdRawRep1 MCF7 CTCF Sg 1 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022658 Stam UW DS16200 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsMcf7CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecInputStdRawRep1 HUVEC In Sg 1 Input HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000468 468 GSM749758 Stam UW DS11470 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHuvecInputStdRawRep1 None RawSignal umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdRawRep2 HUVEC CTCF Sg 2 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000410 410 GSM749749 Stam UW DS11457 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHuvecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdRawRep1 HUVEC CTCF Sg 1 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000410 410 GSM749674 Stam UW DS12395 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHuvecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2InputStdRawRep1 HepG2 In Sg 1 Input HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000470 470 GSM749756 Stam UW DS13599 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHepg2InputStdRawRep1 None RawSignal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdRawRep2 HepG2 CTCF Sg 2 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749683 Stam UW DS11677 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHepg2CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdRawRep1 HepG2 CTCF Sg 1 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749715 Stam UW DS10700 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHepg2CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3InputStdRawRep1 HeLaS3 In Sg 1 Input HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000469 469 GSM749721 Stam UW DS11540 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHelas3InputStdRawRep1 None RawSignal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdRawRep2 HeLaS3 CTCF Sg 2 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-21 wgEncodeEH000398 398 GSM749739 Stam UW DS11167 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHelas3CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdRawRep1 HeLaS3 CTCF Sg 1 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000398 398 GSM749729 Stam UW DS11552 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHelas3CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCd20ro01794InputStdRawRep1 CD20+94 In Sg 1 Input CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002172 2172 GSM1022645 Stam UW DS18982 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsCd20ro01794InputStdRawRep1 None RawSignal B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ RO01794 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCd20ro01778InputStdRawRep1 CD20+78 In Sg 1 Input CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-25 wgEncodeEH002170 2170 GSM1022625 Stam UW DS18984 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsCd20ro01778InputStdRawRep1 None RawSignal B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ RO01778 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549InputStdRawRep1 A549 In Sg 1 Input A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH001904 1904 GSM1022674 Stam UW DS18301 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsA549InputStdRawRep1 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdRawRep2 A549 CTCF Sg 2 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022639 Stam UW DS18302 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsA549CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdRawRep1 A549 CTCF Sg 1 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022640 Stam UW DS18303 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsA549CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562InputStdRawRep1 K562 In Sg 1 Input K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000471 471 GSM749719 Stam UW DS11488 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsK562InputStdRawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdRawRep2 K562 CTCF Sg 2 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-21 2010-06-20 wgEncodeEH000399 399 GSM749733 Stam UW DS11508 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsK562CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdRawRep1 K562 CTCF Sg 1 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-30 2010-03-29 wgEncodeEH000399 399 GSM749690 Stam UW DS11247 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsK562CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878InputStdRawRep1 GM78 In Sg 1 Input GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000463 463 GSM749669 Stam UW DS11883 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12878InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdRawRep2 GM78 CTCF Sg 2 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-21 2010-06-20 wgEncodeEH000394 394 GSM749706 Stam UW DS11165 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12878CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdRawRep1 GM78 CTCF Sg 1 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-06-30 2010-03-29 wgEncodeEH000394 394 GSM749704 Stam UW DS11510 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12878CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsViewPeaks Peaks CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwTfbsWi38CtcfStdPkRep2 WI-38 CTCF Pk 2 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022634 Stam UW DS18348 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsWi38CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38CtcfStdPkRep1 WI-38 CTCF Pk 1 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022637 Stam UW DS18347 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsWi38CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdPkRep2 WERI CTCF Pk 2 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749679 Stam UW DS10408 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsWerirb1CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdPkRep1 WERI CTCF Pk 1 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749768 Stam UW DS10701 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsWerirb1CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdPkRep2 SKRA CTCF Pk 2 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000439 439 GSM749667 Stam UW DS12400 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsSknshraCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdPkRep1 SKRA CTCF Pk 1 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000439 439 GSM749693 Stam UW DS12399 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsSknshraCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdPkRep2 SAEC CTCF Pk 2 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000437 437 GSM749779 Stam UW DS12397 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsSaecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdPkRep1 SAEC CTCF Pk 1 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749684 Stam UW DS12398 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsSaecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdPkRep2 RPTC CTCF Pk 2 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022666 Stam UW DS18337 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsRptecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdPkRep1 RPTC CTCF Pk 1 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022667 Stam UW DS18338 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsRptecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhlfCtcfStdPkRep1 NHLF CTCF Pk 1 CTCF NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002548 2548 GSM1022626 Stam UW DS16349 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsNhlfCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdPkRep2 NHEK CTCF Pk 2 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000406 406 GSM749747 Stam UW DS11556 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsNhekCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdPkRep1 NHEK CTCF Pk 1 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000406 406 GSM749707 Stam UW DS12396 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsNhekCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdPkRep2 NHDF CTCF Pk 2 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022676 Stam UW DS16205 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsNhdfneoCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdPkRep1 NHDF CTCF Pk 1 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022675 Stam UW DS16204 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsNhdfneoCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNb4CtcfStdPkRep1 NB4 CTCF Pk 1 CTCF NB4 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001898 1898 GSM1022643 Stam UW DS16345 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsNb4CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NB4 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdPkRep2 HVMF CTCF Pk 2 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022628 Stam UW DS18572 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHvmfCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdPkRep1 HVMF CTCF Pk 1 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022630 Stam UW DS18571 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHvmfCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdPkRep2 HRpC CTCF Pk 2 CTCF HRPEpiC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000988 988 GSM1022665 Stam UW DS18570 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHrpeCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpIC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdPkRep1 HRpC CTCF Pk 1 CTCF HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000988 988 GSM749673 Stam UW DS16187 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHrpeCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpIC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdPkRep2 HRE CTCF Pk 2 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000405 405 GSM749737 Stam UW DS11574 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHreCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdPkRep1 HRE CTCF Pk 1 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000405 405 GSM749727 Stam UW DS11572 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHreCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdPkRep2 HPF CTCF Pk 2 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749717 Stam UW DS16182 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHpfCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdPkRep1 HPF CTCF Pk 1 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749699 Stam UW DS16181 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHpfCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdPkRep2 HPAF CTCF Pk 2 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749751 Stam UW DS16178 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHpafCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdPkRep1 HPAF CTCF Pk 1 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749681 Stam UW DS16179 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHpafCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdPkRep2 HMF CTCF Pk 2 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749675 Stam UW DS16175 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHmfCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdPkRep1 HMF CTCF Pk 1 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749665 Stam UW DS16176 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHmfCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdPkRep2 HMEC CTCF Pk 2 CTCF HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000419 419 GSM1022631 Stam UW DS18569 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHmecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdPkRep1 HMEC CTCF Pk 1 CTCF HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000419 419 GSM749753 Stam UW DS11255 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHmecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHl60CtcfStdPkRep1 HL60 CTCF Pk 1 CTCF HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000397 397 GSM749688 Stam UW DS9413 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHl60CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdPkRep2 HFMyc CTCF Pk 2 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022669 Stam UW DS18323 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHffmycCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF-Myc CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdPkRep1 HFMyc CTCF Pk 1 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022671 Stam UW DS18322 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHffmycCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF-Myc CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffCtcfStdPkRep1 HFF CTCF Pk 1 CTCF HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002547 2547 GSM1022644 Stam UW DS18318 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHffCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdPkRep2 H293 CTCF Pk 2 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000396 396 GSM749687 Stam UW DS10410 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHek293CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEK293 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdPkRep1 H293 CTCF Pk 1 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000396 396 GSM749668 Stam UW DS10699 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHek293CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEK293 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdPkRep2 HEpC CTCF Pk 2 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749726 Stam UW DS16058 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHeeCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpIC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdPkRep1 HEpC CTCF Pk 1 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749712 Stam UW DS16059 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHeeCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpIC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdPkRep2 HCT16 CTCF Pk 2 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022651 Stam UW DS18568 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHct116CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdPkRep1 HCT16 CTCF Pk 1 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022652 Stam UW DS18710 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHct116CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdPkRep2 HCpC CTCF Pk 2 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749745 Stam UW DS16052 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHcpeCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpIC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdPkRep1 HCpC CTCF Pk 1 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749735 Stam UW DS16051 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHcpeCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpIC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdPkRep2 HCM CTCF Pk 2 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001894 1894 GSM1022677 Stam UW DS18567 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHcmCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdPkRep1 HCM CTCF Pk 1 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001894 1894 GSM1022657 Stam UW DS18566 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHcmCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfaaCtcfStdPkRep1 HCFa CTCF Pk 1 CTCF HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000982 982 GSM749732 Stam UW DS16048 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHcfaaCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCFaa CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdPkRep2 HBMEC CTCF Pk 2 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749710 Stam UW DS16047 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHbmecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdPkRep1 HBMEC CTCF Pk 1 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749743 Stam UW DS16046 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHbmecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdPkRep2 HAsp CTCF Pk 2 CTCF HA-sp std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000989 989 GSM1022668 Stam UW DS18987 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHaspCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdPkRep1 HAsp CTCF Pk 1 CTCF HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000989 989 GSM749696 Stam UW DS16042 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHaspCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdPkRep2 HAc CTCF Pk 2 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001893 1893 GSM1022662 Stam UW DS18312 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHacCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdPkRep1 HAc CTCF Pk 1 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001893 1893 GSM1022661 Stam UW DS18313 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHacCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdPkRep2 GM75 CTCF Pk 2 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-16 2011-03-15 wgEncodeEH000452 452 GSM749670 Stam UW DS11899 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12875CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12875 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdPkRep1 GM75 CTCF Pk 1 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749764 Stam UW DS10993 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12875CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12875 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdPkRep2 GM74 CTCF Pk 2 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000451 451 GSM749741 Stam UW DS10992 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12874CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12874 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdPkRep1 GM74 CTCF Pk 1 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749757 Stam UW DS11503 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12874CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12874 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdPkRep3 GM73 CTCF Pk 3 CTCF GM12873 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000450 450 GSM1022629 Stam UW DS14433 lmax-v1.0 hg19 3 exp wgEncodeUwTfbsGm12873CtcfStdPkRep3 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12873 CTCF TFBS ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdPkRep2 GM73 CTCF Pk 2 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000450 450 GSM749686 Stam UW DS11501 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12873CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12873 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdPkRep1 GM73 CTCF Pk 1 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749730 Stam UW DS10990 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12873CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12873 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdPkRep3 GM72 CTCF Pk 3 CTCF GM12872 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000449 449 GSM1022633 Stam UW DS14432 lmax-v1.0 hg19 3 exp wgEncodeUwTfbsGm12872CtcfStdPkRep3 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12872 CTCF TFBS ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdPkRep2 GM72 CTCF Pk 2 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000449 449 GSM749692 Stam UW DS11500 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12872CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12872 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdPkRep1 GM72 CTCF Pk 1 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749694 Stam UW DS10989 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12872CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12872 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdPkRep3 GM65 CTCF Pk 3 CTCF GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000448 448 GSM1022636 Stam UW DS13756 lmax-v1.0 hg19 3 exp wgEncodeUwTfbsGm12865CtcfStdPkRep3 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 CTCF TFBS ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdPkRep2 GM65 CTCF Pk 2 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000448 448 GSM749725 Stam UW DS10991 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12865CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdPkRep1 GM65 CTCF Pk 1 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749740 Stam UW DS11502 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12865CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdPkRep3 GM64 CTCF Pk 3 CTCF GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000447 447 GSM1022664 Stam UW DS14431 lmax-v1.0 hg19 3 exp wgEncodeUwTfbsGm12864CtcfStdPkRep3 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 CTCF TFBS ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdPkRep2 GM64 CTCF Pk 2 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000447 447 GSM749762 Stam UW DS11499 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12864CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdPkRep1 GM64 CTCF Pk 1 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749676 Stam UW DS10988 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12864CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12801CtcfStdPkRep1 GM01 CTCF Pk 1 CTCF GM12801 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000393 393 GSM749711 Stam UW DS8755 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12801CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12801 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdPkRep2 GM90 CTCF Pk 2 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-29 2010-03-29 wgEncodeEH000392 392 GSM749705 Stam UW DS11520 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm06990CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdPkRep1 GM90 CTCF Pk 1 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-29 2010-03-29 wgEncodeEH000392 392 GSM749708 Stam UW DS11518 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm06990CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdPkRep2 Caco2 CTCF Pk 2 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000404 404 GSM749689 Stam UW DS11674 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsCaco2CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdPkRep1 Caco2 CTCF Pk 1 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749748 Stam UW DS11675 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsCaco2CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdPkRep2 BJ CTCF Pk 2 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH000403 403 GSM749752 Stam UW DS11562 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsBjCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdPkRep1 BJ CTCF Pk 1 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-20 wgEncodeEH000403 403 GSM749677 Stam UW DS11560 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsBjCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdPkRep2 BE2c CTCF Pk 2 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022650 Stam UW DS18308 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsBe2cCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2c CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdPkRep1 BE2c CTCF Pk 1 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022653 Stam UW DS18307 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsBe2cCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2c CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdPkRep2 AoAF CTCF Pk 2 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749736 Stam UW DS16039 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAoafCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdPkRep1 AoAF CTCF Pk 1 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749666 Stam UW DS16040 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAoafCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdPkRep2 AG03 CTCF Pk 2 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749759 Stam UW DS16038 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg10803CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdPkRep1 AG03 CTCF Pk 1 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749714 Stam UW DS16037 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg10803CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdPkRep2 AG19 CTCF Pk 2 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749723 Stam UW DS16036 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg09319CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdPkRep1 AG19 CTCF Pk 1 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749728 Stam UW DS16035 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg09319CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdPkRep2 AG09 CTCF Pk 2 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749680 Stam UW DS16031 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg09309CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdPkRep1 AG09 CTCF Pk 1 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749750 Stam UW DS16032 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg09309CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdPkRep2 AG50 CTCF Pk 2 CTCF AG04450 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH000976 976 GSM1022635 Stam UW DS18603 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg04450CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdPkRep1 AG50 CTCF Pk 1 CTCF AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000976 976 GSM749769 Stam UW DS16029 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg04450CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdPkRep2 AG49 CTCF Pk 2 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749678 Stam UW DS15736 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg04449CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdPkRep1 AG49 CTCF Pk 1 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749695 Stam UW DS15738 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg04449CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdPkRep2 MCF7 CTCF Pk 2 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022663 Stam UW DS16199 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsMcf7CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdPkRep1 MCF7 CTCF Pk 1 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022658 Stam UW DS16200 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsMcf7CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdPkRep2 HUVEC CTCF Pk 2 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000410 410 GSM749749 Stam UW DS11457 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHuvecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdPkRep1 HUVEC CTCF Pk 1 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000410 410 GSM749674 Stam UW DS12395 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHuvecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdPkRep2 HepG2 CTCF Pk 2 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749683 Stam UW DS11677 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHepg2CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdPkRep1 HepG2 CTCF Pk 1 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749715 Stam UW DS10700 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHepg2CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdPkRep2 HeLaS3 CTCF Pk 2 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000398 398 GSM749739 Stam UW DS11167 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHelas3CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdPkRep1 HeLaS3 CTCF Pk 1 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000398 398 GSM749729 Stam UW DS11552 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHelas3CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdPkRep2 A549 CTCF Pk 2 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022639 Stam UW DS18302 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsA549CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdPkRep1 A549 CTCF Pk 1 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022640 Stam UW DS18303 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsA549CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdPkRep2 K562 CTCF Pk 2 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-06-30 2010-03-29 wgEncodeEH000399 399 GSM749733 Stam UW DS11508 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsK562CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdPkRep1 K562 CTCF Pk 1 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-30 2010-03-29 wgEncodeEH000399 399 GSM749690 Stam UW DS11247 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsK562CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdPkRep2 GM78 CTCF Pk 2 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-06-30 2010-03-29 wgEncodeEH000394 394 GSM749706 Stam UW DS11165 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12878CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdPkRep1 GM78 CTCF Pk 1 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-29 2010-03-29 wgEncodeEH000394 394 GSM749704 Stam UW DS11510 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12878CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsViewHot Hotspots CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwTfbsWi38CtcfStdHotspotsRep2 WI-38 CTCF Ht 2 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022634 Stam UW DS18348 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsWi38CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38CtcfStdHotspotsRep1 WI-38 CTCF Ht 1 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022637 Stam UW DS18347 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsWi38CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdHotspotsRep2 WERI CTCF Ht 2 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749679 Stam UW DS10408 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsWerirb1CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdHotspotsRep1 WERI CTCF Ht 1 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749768 Stam UW DS10701 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsWerirb1CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdHotspotsRep2 SKRA CTCF Ht 2 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000439 439 GSM749667 Stam UW DS12400 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsSknshraCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdHotspotsRep1 SKRA CTCF Ht 1 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000439 439 GSM749693 Stam UW DS12399 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsSknshraCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdHotspotsRep2 SAEC CTCF Ht 2 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749779 Stam UW DS12397 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsSaecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdHotspotsRep1 SAEC CTCF Ht 1 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749684 Stam UW DS12398 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsSaecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdHotspotsRep2 RPTC CTCF Ht 2 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022666 Stam UW DS18337 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsRptecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdHotspotsRep1 RPTC CTCF Ht 1 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022667 Stam UW DS18338 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsRptecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhlfCtcfStdHotspotsRep1 NHLF CTCF Ht 1 CTCF NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002548 2548 GSM1022626 Stam UW DS16349 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsNhlfCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHLF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdHotspotsRep2 NHEK CTCF Ht 2 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000406 406 GSM749747 Stam UW DS11556 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsNhekCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdHotspotsRep1 NHEK CTCF Ht 1 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000406 406 GSM749707 Stam UW DS12396 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsNhekCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep2 NHDF CTCF Ht 2 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022676 Stam UW DS16205 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep1 NHDF CTCF Ht 1 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022675 Stam UW DS16204 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNb4CtcfStdHotspotsRep1 NB4 CTCF Ht 1 CTCF NB4 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001898 1898 GSM1022643 Stam UW DS16345 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsNb4CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NB4 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdHotspotsRep2 HVMF CTCF Ht 2 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022628 Stam UW DS18572 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHvmfCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdHotspotsRep1 HVMF CTCF Ht 1 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022630 Stam UW DS18571 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHvmfCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdHotspotsRep2 HRpC CTCF Ht 2 CTCF HRPEpiC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000988 988 GSM1022665 Stam UW DS18570 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHrpeCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpIC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdHotspotsRep1 HRpC CTCF Ht 1 CTCF HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000988 988 GSM749673 Stam UW DS16187 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHrpeCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpIC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdHotspotsRep2 HRE CTCF Ht 2 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000405 405 GSM749737 Stam UW DS11574 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHreCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdHotspotsRep1 HRE CTCF Ht 1 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000405 405 GSM749727 Stam UW DS11572 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHreCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdHotspotsRep2 HPF CTCF Ht 2 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749717 Stam UW DS16182 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHpfCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdHotspotsRep1 HPF CTCF Ht 1 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749699 Stam UW DS16181 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHpfCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdHotspotsRep2 HPAF CTCF Ht 2 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749751 Stam UW DS16178 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHpafCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdHotspotsRep1 HPAF CTCF Ht 1 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749681 Stam UW DS16179 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHpafCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdHotspotsRep2 HMF CTCF Ht 2 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749675 Stam UW DS16175 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHmfCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdHotspotsRep1 HMF CTCF Ht 1 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749665 Stam UW DS16176 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHmfCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdHotspotsRep2 HMEC CTCF Ht 2 CTCF HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000419 419 GSM1022631 Stam UW DS18569 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHmecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdHotspotsRep1 HMEC CTCF Ht 1 CTCF HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000419 419 GSM749753 Stam UW DS11255 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHmecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHl60CtcfStdHotspotsRep1 HL60 CTCF Ht 1 CTCF HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000397 397 GSM749688 Stam UW DS9413 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHl60CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HL-60 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdHotspotsRep2 HFMyc CTCF Ht 2 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022669 Stam UW DS18323 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHffmycCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF-Myc CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdHotspotsRep1 HFMyc CTCF Ht 1 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022671 Stam UW DS18322 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHffmycCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF-Myc CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffCtcfStdHotspotsRep1 HFF CTCF Ht 1 CTCF HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002547 2547 GSM1022644 Stam UW DS18318 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHffCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdHotspotsRep2 H293 CTCF Ht 2 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000396 396 GSM749687 Stam UW DS10410 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHek293CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEK293 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdHotspotsRep1 H293 CTCF Ht 1 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000396 396 GSM749668 Stam UW DS10699 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHek293CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEK293 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdHotspotsRep2 HEpC CTCF Ht 2 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749726 Stam UW DS16058 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHeeCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpIC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdHotspotsRep1 HEpC CTCF Ht 1 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749712 Stam UW DS16059 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHeeCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpIC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdHotspotsRep2 HCT16 CTCF Ht 2 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022651 Stam UW DS18568 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHct116CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdHotspotsRep1 HCT16 CTCF Ht 1 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022652 Stam UW DS18710 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHct116CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdHotspotsRep2 HCpC CTCF Ht 2 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749745 Stam UW DS16052 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHcpeCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpIC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdHotspotsRep1 HCpC CTCF Ht 1 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749735 Stam UW DS16051 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHcpeCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpIC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdHotspotsRep2 HCM CTCF Ht 2 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001894 1894 GSM1022677 Stam UW DS18567 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHcmCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdHotspotsRep1 HCM CTCF Ht 1 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001894 1894 GSM1022657 Stam UW DS18566 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHcmCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfaaCtcfStdHotspotsRep1 HCFa CTCF Ht 1 CTCF HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000982 982 GSM749732 Stam UW DS16048 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHcfaaCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCFaa CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdHotspotsRep2 HBMEC CTCF Ht 2 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749710 Stam UW DS16047 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHbmecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdHotspotsRep1 HBMEC CTCF Ht 1 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749743 Stam UW DS16046 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHbmecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdHotspotsRep2 HAsp CTCF Ht 2 CTCF HA-sp std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000989 989 GSM1022668 Stam UW DS18987 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHaspCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdHotspotsRep1 HAsp CTCF Ht 1 CTCF HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000989 989 GSM749696 Stam UW DS16042 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHaspCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdHotspotsRep2 HAc CTCF Ht 2 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001893 1893 GSM1022662 Stam UW DS18312 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHacCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdHotspotsRep1 HAc CTCF Ht 1 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001893 1893 GSM1022661 Stam UW DS18313 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHacCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdHotspotsRep2 GM75 CTCF Ht 2 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749670 Stam UW DS11899 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12875CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12875 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdHotspotsRep1 GM75 CTCF Ht 1 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749764 Stam UW DS10993 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12875CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12875 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdHotspotsRep2 GM74 CTCF Ht 2 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749741 Stam UW DS10992 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12874CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12874 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdHotspotsRep1 GM74 CTCF Ht 1 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749757 Stam UW DS11503 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12874CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12874 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdHotspotsRep3 GM73 CTCF Ht 3 CTCF GM12873 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000450 450 GSM1022629 Stam UW DS14433 Hotspot-v5.2 hg19 3 exp wgEncodeUwTfbsGm12873CtcfStdHotspotsRep3 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12873 CTCF TFBS ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdHotspotsRep2 GM73 CTCF Ht 2 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749686 Stam UW DS11501 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12873CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12873 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdHotspotsRep1 GM73 CTCF Ht 1 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749730 Stam UW DS10990 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12873CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12873 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdHotspotsRep3 GM72 CTCF Ht 3 CTCF GM12872 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000449 449 GSM1022633 Stam UW DS14432 Hotspot-v5.2 hg19 3 exp wgEncodeUwTfbsGm12872CtcfStdHotspotsRep3 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12872 CTCF TFBS ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdHotspotsRep2 GM72 CTCF Ht 2 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749692 Stam UW DS11500 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12872CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12872 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdHotspotsRep1 GM72 CTCF Ht 1 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749694 Stam UW DS10989 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12872CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12872 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdHotspotsRep3 GM65 CTCF Ht 3 CTCF GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000448 448 GSM1022636 Stam UW DS13756 Hotspot-v5.2 hg19 3 exp wgEncodeUwTfbsGm12865CtcfStdHotspotsRep3 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 CTCF TFBS ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdHotspotsRep2 GM65 CTCF Ht 2 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749725 Stam UW DS10991 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12865CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdHotspotsRep1 GM65 CTCF Ht 1 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749740 Stam UW DS11502 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12865CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdHotspotsRep3 GM64 CTCF Ht 3 CTCF GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000447 447 GSM1022664 Stam UW DS14431 Hotspot-v5.2 hg19 3 exp wgEncodeUwTfbsGm12864CtcfStdHotspotsRep3 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 CTCF TFBS ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdHotspotsRep2 GM64 CTCF Ht 2 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749762 Stam UW DS11499 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12864CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdHotspotsRep1 GM64 CTCF Ht 1 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749676 Stam UW DS10988 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12864CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12801CtcfStdHotspotsRep1 GM01 CTCF Ht 1 CTCF GM12801 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000393 393 GSM749711 Stam UW DS8755 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12801CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12801 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdHotspotsRep2 GM90 CTCF Ht 2 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-21 2010-06-20 wgEncodeEH000392 392 GSM749705 Stam UW DS11520 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm06990CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdHotspotsRep1 GM90 CTCF Ht 1 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-29 2010-03-29 wgEncodeEH000392 392 GSM749708 Stam UW DS11518 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm06990CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdHotspotsRep2 Caco2 CTCF Ht 2 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749689 Stam UW DS11674 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsCaco2CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdHotspotsRep1 Caco2 CTCF Ht 1 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749748 Stam UW DS11675 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsCaco2CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdHotspotsRep2 BJ CTCF Ht 2 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-19 wgEncodeEH000403 403 GSM749752 Stam UW DS11562 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsBjCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdHotspotsRep1 BJ CTCF Ht 1 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-20 wgEncodeEH000403 403 GSM749677 Stam UW DS11560 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsBjCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdHotspotsRep2 BE2c CTCF Ht 2 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022650 Stam UW DS18308 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsBe2cCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2c CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdHotspotsRep1 BE2c CTCF Ht 1 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022653 Stam UW DS18307 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsBe2cCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2c CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdHotspotsRep2 AoAF CTCF Ht 2 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749736 Stam UW DS16039 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAoafCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdHotspotsRep1 AoAF CTCF Ht 1 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749666 Stam UW DS16040 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAoafCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdHotspotsRep2 AG03 CTCF Ht 2 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749759 Stam UW DS16038 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAg10803CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdHotspotsRep1 AG03 CTCF Ht 1 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749714 Stam UW DS16037 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg10803CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdHotspotsRep2 AG19 CTCF Ht 2 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749723 Stam UW DS16036 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAg09319CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdHotspotsRep1 AG19 CTCF Ht 1 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749728 Stam UW DS16035 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg09319CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdHotspotsRep2 AG09 CTCF Ht 2 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749680 Stam UW DS16031 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAg09309CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdHotspotsRep1 AG09 CTCF Ht 1 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749750 Stam UW DS16032 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg09309CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdHotspotsRep2 AG50 CTCF Ht 2 CTCF AG04450 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH000976 976 GSM1022635 Stam UW DS18603 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsAg04450CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdHotspotsRep1 AG50 CTCF Ht 1 CTCF AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000976 976 GSM749769 Stam UW DS16029 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg04450CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdHotspotsRep2 AG49 CTCF Ht 2 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749678 Stam UW DS15736 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAg04449CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdHotspotsRep1 AG49 CTCF Ht 1 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749695 Stam UW DS15738 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg04449CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdHotspotsRep2 MCF7 CTCF Ht 2 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022663 Stam UW DS16199 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsMcf7CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdHotspotsRep1 MCF7 CTCF Ht 1 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022658 Stam UW DS16200 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsMcf7CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdHotspotsRep2 HUVEC CTCF Ht 2 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000410 410 GSM749749 Stam UW DS11457 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHuvecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdHotspotsRep1 HUVEC CTCF Ht 1 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000410 410 GSM749674 Stam UW DS12395 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHuvecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdHotspotsRep2 HepG2 CTCF Ht 2 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749683 Stam UW DS11677 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHepg2CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdHotspotsRep1 HepG2 CTCF Ht 1 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749715 Stam UW DS10700 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHepg2CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdHotspotsRep2 HeLaS3 CTCF Ht 2 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-21 wgEncodeEH000398 398 GSM749739 Stam UW DS11167 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHelas3CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdHotspotsRep1 HeLaS3 CTCF Ht 1 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000398 398 GSM749729 Stam UW DS11552 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHelas3CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdHotspotsRep2 A549 CTCF Ht 2 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022639 Stam UW DS18302 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsA549CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdHotspotsRep1 A549 CTCF Ht 1 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022640 Stam UW DS18303 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsA549CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdHotspotsRep2 K562 CTCF Ht 2 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-21 2010-06-20 wgEncodeEH000399 399 GSM749733 Stam UW DS11508 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsK562CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdHotspotsRep1 K562 CTCF Ht 1 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-30 2010-03-29 wgEncodeEH000399 399 GSM749690 Stam UW DS11247 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsK562CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdHotspotsRep2 GM78 CTCF Ht 2 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-21 2010-06-20 wgEncodeEH000394 394 GSM749706 Stam UW DS11165 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12878CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdHotspotsRep1 GM78 CTCF Ht 1 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-06-30 2010-03-29 wgEncodeEH000394 394 GSM749704 Stam UW DS11510 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12878CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistone UW Histone GSE35583 Histone Modifications by ChIP-seq from ENCODE/University of Washington Regulation Description This track was produced as part of the ENCODE Project. This track displays genome-wide maps of histone modifications in different cell lines using ChIP-seq high-throughput sequencing. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: HotSpots ChIP-seq affinity zones identified using the HotSpot algorithm. Peaks ChIP-seq affinity sites identified as signal peaks within FDR 1.0% affinity zones. Raw Signal The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Cells were cross-linked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using a Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 &#176;C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross-linking in the immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. A quantity of 20-50 ng of ChIP DNA was end-repaired, followed by addition of adenine, ligation to Illumina adapters, and creation of a Solexa library for sequencing. ChIP-seq affinity was directly measured through the raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). ChIP-seq affinity zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). One percent false discovery rate thresholds (FDR 1.0%) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36-mers. ChIP-Seq affinities (Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm. All tracks have a False Discovery Rate of 1% (FDR 1.0%). Verification Data were verified by sequencing biological replicates displaying a correlation coefficient greater than 0.9. Release Notes Release 5 (July 2012) of this track removes experiments with K562/Zinc finger knockouts and adds in some missing inputs. Credits These data were generated by the UW ENCODE group. Contact: Richard Sandstrom References Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwHistoneViewRawSig Sg Signal Histone Modifications by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwHistoneWi38InputStdRawRep1 WI38 In Sg 1 Input WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001903 1903 GSM945245 Stam UW DS18346 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneWi38InputStdRawRep1 None RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38InputOhtamStdRawRep1 WI38 In Sg 1 Input WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002048 2048 GSM945223 Stam UW DS18351 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneWi38InputOhtamStdRawRep1 4OHTAM_20nM_72hr RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 Input 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3StdRawRep2 WI38 H3K4M3 Sg 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18349 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3StdRawRep1 WI38 H3K4M3 Sg 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18350 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdRawRep2 WI38 H3K4M3 Sg 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18354 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdRawRep2 4OHTAM_20nM_72hr RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdRawRep1 WI38 H3K4M3 Sg 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18355 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdRawRep1 4OHTAM_20nM_72hr RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1InputStdRawRep1 WERI In Sg 1 Input WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH000475 475 GSM945318 Stam UW DS11888 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneWerirb1InputStdRawRep1 None RawSignal retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdRawRep2 WERI H3K4M3 Sg 2 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16213 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneWerirb1H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdRawRep1 WERI H3K4M3 Sg 1 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16214 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneWerirb1H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraInputStdRawRep1 SKRA In Sg 1 Input SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000474 474 GSM945317 Stam UW DS11605 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneSknshraInputStdRawRep1 None RawSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdRawRep2 SKRA H3K36M3 Sg 2 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12403 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSknshraH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdRawRep1 SKRA H3K36M3 Sg 1 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12404 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSknshraH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdRawRep2 SKRA H3K27M3 Sg 2 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-20 2010-07-20 wgEncodeEH000440 440 GSM945210 Stam UW DS12215 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSknshraH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdRawRep1 SKRA H3K27M3 Sg 1 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000440 440 GSM945210 Stam UW DS12212 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSknshraH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdRawRep2 SKRA H3K4M3 Sg 2 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11783 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSknshraH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdRawRep1 SKRA H3K4M3 Sg 1 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11782 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSknshraH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcInputStdRawRep1 SKNMC In Sg 1 Input SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001901 1901 GSM945247 Stam UW DS18341 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneSknmcInputStdRawRep1 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdRawRep2 SKNMC H3K4M3 Sg 2 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18345 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneSknmcH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdRawRep1 SKNMC H3K4M3 Sg 1 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18344 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneSknmcH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcInputStdRawRep1 SKMC In Sg 1 Input SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002173 2173 GSM945161 Stam UW DS16208 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneSkmcInputStdRawRep1 None RawSignal skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SKMC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdRawRep2 SKMC H3K4M3 Sg 2 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16212 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneSkmcH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SKMC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdRawRep1 SKMC H3K4M3 Sg 1 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16211 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneSkmcH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SKMC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecInputStdRawRep1 SAEC In Sg 1 Input SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000473 473 GSM945314 Stam UW DS11550 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneSaecInputStdRawRep1 None RawSignal small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdRawRep2 SAEC H3K36M3 Sg 2 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12246 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSaecH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdRawRep1 SAEC H3K36M3 Sg 1 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12243 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSaecH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdRawRep2 SAEC H3K27M3 Sg 2 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000420 420 GSM945200 Stam UW DS12245 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSaecH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdRawRep1 SAEC H3K27M3 Sg 1 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000420 420 GSM945200 Stam UW DS12242 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSaecH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdRawRep2 SAEC H3K4M3 Sg 2 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11579 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSaecH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdRawRep1 SAEC H3K4M3 Sg 1 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11577 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSaecH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecInputStdRawRep1 RPTEC In Sg 1 Input RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002045 2045 GSM945217 Stam UW DS18336 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneRptecInputStdRawRep1 None RawSignal renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdRawRep2 RPTEC H3K4M3 Sg 2 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18339 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneRptecH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdRawRep1 RPTEC H3K4M3 Sg 1 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18340 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneRptecH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1InputStdRawRep1 PANC1 In Sg 1 Input PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001900 1900 GSM945246 Stam UW DS18331 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistonePanc1InputStdRawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdRawRep2 PANC1 H3K4M3 Sg 2 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18334 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistonePanc1H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdRawRep1 PANC1 H3K4M3 Sg 1 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18335 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistonePanc1H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfInputStdRawRep1 NHLF In Sg 1 Input NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001899 1899 GSM945280 Stam UW DS16347 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneNhlfInputStdRawRep1 None RawSignal lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdRawRep2 NHLF H3K4M3 Sg 2 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16350 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneNhlfH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdRawRep1 NHLF H3K4M3 Sg 1 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16351 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneNhlfH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekInputStdRawRep1 NHEK In Sg 1 Input NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000472 472 GSM945313 Stam UW DS11542 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneNhekInputStdRawRep1 None RawSignal epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdRawRep2 NHEK H3K36M3 Sg 2 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12240 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneNhekH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdRawRep1 NHEK H3K36M3 Sg 1 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12237 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneNhekH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdRawRep2 NHEK H3K27M3 Sg 2 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12080 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneNhekH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdRawRep1 NHEK H3K27M3 Sg 1 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12078 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneNhekH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdRawRep2 NHEK H3K4M3 Sg 2 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000415 415 GSM945175 Stam UW DS11557 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneNhekH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdRawRep1 NHEK H3K4M3 Sg 1 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000415 415 GSM945175 Stam UW DS11559 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneNhekH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoInputStdRawRep1 NHDF In Sg 1 Input NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000972 972 GSM945250 Stam UW DS16203 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneNhdfneoInputStdRawRep1 None RawSignal neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdRawRep2 NHDF H3K4M3 Sg 2 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16207 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneNhdfneoH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdRawRep1 NHDF H3K4M3 Sg 1 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16206 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneNhdfneoH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNb4InputStdRawRep1 NB4 In Sg 1 Input NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000970 970 GSM945252 Stam UW DS16344 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneNb4InputStdRawRep1 None RawSignal acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNb4H3k4me3StdRawRep1 NB4 H3K4M3 Sg 1 H3K4me3 NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000969 969 GSM945275 Stam UW DS16346 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneNb4H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapInputStdRawRep1 LNCP In Sg 1 Input LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001897 1897 GSM945282 Stam UW DS18326 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneLncapInputStdRawRep1 None RawSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdRawRep2 LNCP H3K4M3 Sg 2 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18329 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneLncapH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdRawRep1 LNCP H3K4M3 Sg 1 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18330 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneLncapH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatInputStdRawRep1 Jurk In Sg 1 Input Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000966 966 GSM945268 Stam UW DS16193 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneJurkatInputStdRawRep1 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdRawRep2 Jurk H3K4M3 Sg 2 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16196 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneJurkatH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdRawRep1 Jurk H3K4M3 Sg 1 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16197 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneJurkatH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfInputStdRawRep1 HVMF In Sg 1 Input HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000964 964 GSM945266 Stam UW DS16190 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHvmfInputStdRawRep1 None RawSignal villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdRawRep2 HVMF H3K4M3 Sg 2 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16155 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHvmfH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdRawRep1 HVMF H3K4M3 Sg 1 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16156 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHvmfH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeInputStdRawRep1 HRPE In Sg 1 Input HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000962 962 GSM945272 Stam UW DS16014 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHrpeInputStdRawRep1 None RawSignal retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdRawRep2 HRPE H3K4M3 Sg 2 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16188 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHrpeH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdRawRep1 HRPE H3K4M3 Sg 1 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16189 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHrpeH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreInputStdRawRep1 HRE In Sg 1 Input HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000467 467 GSM945257 Stam UW DS11549 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHreInputStdRawRep1 None RawSignal renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdRawRep2 HRE H3K36M3 Sg 2 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12418 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHreH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdRawRep1 HRE H3K36M3 Sg 1 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12234 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHreH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdRawRep2 HRE H3K27M3 Sg 2 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000429 429 GSM945160 Stam UW DS12415 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHreH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdRawRep1 HRE H3K27M3 Sg 1 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000429 429 GSM945160 Stam UW DS12422 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHreH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdRawRep2 HRE H3K4M3 Sg 2 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000409 409 GSM945276 Stam UW DS11573 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHreH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdRawRep1 HRE H3K4M3 Sg 1 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000409 409 GSM945276 Stam UW DS11575 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHreH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfInputStdRawRep1 HPF In Sg 1 Input HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000960 960 GSM945270 Stam UW DS16180 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHpfInputStdRawRep1 None RawSignal pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdRawRep2 HPF H3K4M3 Sg 2 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16183 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHpfH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdRawRep1 HPF H3K4M3 Sg 1 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16184 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHpfH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafInputStdRawRep1 HPAF In Sg 1 Input HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000958 958 GSM945285 Stam UW DS16177 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHpafInputStdRawRep1 None RawSignal pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdRawRep2 HPAF H3K4M3 Sg 2 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16154 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHpafH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdRawRep1 HPAF H3K4M3 Sg 1 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16153 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHpafH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfInputStdRawRep1 HMF In Sg 1 Input HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000956 956 GSM945293 Stam UW DS16174 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHmfInputStdRawRep1 None RawSignal mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdRawRep2 HMF H3K4M3 Sg 2 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16152 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHmfH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdRawRep1 HMF H3K4M3 Sg 1 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16151 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHmfH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecInputStdRawRep1 HMEC In Sg 1 Input HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000466 466 GSM945258 Stam UW DS13600 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHmecInputStdRawRep1 None RawSignal mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k27me3StdRawRep1 HMEC H3K27M3 Sg 1 H3K27me3 HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000408 408 GSM945277 Stam UW DS12082 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHmecH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdRawRep2 HMEC H3K4M3 Sg 2 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15761 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHmecH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdRawRep1 HMEC H3K4M3 Sg 1 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15762 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHmecH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60InputStdRawRep1 HL-60 In Sg 1 Input HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000465 465 GSM945255 Stam UW DS13664 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHl60InputStdRawRep1 None RawSignal promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdRawRep2 HL-60 H3K4M3 Sg 2 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11797 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHl60H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdRawRep1 HL-60 H3K4M3 Sg 1 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11795 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHl60H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycInputStdRawRep1 HFMc In Sg 1 Input HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001896 1896 GSM945281 Stam UW DS18321 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHffmycInputStdRawRep1 None RawSignal foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFFMyc Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdRawRep2 HFMc H3K4M3 Sg 2 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18325 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHffmycH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFFMyc H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdRawRep1 HFMc H3K4M3 Sg 1 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18324 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHffmycH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFFMyc H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffInputStdRawRep1 HFF In Sg 1 Input HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002043 2043 GSM945219 Stam UW DS18316 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHffInputStdRawRep1 None RawSignal foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffH3k04me3StdRawRep1 HFF H3K4M3 Sg 1 H3K4me3 HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002042 2042 GSM945218 Stam UW DS18320 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHffH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293InputStdRawRep1 HEK In Sg 1 Input HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000464 464 GSM945256 Stam UW DS13603 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHek293InputStdRawRep1 None RawSignal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdRawRep2 HEK H3K4M3 Sg 2 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15759 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHek293H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdRawRep1 HEK H3K4M3 Sg 1 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15760 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHek293H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeInputStdRawRep1 HEE In Sg 1 Input HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000952 952 GSM945289 Stam UW DS16057 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHeeInputStdRawRep1 None RawSignal esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdRawRep2 HEE H3K4M3 Sg 2 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16061 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHeeH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdRawRep1 HEE H3K4M3 Sg 1 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16060 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHeeH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116InputStdRawRep1 HCT16 In Sg 1 Input HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000950 950 GSM945287 Stam UW DS16013 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHct116InputStdRawRep1 None RawSignal colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdRawRep2 HCT16 H3K4M3 Sg 2 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16055 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHct116H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdRawRep1 HCT16 H3K4M3 Sg 1 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16056 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHct116H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeInputStdRawRep1 HCPE In Sg 1 Input HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000948 948 GSM945303 Stam UW DS15917 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHcpeInputStdRawRep1 None RawSignal choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpiC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdRawRep2 HCPE H3K4M3 Sg 2 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15757 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHcpeH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpiC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdRawRep1 HCPE H3K4M3 Sg 1 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15758 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHcpeH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpiC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmInputStdRawRep1 HCM In Sg 1 Input HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000946 946 GSM945305 Stam UW DS15916 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHcmInputStdRawRep1 None RawSignal cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdRawRep2 HCM H3K4M3 Sg 2 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15756 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHcmH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdRawRep1 HCM H3K4M3 Sg 1 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15755 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHcmH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfaaInputStdRawRep1 HCFa In Sg 1 Input HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000944 944 GSM945307 Stam UW DS15915 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHcfaaInputStdRawRep1 None RawSignal cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfaaH3k4me3StdRawRep1 HCFa H3K4M3 Sg 1 H3K4me3 HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000943 943 GSM945310 Stam UW DS15754 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHcfaaH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfInputStdRawRep1 HCF In Sg 1 Input HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000942 942 GSM945309 Stam UW DS15914 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHcfInputStdRawRep1 None RawSignal cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdRawRep2 HCF H3K4M3 Sg 2 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15753 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHcfH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdRawRep1 HCF H3K4M3 Sg 1 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15751 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHcfH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecInputStdRawRep1 HBMEC In Sg 1 Input HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000940 940 GSM945311 Stam UW DS15913 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHbmecInputStdRawRep1 None RawSignal brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdRawRep2 HBMEC H3K4M3 Sg 2 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15748 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHbmecH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdRawRep1 HBMEC H3K4M3 Sg 1 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15749 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHbmecH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspInputStdRawRep1 HAsp In Sg 1 Input HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000974 974 GSM945248 Stam UW DS16041 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHaspInputStdRawRep1 None RawSignal astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdRawRep2 HAsp H3K4M3 Sg 2 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16045 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHaspH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdRawRep1 HAsp H3K4M3 Sg 1 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16044 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHaspH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacInputStdRawRep1 HAc In Sg 1 Input HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002165 2165 GSM945227 Stam UW DS18311 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHacInputStdRawRep1 None RawSignal astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdRawRep2 HAc H3K4M3 Sg 2 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18314 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHacH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdRawRep1 HAc H3K4M3 Sg 1 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18315 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHacH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000926 926 GSM945186 Stam UW DS14109 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdRawRep1 None RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdDiffa14dRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002532 2532 GSM945319 Stam UW DS14111 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdDiffa14dRawRep1 diffProtA_14d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input diffProtA 14 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdDiffa9dRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002545 2545 GSM945193 Stam UW DS15393 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdDiffa9dRawRep1 diffProtA_9d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input diffProtA 9 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdDiffa5dRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002544 2544 GSM945194 Stam UW DS14110 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdDiffa5dRawRep1 diffProtA_5d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input diffProtA 5 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdDiffa2dRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002543 2543 GSM945189 Stam UW DS15392 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdDiffa2dRawRep1 diffProtA_2d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input diffProtA 2 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14114 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14115 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14650 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dRawRep2 diffProtA_14d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14123 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dRawRep1 diffProtA_14d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS15386 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dRawRep2 diffProtA_9d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS14648 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dRawRep1 diffProtA_9d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14120 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dRawRep2 diffProtA_5d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14119 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dRawRep1 diffProtA_5d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS14646 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dRawRep2 diffProtA_2d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS15385 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dRawRep1 diffProtA_2d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS14113 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS13428 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14122 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dRawRep2 diffProtA_14d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14649 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dRawRep1 diffProtA_14d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14709 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dRawRep2 diffProtA_9d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14647 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dRawRep1 diffProtA_9d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS14118 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dRawRep2 diffProtA_5d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS13778 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dRawRep1 diffProtA_5d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14708 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dRawRep2 diffProtA_2d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14645 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dRawRep1 diffProtA_2d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS14112 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS13427 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002530 2530 GSM945321 Stam UW DS14707 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dRawRep2 diffProtA_14d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002530 2530 GSM945321 Stam UW DS14121 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dRawRep1 diffProtA_14d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14705 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dRawRep2 diffProtA_9d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14706 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dRawRep1 diffProtA_9d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002531 2531 GSM945322 Stam UW DS14116 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dRawRep2 diffProtA_5d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002531 2531 GSM945322 Stam UW DS13777 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dRawRep1 diffProtA_5d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14703 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dRawRep2 diffProtA_2d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14704 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dRawRep1 diffProtA_2d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12875InputStdRawRep1 GM75 In Sg 1 Input GM12875 std ChipSeq ENCODE Mar 2012 Freeze 2010-06-15 2010-11-18 wgEncodeEH000462 462 GSM945260 Stam UW DS13589 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm12875InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12875H3k04me3StdRawRep1 GM75 H3K4M3 Sg 1 H3K4me3 GM12875 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002041 2041 GSM945221 Stam UW DS18910 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneGm12875H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865InputStdRawRep1 GM65 In Sg 1 Input GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2010-06-15 2010-11-18 wgEncodeEH000458 458 GSM945234 Stam UW DS13590 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm12865InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdRawRep2 GM65 H3K4M3 Sg 2 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002039 2039 GSM945295 Stam UW DS20810 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneGm12865H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdRawRep1 GM65 H3K4M3 Sg 1 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002039 2039 GSM945295 Stam UW DS18707 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneGm12865H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864InputStdRawRep1 GM64 In Sg 1 Input GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2010-06-15 2010-11-18 wgEncodeEH000457 457 GSM945238 Stam UW DS13587 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm12864InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdRawRep2 GM64 H3K4M3 Sg 2 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18900 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneGm12864H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdRawRep1 GM64 H3K4M3 Sg 1 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18706 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneGm12864H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990InputStdRawRep1 GM90 In Sg 1 Input GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000455 455 GSM945237 Stam UW DS11497 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm06990InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdRawRep2 GM90 H3K36M3 Sg 2 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12189 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm06990H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdRawRep1 GM90 H3K36M3 Sg 1 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12192 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm06990H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdRawRep2 GM90 H3K27M3 Sg 2 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000427 427 GSM945205 Stam UW DS12188 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm06990H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdRawRep1 GM90 H3K27M3 Sg 1 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000427 427 GSM945205 Stam UW DS12191 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm06990H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdRawRep2 GM90 H3K4M3 Sg 2 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-12 2010-07-11 wgEncodeEH000417 417 GSM945179 Stam UW DS11519 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm06990H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdRawRep1 GM90 H3K4M3 Sg 1 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-13 2010-07-12 wgEncodeEH000417 417 GSM945179 Stam UW DS11521 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm06990H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2InputStdRawRep1 Caco In Sg 1 Input Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000454 454 GSM945236 Stam UW DS13597 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneCaco2InputStdRawRep1 None RawSignal colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdRawRep2 Caco H3K36M3 Sg 2 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12405 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneCaco2H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdRawRep1 Caco H3K36M3 Sg 1 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12406 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneCaco2H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdRawRep2 Caco H3K27M3 Sg 2 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000425 425 GSM945203 Stam UW DS12218 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneCaco2H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdRawRep1 Caco H3K27M3 Sg 1 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-20 2010-07-20 wgEncodeEH000425 425 GSM945203 Stam UW DS12221 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneCaco2H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdRawRep2 Caco H3K4M3 Sg 2 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11785 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneCaco2H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdRawRep1 Caco H3K4M3 Sg 1 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11784 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneCaco2H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjInputStdRawRep1 BJ In Sg 1 Input BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000453 453 GSM945235 Stam UW DS11544 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneBjInputStdRawRep1 None RawSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdRawRep2 BJ H3K36M3 Sg 2 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12195 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneBjH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdRawRep1 BJ H3K36M3 Sg 1 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12198 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneBjH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdRawRep2 BJ H3K27M3 Sg 2 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-20 2010-07-20 wgEncodeEH000424 424 GSM945204 Stam UW DS12197 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneBjH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdRawRep1 BJ H3K27M3 Sg 1 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000424 424 GSM945204 Stam UW DS12194 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneBjH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdRawRep2 BJ H3K4M3 Sg 2 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000416 416 GSM945178 Stam UW DS11561 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneBjH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdRawRep1 BJ H3K4M3 Sg 1 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-13 2010-07-12 wgEncodeEH000416 416 GSM945178 Stam UW DS11563 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneBjH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cInputStdRawRep1 BE2_C In Sg 1 Input BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001892 1892 GSM945283 Stam UW DS18306 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneBe2cInputStdRawRep1 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdRawRep2 BE2_C H3K4M3 Sg 2 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18310 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneBe2cH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdRawRep1 BE2_C H3K4M3 Sg 1 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18309 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneBe2cH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafInputStdRawRep1 AoAF In Sg 1 Input AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000938 938 GSM945164 Stam UW DS15912 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAoafInputStdRawRep1 None RawSignal aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdRawRep2 AoAF H3K4M3 Sg 2 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15747 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAoafH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdRawRep1 AoAF H3K4M3 Sg 1 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15746 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAoafH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803InputStdRawRep1 AG03 In Sg 1 Input AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000936 936 GSM945171 Stam UW DS15911 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg10803InputStdRawRep1 None RawSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdRawRep2 AG03 H3K4M3 Sg 2 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15745 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg10803H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdRawRep1 AG03 H3K4M3 Sg 1 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15744 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg10803H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319InputStdRawRep1 AG19 In Sg 1 Input AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000934 934 GSM945173 Stam UW DS15910 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg09319InputStdRawRep1 None RawSignal gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdRawRep2 AG19 H3K4M3 Sg 2 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15743 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg09319H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdRawRep1 AG19 H3K4M3 Sg 1 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15742 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg09319H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309InputStdRawRep1 AG09 In Sg 1 Input AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000932 932 GSM945167 Stam UW DS16030 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg09309InputStdRawRep1 None RawSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdRawRep2 AG09 H3K4M3 Sg 2 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16033 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg09309H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdRawRep1 AG09 H3K4M3 Sg 1 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16034 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg09309H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450InputStdRawRep1 AG50 In Sg 1 Input AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000930 930 GSM945169 Stam UW DS15909 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg04450InputStdRawRep1 None RawSignal fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27me3StdRawRep1 AG50 H3K27m3 Rw 1 H3K27me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003036 3036 GSM1010913 Stam UW DS21480 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04450H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27acStdRawRep1 AG50 H3K27ac Rw 1 H3K27ac AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003035 3035 GSM1010912 Stam UW DS21479 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04450H3k27acStdRawRep1 None RawSignal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K27ac Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdRawRep2 AG50 H3K9m3 Raw 2 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21481 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg04450H3k09me3StdRawRep2 None RawSignal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K9me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdRawRep1 AG50 H3K9m3 Raw 1 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21482 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04450H3k09me3StdRawRep1 None RawSignal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K9me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdRawRep2 AG50 H3K4M3 Sg 2 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15741 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg04450H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdRawRep1 AG50 H3K4M3 Sg 1 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15740 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04450H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449InputStdRawRep1 AG49 In Sg 1 Input AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000928 928 GSM945176 Stam UW DS15908 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg04449InputStdRawRep1 None RawSignal fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdRawRep2 AG49 H3K4M3 Sg 2 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15739 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg04449H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdRawRep1 AG49 H3K4M3 Sg 1 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15737 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04449H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746InputStdRawRep1 CD14 In Sg 1 Input Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002169 2169 GSM945224 Stam UW DS18980 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneMonocd14ro1746InputStdRawRep1 None RawSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Monocytes-CD14+ RO 01746 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k27me3StdRawRep1 CD14 H3K27M3 Sg 1 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002167 2167 GSM945301 Stam UW DS19094 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Monocytes-CD14+ RO 01746 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k04me3StdRawRep1 CD14 H3K4M3 Sg 1 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002168 2168 GSM945225 Stam UW DS18981 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Monocytes-CD14+ RO 01746 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7InputStdRawRep1 MCF7 In Sg 1 Input MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000968 968 GSM945274 Stam UW DS16198 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneMcf7InputStdRawRep1 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k04me3StdRawRep2 MCF7 H3K4M3 Sg 2 H3K4me3 MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000967 967 GSM945269 Stam UW DS16201 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneMcf7H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k4me3StdRawRep1 MCF7 H3K4M3 Sg 1 H3K4me3 MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000967 967 GSM945269 Stam UW DS16202 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneMcf7H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecInputStdRawRep1 HUVE In Sg 1 Input HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000468 468 GSM945254 Stam UW DS11470 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHuvecInputStdRawRep1 None RawSignal umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdRawRep2 HUVE H3K36M3 Sg 2 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000431 431 GSM945233 Stam UW DS12225 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHuvecH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdRawRep1 HUVE H3K36M3 Sg 1 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000431 431 GSM945233 Stam UW DS12228 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHuvecH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdRawRep2 HUVE H3K27M3 Sg 2 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-12 wgEncodeEH000411 411 GSM945180 Stam UW DS12224 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHuvecH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdRawRep1 HUVE H3K27M3 Sg 1 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000411 411 GSM945180 Stam UW DS12227 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHuvecH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdRawRep2 HUVE H3K4M3 Sg 2 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000412 412 GSM945181 Stam UW DS11458 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHuvecH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdRawRep1 HUVE H3K4M3 Sg 1 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000412 412 GSM945181 Stam UW DS11460 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHuvecH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2InputStdRawRep1 HepG In Sg 1 Input HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000470 470 GSM945291 Stam UW DS13599 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHepg2InputStdRawRep1 None RawSignal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdRawRep2 HepG H3K36M3 Sg 2 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000446 446 GSM945211 Stam UW DS12075 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHepg2H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdRawRep1 HepG H3K36M3 Sg 1 H3K36me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000446 446 GSM945211 Stam UW DS12207 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHepg2H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdRawRep2 HepG H3K27M3 Sg 2 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12206 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHepg2H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdRawRep1 HepG H3K27M3 Sg 1 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12076 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHepg2H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdRawRep2 HepG H3K4M3 Sg 2 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11780 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHepg2H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdRawRep1 HepG H3K4M3 Sg 1 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11781 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHepg2H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3InputStdRawRep1 HeLa In Sg 1 Input HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000469 469 GSM945253 Stam UW DS11540 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHelas3InputStdRawRep1 None RawSignal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdRawRep2 HeLa H3K36M3 Sg 2 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12201 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHelas3H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdRawRep1 HeLa H3K36M3 Sg 1 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12071 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHelas3H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdRawRep2 HeLa H3K27M3 Sg 2 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12070 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHelas3H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdRawRep1 HeLa H3K27M3 Sg 1 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12072 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHelas3H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdRawRep2 HeLa H3K4M3 Sg 2 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11553 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHelas3H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdRawRep1 HeLa H3K4M3 Sg 1 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11555 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHelas3H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01794InputStdRawRep1 20+94 In Sg 1 Input CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002172 2172 GSM945195 Stam UW DS18982 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneCd20ro01794InputStdRawRep1 None RawSignal B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01794) Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01794H3k04me3StdRawRep3 20+94 H3K4M3 Sg 3 H3K4me3 CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002171 2171 GSM945198 Stam UW DS18983 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwHistoneCd20ro01794H3k04me3StdRawRep3 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01794) H3K4me3 Histone Mod ChIP-seq Raw Sig 3 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778InputStdRawRep1 20+78 In Sg 1 Input CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-25 wgEncodeEH002170 2170 GSM945197 Stam UW DS18984 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneCd20ro01778InputStdRawRep1 None RawSignal B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01778) Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdRawRep2 20+78 H3K4M3 Sg 2 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002166 2166 GSM945229 Stam UW DS18986 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdRawRep1 20+78 H3K4M3 Sg 1 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002166 2166 GSM945229 Stam UW DS18985 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549InputStdRawRep1 A549 In Sg 1 Input A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH001904 1904 GSM945243 Stam UW DS18301 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneA549InputStdRawRep1 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdRawRep2 A549 H3K4M3 Sg 2 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18304 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneA549H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdRawRep1 A549 H3K4M3 Sg 1 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18305 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneA549H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562InputStdRawRep1 K562 In Sg 1 Input K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000471 471 GSM945294 Stam UW DS11488 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneK562InputStdRawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdRawRep2 K562 H3K36M3 Sg 2 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12177 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneK562H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdRawRep1 K562 H3K36M3 Sg 1 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12067 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneK562H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdRawRep2 K562 H3K27M3 Sg 2 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12068 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneK562H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdRawRep1 K562 H3K27M3 Sg 1 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12066 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneK562H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdRawRep2 K562 H3K4M3 Sg 2 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000400 400 GSM945165 Stam UW DS11509 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneK562H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdRawRep1 K562 H3K4M3 Sg 1 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000400 400 GSM945165 Stam UW DS11507 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneK562H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878InputStdRawRep1 GM78 In Sg 1 Input GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000463 463 GSM945259 Stam UW DS11883 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm12878InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdRawRep2 GM78 H3K36M3 Sg 2 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12183 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm12878H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdRawRep1 GM78 H3K36M3 Sg 1 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12186 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm12878H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdRawRep2 GM78 H3K27M3 Sg 2 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000428 428 GSM945196 Stam UW DS12185 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm12878H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdRawRep1 GM78 H3K27M3 Sg 1 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000428 428 GSM945196 Stam UW DS12182 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm12878H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdRawRep2 GM78 H3K4M3 Sg 2 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-12 2010-07-11 wgEncodeEH000395 395 GSM945188 Stam UW DS11511 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm12878H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdRawRep1 GM78 H3K4M3 Sg 1 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-06-30 2010-03-29 wgEncodeEH000395 395 GSM945188 Stam UW DS11513 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm12878H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwHistoneWi38H3k04me3StdPkRep2 WI38 H3K4M3 Pk 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18349 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3StdPkRep1 WI38 H3K4M3 Pk 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18350 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep2 WI38 H3K4M3 Pk 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18354 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep2 4OHTAM_20nM_72hr Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Regions of enriched signal in experiment WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep1 WI38 H3K4M3 Pk 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18355 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep1 4OHTAM_20nM_72hr Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Regions of enriched signal in experiment WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdPkRep2 WERI H3K4M3 Pk 2 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16213 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneWerirb1H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdPkRep1 WERI H3K4M3 Pk 1 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16214 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneWerirb1H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdPkRep2 SKRA H3K36M3 Pk 2 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000441 441 GSM945209 Stam UW DS12403 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSknshraH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdPkRep1 SKRA H3K36M3 Pk 1 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12404 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSknshraH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdPkRep2 SKRA H3K27M3 Pk 2 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000440 440 GSM945210 Stam UW DS12215 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSknshraH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdPkRep1 SKRA H3K27M3 Pk 1 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000440 440 GSM945210 Stam UW DS12212 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSknshraH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdPkRep2 SKRA H3K4M3 Pk 2 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000422 422 GSM945202 Stam UW DS11783 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSknshraH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdPkRep1 SKRA H3K4M3 Pk 1 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11782 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSknshraH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdPkRep2 SKNMC H3K4M3 Pk 2 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18345 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneSknmcH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-MC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdPkRep1 SKNMC H3K4M3 Pk 1 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18344 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneSknmcH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-MC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdPkRep2 SKMC H3K4M3 Pk 2 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16212 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneSkmcH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SKMC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdPkRep1 SKMC H3K4M3 Pk 1 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16211 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneSkmcH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SKMC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdPkRep2 SAEC H3K36M3 Pk 2 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000438 438 GSM945226 Stam UW DS12246 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSaecH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdPkRep1 SAEC H3K36M3 Pk 1 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12243 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSaecH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdPkRep2 SAEC H3K27M3 Pk 2 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000420 420 GSM945200 Stam UW DS12245 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSaecH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdPkRep1 SAEC H3K27M3 Pk 1 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000420 420 GSM945200 Stam UW DS12242 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSaecH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdPkRep2 SAEC H3K4M3 Pk 2 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000421 421 GSM945199 Stam UW DS11579 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSaecH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdPkRep1 SAEC H3K4M3 Pk 1 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11577 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSaecH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdPkRep2 RPTEC H3K4M3 Pk 2 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18339 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneRptecH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdPkRep1 RPTEC H3K4M3 Pk 1 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18340 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneRptecH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdPkRep2 PANC1 H3K4M3 Pk 2 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18334 lmax-v1.0 hg19 2 exp wgEncodeUwHistonePanc1H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PANC-1 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdPkRep1 PANC1 H3K4M3 Pk 1 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18335 lmax-v1.0 hg19 1 exp wgEncodeUwHistonePanc1H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PANC-1 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdPkRep2 NHLF H3K4M3 Pk 2 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16350 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneNhlfH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdPkRep1 NHLF H3K4M3 Pk 1 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16351 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneNhlfH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdPkRep2 NHEK H3K36M3 Pk 2 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000414 414 GSM945174 Stam UW DS12240 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneNhekH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdPkRep1 NHEK H3K36M3 Pk 1 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12237 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneNhekH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdPkRep2 NHEK H3K27M3 Pk 2 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-16 2011-03-15 wgEncodeEH000436 436 GSM945300 Stam UW DS12080 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneNhekH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdPkRep1 NHEK H3K27M3 Pk 1 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12078 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneNhekH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdPkRep2 NHEK H3K4M3 Pk 2 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000415 415 GSM945175 Stam UW DS11557 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneNhekH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdPkRep1 NHEK H3K4M3 Pk 1 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000415 415 GSM945175 Stam UW DS11559 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneNhekH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdPkRep2 NHDF H3K4M3 Pk 2 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16207 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneNhdfneoH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdPkRep1 NHDF H3K4M3 Pk 1 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16206 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneNhdfneoH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNb4H3k4me3StdPkRep1 NB4 H3K4M3 Pk 1 H3K4me3 NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000969 969 GSM945275 Stam UW DS16346 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneNb4H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NB4 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdPkRep2 LNCP H3K4M3 Pk 2 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18329 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneLncapH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment LNCaP H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdPkRep1 LNCP H3K4M3 Pk 1 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18330 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneLncapH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment LNCaP H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdPkRep2 Jurk H3K4M3 Pk 2 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16196 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneJurkatH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Jurkat H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdPkRep1 Jurk H3K4M3 Pk 1 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16197 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneJurkatH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Jurkat H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdPkRep2 HVMF H3K4M3 Pk 2 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16155 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHvmfH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdPkRep1 HVMF H3K4M3 Pk 1 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16156 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHvmfH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdPkRep2 HRPE H3K4M3 Pk 2 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16188 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHrpeH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpIC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdPkRep1 HRPE H3K4M3 Pk 1 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16189 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHrpeH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpIC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdPkRep2 HRE H3K36M3 Pk 2 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000430 430 GSM945232 Stam UW DS12418 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHreH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdPkRep1 HRE H3K36M3 Pk 1 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12234 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHreH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdPkRep2 HRE H3K27M3 Pk 2 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000429 429 GSM945160 Stam UW DS12415 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHreH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdPkRep1 HRE H3K27M3 Pk 1 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-20 2010-07-20 wgEncodeEH000429 429 GSM945160 Stam UW DS12422 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHreH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdPkRep2 HRE H3K4M3 Pk 2 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000409 409 GSM945276 Stam UW DS11573 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHreH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdPkRep1 HRE H3K4M3 Pk 1 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000409 409 GSM945276 Stam UW DS11575 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHreH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdPkRep2 HPF H3K4M3 Pk 2 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16183 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHpfH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdPkRep1 HPF H3K4M3 Pk 1 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16184 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHpfH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdPkRep2 HPAF H3K4M3 Pk 2 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16154 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHpafH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdPkRep1 HPAF H3K4M3 Pk 1 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16153 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHpafH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdPkRep2 HMF H3K4M3 Pk 2 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16152 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHmfH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdPkRep1 HMF H3K4M3 Pk 1 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16151 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHmfH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k27me3StdPkRep1 HMEC H3K27M3 Pk 1 H3K27me3 HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000408 408 GSM945277 Stam UW DS12082 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHmecH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdPkRep2 HMEC H3K4M3 Pk 2 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15761 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHmecH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdPkRep1 HMEC H3K4M3 Pk 1 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15762 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHmecH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdPkRep2 HL-60 H3K4M3 Pk 2 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000418 418 GSM945222 Stam UW DS11797 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHl60H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdPkRep1 HL-60 H3K4M3 Pk 1 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11795 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHl60H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdPkRep2 HFMc H3K4M3 Pk 2 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18325 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHffmycH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFFMyc H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdPkRep1 HFMc H3K4M3 Pk 1 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18324 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHffmycH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFFMyc H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffH3k04me3StdPkRep1 HFF H3K4M3 Pk 1 H3K4me3 HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002042 2042 GSM945218 Stam UW DS18320 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHffH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdPkRep2 HEK H3K4M3 Pk 2 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15759 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHek293H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEK293 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdPkRep1 HEK H3K4M3 Pk 1 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15760 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHek293H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEK293 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdPkRep2 HEE H3K4M3 Pk 2 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16061 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHeeH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpIC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdPkRep1 HEE H3K4M3 Pk 1 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16060 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHeeH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpIC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdPkRep2 HCT16 H3K4M3 Pk 2 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16055 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHct116H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdPkRep1 HCT16 H3K4M3 Pk 1 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16056 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHct116H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdPkRep2 HCPE H3K4M3 Pk 2 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15757 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHcpeH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpiC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdPkRep1 HCPE H3K4M3 Pk 1 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15758 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHcpeH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpiC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdPkRep2 HCM H3K4M3 Pk 2 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15756 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHcmH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdPkRep1 HCM H3K4M3 Pk 1 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15755 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHcmH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfaaH3k4me3StdPkRep1 HCFa H3K4M3 Pk 1 H3K4me3 HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000943 943 GSM945310 Stam UW DS15754 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHcfaaH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCFaa H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdPkRep2 HCF H3K4M3 Pk 2 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15753 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHcfH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdPkRep1 HCF H3K4M3 Pk 1 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15751 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHcfH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdPkRep2 HBMEC H3K4M3 Pk 2 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15748 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHbmecH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdPkRep1 HBMEC H3K4M3 Pk 1 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15749 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHbmecH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdPkRep2 HAsp H3K4M3 Pk 2 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16045 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHaspH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdPkRep1 HAsp H3K4M3 Pk 1 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16044 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHaspH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdPkRep2 HAc H3K4M3 Pk 2 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18314 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHacH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdPkRep1 HAc H3K4M3 Pk 1 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18315 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHacH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14114 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14115 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14650 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dPkRep2 diffProtA_14d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14123 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dPkRep1 diffProtA_14d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS15386 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dPkRep2 diffProtA_9d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS14648 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dPkRep1 diffProtA_9d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14120 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dPkRep2 diffProtA_5d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14119 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dPkRep1 diffProtA_5d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS14646 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dPkRep2 diffProtA_2d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS15385 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dPkRep1 diffProtA_2d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS14113 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS13428 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14122 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dPkRep2 diffProtA_14d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14649 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dPkRep1 diffProtA_14d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14709 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dPkRep2 diffProtA_9d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14647 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dPkRep1 diffProtA_9d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS14118 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dPkRep2 diffProtA_5d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS13778 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dPkRep1 diffProtA_5d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14708 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dPkRep2 diffProtA_2d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14645 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dPkRep1 diffProtA_2d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS14112 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS13427 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002530 2530 GSM945321 Stam UW DS14707 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dPkRep2 diffProtA_14d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002530 2530 GSM945321 Stam UW DS14121 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dPkRep1 diffProtA_14d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14705 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dPkRep2 diffProtA_9d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14706 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dPkRep1 diffProtA_9d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002531 2531 GSM945322 Stam UW DS14116 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dPkRep2 diffProtA_5d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002531 2531 GSM945322 Stam UW DS13777 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dPkRep1 diffProtA_5d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14703 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dPkRep2 diffProtA_2d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14704 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dPkRep1 diffProtA_2d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12875H3k04me3StdPkRep1 GM75 H3K4M3 Pk 1 H3K4me3 GM12875 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002041 2041 GSM945221 Stam UW DS18910 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneGm12875H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12875 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdPkRep2 GM65 H3K4M3 Pk 2 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002039 2039 GSM945295 Stam UW DS20810 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneGm12865H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdPkRep1 GM65 H3K4M3 Pk 1 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002039 2039 GSM945295 Stam UW DS18707 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneGm12865H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdPkRep2 GM64 H3K4M3 Pk 2 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18900 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneGm12864H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdPkRep1 GM64 H3K4M3 Pk 1 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18706 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneGm12864H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdPkRep2 GM90 H3K36M3 Pk 2 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12189 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm06990H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdPkRep1 GM90 H3K36M3 Pk 1 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-22 2010-07-21 wgEncodeEH000444 444 GSM945213 Stam UW DS12192 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm06990H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdPkRep2 GM90 H3K27M3 Pk 2 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2010-06-11 2011-03-11 wgEncodeEH000427 427 GSM945205 Stam UW DS12188 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm06990H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdPkRep1 GM90 H3K27M3 Pk 1 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000427 427 GSM945205 Stam UW DS12191 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm06990H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdPkRep2 GM90 H3K4M3 Pk 2 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2010-06-11 2011-03-11 wgEncodeEH000417 417 GSM945179 Stam UW DS11519 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm06990H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdPkRep1 GM90 H3K4M3 Pk 1 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-13 2010-07-12 wgEncodeEH000417 417 GSM945179 Stam UW DS11521 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm06990H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdPkRep2 Caco H3K36M3 Pk 2 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2010-06-11 2011-03-11 wgEncodeEH000426 426 GSM945206 Stam UW DS12405 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneCaco2H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdPkRep1 Caco H3K36M3 Pk 1 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12406 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneCaco2H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdPkRep2 Caco H3K27M3 Pk 2 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000425 425 GSM945203 Stam UW DS12218 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneCaco2H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdPkRep1 Caco H3K27M3 Pk 1 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-20 2010-07-20 wgEncodeEH000425 425 GSM945203 Stam UW DS12221 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneCaco2H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdPkRep2 Caco H3K4M3 Pk 2 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2010-06-11 2011-03-11 wgEncodeEH000407 407 GSM945162 Stam UW DS11785 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneCaco2H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdPkRep1 Caco H3K4M3 Pk 1 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11784 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneCaco2H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdPkRep2 BJ H3K36M3 Pk 2 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12195 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneBjH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdPkRep1 BJ H3K36M3 Pk 1 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-22 2010-07-21 wgEncodeEH000443 443 GSM945207 Stam UW DS12198 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneBjH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdPkRep2 BJ H3K27M3 Pk 2 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000424 424 GSM945204 Stam UW DS12197 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneBjH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdPkRep1 BJ H3K27M3 Pk 1 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000424 424 GSM945204 Stam UW DS12194 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneBjH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdPkRep2 BJ H3K4M3 Pk 2 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000416 416 GSM945178 Stam UW DS11561 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneBjH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdPkRep1 BJ H3K4M3 Pk 1 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-13 2010-07-12 wgEncodeEH000416 416 GSM945178 Stam UW DS11563 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneBjH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdPkRep2 BE2_C H3K4M3 Pk 2 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18310 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneBe2cH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2_C H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdPkRep1 BE2_C H3K4M3 Pk 1 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18309 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneBe2cH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2_C H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdPkRep2 AoAF H3K4M3 Pk 2 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15747 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAoafH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdPkRep1 AoAF H3K4M3 Pk 1 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15746 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAoafH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdPkRep2 AG03 H3K4M3 Pk 2 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15745 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg10803H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdPkRep1 AG03 H3K4M3 Pk 1 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15744 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg10803H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdPkRep2 AG19 H3K4M3 Pk 2 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15743 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg09319H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdPkRep1 AG19 H3K4M3 Pk 1 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15742 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg09319H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdPkRep2 AG09 H3K4M3 Pk 2 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16033 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg09309H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdPkRep1 AG09 H3K4M3 Pk 1 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16034 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg09309H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27me3StdPkRep1 AG50 H3K27m3 Pk 1 H3K27me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003036 3036 GSM1010913 Stam UW DS21480 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04450H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27acStdPkRep1 AG50 H3K27ac Pk 1 H3K27ac AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003035 3035 GSM1010912 Stam UW DS21479 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04450H3k27acStdPkRep1 None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K27ac Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdPkRep2 AG50 H3K9me3 Pk 2 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21481 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg04450H3k09me3StdPkRep2 None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K9me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdPkRep1 AG50 H3K9me3 Pk 1 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21482 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04450H3k09me3StdPkRep1 None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K9me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdPkRep2 AG50 H3K4M3 Pk 2 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15741 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg04450H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdPkRep1 AG50 H3K4M3 Pk 1 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15740 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04450H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdPkRep2 AG49 H3K4M3 Pk 2 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15739 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg04449H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdPkRep1 AG49 H3K4M3 Pk 1 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15737 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04449H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k27me3StdPkRep1 CD14 H3K27M3 Pk 1 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002167 2167 GSM945301 Stam UW DS19094 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Monocytes-CD14+ RO 01746 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k04me3StdPkRep1 CD14 H3K4M3 Pk 1 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002168 2168 GSM945225 Stam UW DS18981 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Monocytes-CD14+ RO 01746 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k04me3StdPkRep2 MCF7 H3K4M3 Pk 2 H3K4me3 MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000967 967 GSM945269 Stam UW DS16201 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneMcf7H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k4me3StdPkRep1 MCF7 H3K4M3 Pk 1 H3K4me3 MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000967 967 GSM945269 Stam UW DS16202 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneMcf7H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdPkRep2 HUVE H3K36M3 Pk 2 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000431 431 GSM945233 Stam UW DS12225 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHuvecH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdPkRep1 HUVE H3K36M3 Pk 1 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000431 431 GSM945233 Stam UW DS12228 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHuvecH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdPkRep2 HUVE H3K27M3 Pk 2 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000411 411 GSM945180 Stam UW DS12224 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHuvecH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdPkRep1 HUVE H3K27M3 Pk 1 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000411 411 GSM945180 Stam UW DS12227 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHuvecH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdPkRep2 HUVE H3K4M3 Pk 2 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000412 412 GSM945181 Stam UW DS11458 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHuvecH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdPkRep1 HUVE H3K4M3 Pk 1 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000412 412 GSM945181 Stam UW DS11460 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHuvecH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdPkRep2 HepG H3K36M3 Pk 2 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000446 446 GSM945211 Stam UW DS12075 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHepg2H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdPkRep1 HepG H3K36M3 Pk 1 H3K36me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-22 2010-07-21 wgEncodeEH000446 446 GSM945211 Stam UW DS12207 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHepg2H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdPkRep2 HepG H3K27M3 Pk 2 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000433 433 GSM945231 Stam UW DS12206 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHepg2H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdPkRep1 HepG H3K27M3 Pk 1 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12076 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHepg2H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdPkRep2 HepG H3K4M3 Pk 2 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000413 413 GSM945182 Stam UW DS11780 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHepg2H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdPkRep1 HepG H3K4M3 Pk 1 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11781 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHepg2H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdPkRep2 HeLa H3K36M3 Pk 2 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000432 432 GSM945230 Stam UW DS12201 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHelas3H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdPkRep1 HeLa H3K36M3 Pk 1 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12071 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHelas3H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdPkRep2 HeLa H3K27M3 Pk 2 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000442 442 GSM945208 Stam UW DS12070 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHelas3H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdPkRep1 HeLa H3K27M3 Pk 1 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12072 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHelas3H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdPkRep2 HeLa H3K4M3 Pk 2 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000423 423 GSM945201 Stam UW DS11553 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHelas3H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdPkRep1 HeLa H3K4M3 Pk 1 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11555 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHelas3H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01794H3k04me3StdPkRep3 20+94 H3K4M3 Pk 3 H3K4me3 CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002171 2171 GSM945198 Stam UW DS18983 lmax-v1.0 hg19 3 exp wgEncodeUwHistoneCd20ro01794H3k04me3StdPkRep3 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD20+ (RO 01794) H3K4me3 Histone Mod ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdPkRep2 20+78 H3K4M3 Pk 2 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002166 2166 GSM945229 Stam UW DS18986 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdPkRep1 20+78 H3K4M3 Pk 1 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002166 2166 GSM945229 Stam UW DS18985 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdPkRep2 A549 H3K4M3 Pk 2 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18304 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneA549H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdPkRep1 A549 H3K4M3 Pk 1 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18305 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneA549H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdPkRep2 K562 H3K36M3 Pk 2 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000435 435 GSM945302 Stam UW DS12177 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneK562H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdPkRep1 K562 H3K36M3 Pk 1 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12067 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneK562H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdPkRep2 K562 H3K27M3 Pk 2 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000434 434 GSM945228 Stam UW DS12068 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneK562H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdPkRep1 K562 H3K27M3 Pk 1 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12066 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneK562H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdPkRep2 K562 H3K4M3 Pk 2 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000400 400 GSM945165 Stam UW DS11509 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneK562H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdPkRep1 K562 H3K4M3 Pk 1 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000400 400 GSM945165 Stam UW DS11507 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneK562H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdPkRep2 GM78 H3K36M3 Pk 2 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12183 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm12878H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdPkRep1 GM78 H3K36M3 Pk 1 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-22 2010-07-21 wgEncodeEH000445 445 GSM945212 Stam UW DS12186 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm12878H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdPkRep2 GM78 H3K27M3 Pk 2 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000428 428 GSM945196 Stam UW DS12185 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm12878H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdPkRep1 GM78 H3K27M3 Pk 1 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000428 428 GSM945196 Stam UW DS12182 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm12878H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdPkRep2 GM78 H3K4M3 Pk 2 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-06-30 2010-03-29 wgEncodeEH000395 395 GSM945188 Stam UW DS11511 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm12878H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdPkRep1 GM78 H3K4M3 Pk 1 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-06-30 2010-03-29 wgEncodeEH000395 395 GSM945188 Stam UW DS11513 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm12878H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneViewHot Hotspots Histone Modifications by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwHistoneWi38H3k04me3StdHotspotsRep2 WI38 H3K4M3 Ht 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18349 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3StdHotspotsRep1 WI38 H3K4M3 Ht 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18350 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdHotspotsRep2 WI38 H3K4M3 Ht 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18354 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdHotspotsRep2 4OHTAM_20nM_72hr Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdHotspotsRep1 WI38 H3K4M3 Ht 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18355 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdHotspotsRep1 4OHTAM_20nM_72hr Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdHotspotsRep2 WERI H3K4M3 Ht 2 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16213 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneWerirb1H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdHotspotsRep1 WERI H3K4M3 Ht 1 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16214 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneWerirb1H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdHotspotsRep2 SKRA H3K36M3 Ht 2 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12403 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSknshraH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdHotspotsRep1 SKRA H3K36M3 Ht 1 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12404 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSknshraH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdHotspotsRep2 SKRA H3K27M3 Ht 2 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-20 2010-07-20 wgEncodeEH000440 440 GSM945210 Stam UW DS12215 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSknshraH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdHotspotsRep1 SKRA H3K27M3 Ht 1 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000440 440 GSM945210 Stam UW DS12212 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSknshraH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdHotspotsRep2 SKRA H3K4M3 Ht 2 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11783 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSknshraH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdHotspotsRep1 SKRA H3K4M3 Ht 1 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11782 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSknshraH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdHotspotsRep2 SKNMC H3K4M3 Ht 2 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18345 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneSknmcH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-MC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdHotspotsRep1 SKNMC H3K4M3 Ht 1 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18344 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneSknmcH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-MC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdHotspotsRep2 SKMC H3K4M3 Ht 2 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16212 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneSkmcH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SKMC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdHotspotsRep1 SKMC H3K4M3 Ht 1 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16211 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneSkmcH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SKMC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdHotspotsRep2 SAEC H3K36M3 Ht 2 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12246 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSaecH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdHotspotsRep1 SAEC H3K36M3 Ht 1 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12243 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSaecH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdHotspotsRep2 SAEC H3K27M3 Ht 2 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000420 420 GSM945200 Stam UW DS12245 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSaecH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdHotspotsRep1 SAEC H3K27M3 Ht 1 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000420 420 GSM945200 Stam UW DS12242 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSaecH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdHotspotsRep2 SAEC H3K4M3 Ht 2 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11579 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSaecH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdHotspotsRep1 SAEC H3K4M3 Ht 1 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11577 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSaecH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdHotspotsRep2 RPTEC H3K4M3 Ht 2 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18339 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneRptecH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdHotspotsRep1 RPTEC H3K4M3 Ht 1 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18340 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneRptecH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdHotspotsRep2 PANC1 H3K4M3 Ht 2 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18334 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistonePanc1H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm PANC-1 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdHotspotsRep1 PANC1 H3K4M3 Ht 1 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18335 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistonePanc1H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm PANC-1 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdHotspotsRep2 NHLF H3K4M3 Ht 2 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16350 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneNhlfH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHLF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdHotspotsRep1 NHLF H3K4M3 Ht 1 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16351 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneNhlfH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHLF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdHotspotsRep2 NHEK H3K36M3 Ht 2 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12240 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneNhekH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdHotspotsRep1 NHEK H3K36M3 Ht 1 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12237 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneNhekH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdHotspotsRep2 NHEK H3K27M3 Ht 2 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12080 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneNhekH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdHotspotsRep1 NHEK H3K27M3 Ht 1 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12078 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneNhekH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep2 NHEK H3K4M3 Ht 2 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000415 415 GSM945175 Stam UW DS11557 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep1 NHEK H3K4M3 Ht 1 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000415 415 GSM945175 Stam UW DS11559 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdHotspotsRep2 NHDF H3K4M3 Ht 2 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16207 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneNhdfneoH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdHotspotsRep1 NHDF H3K4M3 Ht 1 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16206 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneNhdfneoH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNb4H3k4me3StdHotspotsRep1 NB4 H3K4M3 Ht 1 H3K4me3 NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000969 969 GSM945275 Stam UW DS16346 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneNb4H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NB4 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdHotspotsRep2 LNCP H3K4M3 Ht 2 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18329 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneLncapH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm LNCaP H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdHotspotsRep1 LNCP H3K4M3 Ht 1 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18330 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneLncapH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm LNCaP H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdHotspotsRep2 Jurk H3K4M3 Ht 2 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16196 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneJurkatH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Jurkat H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdHotspotsRep1 Jurk H3K4M3 Ht 1 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16197 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneJurkatH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Jurkat H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdHotspotsRep2 HVMF H3K4M3 Ht 2 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16155 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHvmfH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdHotspotsRep1 HVMF H3K4M3 Ht 1 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16156 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHvmfH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdHotspotsRep2 HRPE H3K4M3 Ht 2 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16188 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHrpeH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpIC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdHotspotsRep1 HRPE H3K4M3 Ht 1 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16189 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHrpeH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpIC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdHotspotsRep2 HRE H3K36M3 Ht 2 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12418 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHreH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdHotspotsRep1 HRE H3K36M3 Ht 1 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12234 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHreH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdHotspotsRep2 HRE H3K27M3 Ht 2 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000429 429 GSM945160 Stam UW DS12415 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHreH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdHotspotsRep1 HRE H3K27M3 Ht 1 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000429 429 GSM945160 Stam UW DS12422 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHreH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdHotspotsRep2 HRE H3K4M3 Ht 2 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000409 409 GSM945276 Stam UW DS11573 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHreH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdHotspotsRep1 HRE H3K4M3 Ht 1 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000409 409 GSM945276 Stam UW DS11575 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHreH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdHotspotsRep2 HPF H3K4M3 Ht 2 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16183 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHpfH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdHotspotsRep1 HPF H3K4M3 Ht 1 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16184 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHpfH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdHotspotsRep2 HPAF H3K4M3 Ht 2 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16154 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHpafH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdHotspotsRep1 HPAF H3K4M3 Ht 1 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16153 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHpafH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep2 HMF H3K4M3 Ht 2 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16152 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep1 HMF H3K4M3 Ht 1 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16151 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k27me3StdHotspotsRep1 HMEC H3K27M3 Ht 1 H3K27me3 HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000408 408 GSM945277 Stam UW DS12082 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHmecH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdHotspotsRep2 HMEC H3K4M3 Ht 2 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15761 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHmecH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdHotspotsRep1 HMEC H3K4M3 Ht 1 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15762 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHmecH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdHotspotsRep2 HL-60 H3K4M3 Ht 2 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11797 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHl60H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HL-60 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdHotspotsRep1 HL-60 H3K4M3 Ht 1 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11795 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHl60H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HL-60 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdHotspotsRep2 HFMc H3K4M3 Ht 2 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18325 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneHffmycH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFFMyc H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdHotspotsRep1 HFMc H3K4M3 Ht 1 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18324 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneHffmycH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFFMyc H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffH3k04me3StdHotspotsRep1 HFF H3K4M3 Ht 1 H3K4me3 HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002042 2042 GSM945218 Stam UW DS18320 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneHffH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdHotspotsRep2 HEK H3K4M3 Ht 2 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15759 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHek293H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEK293 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdHotspotsRep1 HEK H3K4M3 Ht 1 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15760 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHek293H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEK293 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdHotspotsRep2 HEE H3K4M3 Ht 2 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16061 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHeeH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpIC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdHotspotsRep1 HEE H3K4M3 Ht 1 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16060 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHeeH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpIC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdHotspotsRep2 HCT16 H3K4M3 Ht 2 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16055 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHct116H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdHotspotsRep1 HCT16 H3K4M3 Ht 1 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16056 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHct116H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdHotspotsRep2 HCPE H3K4M3 Ht 2 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15757 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHcpeH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpiC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdHotspotsRep1 HCPE H3K4M3 Ht 1 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15758 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHcpeH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpiC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdHotspotsRep2 HCM H3K4M3 Ht 2 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15756 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHcmH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdHotspotsRep1 HCM H3K4M3 Ht 1 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15755 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHcmH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfaaH3k4me3StdHotspotsRep1 HCFa H3K4M3 Ht 1 H3K4me3 HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000943 943 GSM945310 Stam UW DS15754 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHcfaaH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCFaa H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdHotspotsRep2 HCF H3K4M3 Ht 2 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15753 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHcfH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdHotspotsRep1 HCF H3K4M3 Ht 1 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15751 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHcfH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdHotspotsRep2 HBMEC H3K4M3 Ht 2 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15748 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHbmecH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdHotspotsRep1 HBMEC H3K4M3 Ht 1 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15749 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHbmecH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdHotspotsRep2 HAsp H3K4M3 Ht 2 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16045 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHaspH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdHotspotsRep1 HAsp H3K4M3 Ht 1 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16044 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHaspH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdHotspotsRep2 HAc H3K4M3 Ht 2 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18314 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneHacH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdHotspotsRep1 HAc H3K4M3 Ht 1 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18315 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneHacH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14114 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14115 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14650 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dHotspotsRep2 diffProtA_14d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14123 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dHotspotsRep1 diffProtA_14d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS15386 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dHotspotsRep2 diffProtA_9d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS14648 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dHotspotsRep1 diffProtA_9d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14120 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep2 diffProtA_5d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14119 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep1 diffProtA_5d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS14646 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dHotspotsRep2 diffProtA_2d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS15385 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dHotspotsRep1 diffProtA_2d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS14113 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS13428 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14122 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dHotspotsRep2 diffProtA_14d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14649 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dHotspotsRep1 diffProtA_14d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14709 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep2 diffProtA_9d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14647 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep1 diffProtA_9d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS14118 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dHotspotsRep2 diffProtA_5d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS13778 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dHotspotsRep1 diffProtA_5d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14708 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep2 diffProtA_2d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14645 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep1 diffProtA_2d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS14112 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS13427 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002530 2530 GSM945321 Stam UW DS14707 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dHotspotsRep2 diffProtA_14d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002530 2530 GSM945321 Stam UW DS14121 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dHotspotsRep1 diffProtA_14d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14705 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dHotspotsRep2 diffProtA_9d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14706 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dHotspotsRep1 diffProtA_9d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002531 2531 GSM945322 Stam UW DS14116 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dHotspotsRep2 diffProtA_5d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002531 2531 GSM945322 Stam UW DS13777 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dHotspotsRep1 diffProtA_5d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14703 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dHotspotsRep2 diffProtA_2d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14704 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dHotspotsRep1 diffProtA_2d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12875H3k04me3StdHotspotsRep1 GM75 H3K4M3 Ht 1 H3K4me3 GM12875 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002041 2041 GSM945221 Stam UW DS18910 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneGm12875H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12875 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdHotspotsRep2 GM65 H3K4M3 Ht 2 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002039 2039 GSM945295 Stam UW DS20810 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneGm12865H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdHotspotsRep1 GM65 H3K4M3 Ht 1 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002039 2039 GSM945295 Stam UW DS18707 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneGm12865H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdHotspotsRep2 GM64 H3K4M3 Ht 2 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18900 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneGm12864H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdHotspotsRep1 GM64 H3K4M3 Ht 1 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18706 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneGm12864H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdHotspotsRep2 GM90 H3K36M3 Ht 2 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12189 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm06990H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdHotspotsRep1 GM90 H3K36M3 Ht 1 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12192 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm06990H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdHotspotsRep2 GM90 H3K27M3 Ht 2 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000427 427 GSM945205 Stam UW DS12188 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm06990H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdHotspotsRep1 GM90 H3K27M3 Ht 1 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000427 427 GSM945205 Stam UW DS12191 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm06990H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdHotspotsRep2 GM90 H3K4M3 Ht 2 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-12 2010-07-11 wgEncodeEH000417 417 GSM945179 Stam UW DS11519 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm06990H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdHotspotsRep1 GM90 H3K4M3 Ht 1 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-13 2010-07-12 wgEncodeEH000417 417 GSM945179 Stam UW DS11521 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm06990H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdHotspotsRep2 Caco H3K36M3 Ht 2 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12405 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneCaco2H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdHotspotsRep1 Caco H3K36M3 Ht 1 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12406 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneCaco2H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdHotspotsRep2 Caco H3K27M3 Ht 2 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000425 425 GSM945203 Stam UW DS12218 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneCaco2H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdHotspotsRep1 Caco H3K27M3 Ht 1 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-20 2010-07-20 wgEncodeEH000425 425 GSM945203 Stam UW DS12221 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneCaco2H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdHotspotsRep2 Caco H3K4M3 Ht 2 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11785 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneCaco2H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdHotspotsRep1 Caco H3K4M3 Ht 1 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11784 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneCaco2H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdHotspotsRep2 BJ H3K36M3 Ht 2 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12195 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneBjH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdHotspotsRep1 BJ H3K36M3 Ht 1 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12198 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneBjH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdHotspotsRep2 BJ H3K27M3 Ht 2 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-20 2010-07-20 wgEncodeEH000424 424 GSM945204 Stam UW DS12197 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneBjH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdHotspotsRep1 BJ H3K27M3 Ht 1 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000424 424 GSM945204 Stam UW DS12194 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneBjH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdHotspotsRep2 BJ H3K4M3 Ht 2 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000416 416 GSM945178 Stam UW DS11561 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneBjH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdHotspotsRep1 BJ H3K4M3 Ht 1 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-13 2010-07-12 wgEncodeEH000416 416 GSM945178 Stam UW DS11563 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneBjH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdHotspotsRep2 BE2_C H3K4M3 Ht 2 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18310 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneBe2cH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2_C H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdHotspotsRep1 BE2_C H3K4M3 Ht 1 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18309 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneBe2cH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2_C H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdHotspotsRep2 AoAF H3K4M3 Ht 2 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15747 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAoafH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdHotspotsRep1 AoAF H3K4M3 Ht 1 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15746 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAoafH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdHotspotsRep2 AG03 H3K4M3 Ht 2 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15745 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg10803H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdHotspotsRep1 AG03 H3K4M3 Ht 1 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15744 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg10803H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdHotspotsRep2 AG19 H3K4M3 Ht 2 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15743 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg09319H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdHotspotsRep1 AG19 H3K4M3 Ht 1 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15742 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg09319H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdHotspotsRep2 AG09 H3K4M3 Ht 2 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16033 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg09309H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdHotspotsRep1 AG09 H3K4M3 Ht 1 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16034 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg09309H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27me3StdHotspotsRep1 AG50 H3K27m3 Ht 1 H3K27me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003036 3036 GSM1010913 Stam UW DS21480 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneAg04450H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27acStdHotspotsRep1 AG50 H3K27ac Ht 1 H3K27ac AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003035 3035 GSM1010912 Stam UW DS21479 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneAg04450H3k27acStdHotspotsRep1 None Hotspots Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K27ac Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdHotspotsRep2 AG50 H3K9me3 Ht 2 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21481 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneAg04450H3k09me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K9me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdHotspotsRep1 AG50 H3K9me3 Ht 1 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21482 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneAg04450H3k09me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K9me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdHotspotsRep2 AG50 H3K4M3 Ht 2 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15741 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg04450H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdHotspotsRep1 AG50 H3K4M3 Ht 1 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15740 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg04450H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdHotspotsRep2 AG49 H3K4M3 Ht 2 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15739 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg04449H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdHotspotsRep1 AG49 H3K4M3 Ht 1 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15737 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg04449H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k27me3StdHotspotsRep1 CD14 H3K27M3 Ht 1 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002167 2167 GSM945301 Stam UW DS19094 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Monocytes-CD14+ RO 01746 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k04me3StdHotspotsRep1 CD14 H3K4M3 Ht 1 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002168 2168 GSM945225 Stam UW DS18981 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Monocytes-CD14+ RO 01746 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k04me3StdHotspotsRep2 MCF7 H3K4M3 Ht 2 H3K4me3 MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000967 967 GSM945269 Stam UW DS16201 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneMcf7H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k4me3StdHotspotsRep1 MCF7 H3K4M3 Ht 1 H3K4me3 MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000967 967 GSM945269 Stam UW DS16202 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneMcf7H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdHotspotsRep2 HUVE H3K36M3 Ht 2 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000431 431 GSM945233 Stam UW DS12225 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHuvecH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdHotspotsRep1 HUVE H3K36M3 Ht 1 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000431 431 GSM945233 Stam UW DS12228 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHuvecH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdHotspotsRep2 HUVE H3K27M3 Ht 2 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-12 wgEncodeEH000411 411 GSM945180 Stam UW DS12224 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHuvecH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdHotspotsRep1 HUVE H3K27M3 Ht 1 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000411 411 GSM945180 Stam UW DS12227 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHuvecH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdHotspotsRep2 HUVE H3K4M3 Ht 2 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000412 412 GSM945181 Stam UW DS11458 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHuvecH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdHotspotsRep1 HUVE H3K4M3 Ht 1 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000412 412 GSM945181 Stam UW DS11460 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHuvecH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdHotspotsRep2 HepG H3K36M3 Ht 2 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000446 446 GSM945211 Stam UW DS12075 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHepg2H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdHotspotsRep1 HepG H3K36M3 Ht 1 H3K36me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000446 446 GSM945211 Stam UW DS12207 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHepg2H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep2 HepG H3K27M3 Ht 2 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12206 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep1 HepG H3K27M3 Ht 1 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12076 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdHotspotsRep2 HepG H3K4M3 Ht 2 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11780 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHepg2H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdHotspotsRep1 HepG H3K4M3 Ht 1 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11781 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHepg2H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdHotspotsRep2 HeLa H3K36M3 Ht 2 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12201 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHelas3H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdHotspotsRep1 HeLa H3K36M3 Ht 1 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12071 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHelas3H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdHotspotsRep2 HeLa H3K27M3 Ht 2 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12070 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHelas3H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdHotspotsRep1 HeLa H3K27M3 Ht 1 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12072 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHelas3H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdHotspotsRep2 HeLa H3K4M3 Ht 2 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11553 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHelas3H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdHotspotsRep1 HeLa H3K4M3 Ht 1 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11555 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHelas3H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01794H3k04me3StdHotspotsRep3 20+94 H3K4M3 Ht 3 H3K4me3 CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002171 2171 GSM945198 Stam UW DS18983 Hotspot-v5.2 hg19 3 exp wgEncodeUwHistoneCd20ro01794H3k04me3StdHotspotsRep3 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CD20+ (RO 01794) H3K4me3 Histone Mod ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdHotspotsRep2 20+78 H3K4M3 Ht 2 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002166 2166 GSM945229 Stam UW DS18986 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdHotspotsRep1 20+78 H3K4M3 Ht 1 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002166 2166 GSM945229 Stam UW DS18985 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdHotspotsRep2 A549 H3K4M3 Ht 2 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18304 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneA549H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdHotspotsRep1 A549 H3K4M3 Ht 1 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18305 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneA549H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdHotspotsRep2 K562 H3K36M3 Ht 2 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12177 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneK562H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdHotspotsRep1 K562 H3K36M3 Ht 1 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12067 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneK562H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdHotspotsRep2 K562 H3K27M3 Ht 2 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12068 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneK562H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdHotspotsRep1 K562 H3K27M3 Ht 1 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12066 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneK562H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdHotspotsRep2 K562 H3K4M3 Ht 2 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000400 400 GSM945165 Stam UW DS11509 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneK562H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdHotspotsRep1 K562 H3K4M3 Ht 1 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000400 400 GSM945165 Stam UW DS11507 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneK562H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdHotspotsRep2 GM78 H3K36M3 Ht 2 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12183 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm12878H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdHotspotsRep1 GM78 H3K36M3 Ht 1 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12186 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm12878H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdHotspotsRep2 GM78 H3K27M3 Ht 2 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000428 428 GSM945196 Stam UW DS12185 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm12878H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdHotspotsRep1 GM78 H3K27M3 Ht 1 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000428 428 GSM945196 Stam UW DS12182 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm12878H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdHotspotsRep2 GM78 H3K4M3 Ht 2 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-12 2010-07-11 wgEncodeEH000395 395 GSM945188 Stam UW DS11511 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm12878H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdHotspotsRep1 GM78 H3K4M3 Ht 1 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-06-30 2010-03-29 wgEncodeEH000395 395 GSM945188 Stam UW DS11513 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm12878H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
dbSnp153Composite dbSNP 153 Short Genetic Variants from dbSNP release 153 Variation Description This track shows short genetic variants (up to approximately 50 base pairs) from dbSNP build 153: single-nucleotide variants (SNVs), small insertions, deletions, and complex deletion/insertions (indels), relative to the reference genome assembly. Most variants in dbSNP are rare, not true polymorphisms, and some variants are known to be pathogenic. For hg38 (GRCh38), approximately 667 million distinct variants (RefSNP clusters with rs# ids) have been mapped to more than 702 million genomic locations including alternate haplotype and fix patch sequences. dbSNP remapped variants from hg38 to hg19 (GRCh37); approximately 658 million distinct variants were mapped to more than 683 million genomic locations including alternate haplotype and fix patch sequences (not all of which are included in UCSC's hg19). This track includes four subtracks of variants: All dbSNP (153): the entire set (683 million for hg19, 702 million for hg38) Common dbSNP (153): approximately 15 million variants with a minor allele frequency (MAF) of at least 1% (0.01) in the 1000 Genomes Phase 3 dataset. Variants in the Mult. subset (below) are excluded. ClinVar dbSNP (153): approximately 455,000 variants mentioned in ClinVar. Note: that includes both benign and pathogenic (as well as uncertain) variants. Variants in the Mult. subset (below) are excluded. Mult. dbSNP (153): variants that have been mapped to multiple chromosomes, for example chr1 and chr2, raising the question of whether the variant is really a variant or just a difference between duplicated sequences. There are some exceptions in which a variant is mapped to more than one reference sequence, but not culled into this set: A variant may appear in both X and Y pseudo-autosomal regions (PARs) without being included in this set. A variant may also appear in a main chromosome as well as an alternate haplotype or fix patch sequence assigned to that chromosome. A fifth subtrack highlights coordinate ranges to which dbSNP mapped a variant but with genomic coordinates that are not internally consistent, i.e. different coordinate ranges were provided when describing different alleles. This can occur due to a bug with mapping variants from one assembly sequence to another when there is an indel difference between the assembly sequences: Map Err (153): around 120,000 mappings of 55,000 distinct rsIDs for hg19 and 149,000 mappings of 86,000 distinct rsIDs for hg38. Interpreting and Configuring the Graphical Display SNVs and pure deletions are displayed as boxes covering the affected base(s). Pure insertions are drawn as single-pixel tickmarks between the base before and the base after the insertion. Insertions and/or deletions in repetitive regions may be represented by a half-height box showing uncertainty in placement, followed by a full-height box showing the number of deleted bases, or a full-height tickmark to indicate an insertion. When an insertion or deletion falls in a repetitive region, the placement may be ambiguous. For example, if the reference genome contains "TAAAG" but some individuals have "TAAG" at the same location, then the variant is a deletion of a single A relative to the reference genome. However, which A was deleted? There is no way to tell whether the first, second or third A was removed. Different variant mapping tools may place the deletion at different bases in the reference genome. To reduce errors in merging variant calls made with different left vs. right biases, dbSNP made a major change in its representation of deletion/insertion variants in build 152. Now, instead of assigning a single-base genomic location at one of the A's, dbSNP expands the coordinates to encompass the whole repetitive region, so the variant is represented as a deletion of 3 A's combined with an insertion of 2 A's. In the track display, there will be a half-height box covering the first two A's, followed by a full-height box covering the third A, to show a net loss of one base but an uncertain placement within the three A's. Variants are colored according to functional effect on genes annotated by dbSNP: Protein-altering variants and splice site variants are red. Synonymous codon variants are green. Non-coding transcript or Untranslated Region (UTR) variants are blue. On the track controls page, several variant properties can be included or excluded from the item labels: rs# identifier assigned by dbSNP, reference/alternate alleles, major/minor alleles (when available) and minor allele frequency (when available). Allele frequencies are reported independently by twelve projects (some of which may have overlapping sets of samples): 1000Genomes: The 1000 Genomes Phase 3 dataset contains data for 2,504 individuals from 26 populations. GnomAD exomes: The gnomAD v2.1 exome dataset comprises a total of 16 million SNVs and 1.2 million indels from 125,748 exomes in 14 populations. TOPMED: The TOPMED dataset contains phase 3 data from freeze 5 panel that include more than 60,000 individuals. The approximate ethnic breakdown is European(52%), African (31%), Hispanic or Latino (10%), and East Asian (7%) ancestry. PAGE STUDY: The PAGE Study: How Genetic Diversity Improves Our Understanding of the Architecture of Complex Traits. GnomAD genomes: The gnomAD v2.1 genome dataset includes 229 million SNVs and 33 million indels from 15,708 genomes in 9 populations. GoESP: The NHLBI Grand Opportunity Exome Sequencing Project (GO-ESP) dataset contains 6503 samples drawn from multiple ESP cohorts and represents all of the ESP exome variant data. Estonian: Genetic variation in the Estonian population: pharmacogenomics study of adverse drug effects using electronic health records. ALSPAC: The UK10K - Avon Longitudinal Study of Parents and Children project contains 1927 sample including individuals obtained from the ALSPAC population. This population contains more than 14,000 mothers enrolled during pregnancy in 1991 and 1992. TWINSUK: The UK10K - TwinsUK project contains 1854 samples from the Department of Twin Research and Genetic Epidemiology (DTR). The DTR dataset contains data obtained from the 11,000 identical and non-identical twins between the ages of 16 and 85 years old. NorthernSweden: Whole-genome sequenced control population in northern Sweden reveals subregional genetic differences. This population consists of 300 whole genome sequenced human samples selected from the county of Vasterbotten in northern Sweden. To be selected for inclusion into the population, the individuals had to have reached at least 80 years of age and have no diagnosed cancer. Vietnamese: The Vietnamese Genetic Variation Database includes about 25 million variants (SNVs and indels) from 406 genomes and 305 exomes of unrelated healthy Kinh Vietnamese (KHV) people. The project from which to take allele frequency data defaults to 1000 Genomes but can be set to any of those projects. Using the track controls, variants can be filtered by minimum minor allele frequency (MAF) variation class/type (e.g. SNV, insertion, deletion) functional effect on a gene (e.g. synonymous, frameshift, intron, upstream) assorted features and anomalies noted by UCSC during processing of dbSNP's data Interesting and anomalous conditions noted by UCSC While processing the information downloaded from dbSNP, UCSC annotates some properties of interest. These are noted on the item details page, and may be useful to include or exclude affected variants. Some are purely informational: keyword in data file (dbSnp153.bb) # in hg19# in hg38description clinvar 454678 453996 Variant is in ClinVar. clinvarBenign 143864 143736 Variant is in ClinVar with clinical significance of benign and/or likely benign. clinvarConflicting 7932 7950 Variant is in ClinVar with reports of both benign and pathogenic significance. clinvarPathogenic 96242 95262 Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic. commonAll 12184521 12438655 Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all projects reporting frequencies. commonSome 20541190 20902944 Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all, projects reporting frequencies. diffMajor 1377831 1399109 Different frequency sources have different major alleles. overlapDiffClass 107015341 110007682 This variant overlaps another variant with a different type/class. overlapSameClass 16915239 17291289 This variant overlaps another with the same type/class but different start/end. rareAll 662601770 681696398 Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in all projects reporting frequencies, or has no frequency data. rareSome 670958439 690160687 Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in some, but not all, projects reporting frequencies, or has no frequency data. revStrand 3813702 4532511 Alleles are displayed on the + strand at the current position. dbSNP's alleles are displayed on the + strand of a different assembly sequence, so dbSNP's variant page shows alleles that are reverse-complemented with respect to the alleles displayed above. while others may indicate that the reference genome contains a rare variant or sequencing issue: keyword in data file (dbSnp153.bb) # in hg19# in hg38description refIsAmbiguous 101 111 The reference genome allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G', or 'N' for 'any base'). refIsMinor 3272116 3360435 The reference genome allele is not the major allele in at least one project. refIsRare 136547 160827 The reference genome allele is rare (i.e. allele frequency refIsSingleton 37832 50927 The reference genome allele has never been observed in a population sequencing project reporting frequencies. refMismatch 4 33 The reference genome allele reported by dbSNP differs from the GenBank assembly sequence. This is very rare and in all cases observed so far, the GenBank assembly has an 'N' while the RefSeq assembly used by dbSNP has a less ambiguous character such as 'R'. and others may indicate an anomaly or problem with the variant data: keyword in data file (dbSnp153.bb) # in hg19# in hg38description altIsAmbiguous 10755 10888 At least one alternate allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G'). For alleles containing more than one ambiguous base, this may create a combinatoric explosion of possible alleles. classMismatch 5998 6216 Variation class/type is inconsistent with alleles mapped to this genome assembly. clusterError 114826 128306 This variant has the same start, end and class as another variant; they probably should have been merged into one variant. freqIncomplete 3922 4673 At least one project reported counts for only one allele which implies that at least one allele is missing from the report; that project's frequency data are ignored. freqIsAmbiguous 7656 7756 At least one allele reported by at least one project that reports frequencies contains an IUPAC ambiguous base. freqNotMapped 2685 6590 At least one project reported allele frequencies relative to a different assembly; However, dbSNP does not include a mapping of this variant to that assembly, which implies a problem with mapping the variant across assemblies. The mapping on this assembly may have an issue; evaluate carefully vs. original submissions, which you can view by clicking through to dbSNP above. freqNotRefAlt 17694 32170 At least one allele reported by at least one project that reports frequencies does not match any of the reference or alternate alleles listed by dbSNP. multiMap 562180 132123 This variant has been mapped to more than one distinct genomic location. otherMapErr 114095 204219 At least one other mapping of this variant has erroneous coordinates. The mapping(s) with erroneous coordinates are excluded from this track and are included in the Map Err subtrack. Sometimes despite this mapping having legal coordinates, there may still be an issue with this mapping's coordinates and alleles; you may want to click through to dbSNP to compare the initial submission's coordinates and alleles. In hg19, 55454 distinct rsIDs are affected; in hg38, 86636. Data Sources and Methods dbSNP has collected genetic variant reports from researchers worldwide for more than 20 years. Since the advent of next-generation sequencing methods and the population sequencing efforts that they enable, dbSNP has grown exponentially, requiring a new data schema, computational pipeline, web infrastructure, and download files. (Holmes et al.) The same challenges of exponential growth affected UCSC's presentation of dbSNP variants, so we have taken the opportunity to change our internal representation and import pipeline. Most notably, flanking sequences are no longer provided by dbSNP, because most submissions have been genomic variant calls in VCF format as opposed to independent sequences. We downloaded JSON files available from dbSNP at ftp://ftp.ncbi.nlm.nih.gov/snp/archive/b153/JSON/, extracted a subset of the information about each variant, and collated it into a bigBed file using the bigDbSnp.as schema with the information necessary for filtering and displaying the variants, as well as a separate file containing more detailed information to be displayed on each variant's details page (dbSnpDetails.as schema). Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. Since dbSNP has grown to include approximately 700 million variants, the size of the All dbSNP (153) subtrack can cause the Table Browser and Data Integrator to time out, leading to a blank page or truncated output, unless queries are restricted to a chromosomal region, to particular defined regions, to a specific set of rs# IDs (which can be pasted/uploaded into the Table Browser), or to one of the subset tracks such as Common (~15 million variants) or ClinVar (~0.5M variants). For automated analysis, the track data files can be downloaded from the downloads server for hg19 and hg38. file format subtrack dbSnp153.bb hg19 hg38 bigDbSnp (bigBed4+13) All dbSNP (153) dbSnp153ClinVar.bb hg19 hg38 bigDbSnp (bigBed4+13) ClinVar dbSNP (153) dbSnp153Common.bb hg19 hg38 bigDbSnp (bigBed4+13) Common dbSNP (153) dbSnp153Mult.bb hg19 hg38 bigDbSnp (bigBed4+13) Mult. dbSNP (153) dbSnp153BadCoords.bb hg19 hg38 bigBed4 Map Err (153) dbSnp153Details.tab.gz gzip-compressed tab-separated text Detailed variant properties, independent of genome assembly version Several utilities for working with bigBed-formatted binary files can be downloaded here. Run a utility with no arguments to see a brief description of the utility and its options. bigBedInfo provides summary statistics about a bigBed file including the number of items in the file. With the -as option, the output includes an autoSql definition of data columns, useful for interpreting the column values. bigBedToBed converts the binary bigBed data to tab-separated text. Output can be restricted to a particular region by using the -chrom, -start and -end options. bigBedNamedItems extracts rows for one or more rs# IDs. Example: retrieve all variants in the region chr1:200001-200400 bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp153.bb -chrom=chr1 -start=200000 -end=200400 stdout Example: retrieve variant rs6657048 bigBedNamedItems dbSnp153.bb rs6657048 stdout Example: retrieve all variants with rs# IDs in file myIds.txt bigBedNamedItems -nameFile dbSnp153.bb myIds.txt dbSnp153.myIds.bed The columns in the bigDbSnp/bigBed files and dbSnp153Details.tab.gz file are described in bigDbSnp.as and dbSnpDetails.as respectively. For columns that contain lists of allele frequency data, the order of projects providing the data listed is as follows: 1000Genomes GnomAD exomes TOPMED PAGE STUDY GnomAD genomes GoESP Estonian ALSPAC TWINSUK NorthernSweden Vietnamese UCSC also has an API that can be used to retrieve values from a particular chromosome range. A list of rs# IDs can be pasted/uploaded in the Variant Annotation Integrator tool to find out which genes (if any) the variants are located in, as well as functional effect such as intron, coding-synonymous, missense, frameshift, etc. Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information. References Holmes JB, Moyer E, Phan L, Maglott D, Kattman B. SPDI: Data Model for Variants and Applications at NCBI. Bioinformatics. 2019 Nov 18;. PMID: 31738401 Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K, Clark K, Connor R, Fiorini N, Funk K, Hefferon T et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2019 Jan 8;47(D1):D23-D28. PMID: 30395293; PMC: PMC6323993 Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
dbSnpArchive dbSNP Archive dbSNP Track Archive Variation Description This composite track contains information about single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP, available from ftp.ncbi.nih.gov/snp. You can click into each track for a version/subset-specific description. This collection includes numbered versions of the entire dbSNP datasets (All SNP) as well as three tracks with subsets of the items in that version. Here is information on each of the subsets: dbSNP 153: The dbSNP build 153 is composed of 5 subtracks. Click the track for a description of the subtracks. Common SNPs: SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs: SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs: SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF >= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF >= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/database/ (for human, organism_tax_id = human_9606; for mouse, organism_tax_id = mouse_10090). The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/rs_fasta/ Coordinates, orientation, location type and dbSNP reference allele data were obtained from files like b138_SNPContigLoc.bcp.gz and b138_ContigInfo.bcp.gz. b138_SNPMapInfo.bcp.gz provides the alignment weights. Functional classification was obtained from files like b138_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation files can be downloaded in their entirety for hg38, hg19, and mm10 as (snp*.txt.gz). You can also make queries using the UCSC Genome Browser JSON API or public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download in the genome's snp*Mask folder. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exlcude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
dbSnp153ViewVariants Variants Short Genetic Variants from dbSNP release 153 Variation 
dbSnp153 All dbSNP(153) All Short Genetic Variants from dbSNP Release 153 Variation 
dbSnp153Mult dbSNP(153) Mult. Short Genetic Variants from dbSNP Release 153 that Map to Multiple Genomic Loci Variation 
dbSnp153ClinVar dbSNP(153) in ClinVar Short Genetic Variants from dbSNP Release 153 Included in ClinVar Variation 
dbSnp153Common Common dbSNP(153) Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153 Variation 
dbSnp153ViewErrs Mapping Errors Short Genetic Variants from dbSNP release 153 Variation 
dbSnp153BadCoords Map Err dbSnp(153) Mappings with Inconsistent Coordinates from dbSNP 153 Variation 
snp151Common Common SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 151, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have a minor allele frequency (MAF) of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. Allele counts from all submissions that include frequency data are combined when determining MAF, so for example the allele counts from the 1000 Genomes Project and an independent submitter may be combined for the same variant. dbSNP provides download files in the Variant Call Format (VCF) that include a "COMMON" flag in the INFO column. That is determined by a different method, and is generally a superset of the UCSC Common set. dbSNP uses frequency data from the 1000 Genomes Project only, and considers a variant COMMON if it has a MAF of at least 0.01 in any of the five super-populations: African (AFR) Admixed American (AMR) East Asian (EAS) European (EUR) South Asian (SAS) In build 151, dbSNP marks approximately 38M variants as COMMON; 23M of those have a global MAF &lt; 0.01. The remainder should be in agreement with UCSC's Common subset. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(151) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(151) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly. All SNPs(151) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b151_SNPContigLoc_N.bcp.gz and b151_ContigInfo_N.bcp.gz. (N = 105 for hg19, 108 for hg38) b151_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b151_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp151*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp151 All SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 151, available from ftp.ncbi.nlm.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(151): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(151): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(151): SNPs that have been mapped to multiple locations in the reference genome assembly. There are very few SNPs in this category because dbSNP has been filtering out almost all multiple-mapping SNPs since build 149. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(151) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(151) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly. All SNPs(151) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b151_SNPContigLoc_N.bcp.gz and b151_ContigInfo_N.bcp.gz. (N = 105 for hg19, 108 for hg38) b151_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b151_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp151*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp151Flagged Flagged SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 151, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(151) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(151) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly. All SNPs(151) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b151_SNPContigLoc_N.bcp.gz and b151_ContigInfo_N.bcp.gz. (N = 105 for hg19, 108 for hg38) b151_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b151_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp151*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp151Mult Mult. SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 151, available from ftp.ncbi.nlm.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(151): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(151): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(151): SNPs that have been mapped to multiple locations in the reference genome assembly. There are very few SNPs in this category because dbSNP has been filtering out almost all multiple-mapping SNPs since build 149. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(151) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(151) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly. All SNPs(151) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b151_SNPContigLoc_N.bcp.gz and b151_ContigInfo_N.bcp.gz. (N = 105 for hg19, 108 for hg38) b151_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b151_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp151*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp150 All SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 150, available from ftp.ncbi.nlm.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(150): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(150): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(150): SNPs that have been mapped to multiple locations in the reference genome assembly. There are very few SNPs in this category because dbSNP has been filtering out almost all multiple-mapping SNPs since build 149. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(150) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(150) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly. All SNPs(150) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b150_SNPContigLoc_N.bcp.gz and b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b150_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b150_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp150*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp150Common Common SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 150, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have a minor allele frequency (MAF) of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. Allele counts from all submissions that include frequency data are combined when determining MAF, so for example the allele counts from the 1000 Genomes Project and an independent submitter may be combined for the same variant. dbSNP provides download files in the Variant Call Format (VCF) that include a "COMMON" flag in the INFO column. That is determined by a different method, and is generally a superset of the UCSC Common set. dbSNP uses frequency data from the 1000 Genomes Project only, and considers a variant COMMON if it has a MAF of at least 0.01 in any of the five super-populations: African (AFR) Admixed American (AMR) East Asian (EAS) European (EUR) South Asian (SAS) In build 151 (which has replaced build 150 on the dbSNP web and download site), dbSNP marks approximately 38M variants as COMMON; 23M of those have a global MAF &lt; 0.01. The remainder should be in agreement with UCSC's Common subset. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(150) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(150) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly. All SNPs(150) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b150_SNPContigLoc_N.bcp.gz and b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b150_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b150_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp150*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp150Flagged Flagged SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 150, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(150) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(150) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly. All SNPs(150) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b150_SNPContigLoc_N.bcp.gz and b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b150_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b150_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp150*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp150Mult Mult. SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 150, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. Since build 149, dbSNP has been filtering out almost all such "SNPs" so there are very few items in this track. The default maximum weight for this track is 3, unlike the other dbSNP build 150 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(150) track because of its maximum weight filter. The remainder of this page is identical on the following tracks: Common SNPs(150) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(150) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly. All SNPs(150) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b150_SNPContigLoc_N.bcp.gz and b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b150_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b150_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp150*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp147 All SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 147, available from ftp.ncbi.nlm.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(147): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(147): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(147): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(147) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(147) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly. All SNPs(147) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are always colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b147_SNPContigLoc_N.bcp.gz and b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b147_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b147_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp147*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp147Common Common SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 147, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(147) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(147) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly. All SNPs(147) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are always colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b147_SNPContigLoc_N.bcp.gz and b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b147_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b147_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp147*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp147Flagged Flagged SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 147, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(147) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(147) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly. All SNPs(147) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are always colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b147_SNPContigLoc_N.bcp.gz and b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b147_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b147_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp147*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp147Mult Mult. SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 147, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The default maximum weight for this track is 3, unlike the other dbSNP build 147 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(147) track because of its maximum weight filter. The remainder of this page is identical on the following tracks: Common SNPs(147) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(147) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly. All SNPs(147) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are always colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b147_SNPContigLoc_N.bcp.gz and b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b147_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b147_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp147*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp146 All SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 146, available from ftp.ncbi.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(146): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(146): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(146): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(146) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(146) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly. All SNPs(146) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b146_SNPContigLoc_N.bcp.gz and b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b146_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b146_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp146*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp146Common Common SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 146, available from ftp.ncbi.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(146) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(146) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly. All SNPs(146) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b146_SNPContigLoc_N.bcp.gz and b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b146_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b146_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp146*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp146Flagged Flagged SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 146, available from ftp.ncbi.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(146) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(146) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly. All SNPs(146) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b146_SNPContigLoc_N.bcp.gz and b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b146_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b146_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp146*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp146Mult Mult. SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 146, available from ftp.ncbi.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The default maximum weight for this track is 3, unlike the other dbSNP build 146 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(146) track because of its maximum weight filter. The remainder of this page is identical on the following tracks: Common SNPs(146) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(146) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly. All SNPs(146) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b146_SNPContigLoc_N.bcp.gz and b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b146_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b146_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp146*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp144 All SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 144, available from ftp.ncbi.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(144): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(144): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(144): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(144) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(144) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly. All SNPs(144) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b144_SNPContigLoc_N.bcp.gz and b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b144_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b144_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp144*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp144Common Common SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 144, available from ftp.ncbi.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(144) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(144) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly. All SNPs(144) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b144_SNPContigLoc_N.bcp.gz and b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b144_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b144_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp144*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp144Flagged Flagged SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 144, available from ftp.ncbi.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(144) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(144) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly. All SNPs(144) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b144_SNPContigLoc_N.bcp.gz and b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b144_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b144_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp144*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp144Mult Mult. SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 144, available from ftp.ncbi.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The default maximum weight for this track is 3, unlike the other dbSNP build 144 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(144) track because of its maximum weight filter. The remainder of this page is identical on the following tracks: Common SNPs(144) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(144) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly. All SNPs(144) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b144_SNPContigLoc_N.bcp.gz and b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b144_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b144_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp144*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp142 All SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 142, available from ftp.ncbi.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(142): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(142): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(142): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(142) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(142) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly. All SNPs(142) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b142_SNPContigLoc_N.bcp.gz and b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38) b142_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b142_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp142*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp142Common Common SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 142, available from ftp.ncbi.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(142) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(142) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly. All SNPs(142) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b142_SNPContigLoc_N.bcp.gz and b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38) b142_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b142_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp142*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp142Flagged Flagged SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 142, available from ftp.ncbi.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(142) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(142) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly. All SNPs(142) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b142_SNPContigLoc_N.bcp.gz and b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38) b142_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b142_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp142*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp142Mult Mult. SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 142, available from ftp.ncbi.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The default maximum weight for this track is 3, unlike the other dbSNP build 142 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(142) track because of its maximum weight filter. The remainder of this page is identical on the following tracks: Common SNPs(142) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(142) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly. All SNPs(142) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b142_SNPContigLoc_N.bcp.gz and b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38) b142_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b142_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp142*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp141 All SNPs(141) Simple Nucleotide Polymorphisms (dbSNP 141) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 141, available from ftp.ncbi.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(141): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(141): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(141): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(141) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(141) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(141) - SNPs mapping in more than one place on reference assembly. All SNPs(141) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/database/ (for human, organism_tax_id = human_9606; for mouse, organism_tax_id = mouse_10090). The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/rs_fasta/ Coordinates, orientation, location type and dbSNP reference allele data were obtained from b141_SNPContigLoc.bcp.gz and b141_ContigInfo.bcp.gz. b141_SNPMapInfo.bcp.gz provided the alignment weights. Functional classification was obtained from b141_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp141*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp141Common Common SNPs(141) Simple Nucleotide Polymorphisms (dbSNP 141) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 141, available from ftp.ncbi.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(141) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(141) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(141) - SNPs mapping in more than one place on reference assembly. All SNPs(141) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/database/ (for human, organism_tax_id = human_9606; for mouse, organism_tax_id = mouse_10090). The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/rs_fasta/ Coordinates, orientation, location type and dbSNP reference allele data were obtained from b141_SNPContigLoc.bcp.gz and b141_ContigInfo.bcp.gz. b141_SNPMapInfo.bcp.gz provided the alignment weights. Functional classification was obtained from b141_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp141*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
dbSnp155Composite dbSNP 155 Short Genetic Variants from dbSNP release 155 Variation Description This track shows short genetic variants (up to approximately 50 base pairs) from dbSNP build 155: single-nucleotide variants (SNVs), small insertions, deletions, and complex deletion/insertions (indels), relative to the reference genome assembly. Most variants in dbSNP are rare, not true polymorphisms, and some variants are known to be pathogenic. For hg38 (GRCh38), approximately 998 million distinct variants (RefSNP clusters with rs# ids) have been mapped to more than 1.06 billion genomic locations including alternate haplotype and fix patch sequences. dbSNP remapped variants from hg38 to hg19 (GRCh37); approximately 981 million distinct variants were mapped to more than 1.02 billion genomic locations including alternate haplotype and fix patch sequences (not all of which are included in UCSC's hg19). This track includes four subtracks of variants: All dbSNP (155): the entire set (1.02 billion for hg19, 1.06 billion for hg38) Common dbSNP (155): approximately 15 million variants with a minor allele frequency (MAF) of at least 1% (0.01) in the 1000 Genomes Phase 3 dataset. Variants in the Mult. subset (below) are excluded. ClinVar dbSNP (155): approximately 820,000 variants mentioned in ClinVar. Note: that includes both benign and pathogenic (as well as uncertain) variants. Variants in the Mult. subset (below) are excluded. Mult. dbSNP (155): variants that have been mapped to multiple chromosomes, for example chr1 and chr2, raising the question of whether the variant is really a variant or just a difference between duplicated sequences. There are some exceptions in which a variant is mapped to more than one reference sequence, but not culled into this set: A variant may appear in both X and Y pseudo-autosomal regions (PARs) without being included in this set. A variant may also appear in a main chromosome as well as an alternate haplotype or fix patch sequence assigned to that chromosome. A fifth subtrack highlights coordinate ranges to which dbSNP mapped a variant but with genomic coordinates that are not internally consistent, i.e. different coordinate ranges were provided when describing different alleles. This can occur due to a bug with mapping variants from one assembly sequence to another when there is an indel difference between the assembly sequences: Map Err (155): around 134,000 mappings of 88,000 distinct rsIDs for hg19 and 178,000 mappings of 108,000 distinct rsIDs for hg38. Interpreting and Configuring the Graphical Display SNVs and pure deletions are displayed as boxes covering the affected base(s). Pure insertions are drawn as single-pixel tickmarks between the base before and the base after the insertion. Insertions and/or deletions in repetitive regions may be represented by a half-height box showing uncertainty in placement, followed by a full-height box showing the number of deleted bases, or a full-height tickmark to indicate an insertion. When an insertion or deletion falls in a repetitive region, the placement may be ambiguous. For example, if the reference genome contains "TAAAG" but some individuals have "TAAG" at the same location, then the variant is a deletion of a single A relative to the reference genome. However, which A was deleted? There is no way to tell whether the first, second or third A was removed. Different variant mapping tools may place the deletion at different bases in the reference genome. To reduce errors in merging variant calls made with different left vs. right biases, dbSNP made a major change in its representation of deletion/insertion variants in build 152. Now, instead of assigning a single-base genomic location at one of the A's, dbSNP expands the coordinates to encompass the whole repetitive region, so the variant is represented as a deletion of 3 A's combined with an insertion of 2 A's. In the track display, there will be a half-height box covering the first two A's, followed by a full-height box covering the third A, to show a net loss of one base but an uncertain placement within the three A's. Variants are colored according to functional effect on genes annotated by dbSNP: Protein-altering variants and splice site variants are red. Synonymous codon variants are green. Non-coding transcript or Untranslated Region (UTR) variants are blue. On the track controls page, several variant properties can be included or excluded from the item labels: rs# identifier assigned by dbSNP, reference/alternate alleles, major/minor alleles (when available) and minor allele frequency (when available). Allele frequencies are reported independently by the project (some of which may have overlapping sets of samples): 1000Genomes: The 1000 Genomes dataset contains data for 2,504 individuals from 26 populations. dbGaP_PopFreq: The new source of dbGaP aggregated frequency data (>1 Million Subjects) provided by dbSNP. TOPMED: The TOPMED dataset contains freeze 8 panel that includes about 158,000 individuals. The approximate ethnic breakdown is European(41%), African (31%), Hispanic or Latino (15%), East Asian (9%), and unknown (4%) ancestry. KOREAN: The Korean Reference Genome Database contains data for 1,465 Korean individuals. SGDP_PRJ: The Simons Genome Diversity Project dataset contains 263 C-panel fully public samples and 16 B-panel fully public samples for a total of 279 samples. Qatari: The dataset contains initial mappings of the genomes of more than 1,000 Qatari nationals. NorthernSweden: The dataset contains 300 whole-genome sequenced human samples from the county of Vasterbotten in northern Sweden. Siberian: The dataset contains paired-end whole-genome sequencing data of 28 modern-day humans from Siberia and Western Russia. TWINSUK: The UK10K - TwinsUK project contains 1854 samples from the Department of Twin Research and Genetic Epidemiology (DTR). The dataset contains data obtained from the 11,000 identical and non-identical twins between the ages of 16 and 85 years old. TOMMO: The Tohoku Medical Megabank Project contains an allele frequency panel of 3552 Japanese individuals, including the X chromosome. ALSPAC: The UK10K - Avon Longitudinal Study of Parents and Children project contains 1927 sample including individuals obtained from the ALSPAC population. This population contains more than 14,000 mothers enrolled during pregnancy in 1991 and 1992. GENOME_DK: The dataset contains the sequencing of Danish parent-offspring trios to determine genomic variation within the Danish population. GnomAD: The gnomAD genome dataset includes a catalog containing 602M SNVs and 105M indels based on the whole-genome sequencing of 71,702 samples mapped to the GRCh38 build of the human reference genome. GoNL: The Genome of the Netherlands (GoNL) Project characterizes DNA sequence variation, common and rare, for SNVs and short insertions and deletions (indels) and large deletions in 769 individuals of Dutch ancestry selected from five biobanks under the auspices of the Dutch hub of the Biobanking and Biomolecular Research Infrastructure (BBMRI-NL). Estonian: The dataset contains genetic variation in the Estonian population: pharmacogenomics study of adverse drug effects using electronic health records. Vietnamese: The Kinh Vietnamese database contains 24.81 million variants (22.47 million single nucleotide polymorphisms (SNPs) and 2.34 million indels), of which 0.71 million variants are novel. Korea1K: The dataset contains 1,094 Korean personal genomes with clinical information. HapMap: (HapMap is being retired.) The International HapMap Project contains samples from African, Asian, or European populations. PRJEB36033: The dataset contains ancient Sardinia genome-wide 1240k capture data from 70 ancient Sardinians. HGDP_Stanford: The Stanford HGDP SNP genotyping data consists of ~660,918 tag SNPs in autosomes, chromosome X and Y, the pseudoautosomal region, and mitochondrial DNA, typed across 1043 individuals from all panel populations. Daghestan: The dataset contains genotypes of >550 000 autosomal single-nucleotide polymorphisms (SNPs) in a set of 14 population isolates speaking Nakh-Daghestanian (ND) languages. PAGE_STUDY: The PAGE Study: How Genetic Diversity Improves Our Understanding of the Architecture of Complex Traits. Chileans: The dataset consists of genetic variation on the Chileans using genotype data on ~685,944 SNPs from 313 individuals across the whole-continental country. MGP: MGP contains aggregated information on 267 healthy individuals, representative of the Spanish population that were used as controls in the MGP (Medical Genome Project). PRJEB37584: The dataset contains genome-wide genotype analysis that identified copy number variations in cranial meningiomas in Chinese patients, and demonstrated diverse CNV burdens among individuals with diverse clinical features. GoESP: The NHLBI Grand Opportunity Exome Sequencing Project (GO-ESP) dataset contains 6503 samples drawn from multiple ESP cohorts and represents all of the ESP exome variant data. ExAC: The Exome Aggregation Consortium (ExAC) dataset contains 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies. Individuals affected by severe pediatric disease have been removed. GnomAD_exomes: The gnomAD v2.1 exome dataset comprises a total of 16 million SNVs and 1.2 million indels from 125,748 exomes in 14 populations. FINRISK: The FINRISK cohorts comprise the respondents of representative, cross-sectional population surveys that are carried out every 5 years since 1972, to assess the risk factors of chronic diseases (e.g. CVD, diabetes, obesity, cancer) and health behavior in the working age population. PharmGKB: The dataset contains aggregated frequency data for all PharmGKB submissions. PRJEB37766: The Mexican Genomic Database for Addiction Research. The project from which to take allele frequency data defaults to 1000 Genomes but can be set to any of those projects. Using the track controls, variants can be filtered by minimum minor allele frequency (MAF) variation class/type (e.g. SNV, insertion, deletion) functional effect on a gene (e.g. synonymous, frameshift, intron, upstream) assorted features and anomalies noted by UCSC during processing of dbSNP's data Interesting and anomalous conditions noted by UCSC While processing the information downloaded from dbSNP, UCSC annotates some properties of interest. These are noted on the item details page, and may be useful to include or exclude affected variants. Some are purely informational: keyword in data file (dbSnp155.bb) # in hg19# in hg38description clinvar 627817 630503 Variant is in ClinVar. clinvarBenign 275541 276409 Variant is in ClinVar with clinical significance of benign and/or likely benign. clinvarConflicting 16925 16834 Variant is in ClinVar with reports of both benign and pathogenic significance. clinvarPathogenic 56373 56475 Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic. commonAll 14904503 15862783 Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all projects reporting frequencies. commonSome 59633864 62095091 Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all, projects reporting frequencies. diffMajor 12748733 13073288 Different frequency sources have different major alleles. overlapDiffClass 198945442 207101421 This variant overlaps another variant with a different type/class. overlapSameClass 29281958 30301090 This variant overlaps another with the same type/class but different start/end. rareAll 906113910 938985356 Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in all projects reporting frequencies, or has no frequency data. rareSome 950843271 985217664 Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in some, but not all, projects reporting frequencies, or has no frequency data. revStrand 5540864 6770772 Alleles are displayed on the + strand at the current position. dbSNP's alleles are displayed on the + strand of a different assembly sequence, so dbSNP's variant page shows alleles that are reverse-complemented with respect to the alleles displayed above. while others may indicate that the reference genome contains a rare variant or sequencing issue: keyword in data file (dbSnp155.bb) # in hg19# in hg38description refIsAmbiguous 19 41 The reference genome allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G', or 'N' for 'any base'). refIsMinor 14950212 15386394 The reference genome allele is not the major allele in at least one project. refIsRare 793081 822757 The reference genome allele is rare (i.e. allele frequency refIsSingleton 694310 712794 The reference genome allele has never been observed in a population sequencing project reporting frequencies. refMismatch 1 18 The reference genome allele reported by dbSNP differs from the GenBank assembly sequence. This is very rare and in all cases observed so far, the GenBank assembly has an 'N' while the RefSeq assembly used by dbSNP has a less ambiguous character such as 'R'. and others may indicate an anomaly or problem with the variant data: keyword in data file (dbSnp155.bb) # in hg19# in hg38description altIsAmbiguous 5294 5361 At least one alternate allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G'). For alleles containing more than one ambiguous base, this may create a combinatoric explosion of possible alleles. classMismatch 13289 18475 Variation class/type is inconsistent with alleles mapped to this genome assembly. clusterError 373258 459130 This variant has the same start, end and class as another variant; they probably should have been merged into one variant. freqIncomplete 0 0 At least one project reported counts for only one allele which implies that at least one allele is missing from the report; that project's frequency data are ignored. freqIsAmbiguous 4332 4399 At least one allele reported by at least one project that reports frequencies contains an IUPAC ambiguous base. freqNotMapped 1149972 1141935 At least one project reported allele frequencies relative to a different assembly; However, dbSNP does not include a mapping of this variant to that assembly, which implies a problem with mapping the variant across assemblies. The mapping on this assembly may have an issue; evaluate carefully vs. original submissions, which you can view by clicking through to dbSNP above. freqNotRefAlt 74139 110646 At least one allele reported by at least one project that reports frequencies does not match any of the reference or alternate alleles listed by dbSNP. multiMap 799777 286666 This variant has been mapped to more than one distinct genomic location. otherMapErr 91260 195051 At least one other mapping of this variant has erroneous coordinates. The mapping(s) with erroneous coordinates are excluded from this track and are included in the Map Err subtrack. Sometimes despite this mapping having legal coordinates, there may still be an issue with this mapping's coordinates and alleles; you may want to click through to dbSNP to compare the initial submission's coordinates and alleles. In hg19, 55454 distinct rsIDs are affected; in hg38, 86636. Data Sources and Methods dbSNP has collected genetic variant reports from researchers worldwide for more than 20 years. Since the advent of next-generation sequencing methods and the population sequencing efforts that they enable, dbSNP has grown exponentially, requiring a new data schema, computational pipeline, web infrastructure, and download files. (Holmes et al.) The same challenges of exponential growth affected UCSC's presentation of dbSNP variants, so we have taken the opportunity to change our internal representation and import pipeline. Most notably, flanking sequences are no longer provided by dbSNP, because most submissions have been genomic variant calls in VCF format as opposed to independent sequences. We downloaded JSON files available from dbSNP at http://ftp.ncbi.nlm.nih.gov/snp/archive/b155/JSON/, extracted a subset of the information about each variant, and collated it into a bigBed file using the bigDbSnp.as schema with the information necessary for filtering and displaying the variants, as well as a separate file containing more detailed information to be displayed on each variant's details page (dbSnpDetails.as schema). Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. Since dbSNP has grown to include over 1 billion variants, the size of the All dbSNP (155) subtrack can cause the Table Browser and Data Integrator to time out, leading to a blank page or truncated output, unless queries are restricted to a chromosomal region, to particular defined regions, to a specific set of rs# IDs (which can be pasted/uploaded into the Table Browser), or to one of the subset tracks such as Common (~15 million variants) or ClinVar (~0.8M variants). For automated analysis, the track data files can be downloaded from the downloads server for hg19 and hg38. file format subtrack dbSnp155.bb hg19 hg38 bigDbSnp (bigBed4+13) All dbSNP (155) dbSnp155ClinVar.bb hg19 hg38 bigDbSnp (bigBed4+13) ClinVar dbSNP (155) dbSnp155Common.bb hg19 hg38 bigDbSnp (bigBed4+13) Common dbSNP (155) dbSnp155Mult.bb hg19 hg38 bigDbSnp (bigBed4+13) Mult. dbSNP (155) dbSnp155BadCoords.bb hg19 hg38 bigBed4 Map Err (155) dbSnp155Details.tab.gz gzip-compressed tab-separated text Detailed variant properties, independent of genome assembly version Several utilities for working with bigBed-formatted binary files can be downloaded here. Run a utility with no arguments to see a brief description of the utility and its options. bigBedInfo provides summary statistics about a bigBed file including the number of items in the file. With the -as option, the output includes an autoSql definition of data columns, useful for interpreting the column values. bigBedToBed converts the binary bigBed data to tab-separated text. Output can be restricted to a particular region by using the -chrom, -start and -end options. bigBedNamedItems extracts rows for one or more rs# IDs. Example: retrieve all variants in the region chr1:200001-200400 bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp155.bb -chrom=chr1 -start=200000 -end=200400 stdout Example: retrieve variant rs6657048 bigBedNamedItems dbSnp155.bb rs6657048 stdout Example: retrieve all variants with rs# IDs in a file (myIds.txt) and output to another file (dbSnp155.myIds.bed) bigBedNamedItems -nameFile dbSnp155.bb myIds.txt dbSnp155.myIds.bed The columns in the bigDbSnp/bigBed files and dbSnp155Details.tab.gz file are described in bigDbSnp.as and dbSnpDetails.as respectively. For columns that contain lists of allele frequency data, the order of projects providing the data listed is as follows: 1000Genomes dbGaP_PopFreq TOPMED KOREAN SGDP_PRJ Qatari NorthernSweden Siberian TWINSUK TOMMO ALSPAC GENOME_DK GnomAD GoNL Estonian Vietnamese Korea1K HapMap PRJEB36033 HGDP_Stanford Daghestan PAGE_STUDY Chileans MGP PRJEB37584 GoESP ExAC GnomAD_exomes FINRISK PharmGKB PRJEB37766 The functional effect (maxFuncImpact) for each variant contains the Sequence Ontology (SO) ID for the greatest functional impact on the gene. This field contains a 0 when no SO terms are annotated on the variant. UCSC also has an API that can be used to retrieve values from a particular chromosome range. A list of rs# IDs can be pasted/uploaded in the Variant Annotation Integrator tool to find out which genes (if any) the variants are located in, as well as functional effect such as intron, coding-synonymous, missense, frameshift, etc. Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information. References Holmes JB, Moyer E, Phan L, Maglott D, Kattman B. SPDI: Data Model for Variants and Applications at NCBI. Bioinformatics. 2019 Nov 18;. PMID: 31738401 Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K, Clark K, Connor R, Fiorini N, Funk K, Hefferon T et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2019 Jan 8;47(D1):D23-D28. PMID: 30395293; PMC: PMC6323993 Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
dbSnp155ViewVariants Variants Short Genetic Variants from dbSNP release 155 Variation 
dbSnp155 All dbSNP(155) All Short Genetic Variants from dbSNP Release 155 Variation 
dbSnp155Mult Mult. dbSNP(155) Short Genetic Variants from dbSNP Release 155 that Map to Multiple Genomic Loci Variation 
dbSnp155ClinVar ClinVar dbSNP(155) Short Genetic Variants from dbSNP Release 155 Included in ClinVar Variation 
dbSnp155Common Common dbSNP(155) Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 155 Variation 
dbSnp155ViewErrs Mapping Errors Short Genetic Variants from dbSNP release 155 Variation 
dbSnp155BadCoords Map Err dbSnp(155) Mappings with Inconsistent Coordinates from dbSNP 155 Variation 
snp141Flagged Flagged SNPs(141) Simple Nucleotide Polymorphisms (dbSNP 141) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 141, available from ftp.ncbi.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(141) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(141) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(141) - SNPs mapping in more than one place on reference assembly. All SNPs(141) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/database/ (for human, organism_tax_id = human_9606; for mouse, organism_tax_id = mouse_10090). The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/rs_fasta/ Coordinates, orientation, location type and dbSNP reference allele data were obtained from b141_SNPContigLoc.bcp.gz and b141_ContigInfo.bcp.gz. b141_SNPMapInfo.bcp.gz provided the alignment weights. Functional classification was obtained from b141_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp141*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp138 All SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 138, available from ftp.ncbi.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(138): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(138): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(138): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks for all assemblies and versions: Common SNPs(138) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(138) - SNPs not necessarily a risk allele! Mult. SNPs(138) - SNPs mapping in more than one place on reference assembly. All SNPs(138) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF >= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF >= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/database/ (for human, organism_tax_id = human_9606; for mouse, organism_tax_id = mouse_10090). The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/rs_fasta/ Coordinates, orientation, location type and dbSNP reference allele data were obtained from b138_SNPContigLoc.bcp.gz and b138_ContigInfo.bcp.gz. b138_SNPMapInfo.bcp.gz provided the alignment weights. Functional classification was obtained from b138_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38, hg19, mm10, susScr3, bosTau7, and galGal4 (snp138*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exlcude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp138Common Common SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 138, available from ftp.ncbi.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks for all assemblies and versions: Common SNPs(138) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(138) - SNPs not necessarily a risk allele! Mult. SNPs(138) - SNPs mapping in more than one place on reference assembly. All SNPs(138) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF >= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF >= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/database/ (for human, organism_tax_id = human_9606; for mouse, organism_tax_id = mouse_10090). The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/rs_fasta/ Coordinates, orientation, location type and dbSNP reference allele data were obtained from b138_SNPContigLoc.bcp.gz and b138_ContigInfo.bcp.gz. b138_SNPMapInfo.bcp.gz provided the alignment weights. Functional classification was obtained from b138_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38, hg19, mm10, susScr3, bosTau7, and galGal4 (snp138*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exlcude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp138Flagged Flagged SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) Flagged as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 138, available from ftp.ncbi.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks for all assemblies and versions: Common SNPs(138) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(138) - SNPs not necessarily a risk allele! Mult. SNPs(138) - SNPs mapping in more than one place on reference assembly. All SNPs(138) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF >= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF >= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/database/ (for human, organism_tax_id = human_9606; for mouse, organism_tax_id = mouse_10090). The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/rs_fasta/ Coordinates, orientation, location type and dbSNP reference allele data were obtained from b138_SNPContigLoc.bcp.gz and b138_ContigInfo.bcp.gz. b138_SNPMapInfo.bcp.gz provided the alignment weights. Functional classification was obtained from b138_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38, hg19, mm10, susScr3, bosTau7, and galGal4 (snp138*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exlcude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp138Mult Mult. SNPs(138) Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 138, available from ftp.ncbi.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The default maximum weight for this track is 3, unlike the other dbSNP build 138 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(138) track because of its maximum weight filter. The remainder of this page is identical on the following tracks for all assemblies and versions: Common SNPs(138) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(138) - SNPs not necessarily a risk allele! Mult. SNPs(138) - SNPs mapping in more than one place on reference assembly. All SNPs(138) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF >= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF >= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/database/ (for human, organism_tax_id = human_9606; for mouse, organism_tax_id = mouse_10090). The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/rs_fasta/ Coordinates, orientation, location type and dbSNP reference allele data were obtained from b138_SNPContigLoc.bcp.gz and b138_ContigInfo.bcp.gz. b138_SNPMapInfo.bcp.gz provided the alignment weights. Functional classification was obtained from b138_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38, hg19, mm10, susScr3, bosTau7, and galGal4 (snp138*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exlcude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
cons100way Conservation Vertebrate Multiz Alignment & Conservation (100 Species) Comparative Genomics Downloads for data in this track are available: Multiz alignments (MAF format), and phylogenetic trees PhyloP conservation (WIG format) PhastCons conservation (WIG format) Description This track shows multiple alignments of 100 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track. PHAST/Multiz are built from chains ("alignable") and nets ("syntenic"), see the documentation of the Chain/Net tracks for a description of the complete alignment process. PhastCons is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites). Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1. Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data, and both were run with the same parameters. UCSC has repeatmasked and aligned all genome assemblies, and provides all the sequences for download. For genome assemblies not available in the genome browser, there are alternative assembly hub genome browsers. Missing sequence in any assembly is highlighted in the track display by regions of yellow when zoomed out and by Ns when displayed at base level (see Gap Annotation, below). Primate subset OrganismSpeciesRelease dateUCSC versionAlignment type BaboonPapio hamadryasNov 2008Baylor Pham_1.0/papHam1Reciprocal best net BushbabyOtolemur garnettiiMar 2011Broad/otoGar3Syntenic net ChimpPan troglodytesFeb 2011CSAC 2.1.4/panTro4Syntenic net Crab-eating macaqueMacaca fascicularisJun 2013Macaca_fascicularis_5.0/macFas5Syntenic net GibbonNomascus leucogenysOct 2012GGSC Nleu3.0/nomLeu3Syntenic net GorillaGorilla gorilla gorillaMay 2011gorGor3.1/gorGor3Reciprocal best net Green monkeyChlorocebus sabaeusJun 2013Chlorocebus_sabeus 1.0/chlSab1Syntenic net HumanHomo sapiensFeb 2009GRCh37/hg19reference species MarmosetCallithrix jacchusMar 2009WUGSC 3.2/calJac3Syntenic net OrangutanPongo pygmaeus abeliiJuly 2007WUGSC 2.0.2/ponAbe2Reciprocal best net RhesusMacaca mulattaOct 2010BGI CR_1.0/rheMac3Syntenic net Squirrel monkeySaimiri boliviensisOct 2011Broad/saiBol1Syntenic net Euarchontoglires subset Brush-tailed ratOctodon degusApr 2012OctDeg1.0/octDeg1Syntenic net ChinchillaChinchilla lanigeraMay 2012 ChiLan1.0/chiLan1Syntenic net Chinese hamsterCricetulus griseusJul 2013C_griseus_v1.0/criGri1Syntenic net Chinese tree shrewTupaia chinensisJan 2013TupChi_1.0/tupChi1Syntenic net Golden hamsterMesocricetus auratusMar 2013MesAur1.0/mesAur1Syntenic net Guinea pigCavia porcellusFeb 2008Broad/cavPor3Syntenic net Lesser Egyptian jerboaJaculus jaculusMay 2012JacJac1.0/jacJac1Syntenic net MouseMus musculusDec 2011GRCm38/mm10Syntenic net Naked mole-ratHeterocephalus glaberJan 2012Broad HetGla_female_1.0/hetGla2Syntenic net PikaOchotona princepsMay 2012OchPri3.0/ochPri3Syntenic net Prairie voleMicrotus ochrogasterOct 2012MicOch1.0/micOch1Syntenic net RabbitOryctolagus cuniculusApr 2009Broad/oryCun2Syntenic net RatRattus norvegicusMar 2012RGSC 5.0/rn5Syntenic net SquirrelSpermophilus tridecemlineatusNov 2011Broad/speTri2Syntenic net Laurasiatheria subset AlpacaVicugna pacosMar 2013Vicugna_pacos-2.0.1/vicPac2Syntenic net Bactrian camelCamelus ferusDec 2011CB1/camFer1Syntenic net Big brown batEptesicus fuscusJul 2012EptFus1.0/eptFus1Syntenic net Black flying-foxPteropus alectoAug 2012ASM32557v1/pteAle1Syntenic net CatFelis catusSep 2011ICGSC Felis_catus 6.2/felCat5Syntenic net CowBos taurusOct 2011Baylor Btau_4.6.1/bosTau7Syntenic net David's myotis batMyotis davidiiAug 2012ASM32734v1/myoDav1Syntenic net DogCanis lupus familiarisSep 2011Broad CanFam3.1/canFam3Syntenic net DolphinTursiops truncatusOct 2011Baylor Ttru_1.4/turTru2Reciprocal best net Domestic goatCapra hircusMay 2012CHIR_1.0/capHir1Syntenic net Ferret Mustela putorius furoApr 2011MusPutFur1.0/musFur1Syntenic net HedgehogErinaceus europaeusMay 2012EriEur2.0/eriEur2Syntenic net HorseEquus caballusSep 2007Broad/equCab2Syntenic net Killer whaleOrcinus orcaJan 2013Oorc_1.1/orcOrc1Syntenic net Little brown batMyotis lucifugusJul 2010Broad Institute Myoluc2.0/myoLuc2Syntenic net MegabatPteropus vampyrusJul 2008Broad/pteVam1Reciprocal best net Pacific walrusOdobenus rosmarus divergensJan 2013Oros_1.0/odoRosDiv1Syntenic net PandaAiluropoda melanoleucaDec 2009BGI-Shenzhen 1.0/ailMel1Syntenic net PigSus scrofaAug 2011SGSC Sscrofa10.2/susScr3Syntenic net SheepOvis ariesAug 2012ISGC Oar_v3.1/oviAri3Syntenic net ShrewSorex araneusAug 2008Broad/sorAra2Syntenic net Star-nosed moleCondylura cristataMar 2012ConCri1.0/conCri1Syntenic net Tibetan antelopePantholops hodgsoniiMay 2013PHO1.0/panHod1Syntenic net Weddell sealLeptonychotes weddelliiMar 2013LepWed1.0/lepWed1Reciprocal best net White rhinocerosCeratotherium simumMay 2012CerSimSim1.0/cerSim1Syntenic net Afrotheria subset AardvarkOrycteropus afer aferMay 2012OryAfe1.0/oryAfe1Syntenic net Cape elephant shrewElephantulus edwardiiAug 2012EleEdw1.0/eleEdw1Syntenic net Cape golden moleChrysochloris asiaticaAug 2012ChrAsi1.0/chrAsi1Syntenic net ElephantLoxodonta africanaJul 2009Broad/loxAfr3Syntenic net ManateeTrichechus manatus latirostrisOct 2011Broad v1.0/triMan1Syntenic net TenrecEchinops telfairiNov 2012Broad/echTel2Syntenic net Mammal subset ArmadilloDasypus novemcinctusDec 2011Baylor/dasNov3Syntenic net OpossumMonodelphis domesticaOct 2006Broad/monDom5Net PlatypusOrnithorhynchus anatinusMar 2007WUGSC 5.0.1/ornAna1Reciprocal best net Tasmanian devilSarcophilus harrisiiFeb 2011WTSI Devil_ref v7.0/sarHar1Net WallabyMacropus eugeniiSep 2009TWGS Meug_1.1/macEug2Reciprocal best net Aves subset BudgerigarMelopsittacus undulatusSep 2011WUSTL v6.3/melUnd1Net ChickenGallus gallusNov 2011ICGSC Gallus_gallus-4.0/galGal4Net Collared flycatcherFicedula albicollisJun 2013FicAlb1.5/ficAlb2Net Mallard duckAnas platyrhynchosApr 2013BGI_duck_1.0/anaPla1Net Medium ground finchGeospiza fortisApr 2012GeoFor_1.0/geoFor1Net ParrotAmazona vittataJan 2013AV1/amaVit1Net Peregrine falconFalco peregrinusFeb 2013F_peregrinus_v1.0/falPer1Net Rock pigeonColumba liviaFeb 2013Cliv_1.0/colLiv1Net Saker falconFalco cherrugFeb 2013F_cherrug_v1.0/falChe1Net Scarlet macawAra macaoJun 2013SMACv1.1/araMac1Net Tibetan ground jayPseudopodoces humilisJan 2013PseHum1.0/pseHum1Net TurkeyMeleagris gallopavoDec 2009TGC Turkey_2.01/melGal1Net White-throated sparrowZonotrichia albicollisApr 2013ASM38545v1/zonAlb1Net Zebra finchTaeniopygia guttataFeb 2013WashU taeGut324/taeGut2Net Sarcopterygii subset American alligatorAlligator mississippiensisAug 2012allMis0.2/allMis1Net Chinese softshell turtlePelodiscus sinensisOct 2011PelSin_1.0/pelSin1Net CoelacanthLatimeria chalumnaeAug 2011Broad/latCha1Net Green seaturtleChelonia mydasMar 2013CheMyd_1.0/cheMyd1Net LizardAnolis carolinensisMay 2010Broad AnoCar2.0/anoCar2Net Painted turtleChrysemys picta belliiDec 2011v3.0.1/chrPic1Net Spiny softshell turtleApalone spiniferaMay 2013ASM38561v1/apaSpi1Net X. tropicalisXenopus tropicalisSep 2012JGI 7.0/xenTro7Net Fish subset Atlantic codGadus morhuaMay 2010Genofisk GadMor_May2010/gadMor1Net Burton's mouthbreederHaplochromis burtoniOct 2011AstBur1.0/hapBur1Net FuguTakifugu rubripesOct 2011FUGU5/fr3Net LampreyPetromyzon marinusSep 2010WUGSC 7.0/petMar2Net MedakaOryzias latipesOct 2005NIG/UT MEDAKA1/oryLat2Net Mexican tetra (cavefish)Astyanax mexicanusApr 2013Astyanax_mexicanus-1.0.2/astMex1Net Nile tilapiaOreochromis niloticusJan 2011Broad oreNil1.1/oreNil2Net Princess of BurundiNeolamprologus brichardiMay 2011NeoBri1.0/neoBri1Net Pundamilia nyerereiPundamilia nyerereiOct 2011PunNye1.0/punNye1Net Southern platyfishXiphophorus maculatusJan 2012Xiphophorus_maculatus-4.4.2/xipMac1Net Spotted garLepisosteus oculatusDec 2011LepOcu1/lepOcu1Net SticklebackGasterosteus aculeatusFeb 2006Broad/gasAcu1Net TetraodonTetraodon nigroviridisMar 2007Genoscope 8.0/tetNig2Net Yellowbelly pufferfishTakifugu flavidusMay 2013version 1 of Takifugu flavidus genome/takFla1Net Zebra mbunaMaylandia zebraMar 2012MetZeb1.1/mayZeb1Net ZebrafishDanio rerioJul 2010Zv9/danRer7Net Table 1. Genome assemblies included in the 100-way Conservation track. Display Conventions and Configuration In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options. Pairwise alignments of each species to the human genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons. Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display. To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment. Gap Annotation The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used: Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the human genome or a lineage-specific deletion between the aligned blocks in the aligning species. Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species. Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species. Genomic Breaks Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows: Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement. Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the human genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence. Base Level When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the human sequence at those alignment positions relative to the longest non-human sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a &quot;*&quot; is displayed; other gap sizes are indicated by &quot;+&quot;. Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes: No codon translation: The gene annotation is not used; the bases are displayed without translation. Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment. Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding. Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation. Codon translation uses the following gene tracks as the basis for translation: Gene TrackSpecies UCSC GenesHuman, Mouse RefSeq GenesCow, Frog (X. tropicalis) Ensembl Genes v73Atlantic cod, Bushbaby, Cat, Chicken, Chimp, Coelacanth, Dog, Elephant, Ferret, Fugu, Gorilla, Horse, Lamprey, Little brown bat, Lizard, Mallard duck, Marmoset, Medaka, Orangutan, Panda, Pig, Platypus, Rat, Soft-shell Turtle, Southern platyfish, Squirrel, Tasmanian devil, Tetraodon, Zebrafish no annotationAardvark, Alpaca, American alligator, Armadillo, Baboon, Bactrian camel, Big brown bat, Black flying-fox, Brush-tailed rat, Budgerigar, Burton's mouthbreeder, Cape elephant shrew, Cape golden mole, Chinchilla, Chinese hamster, Chinese tree shrew, Collared flycatcher, Crab-eating macaque, David's myotis (bat), Dolphin, Domestic goat, Gibbon, Golden hamster, Green monkey, Green seaturtle, Hedgehog, Killer whale, Lesser Egyptian jerboa, Manatee, Medium ground finch, Mexican tetra (cavefish), Naked mole-rat, Nile tilapia, Pacific walrus, Painted turtle, Parrot, Peregrine falcon, Pika, Prairie vole, Princess of Burundi, Pundamilia nyererei, Rhesus, Rock pigeon, Saker falcon, Scarlet Macaw, Sheep, Shrew, Spiny softshell turtle, Spotted gar, Squirrel monkey, Star-nosed mole, Tawny puffer fish, Tenrec, Tibetan antelope, Tibetan ground jay, Wallaby, Weddell seal, White rhinoceros, White-throated sparrow, Zebra Mbuna, Zebra finch Table 2. Gene tracks used for codon translation. Methods Pairwise alignments with the human genome were generated for each species using lastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks. An additional filtering step was introduced in the generation of the 60-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query (&quot;reciprocal best&quot;). The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display. Phylogenetic Tree Model Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The all-species tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 60-way alignment (msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene set, filtered to select single-coverage long transcripts. This same tree model was used in the phyloP calculations; however, the background frequencies were modified to maintain reversibility. The resulting tree model: all species. PhastCons Conservation The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005. The phastCons parameters used were: expected-length=45, target-coverage=0.3, rho=0.3. PhyloP Conservation The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements ( http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC). Conserved Elements The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full". Credits This track was created using the following programs: Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC). MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC Tree image generator: phyloPng by Galt Barber, UCSC Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community. Thanks to Giacomo Bernardi for help with the fish relationships. References Phylo-HMMs, phastCons, and phyloP: Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911 Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823 Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216 Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396 Chain/Net: Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Multiz: Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317 Lastz (formerly Blastz): Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 Phylogenetic Tree: Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200 
cons100wayViewalign Multiz Alignments Vertebrate Multiz Alignment & Conservation (100 Species) Comparative Genomics 
multiz100way Multiz Align Multiz Alignments of 100 Vertebrates Comparative Genomics 
cons100wayViewphastcons Element Conservation (phastCons) Vertebrate Multiz Alignment & Conservation (100 Species) Comparative Genomics 
phastCons100way 100 Vert. Cons 100 vertebrates conservation by PhastCons Comparative Genomics 
cons100wayViewelements Conserved Elements Vertebrate Multiz Alignment & Conservation (100 Species) Comparative Genomics 
phastConsElements100way 100 Vert. El 100 vertebrates Conserved Elements Comparative Genomics 
cons100wayViewphyloP Basewise Conservation (phyloP) Vertebrate Multiz Alignment & Conservation (100 Species) Comparative Genomics 
phyloP100wayAll 100 Vert. Cons 100 vertebrates Basewise Conservation by PhyloP Comparative Genomics 
cpgIslandExt CpG Islands CpG Islands (Islands < 300 Bases are Light Green) Regulation Description CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. By default, only the masked version of the track is displayed. To view the unmasked version, change the visibility settings in the track controls at the top of this page. Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. The track CpG Islands is constructed on the sequence after all masked sequence is removed. The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula (cited in Gardiner-Garden et al. (1987)): Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. The calculation of the track data is performed by the following command sequence: twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \ | cpg_lh /dev/stdin 2&gt; cpg_lh.err \ | awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2; printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \ | sort -k1,1 -k2,2n &gt; cpgIsland.bed The unmasked track data is constructed from twoBitToFa -noMask output for the twoBitToFa command. Data access CpG islands and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/. The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447 
cpgIslandSuper CpG Islands CpG Islands (Islands < 300 Bases are Light Green) Regulation Description CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. By default, only the masked version of the track is displayed. To view the unmasked version, change the visibility settings in the track controls at the top of this page. Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. The track CpG Islands is constructed on the sequence after all masked sequence is removed. The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula (cited in Gardiner-Garden et al. (1987)): Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. The calculation of the track data is performed by the following command sequence: twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \ | cpg_lh /dev/stdin 2&gt; cpg_lh.err \ | awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2; printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \ | sort -k1,1 -k2,2n &gt; cpgIsland.bed The unmasked track data is constructed from twoBitToFa -noMask output for the twoBitToFa command. Data access CpG islands and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/. The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447 
fixSeqLiftOverPsl Fix Patches Reference Assembly Fix Patch Sequence Alignments Mapping and Sequencing Description This track shows alignments of fix patch sequences to main chromosome sequences in the reference genome assembly. When errors are corrected in the reference genome assembly, the Genome Reference Consortium (GRC) adds fix patch sequences containing the corrected regions. This strikes a balance between providing the most complete and correct genome sequence, while maintaining stable chromosome coordinates for the original assembly sequences. Fix patches are often associated with incident reports displayed in the GRC Incidents track. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. Mismatching bases are highlighted in red. Several types of alignment gap may also be colored; for more information, see Alignment Insertion/Deletion Display Options. Credits The alignments were provided by NCBI as GFF files and translated into the PSL representation for browser display by UCSC. 
knownGene GENCODE V47lift37 GENCODE V47lift37 Genes and Gene Predictions Description The GENCODE Genes track (version 47, September 2024) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. By default, only the basic gene set is displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts that GENCODE believes will be useful to the majority of users. The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes are not displayed by default. It contains annotations on the reference chromosomes as well as assembly patches and alternative loci (haplotypes). Statistics for the v47 release can be found in the GENCODE site for this build. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. It includes options to display the entire GENCODE set and pseudogenes. To customize these options, the respective boxes can be checked or unchecked at the top of this description page. This track also includes a variety of labels which identify the transcripts when visibility is set to &quot;full&quot; or &quot;pack&quot;. Gene symbols (e.g. NIPA1) are displayed by default, but additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene and transcript names can be found in our FAQ. This track, in general, follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. Coloring for the gene annotations is based on the annotation type: coding: protein coding transcripts, including polymorphic pseudogenes non-coding: non-protein coding transcripts pseudogene: pseudogene transcript annotations problem: problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. There is also an option to display the data as a density graph, which can be helpful for visualizing the distribution of items over a region. Squishy-pack Display Within a gene using the pack display mode, transcripts below a specified rank will be condensed into a view similar to squish mode. The transcript ranking approach is preliminary and will change in future releases. The transcripts rankings are defined by the following criteria for protein-coding and non-coding genes: Protein_coding genes MANE or Ensembl canonical 1st: MANE Select / Ensembl canonical 2nd: MANE Plus Clinical Coding biotypes 1st: protein_coding and protein_coding_LoF 2nd: NMDs and NSDs 3rd: retained intron and protein_coding_CDS_not_defined Completeness 1st: full length 2nd: CDS start/end not found CARS score (only for coding transcripts) Transcript genomic span and length (only for non-coding transcripts) Non-coding genes Transcript biotype 1st: transcript biotype identical to gene biotype Ensembl canonical GENCODE basic Transcript genomic span Transcript length Methods The GENCODE v47 track was built from the GENCODE downloads file gencode.v47.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources were correlated with the GENCODE data to build association tables. The lift to GRCh37/hg19 made use of the lift mechanism described here. Related Data The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a downloadable file. One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list is then available on the table menu. Data access GENCODE Genes and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. The genePred format files for hg38 are available from our downloads directory or in our GTF download directory. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. Credits The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a computational pipeline developed by Jim Kent and Brian Raney. This version of the track was generated by Jonathan Casper. References Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. PMID: 36420896; PMC: PMC9825462 A full list of GENCODE publications is available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
gtexGeneV8 GTEx Gene V8 Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019) Expression Description The NIH Genotype-Tissue Expression (GTEx) project was created to establish a sample and data resource for studies on the relationship between genetic variation and gene expression in multiple human tissues. This track shows median gene expression levels in 52 tissues and 2 cell lines, based on RNA-seq data from the GTEx final data release (V8, August 2019). This release is based on data from 17,382 tissue samples obtained from 948 adult post-mortem individuals. Display Conventions In Full and Pack display modes, expression for each gene is represented by a colored bargraph, where the height of each bar represents the median expression level across all samples for a tissue, and the bar color indicates the tissue. Tissue colors were assigned to conform to the GTEx Consortium publication conventions. &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The bargraph display has the same width and tissue order for all genes. Mouse hover over a bar will show the tissue and median expression level. The Squish display mode draws a rectangle for each gene, colored to indicate the tissue with highest expression level if it contributes more than 10% to the overall expression (and colored black if no tissue predominates). In Dense mode, the darkness of the grayscale rectangle displayed for the gene reflects the total median expression level across all tissues. The GTEx transcript model used to quantify expression level is displayed below the graph, colored to indicate the transcript class (coding, noncoding, pseudogene, problem), following GENCODE conventions. Click-through on a graph displays a boxplot of expression level quartiles with outliers, per tissue, along with a link to the corresponding gene page on the GTEx Portal. The track configuration page provides controls to limit the genes and tissues displayed, and to select raw or log transformed expression level display. Methods Tissue samples were obtained using the GTEx standard operating procedures for informed consent and tissue collection, in conjunction with the National Cancer Institute Biorepositories and Biospecimen. All tissue specimens were reviewed by pathologists to characterize and verify organ source. Images from stained tissue samples can be viewed via the NCI histopathology viewer. The Qiagen PAXgene non-formalin tissue preservation product was used to stabilize tissue specimens without cross-linking biomolecules. RNA-seq was performed by the GTEx Laboratory, Data Analysis and Coordinating Center (LDACC) at the Broad Institute. The Illumina TruSeq protocol was used to create an unstranded polyA+ library sequenced on the Illumina HiSeq 2000 and HiSeq 2500 platforms to produce 76-bp paired end reads with a coverage goal of 50M (median achieved was ~82M total reads). Sequence reads were aligned to the hg38/GRCh38 human genome using STAR v2.5.3a assisted by the GENCODE 26 transcriptome definition. The alignment pipeline is available here. Gene annotations were produced using a custom isoform collapsing procedure that excluded retained intron and read through transcripts, merged overlapping exon intervals and then excluded exon intervals overlapping between genes. Gene expression levels in TPM were called via the RNA-SeQC tool (v1.1.9), after filtering for unique mapping, proper pairing, and exon overlap. For further method details, see the GTEx Portal Documentation page. UCSC obtained the gene-level expression files, gene annotations and sample metadata from the GTEx Portal Download page. Median expression level in TPM was computed per gene/per tissue. Subject and Sample Characteristics The scientific goal of the GTEx project required that the donors and their biospecimen present with no evidence of disease. The tissue types collected were chosen based on their clinical significance, logistical feasibility and their relevance to the scientific goal of the project and the research community. Summary plots of GTEx sample characteristics are available at the GTEx Portal Tissue Summary page. Data Access The raw data for the GTEx Gene expression track can be accessed interactively through the Table Browser or Data Integrator. Metadata can be found in the connected tables below. gtexGeneModelV8 describes the gene names and coordinates in genePred format. hgFixed.gtexTissueV8 lists each of the 53 tissues in alphabetical order, corresponding to the comma separated expression values in gtexGeneV8. hgFixed.gtexSampleDataV8 has TPM expression scores for each individual gene-sample data point, connected to gtexSampleV8. hgFixed.gtexSampleV8 contains metadata about sample time, collection site, and tissue, connected to the donor field in the gtexDonorV8 table. hgFixed.gtexDonorV8 has anonymized information on the tissue donor. For automated analysis and downloads, the track data files can be downloaded from our downloads server or the JSON API. Individual regions or the whole genome annotation can be accessed as text using our utility bigBedToBed. Instructions for downloading the utility can be found here. That utility can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/gtex/gtexGeneV8.bb -chrom=chr21 -start=0 -end=100000000 stdout Data can also be obtained directly from GTEx at the following link: https://gtexportal.org/home/datasets Credits Statistical analysis and data interpretation was performed by The GTEx Consortium Analysis Working Group. Data was provided by the GTEx LDACC at The Broad Institute of MIT and Harvard. References GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science. 2020 Sep 11;369(6509):1318-1330. PMID: 32913098; PMC: PMC7737656 GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun;45(6):580-5. PMID: 23715323; PMC: PMC4010069 Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, DeLuca DS, Peter-Demchok J, Gelfand ET et al. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. Biopreserv Biobank. 2015 Oct;13(5):311-9. PMID: 26484571; PMC: PMC4675181 Mel&#233; M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ et al. Human genomics. The human transcriptome across tissues and individuals. Science. 2015 May 8;348(6235):660-5. PMID: 25954002; PMC: PMC4547472 DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012 Jun 1;28(11):1530-2. PMID: 22539670; PMC: PMC3356847 
jarvis JARVIS JARVIS: score to prioritize non-coding regions for disease relevance Phenotype and Literature Description The "Constraint scores" container track includes several subtracks showing the results of constraint prediction algorithms. These try to find regions of negative selection, where variations likely have functional impact. The algorithms do not use multi-species alignments to derive evolutionary constraint, but use primarily human variation, usually from variants collected by gnomAD (see the gnomAD V2 or V3 tracks on hg19 and hg38) or TOPMED (contained in our dbSNP tracks and available as a filter). One of the subtracks is based on UK Biobank variants, which are not available publicly, so we have no track with the raw data. The number of human genomes that are used as the input for these scores are 76k, 53k and 110k for gnomAD, TOPMED and UK Biobank, respectively. Note that another important constraint score, gnomAD constraint, is not part of this container track but can be found in the hg38 gnomAD track. The algorithms included in this track are: JARVIS - "Junk" Annotation genome-wide Residual Variation Intolerance Score: JARVIS scores were created by first scanning the entire genome with a sliding-window approach (using a 1-nucleotide step), recording the number of all TOPMED variants and common variants, irrespective of their predicted effect, within each window, to eventually calculate a single-nucleotide resolution genome-wide residual variation intolerance score (gwRVIS). That score, gwRVIS was then combined with primary genomic sequence context, and additional genomic annotations with a multi-module deep learning framework to infer pathogenicity of noncoding regions that still remains naive to existing phylogenetic conservation metrics. The higher the score, the more deleterious the prediction. This score covers the entire genome, except the gaps. HMC - Homologous Missense Constraint: Homologous Missense Constraint (HMC) is a amino acid level measure of genetic intolerance of missense variants within human populations. For all assessable amino-acid positions in Pfam domains, the number of missense substitutions directly observed in gnomAD (Observed) was counted and compared to the expected value under a neutral evolution model (Expected). The upper limit of a 95% confidence interval for the Observed/Expected ratio is defined as the HMC score. Missense variants disrupting the amino-acid positions with HMC&lt;0.8 are predicted to be likely deleterious. This score only covers PFAM domains within coding regions. MetaDome - Tolerance Landscape Score (hg19 only): MetaDome Tolerance Landscape scores are computed as a missense over synonymous variant count ratio, which is calculated in a sliding window (with a size of 21 codons/residues) to provide a per-position indication of regional tolerance to missense variation. The variant database was gnomAD and the score corrected for codon composition. Scores &lt;0.7 are considered intolerant. This score covers only coding regions. MTR - Missense Tolerance Ratio (hg19 only): Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence. It is estimated across sliding windows of 31 codons (default) and uses observed standing variation data from the WES component of gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores were computed using Ensembl v95 release. The number of gnomAD 2 exomes used here is higher than the number of gnomAD 3 samples (125 exoms versus 76k full genomes), but this score only covers coding regions. UK Biobank depletion rank score (hg38 only): Halldorsson et al. tabulated the number of UK Biobank variants in each 500bp window of the genome and compared this number to an expected number given the heptamer nucleotide composition of the window and the fraction of heptamers with a sequence variant across the genome and their mutational classes. A variant depletion score was computed for every overlapping set of 500-bp windows in the genome with a 50-bp step size. They then assigned a rank (depletion rank (DR)) from 0 (most depletion) to 100 (least depletion) for each 500-bp window. Since the windows are overlapping, we plot the value only in the central 50bp of the 500bp window, following advice from the author of the score, Hakon Jonsson, deCODE Genetics. He suggested that the value of the central window, rather than the worst possible score of all overlapping windows, is the most informative for a position. This score covers almost the entire genome, only very few regions were excluded, where the genome sequence had too many gap characters. Display Conventions and Configuration JARVIS JARVIS scores are shown as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The scores were downloaded and converted to a single bigWig file. Move the mouse over the bars to display the exact values. A horizontal line is shown at the 0.733 value which signifies the 90th percentile. See hg19 makeDoc and hg38 makeDoc. Interpretation: The authors offer a suggested guideline of > 0.9998 for identifying higher confidence calls and minimizing false positives. In addition to that strict threshold, the following two more relaxed cutoffs can be used to explore additional hits. Note that these thresholds are offered as guidelines and are not necessarily representative of pathogenicity. PercentileJARVIS score threshold 99th0.9998 95th0.9826 90th0.7338 HMC HMC scores are displayed as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The highly-constrained cutoff of 0.8 is indicated with a line. Interpretation: A protein residue with HMC score &lt;1 indicates that missense variants affecting the homologous residues are significantly under negative selection (P-value &lt; 0.05) and likely to be deleterious. A more stringent score threshold of HMC&lt;0.8 is recommended to prioritize predicted disease-associated variants. MetaDome MetaDome data can be found on two tracks, MetaDome and MetaDome All Data. The MetaDome track should be used by default for data exploration. In this track the raw data containing the MetaDome tolerance scores were converted into a signal ("wiggle") track. Since this data was computed on the proteome, there was a small amount of coordinate overlap, roughly 0.42%. In these regions the lowest possible score was chosen for display in the track to maintain sensitivity. For this reason, if a protein variant is being evaluated, the MetaDome All Data track can be used to validate the score. More information on this data can be found in the MetaDome FAQ. Interpretation: The authors suggest the following guidelines for evaluating intolerance. By default, the MetaDome track displays a horizontal line at 0.7 which signifies the first intolerant bin. For more information see the MetaDome publication. ClassificationMetaDome Tolerance Score Highly intolerant&le; 0.175 Intolerant&le; 0.525 Slightly intolerant&le; 0.7 MTR MTR data can be found on two tracks, MTR All data and MTR Scores. In the MTR Scores track the data has been converted into 4 separate signal tracks representing each base pair mutation, with the lowest possible score shown when multiple transcripts overlap at a position. Overlaps can happen since this score is derived from transcripts and multiple transcripts can overlap. A horizontal line is drawn on the 0.8 score line to roughly represent the 25th percentile, meaning the items below may be of particular interest. It is recommended that the data be explored using this version of the track, as it condenses the information substantially while retaining the magnitude of the data. Any specific point mutations of interest can then be researched in the MTR All data track. This track contains all of the information from MTRV2 including more than 3 possible scores per base when transcripts overlap. A mouse-over on this track shows the ref and alt allele, as well as the MTR score and the MTR score percentile. Filters are available for MTR score, False Discovery Rate (FDR), MTR percentile, and variant consequence. By default, only items in the bottom 25 percentile are shown. Items in the track are colored according to their MTR percentile: Green items MTR percentiles over 75 Black items MTR percentiles between 25 and 75 Red items MTR percentiles below 25 Blue items No MTR score Interpretation: Regions with low MTR scores were seen to be enriched with pathogenic variants. For example, ClinVar pathogenic variants were seen to have an average score of 0.77 whereas ClinVar benign variants had an average score of 0.92. Further validation using the FATHMM cancer-associated training dataset saw that scores less than 0.5 contained 8.6% of the pathogenic variants while only containing 0.9% of neutral variants. In summary, lower scores are more likely to represent pathogenic variants whereas higher scores could be pathogenic, but have a higher chance to be a false positive. For more information see the MTR-Viewer publication. Methods JARVIS Scores were downloaded and converted to a single bigWig file. See the hg19 makeDoc and the hg38 makeDoc for more info. HMC Scores were downloaded and converted to .bedGraph files with a custom Python script. The bedGraph files were then converted to bigWig files, as documented in our makeDoc hg19 build log. MetaDome The authors provided a bed file containing codon coordinates along with the scores. This file was parsed with a python script to create the two tracks. For the first track the scores were aggregated for each coordinate, then the lowest score chosen for any overlaps and the result written out to bedGraph format. The file was then converted to bigWig with the bedGraphToBigWig utility. For the second track the file was reorganized into a bed 4+3 and conveted to bigBed with the bedToBigBed utility. See the hg19 makeDoc for details including the build script. The raw MetaDome data can also be accessed via their Zenodo handle. MTR V2 file was downloaded and columns were reshuffled as well as itemRgb added for the MTR All data track. For the MTR Scores track the file was parsed with a python script to pull out the highest possible MTR score for each of the 3 possible mutations at each base pair and 4 tracks built out of these values representing each mutation. See the hg19 makeDoc entry on MTR for more info. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/hmc/hmc.bw stdout Please refer to our Data Access FAQ for more information. Credits Thanks to Jean-Madeleine Desainteagathe (APHP Paris, France) for suggesting the JARVIS, MTR, HMC tracks. Thanks to Xialei Zhang for providing the HMC data file and to Dimitrios Vitsios and Slave Petrovski for helping clean up the hg38 JARVIS files for providing guidance on interpretation. Additional thanks to Laurens van de Wiel for providing the MetaDome data as well as guidance on the track development and interpretation. References Vitsios D, Dhindsa RS, Middleton L, Gussow AB, Petrovski S. Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. Nat Commun. 2021 Mar 8;12(1):1504. PMID: 33686085; PMC: PMC7940646 Xiaolei Zhang, Pantazis I. Theotokis, Nicholas Li, the SHaRe Investigators, Caroline F. Wright, Kaitlin E. Samocha, Nicola Whiffin, James S. Ware Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery. Medrxiv 2022.02.16.22271023 Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat. 2019 Aug;40(8):1030-1038. PMID: 31116477; PMC: PMC6772141 Silk M, Petrovski S, Ascher DB. MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 2019 Jul 2;47(W1):W121-W126. PMID: 31170280; PMC: PMC6602522 Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO et al. The sequences of 150,119 genomes in the UK Biobank. Nature. 2022 Jul;607(7920):732-740. PMID: 35859178; PMC: PMC9329122 
constraintSuper Constraint scores Human constraint scores Phenotype and Literature Description The "Constraint scores" container track includes several subtracks showing the results of constraint prediction algorithms. These try to find regions of negative selection, where variations likely have functional impact. The algorithms do not use multi-species alignments to derive evolutionary constraint, but use primarily human variation, usually from variants collected by gnomAD (see the gnomAD V2 or V3 tracks on hg19 and hg38) or TOPMED (contained in our dbSNP tracks and available as a filter). One of the subtracks is based on UK Biobank variants, which are not available publicly, so we have no track with the raw data. The number of human genomes that are used as the input for these scores are 76k, 53k and 110k for gnomAD, TOPMED and UK Biobank, respectively. Note that another important constraint score, gnomAD constraint, is not part of this container track but can be found in the hg38 gnomAD track. The algorithms included in this track are: JARVIS - "Junk" Annotation genome-wide Residual Variation Intolerance Score: JARVIS scores were created by first scanning the entire genome with a sliding-window approach (using a 1-nucleotide step), recording the number of all TOPMED variants and common variants, irrespective of their predicted effect, within each window, to eventually calculate a single-nucleotide resolution genome-wide residual variation intolerance score (gwRVIS). That score, gwRVIS was then combined with primary genomic sequence context, and additional genomic annotations with a multi-module deep learning framework to infer pathogenicity of noncoding regions that still remains naive to existing phylogenetic conservation metrics. The higher the score, the more deleterious the prediction. This score covers the entire genome, except the gaps. HMC - Homologous Missense Constraint: Homologous Missense Constraint (HMC) is a amino acid level measure of genetic intolerance of missense variants within human populations. For all assessable amino-acid positions in Pfam domains, the number of missense substitutions directly observed in gnomAD (Observed) was counted and compared to the expected value under a neutral evolution model (Expected). The upper limit of a 95% confidence interval for the Observed/Expected ratio is defined as the HMC score. Missense variants disrupting the amino-acid positions with HMC&lt;0.8 are predicted to be likely deleterious. This score only covers PFAM domains within coding regions. MetaDome - Tolerance Landscape Score (hg19 only): MetaDome Tolerance Landscape scores are computed as a missense over synonymous variant count ratio, which is calculated in a sliding window (with a size of 21 codons/residues) to provide a per-position indication of regional tolerance to missense variation. The variant database was gnomAD and the score corrected for codon composition. Scores &lt;0.7 are considered intolerant. This score covers only coding regions. MTR - Missense Tolerance Ratio (hg19 only): Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence. It is estimated across sliding windows of 31 codons (default) and uses observed standing variation data from the WES component of gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores were computed using Ensembl v95 release. The number of gnomAD 2 exomes used here is higher than the number of gnomAD 3 samples (125 exoms versus 76k full genomes), but this score only covers coding regions. UK Biobank depletion rank score (hg38 only): Halldorsson et al. tabulated the number of UK Biobank variants in each 500bp window of the genome and compared this number to an expected number given the heptamer nucleotide composition of the window and the fraction of heptamers with a sequence variant across the genome and their mutational classes. A variant depletion score was computed for every overlapping set of 500-bp windows in the genome with a 50-bp step size. They then assigned a rank (depletion rank (DR)) from 0 (most depletion) to 100 (least depletion) for each 500-bp window. Since the windows are overlapping, we plot the value only in the central 50bp of the 500bp window, following advice from the author of the score, Hakon Jonsson, deCODE Genetics. He suggested that the value of the central window, rather than the worst possible score of all overlapping windows, is the most informative for a position. This score covers almost the entire genome, only very few regions were excluded, where the genome sequence had too many gap characters. Display Conventions and Configuration JARVIS JARVIS scores are shown as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The scores were downloaded and converted to a single bigWig file. Move the mouse over the bars to display the exact values. A horizontal line is shown at the 0.733 value which signifies the 90th percentile. See hg19 makeDoc and hg38 makeDoc. Interpretation: The authors offer a suggested guideline of > 0.9998 for identifying higher confidence calls and minimizing false positives. In addition to that strict threshold, the following two more relaxed cutoffs can be used to explore additional hits. Note that these thresholds are offered as guidelines and are not necessarily representative of pathogenicity. PercentileJARVIS score threshold 99th0.9998 95th0.9826 90th0.7338 HMC HMC scores are displayed as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The highly-constrained cutoff of 0.8 is indicated with a line. Interpretation: A protein residue with HMC score &lt;1 indicates that missense variants affecting the homologous residues are significantly under negative selection (P-value &lt; 0.05) and likely to be deleterious. A more stringent score threshold of HMC&lt;0.8 is recommended to prioritize predicted disease-associated variants. MetaDome MetaDome data can be found on two tracks, MetaDome and MetaDome All Data. The MetaDome track should be used by default for data exploration. In this track the raw data containing the MetaDome tolerance scores were converted into a signal ("wiggle") track. Since this data was computed on the proteome, there was a small amount of coordinate overlap, roughly 0.42%. In these regions the lowest possible score was chosen for display in the track to maintain sensitivity. For this reason, if a protein variant is being evaluated, the MetaDome All Data track can be used to validate the score. More information on this data can be found in the MetaDome FAQ. Interpretation: The authors suggest the following guidelines for evaluating intolerance. By default, the MetaDome track displays a horizontal line at 0.7 which signifies the first intolerant bin. For more information see the MetaDome publication. ClassificationMetaDome Tolerance Score Highly intolerant&le; 0.175 Intolerant&le; 0.525 Slightly intolerant&le; 0.7 MTR MTR data can be found on two tracks, MTR All data and MTR Scores. In the MTR Scores track the data has been converted into 4 separate signal tracks representing each base pair mutation, with the lowest possible score shown when multiple transcripts overlap at a position. Overlaps can happen since this score is derived from transcripts and multiple transcripts can overlap. A horizontal line is drawn on the 0.8 score line to roughly represent the 25th percentile, meaning the items below may be of particular interest. It is recommended that the data be explored using this version of the track, as it condenses the information substantially while retaining the magnitude of the data. Any specific point mutations of interest can then be researched in the MTR All data track. This track contains all of the information from MTRV2 including more than 3 possible scores per base when transcripts overlap. A mouse-over on this track shows the ref and alt allele, as well as the MTR score and the MTR score percentile. Filters are available for MTR score, False Discovery Rate (FDR), MTR percentile, and variant consequence. By default, only items in the bottom 25 percentile are shown. Items in the track are colored according to their MTR percentile: Green items MTR percentiles over 75 Black items MTR percentiles between 25 and 75 Red items MTR percentiles below 25 Blue items No MTR score Interpretation: Regions with low MTR scores were seen to be enriched with pathogenic variants. For example, ClinVar pathogenic variants were seen to have an average score of 0.77 whereas ClinVar benign variants had an average score of 0.92. Further validation using the FATHMM cancer-associated training dataset saw that scores less than 0.5 contained 8.6% of the pathogenic variants while only containing 0.9% of neutral variants. In summary, lower scores are more likely to represent pathogenic variants whereas higher scores could be pathogenic, but have a higher chance to be a false positive. For more information see the MTR-Viewer publication. Methods JARVIS Scores were downloaded and converted to a single bigWig file. See the hg19 makeDoc and the hg38 makeDoc for more info. HMC Scores were downloaded and converted to .bedGraph files with a custom Python script. The bedGraph files were then converted to bigWig files, as documented in our makeDoc hg19 build log. MetaDome The authors provided a bed file containing codon coordinates along with the scores. This file was parsed with a python script to create the two tracks. For the first track the scores were aggregated for each coordinate, then the lowest score chosen for any overlaps and the result written out to bedGraph format. The file was then converted to bigWig with the bedGraphToBigWig utility. For the second track the file was reorganized into a bed 4+3 and conveted to bigBed with the bedToBigBed utility. See the hg19 makeDoc for details including the build script. The raw MetaDome data can also be accessed via their Zenodo handle. MTR V2 file was downloaded and columns were reshuffled as well as itemRgb added for the MTR All data track. For the MTR Scores track the file was parsed with a python script to pull out the highest possible MTR score for each of the 3 possible mutations at each base pair and 4 tracks built out of these values representing each mutation. See the hg19 makeDoc entry on MTR for more info. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/hmc/hmc.bw stdout Please refer to our Data Access FAQ for more information. Credits Thanks to Jean-Madeleine Desainteagathe (APHP Paris, France) for suggesting the JARVIS, MTR, HMC tracks. Thanks to Xialei Zhang for providing the HMC data file and to Dimitrios Vitsios and Slave Petrovski for helping clean up the hg38 JARVIS files for providing guidance on interpretation. Additional thanks to Laurens van de Wiel for providing the MetaDome data as well as guidance on the track development and interpretation. References Vitsios D, Dhindsa RS, Middleton L, Gussow AB, Petrovski S. Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. Nat Commun. 2021 Mar 8;12(1):1504. PMID: 33686085; PMC: PMC7940646 Xiaolei Zhang, Pantazis I. Theotokis, Nicholas Li, the SHaRe Investigators, Caroline F. Wright, Kaitlin E. Samocha, Nicola Whiffin, James S. Ware Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery. Medrxiv 2022.02.16.22271023 Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat. 2019 Aug;40(8):1030-1038. PMID: 31116477; PMC: PMC6772141 Silk M, Petrovski S, Ascher DB. MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 2019 Jul 2;47(W1):W121-W126. PMID: 31170280; PMC: PMC6602522 Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO et al. The sequences of 150,119 genomes in the UK Biobank. Nature. 2022 Jul;607(7920):732-740. PMID: 35859178; PMC: PMC9329122 
omimAvSnp OMIM Alleles OMIM Allelic Variant Phenotypes Phenotype and Literature Description NOTE: OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the OMIM database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. Further, please be sure to click through to omim.org for the very latest, as they are continually updating data. NOTE ABOUT DOWNLOADS: OMIM is the property of Johns Hopkins University and is not available for download or mirroring by any third party without their permission. Please see OMIM for downloads. OMIM is a compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known Mendelian disorders and over 12,000 genes. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. This database was initiated in the early 1960s by Dr. Victor A. McKusick as a catalog of Mendelian traits and disorders, entitled Mendelian Inheritance in Man (MIM). The OMIM data are separated into three separate tracks: OMIM Alellic Variant Phenotypes (OMIM Alleles) &nbsp;&nbsp;&nbsp;&nbsp;Variants in the OMIM database that have associated dbSNP identifiers. OMIM Gene Phenotypes (OMIM Genes) &nbsp;&nbsp;&nbsp;&nbsp;The genomic positions of gene entries in the OMIM database. The coloring indicates the associated OMIM phenotype map key. OMIM Cytogenetic Loci Phenotypes - Gene Unknown (OMIM Cyto Loci) &nbsp;&nbsp;&nbsp;&nbsp;Regions known to be associated with a phenotype, but for which no specific gene is known to be causative. This track also includes known multi-gene syndromes. This track shows the allelic variants in the Online Mendelian Inheritance in Man (OMIM) database that have associated dbSNP identifiers. Display Conventions and Configuration Genomic positions of OMIM allelic variants are marked by solid blocks, which appear as tick marks when zoomed out. The details page for each variant displays the allelic variant description, the amino acid replacement, and the associated dbSNP and/or ClinVar identifiers with links to the variant's details at those resources. The descriptions of OMIM entries are shown on the main browser display when Full display mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry. Methods This track was constructed as follows: The OMIM allelic variant data file mimAV.txt was obtained from OMIM and loaded into the MySQL table omimAv. The genomic position for each allelic variant in omimAv with an associated dbSnp identifier was obtained from the snp151 table. The OMIM AV identifiers and their corresponding genomic positions from dbSNP were then loaded into the omimAvSnp table. Data Updates This track is automatically updated once a week from OMIM data. The most recent update time is shown at the top of the track documentation page. Data Access Because OMIM has only allowed Data queries within individual chromosomes, no download files are available from the Genome Browser. Full genome datasets can be downloaded directly from the OMIM Downloads page. All genome-wide downloads are freely available from OMIM after registration. If you need the OMIM data in exactly the format of the UCSC Genome Browser, for example if you are running a UCSC Genome Browser local installation (a partial &quot;mirror&quot;), please create a user account on omim.org and contact OMIM via https://omim.org/contact. Send them your OMIM account name and request access to the UCSC Genome Browser 'entitlement'. They will then grant you access to a MySQL/MariaDB data dump that contains all UCSC Genome Browser OMIM tables. UCSC offers queries within chromosomes from Table Browser that include a variety of filtering options and cross-referencing other datasets using our Data Integrator tool. UCSC also has an API that can be used to retrieve data in JSON format from a particular chromosome range. Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information. Credits Thanks to OMIM and NCBI for the use of their data. This track was constructed by Fan Hsu, Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group. References Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. PMID: 18842627; PMC: PMC2686440 Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7. PMID: 15608251; PMC: PMC539987 
omimContainer OMIM Online Mendelian Inheritance in Man Phenotype and Literature OMIM is a compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known Mendelian disorders and over 12,000 genes. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. This database was initiated in the early 1960s by Dr. Victor A. McKusick as a catalog of Mendelian traits and disorders, entitled Mendelian Inheritance in Man (MIM). The OMIM data are separated into three separate tracks: OMIM Alellic Variant Phenotypes (OMIM Alleles) - Variants in the OMIM database that have associated dbSNP identifiers. OMIM Gene Phenotypes (OMIM Genes) - The genomic positions of gene entries in the OMIM database. The coloring indicates the associated OMIM phenotype map key. OMIM Cytogenetic Loci Phenotypes: Gene Unknown (OMIM Cyto Loci) - Regions known to be associated with a phenotype, but for which no specific gene is known to be causative. This track also includes known multi-gene syndromes. Clicking into the individual tracks provides additional information including display conventions. 
pubs Publications Publications: Sequences in Scientific Articles Phenotype and Literature Description This track is based on text-mining of full-text biomedical articles and includes two types of subtracks: Sequences found in publications, grouped by article and searched in genomes with BLAT Identifiers in publications that directly relate to chromosome locations (e.g., gene symbols, SNP identifiers, etc) Both sources of information are linked to the respective articles. Background information on how permission to full-text data was obtained can be found on the project website. Display Convention and Configuration The sequence subtrack indicates the location of sequences in publications mapped back to the genome, annotated with the first author and the year of the publication. All matches of one article are grouped ("chained") together. Article titles are shown when you move the mouse cursor over the features. Thicker parts of the features (exons) represent matching sequences, connected by thin lines to matches from the same article within 30 kbp. The subtrack "individual sequence matches" activates automatically when the user clicks a sequence match and follows the link "Show sequence matches individually" from the details page. Mouse-overs show flanking text around the sequence, and clicking features links to BLAT alignments. All other subtracks (i.e. bands, genes, SNPs) show the number of matching articles as the feature description. Clicking on them shows the sentences and sections in articles where the identifiers were found. The track configuration includes a keyword and year filter. Keywords are space-separated and are searched in the article's title, author list, and abstract. Data The track is based on text from biomedical research articles, obtained as part of the UCSC Genocoding Project. The current dataset consists of about 600,000 files (main text and supplementary files) from PubMed Central (Open-Access set) and around 6 million text files (main text) from Elsevier (as part of the Sciverse Apps program). Methods All file types (including XML, raw ASCII, PDFs and various Microsoft Office formats (Excel, Word, PowerPoint)) were converted to text. The results were processed to find groups of words that look like DNA/RNA sequences or words that look like protein sequences. These were then mapped with BLAT to the human genome and these model organisms: mouse (mm9), rat (rn4), zebrafish (danRer6), Drosophila melanogaster (dm3), X. tropicalis (xenTro2), Medaka (oryLat2), C. intestinalis (ci2), C. elegans (ce6) and yeast (sacCer2). The pipeline roughly proceeds through these steps: For sequences, the best match across all genomes is used, if it is longer than 17 bp and matches at 90% identity. Two sets of BLAT parameters are tried, the default ones for sequences longer than 25 bp, very sensitive ones (stepSize=5) for shorter sequences. Sequences are mapped to genomic DNA. Those that do not match are mapped to RefSeq cDNAs. Hits from the same article that are closer than 30 kbp are joined into one feature (shown as exon-blocks on the browser). All parts of a joined feature have to match at least 25 bp. Non-unique hits are kept in the joined feature with the most members. Joined features with identical members in two different genomes are kept in both genomes. Note that due to the 90% identity filter, some sequences do not match anywhere in the genome. Examples include primers with added restriction sites, mutation primers, or any other sequence that joins or mixes two pieces of genomic DNA not part of RefSeq. Also note that some gene symbols correspond to English words which can sometimes lead to many false positives. Credits Software and processing by Maximilian Haeussler. UCSC Track visualisation by Larry Meyer and Hiram Clawson. Elsevier support by Max Berenstein, Raphael Sidi, Judd Dunham, Scott Robbins and colleagues. Original version written at the Bergman Lab, University of Manchester, UK. Testing by Mary Mangan, OpenHelix Inc, and Greg Roe, UCSC. Feedback Please send ideas, comments or feedback on this track to &#109;a&#120;&#64;&#115;&#111;&#101;.uc&#115;&#99;.e&#100;&#117;. We are very interested in getting access to more articles from publishers for this dataset; see the project website. References Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM, Open Regulatory Annotation Consortium. Text-mining assisted regulatory annotation. Genome Biol. 2008;9(2):R31. PMID: 18271954; PMC: PMC2374703 Haeussler M, Gerner M, Bergman CM. Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics. 2011 Apr 1;27(7):980-6. PMID: 21325301; PMC: PMC3065681 Van Noorden R. Trouble at the text mine. Nature. 2012 Mar 7;483(7388):134-5. 
pubsMarkerSnp SNPs SNPs in Publications Phenotype and Literature 
pubsMarkerGene Genes Gene Symbols in Publications Phenotype and Literature 
pubsMarkerBand Bands Cytogenetic Bands in Publications Phenotype and Literature 
pubsBlat Sequences Sequences in Articles: PubmedCentral and Elsevier Phenotype and Literature 
pubsBlatPsl Indiv. Seq. Matches Individual Sequence Matches of One Selected Article from Sequences Track Phenotype and Literature 
rmsk RepeatMasker Repeating Elements by RepeatMasker Repeats Description This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below. Some newer assemblies have been made with Dfam, not Repbase. You can find the details for how we make our database data here in our &quot;makeDb/doc/&quot; directory. When analyzing the data tables of this track, keep in mind that Repbase is not the same as the Repeatmasker sequence database and that the repeat names in the Repeatmasker output are not the same as the sequence names in the Repeatmasker database. Concretely, you can find a name such as "L1PA4" in the Repeatmasker output and this track, but there is not necessarily a single sequence "L1PA4" in the Repeatmasker database. This is because Repeatmasker creates annotations by joining matches to partial pieces of the database together so there is no 1:1 relationship between its sequence database and the annotations. To learn more, you can read the Repeatmasker paper, its source code or reach out to the Repeatmasker authors, your local expert on transposable elements or us. Display Conventions and Configuration In full display mode, this track displays up to ten different classes of repeats: Short interspersed nuclear elements (SINE), which include ALUs Long interspersed nuclear elements (LINE) Long terminal repeat elements (LTR), which include retroposons DNA repeat elements (DNA) Simple repeats (micro-satellites) Low complexity repeats Satellite repeats RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA) Other repeats, which includes class RC (Rolling Circle) Unknown The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. The higher the combined number of these, the lighter the shading. A &quot;?&quot; at the end of the &quot;Family&quot; or &quot;Class&quot; (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the &quot;?&quot; will be removed or the classification will be changed. Methods Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the FAQ for more information. Credits Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track. References Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010. Repbase Update is described in: Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072 For a discussion of repeats in mammalian genomes, see: Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616 Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846 
spliceAIsnvs SpliceAI SNVs SpliceAI SNVs (unmasked) Phenotype and Literature Important: The SpliceAI data on the UCSC Genome Browser is directly from Illumina (See Data Access below). However, since SpliceAI refers to the algorithm, and not the computed dataset, the data on the Broad server or other sources may have some differences between them. Description SpliceAI is an open-source deep learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. Such variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms. SpliceAI was developed at Illumina; a lookup tool is provided by the Broad institute. Why are some variants not scored by SpliceAI? SpliceAI only annotates variants within genes defined by the gene annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome ends (5kb on either side), deletions of length greater than twice the input parameter -D, or inconsistent with the reference fasta file. What are the differeneces between masked and unmasked tracks? The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites and weakening unannotated splice sites, which are typically much less pathogenic than weakening annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative splicing analysis and masked tracks for variant interpretation. Display Conventions and Interpretation Variants are colored according to Walker et al. 2023 splicing imact: Predicted impact on splicing: Score &gt;&#61; 0.2 Not informative: Score &lt; 0.2 and &gt; 0.1 No impact on splicing: Score &lt;&#61; 0.1 Mouseover on items shows the variant, gene name, type of change (donor gain/loss, acceptor gain/loss), location of affected cryptic splice, and spliceAI score. Clicking on any item brings up a table with this information. The scores range from 0 to 1 and can be interpreted as the probability of the variant being splice-altering. In the paper, a detailed characterization is provided for 0.2 (high recall), 0.5 (recommended), and 0.8 (high precision) cutoffs. Methods The data were downloaded from Illumina. The spliceAI scores are represented in the VCF INFO field as SpliceAI=G|OR4F5|0.01|0.00|0.00|0.00|-32|49|-40|-31 Here, the pipe-separated fields contain ALT allele Gene name Acceptor gain score Acceptor loss score Donor gain score Donor loss score Relative location of affected cryptic acceptor Relative location of affected acceptor Relative location of affected cryptic donor Relative location of affected donor Since most of the values are 0 or almost 0, we selected only those variants with a score equal to or greater than 0.02. The complete processing of this track can be found in the makedoc. Data Access These data are not available for download from the Genome Browser. The raw data can be found directly on Illumina. See below for a copy of the license restrictions pertaining to these data. License FOR ACADEMIC AND NOT-FOR-PROFIT RESEARCH USE ONLY. The SpliceAI scores are made available by Illumina only for academic or not-for-profit research only. By accessing the SpliceAI data, you acknowledge and agree that you may only use this data for your own personal academic or not-for-profit research only, and not for any other purposes. You may not use this data for any for-profit, clinical, or other commercial purpose without obtaining a commercial license from Illumina, Inc. References Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB et al. Predicting Splicing from Primary Sequence with Deep Learning. Cell. 2019 Jan 24;176(3):535-548.e24. PMID: 30661751 Walker LC, Hoya M, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A et al. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet. 2023 Jul 6;110(7):1046-1067. PMID: 37352859; PMC: PMC10357475 
spliceAI SpliceAI SpliceAI: Splice Variant Prediction Score Phenotype and Literature Important: The SpliceAI data on the UCSC Genome Browser is directly from Illumina (See Data Access below). However, since SpliceAI refers to the algorithm, and not the computed dataset, the data on the Broad server or other sources may have some differences between them. Description SpliceAI is an open-source deep learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. Such variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms. SpliceAI was developed at Illumina; a lookup tool is provided by the Broad institute. Why are some variants not scored by SpliceAI? SpliceAI only annotates variants within genes defined by the gene annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome ends (5kb on either side), deletions of length greater than twice the input parameter -D, or inconsistent with the reference fasta file. What are the differeneces between masked and unmasked tracks? The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites and weakening unannotated splice sites, which are typically much less pathogenic than weakening annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative splicing analysis and masked tracks for variant interpretation. Display Conventions and Interpretation Variants are colored according to Walker et al. 2023 splicing imact: Predicted impact on splicing: Score &gt;&#61; 0.2 Not informative: Score &lt; 0.2 and &gt; 0.1 No impact on splicing: Score &lt;&#61; 0.1 Mouseover on items shows the variant, gene name, type of change (donor gain/loss, acceptor gain/loss), location of affected cryptic splice, and spliceAI score. Clicking on any item brings up a table with this information. The scores range from 0 to 1 and can be interpreted as the probability of the variant being splice-altering. In the paper, a detailed characterization is provided for 0.2 (high recall), 0.5 (recommended), and 0.8 (high precision) cutoffs. Methods The data were downloaded from Illumina. The spliceAI scores are represented in the VCF INFO field as SpliceAI=G|OR4F5|0.01|0.00|0.00|0.00|-32|49|-40|-31 Here, the pipe-separated fields contain ALT allele Gene name Acceptor gain score Acceptor loss score Donor gain score Donor loss score Relative location of affected cryptic acceptor Relative location of affected acceptor Relative location of affected cryptic donor Relative location of affected donor Since most of the values are 0 or almost 0, we selected only those variants with a score equal to or greater than 0.02. The complete processing of this track can be found in the makedoc. Data Access These data are not available for download from the Genome Browser. The raw data can be found directly on Illumina. See below for a copy of the license restrictions pertaining to these data. License FOR ACADEMIC AND NOT-FOR-PROFIT RESEARCH USE ONLY. The SpliceAI scores are made available by Illumina only for academic or not-for-profit research only. By accessing the SpliceAI data, you acknowledge and agree that you may only use this data for your own personal academic or not-for-profit research only, and not for any other purposes. You may not use this data for any for-profit, clinical, or other commercial purpose without obtaining a commercial license from Illumina, Inc. References Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB et al. Predicting Splicing from Primary Sequence with Deep Learning. Cell. 2019 Jan 24;176(3):535-548.e24. PMID: 30661751 Walker LC, Hoya M, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A et al. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet. 2023 Jul 6;110(7):1046-1067. PMID: 37352859; PMC: PMC10357475 
Enhancers Enhancers FANTOM5: Enhancers Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
fantom5 FANTOM5 FANTOM5: Mapped transcription start sites (TSS) and their usage Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
FANTOM-NET_Enhancers FANTOM-NET Enhancers FANTOM5: FANTOM-NET Enhancers Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
lincRNAsAllCellTypeTopView lincRNA RNA-Seq Reads lincRNA RNA-Seq reads expression abundances Genes and Gene Predictions Description This track displays the Human Body Map lincRNAs (large intergenic non coding RNAs) and TUCPs (transcripts of uncertain coding potential), as well as their expression levels across 22 human tissues and cell lines. The Human Body Map catalog was generated by integrating previously existing annotation sources with transcripts that were de-novo assembled from RNA-Seq data. These transcripts were collected from ~4 billion RNA-Seq reads across 24 tissues and cell types. Expression abundance was estimated by Cufflinks (Trapnell et al., 2010) based on RNA-Seq. Expression abundances were estimated on the gene locus level, rather than for each transcript separately and are given as raw FPKM. The prefixes tcons_ and tcons_l2_ are used to describe lincRNAs and TUCP transcripts, respectively. Specific details about the catalog generation and data sets used for this study can be found in Cabili et al (2011). Extended characterization of each transcript in the human body map catalog can be found at the Human lincRNA Catalog website. Expression abundance scores range from 0 to 1000, and are displayed from light blue to dark blue respectively: 01000 Credits The body map RNA-Seq data was kindly provided by the Gene Expression Applications research group at Illumina. References Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15;25(18):1915-27. PMID: 21890647; PMC: PMC3185964 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. PMID: 20436464; PMC: PMC3146043 
lincRNAs lincRNAs Human Body Map lincRNAs and TUCP Transcripts Genes and Gene Predictions Description This track displays the Human Body Map lincRNAs (large intergenic non coding RNAs) and TUCPs (transcripts of uncertain coding potential), as well as their expression levels across 22 human tissues and cell lines. The Human Body Map catalog was generated by integrating previously existing annotation sources with transcripts that were de-novo assembled from RNA-Seq data. These transcripts were collected from ~4 billion RNA-Seq reads across 24 tissues and cell types. Expression abundance was estimated by Cufflinks (Trapnell et al., 2010) based on RNA-Seq. Expression abundances were estimated on the gene locus level, rather than for each transcript separately and are given as raw FPKM. The prefixes tcons_ and tcons_l2_ are used to describe lincRNAs and TUCP transcripts, respectively. Specific details about the catalog generation and data sets used for this study can be found in Cabili et al (2011). Extended characterization of each transcript in the human body map catalog can be found at the Human lincRNA Catalog website. Expression abundance scores range from 0 to 1000, and are displayed from light blue to dark blue respectively: 01000 Credits The body map RNA-Seq data was kindly provided by the Gene Expression Applications research group at Illumina. References Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15;25(18):1915-27. PMID: 21890647; PMC: PMC3185964 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. PMID: 20436464; PMC: PMC3146043 
lincRNAsAllCellType lincRNAsAllCellType lincRNA RNA-Seq reads expression abundances Genes and Gene Predictions 
lincRNAsCTWhiteBloodCell WhiteBloodCell lincRNAs from whitebloodcell Genes and Gene Predictions 
lincRNAsCTThyroid Thyroid lincRNAs from thyroid Genes and Gene Predictions 
lincRNAsCTTestes_R Testes_R lincRNAs from testes_r Genes and Gene Predictions 
lincRNAsCTTestes Testes lincRNAs from testes Genes and Gene Predictions 
lincRNAsCTSkeletalMuscle SkeletalMuscle lincRNAs from skeletalmuscle Genes and Gene Predictions 
lincRNAsCTProstate Prostate lincRNAs from prostate Genes and Gene Predictions 
lincRNAsCTPlacenta_R Placenta_R lincRNAs from placenta_r Genes and Gene Predictions 
lincRNAsCTOvary Ovary lincRNAs from ovary Genes and Gene Predictions 
lincRNAsCTLymphNode LymphNode lincRNAs from lymphnode Genes and Gene Predictions 
lincRNAsCTLung Lung lincRNAs from lung Genes and Gene Predictions 
lincRNAsCTLiver Liver lincRNAs from liver Genes and Gene Predictions 
lincRNAsCTKidney Kidney lincRNAs from kidney Genes and Gene Predictions 
lincRNAsCThLF_r2 hLF_r2 lincRNAs from hlf_r2 Genes and Gene Predictions 
lincRNAsCThLF_r1 hLF_r1 lincRNAs from hlf_r1 Genes and Gene Predictions 
lincRNAsCTHeart Heart lincRNAs from heart Genes and Gene Predictions 
lincRNAsCTForeskin_R Foreskin_R lincRNAs from foreskin_r Genes and Gene Predictions 
lincRNAsCTColon Colon lincRNAs from colon Genes and Gene Predictions 
lincRNAsCTBreast Breast lincRNAs from breast Genes and Gene Predictions 
lincRNAsCTBrain_R Brain_R lincRNAs from brain_r Genes and Gene Predictions 
lincRNAsCTBrain Brain lincRNAs from brain Genes and Gene Predictions 
lincRNAsCTAdrenal Adrenal lincRNAs from adrenal Genes and Gene Predictions 
lincRNAsCTAdipose Adipose lincRNAs from adipose Genes and Gene Predictions 
spliceAIindels SpliceAI indels SpliceAI Indels (unmasked) Phenotype and Literature Important: The SpliceAI data on the UCSC Genome Browser is directly from Illumina (See Data Access below). However, since SpliceAI refers to the algorithm, and not the computed dataset, the data on the Broad server or other sources may have some differences between them. Description SpliceAI is an open-source deep learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. Such variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms. SpliceAI was developed at Illumina; a lookup tool is provided by the Broad institute. Why are some variants not scored by SpliceAI? SpliceAI only annotates variants within genes defined by the gene annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome ends (5kb on either side), deletions of length greater than twice the input parameter -D, or inconsistent with the reference fasta file. What are the differeneces between masked and unmasked tracks? The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites and weakening unannotated splice sites, which are typically much less pathogenic than weakening annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative splicing analysis and masked tracks for variant interpretation. Display Conventions and Interpretation Variants are colored according to Walker et al. 2023 splicing imact: Predicted impact on splicing: Score &gt;&#61; 0.2 Not informative: Score &lt; 0.2 and &gt; 0.1 No impact on splicing: Score &lt;&#61; 0.1 Mouseover on items shows the variant, gene name, type of change (donor gain/loss, acceptor gain/loss), location of affected cryptic splice, and spliceAI score. Clicking on any item brings up a table with this information. The scores range from 0 to 1 and can be interpreted as the probability of the variant being splice-altering. In the paper, a detailed characterization is provided for 0.2 (high recall), 0.5 (recommended), and 0.8 (high precision) cutoffs. Methods The data were downloaded from Illumina. The spliceAI scores are represented in the VCF INFO field as SpliceAI=G|OR4F5|0.01|0.00|0.00|0.00|-32|49|-40|-31 Here, the pipe-separated fields contain ALT allele Gene name Acceptor gain score Acceptor loss score Donor gain score Donor loss score Relative location of affected cryptic acceptor Relative location of affected acceptor Relative location of affected cryptic donor Relative location of affected donor Since most of the values are 0 or almost 0, we selected only those variants with a score equal to or greater than 0.02. The complete processing of this track can be found in the makedoc. Data Access These data are not available for download from the Genome Browser. The raw data can be found directly on Illumina. See below for a copy of the license restrictions pertaining to these data. License FOR ACADEMIC AND NOT-FOR-PROFIT RESEARCH USE ONLY. The SpliceAI scores are made available by Illumina only for academic or not-for-profit research only. By accessing the SpliceAI data, you acknowledge and agree that you may only use this data for your own personal academic or not-for-profit research only, and not for any other purposes. You may not use this data for any for-profit, clinical, or other commercial purpose without obtaining a commercial license from Illumina, Inc. References Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB et al. Predicting Splicing from Primary Sequence with Deep Learning. Cell. 2019 Jan 24;176(3):535-548.e24. PMID: 30661751 Walker LC, Hoya M, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A et al. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet. 2023 Jul 6;110(7):1046-1067. PMID: 37352859; PMC: PMC10357475 
wgEncodeRegTxn Transcription Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE Regulation Description This track shows transcription levels for several cell types as assayed by high-throughput sequencing of polyadenylated RNA (RNA-seq). Additional views of this dataset and additional documentation on the methods used for this track are available at the ENCODE Caltech RNA-seq page. The data shown here are derived from the Raw Signal view from the paired 75-mer 200 bp insert size reads. The two replicates of the signal were pooled and normalized so that the total genome-wide signal sums to 10 billion. Display Conventions and Configuration By default, this track uses a transparent overlay method of displaying data from a number of cell lines in the same vertical space. Each of the cell lines in this track is associated with a particular color and these cell line colors are consistent across all tracks that are part of the ENCODE Regulation supertrack. These colors are relatively light and saturated so as to work best with the transparent overlay. Unfortunately, outside the ENCODE Regulation tracks, older cell line color conventions are used that don't match the cell line colors used in the ENCODE Regulation tracks. The older colors were not used in the ENCODE Regulation tracks because they were too dark for the transparent overlay. Credits This track shows data from the Wold Lab at Caltech, as part of the ENCODE Project Consortium. Release Notes This is release 2 (July 2012) of this track which includes two new subtracks for HeLa-S3 and HepG2. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeReg ENCODE Regulation Integrated Regulation from ENCODE Regulation Description These tracks contain information relevant to the regulation of transcription from the ENCODE project. The Transcription track shows transcription levels assayed by sequencing of polyadenylated RNA from a variety of cell types. The Overlayed H3K4Me1 and Overlayed H3K27Ac tracks show where modification of histone proteins is suggestive of enhancer and, to a lesser extent, other regulatory activity. These histone modifications, particularly H3K4Me1, are quite broad. The actual enhancers are typically just a small portion of the area marked by these histone modifications. The Overlay H3K4Me3 track shows a histone mark associated with promoters. The DNase Clusters track shows regions where the chromatin is hypersensitive to cutting by the DNase enzyme, which has been assayed in a large number of cell types. Regulatory regions, in general, tend to be DNase sensitive, and promoters are particularly DNase sensitive. The Txn Factor ChIP tracks show DNA regions where transcription factors, proteins responsible for modulating gene transcription, bind as assayed by chromatin immunoprecipitation with antibodies specific to the transcription factor followed by sequencing of the precipitated DNA (ChIP-seq). These tracks complement each other and together can shed much light on regulatory DNA. The histone marks are informative at a high level, but they have a resolution of just ~200 bases and do not provide much in the way of functional detail. The DNase hypersensitive assay is higher in resolution at the DNA level and can be done on a large number of cell types since it's just a single assay. At the functional level, DNase hypersensitivity suggests that a region is very likely to be regulatory in nature, but provides little information beyond that. The transcription factor ChIP assay has a high resolution at the DNA level, and, due to the very specific nature of the transcription factors, is often informative with respect to functional detail. However, since each transcription factor must be assayed separately, the information is only available for a limited number of transcription factors on a limited number of cell lines. Though each assay has its strengths and weaknesses, the fact that all of these assays are relatively independent of each other gives increased confidence when multiple tracks are suggesting a regulatory function for a region. For additional information please click on the hyperlinks for the individual tracks above. Also note that additional histone marks and transcription information is available in other ENCODE tracks. This integrative Super-track just shows a selection of the most informative data of general interest. Display conventions By default, the transcription and histone mark displays use a transparent overlay method of displaying data from a number of cell lines in a single track. Each of the cell lines in this track is associated with a particular color, and these colors are relatively light and saturated so as to work best with the transparent overlay. Unfortunately, outside the ENCODE Regulation tracks, older cell line color conventions are used that don't match the cell line colors used in the ENCODE Regulation tracks. The older colors were not used in the ENCODE Regulation tracks because they were too dark for the transparent overlay. The DNase and Transcription Factor ChIP tracks contain information on so many cell lines that a color convention is inadequate. Instead, these tracks show gray boxes where the darkness of the box is proportional to the maximum value seen in any cell line in that region. Clicking on the item takes you to a details page where the values for each cell line assayed are displayed. Data Access The raw data for ENCODE 3 Regulation tracks can be accessed from Table Browser or combined with other data-sets through Data Integrator. For automated analysis and downloads, the track data files can be downloaded from our downloads server or queried using the JSON API or Public SQL. Individual regions or the whole genome annotation can be accessed as text using our utility bigBedToBed. Instructions for downloading the utility can be found here. That utility can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/wgEncodeRegDnase/wgEncodeRegDnaseUwA549Hotspot.broadPeak.bb -chrom=chr21 -start=0 -end=100000000 stdout For sorting transcription factor binding sites by cell type, we recommend you use the following download file for hg19. Credits Specific labs and contributors for these datasets are listed in the Credits section of the individual tracks in this super-track. The integrative view presented here was developed by Jim Kent at UCSC. Data Use Policy Users may freely download, analyze and publish results based on any ENCODE data without restrictions. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE production laboratory(s) that generated the datasets used, as described in Citing ENCODE. 
wgEncodeRegTxnCaltechRnaSeqNhlfR2x75Il200SigPooled NHLF NHLF RnaSeq 2011-01-22 2011-10-21 Myers Caltech cell TH1014 2x75 longPolyA wgEncodeRegTxnCaltechRnaSeqNhlfR2x75Il200SigPooled Signal lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal Transcription of NHLF cells from ENCODE Regulation 
wgEncodeRegTxnCaltechRnaSeqNhekR2x75Il200SigPooled NHEK NHEK RnaSeq 2011-01-22 2011-10-21 Myers Caltech cell TH1014 2x75 longPolyA wgEncodeRegTxnCaltechRnaSeqNhekR2x75Il200SigPooled Signal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal Transcription of NHEK cells from ENCODE Regulation 
wgEncodeRegTxnCaltechRnaSeqK562R2x75Il200SigPooled K562 K562 RnaSeq 2011-01-22 2011-10-21 Myers Caltech cell TH1014 2x75 longPolyA wgEncodeRegTxnCaltechRnaSeqK562R2x75Il200SigPooled Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal Transcription of K562 cells from ENCODE Regulation 
wgEncodeRegTxnCaltechRnaSeqHuvecR2x75Il200SigPooled HUVEC HUVEC RnaSeq 2011-01-22 2011-10-21 Myers Caltech cell TH1014 2x75 longPolyA wgEncodeRegTxnCaltechRnaSeqHuvecR2x75Il200SigPooled Signal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal Transcription of HUVEC cells from ENCODE Regulation 
wgEncodeRegTxnCaltechRnaSeqHsmmR2x75Il200SigPooled HSMM HSMM RnaSeq 2011-01-22 2011-10-21 Myers Caltech cell TH1014 2x75 longPolyA wgEncodeRegTxnCaltechRnaSeqHsmmR2x75Il200SigPooled Signal skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal Transcription of HSMM cells from ENCODE Regulation 
wgEncodeRegTxnCaltechRnaSeqHepg2R2x75Il200SigPooled HepG2 HepG2 RnaSeq 2011-01-22 2010-01-12 2010-10-11 wgEncodeEH000127 127 Myers Caltech cell TH1014 hg18 2x75 longPolyA wgEncodeRegTxnCaltechRnaSeqHepg2R2x75Il200SigPooled Signal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal Transcription of HepG2 cells from ENCODE Regulation 
wgEncodeRegTxnCaltechRnaSeqHelas3R2x75Il200SigPooled HeLa-S3 HeLa-S3 RnaSeq 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 Myers Caltech cell TH1014 hg18 2x75 longPolyA wgEncodeRegTxnCaltechRnaSeqHelas3R2x75Il200SigPooled Signal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal Transcription of HeLa-S3 cells from ENCODE Regulation 
wgEncodeRegTxnCaltechRnaSeqH1hescR2x75Il200SigPooled H1-hESC H1-hESC RnaSeq 2011-01-22 2011-10-21 Myers Caltech cell TH1014 2x75 longPolyA wgEncodeRegTxnCaltechRnaSeqH1hescR2x75Il200SigPooled Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal Transcription of H1-hESC cells from ENCODE Regulation 
wgEncodeRegTxnCaltechRnaSeqGm12878R2x75Il200SigPooled GM12878 GM12878 RnaSeq 2011-01-22 2011-10-21 Myers Caltech cell TH1014 2x75 longPolyA wgEncodeRegTxnCaltechRnaSeqGm12878R2x75Il200SigPooled Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal Transcription of GM12878 cells from ENCODE Regulation 
enhancer_promoter_correlations_distances_cell_type Enhancer - promoter correlations distances cell type FANTOM5: Enhancer - promoter correlations distances cell type Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
enhancer_promoter_correlations_distances_organ Enhancer - promoter correlations distances organ FANTOM5: Enhancer - promoter correlations distances organ Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
wgEncodeRegMarkH3k4me1 Layered H3K4Me1 H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE Regulation Description Chemical modifications (e.g. methylation and acylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. A specific modification of a specific histone protein is called a histone mark. This track shows the levels of enrichment of the H3K4Me1 histone mark across the genome as determined by a ChIP-seq assay. The H3K4me1 histone mark is the mono-methylation of lysine 4 of the H3 histone protein, and it is associated with enhancers and with DNA regions downstream of transcription starts. Additional histone marks and other chromatin associated ChIP-seq data is available at the Broad Histone page. Display conventions By default this track uses a transparent overlay method of displaying data from a number of cell lines in the same vertical space. Each of the cell lines in this track is associated with a particular color, and these cell line colors are consistent across all tracks that are part of the ENCODE Regulation supertrack. These colors are relatively light and saturated so as to work best with the transparent overlay. Unfortunately, outside the ENCODE Regulation tracks, older cell line color conventions are used that don't match the cell line colors used in the ENCODE Regulation tracks. The older colors were not used in the ENCODE Regulation tracks because they were too dark for the transparent overlay. Credits This track shows data from the Bernstein Lab at the Broad Institute. The Bernstein lab is part of the ENCODE consortium. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeRegMarkH3k4me1Nhlf NHLF H3K4Me1 Mark (Often Found Near Regulatory Elements) on NHLF Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me1Nhek NHEK H3K4Me1 Mark (Often Found Near Regulatory Elements) on NHEK Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me1K562 K562 H3K4Me1 Mark (Often Found Near Regulatory Elements) on K562 Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me1Huvec HUVEC H3K4Me1 Mark (Often Found Near Regulatory Elements) on HUVEC Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me1Hsmm HSMM H3K4Me1 Mark (Often Found Near Regulatory Elements) on HSMM Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me1H1hesc H1-hESC H3K4Me1 Mark (Often Found Near Regulatory Elements) on H1-hESC Cells from ENCODE Regulation 
wgEncodeBroadHistoneGm12878H3k4me1StdSig GM12878 H3K4me1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000033 33 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H3K4Me1 Mark (Often Found Near Regulatory Elements) on GM12878 Cells from ENCODE Regulation 
spliceAIsnvsMasked SpliceAI SNVs (masked) SpliceAI SNVs (masked) Phenotype and Literature Important: The SpliceAI data on the UCSC Genome Browser is directly from Illumina (See Data Access below). However, since SpliceAI refers to the algorithm, and not the computed dataset, the data on the Broad server or other sources may have some differences between them. Description SpliceAI is an open-source deep learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. Such variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms. SpliceAI was developed at Illumina; a lookup tool is provided by the Broad institute. Why are some variants not scored by SpliceAI? SpliceAI only annotates variants within genes defined by the gene annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome ends (5kb on either side), deletions of length greater than twice the input parameter -D, or inconsistent with the reference fasta file. What are the differeneces between masked and unmasked tracks? The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites and weakening unannotated splice sites, which are typically much less pathogenic than weakening annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative splicing analysis and masked tracks for variant interpretation. Display Conventions and Interpretation Variants are colored according to Walker et al. 2023 splicing imact: Predicted impact on splicing: Score &gt;&#61; 0.2 Not informative: Score &lt; 0.2 and &gt; 0.1 No impact on splicing: Score &lt;&#61; 0.1 Mouseover on items shows the variant, gene name, type of change (donor gain/loss, acceptor gain/loss), location of affected cryptic splice, and spliceAI score. Clicking on any item brings up a table with this information. The scores range from 0 to 1 and can be interpreted as the probability of the variant being splice-altering. In the paper, a detailed characterization is provided for 0.2 (high recall), 0.5 (recommended), and 0.8 (high precision) cutoffs. Methods The data were downloaded from Illumina. The spliceAI scores are represented in the VCF INFO field as SpliceAI=G|OR4F5|0.01|0.00|0.00|0.00|-32|49|-40|-31 Here, the pipe-separated fields contain ALT allele Gene name Acceptor gain score Acceptor loss score Donor gain score Donor loss score Relative location of affected cryptic acceptor Relative location of affected acceptor Relative location of affected cryptic donor Relative location of affected donor Since most of the values are 0 or almost 0, we selected only those variants with a score equal to or greater than 0.02. The complete processing of this track can be found in the makedoc. Data Access These data are not available for download from the Genome Browser. The raw data can be found directly on Illumina. See below for a copy of the license restrictions pertaining to these data. License FOR ACADEMIC AND NOT-FOR-PROFIT RESEARCH USE ONLY. The SpliceAI scores are made available by Illumina only for academic or not-for-profit research only. By accessing the SpliceAI data, you acknowledge and agree that you may only use this data for your own personal academic or not-for-profit research only, and not for any other purposes. You may not use this data for any for-profit, clinical, or other commercial purpose without obtaining a commercial license from Illumina, Inc. References Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB et al. Predicting Splicing from Primary Sequence with Deep Learning. Cell. 2019 Jan 24;176(3):535-548.e24. PMID: 30661751 Walker LC, Hoya M, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A et al. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet. 2023 Jul 6;110(7):1046-1067. PMID: 37352859; PMC: PMC10357475 
robustPeaks TSS peaks FANTOM5: DPI peak, robust set Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
wgEncodeRegMarkH3k4me3 Layered H3K4Me3 H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE Regulation Description Chemical modifications (e.g. methylation and acylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. A specific modification of a specific histone protein is called a histone mark. This track shows the levels of enrichment of the H3K4Me3 histone mark across the genome as determined by a ChIP-seq assay. The H3K4Me3 histone mark is the tri-methylation of lysine 4 of the H3 histone protein, and it is associated with promoters that are active or poised to be activated. Additional histone marks and other chromatin associated ChIP-seq data is available at the Broad Histone page. Display conventions By default this track uses a transparent overlay method of displaying data from a number of cell lines in the same vertical space. Each of the cell lines in this track is associated with a particular color, and these cell line colors are consistent across all tracks that are part of the ENCODE Regulation supertrack. These colors are relatively light and saturated so as to work best with the transparent overlay. Unfortunately, outside the ENCODE Regulation tracks, older cell line color conventions are used that don't match the cell line colors used in the ENCODE Regulation tracks. The older colors were not used in the ENCODE Regulation tracks because they were too dark for the transparent overlay. Credits This track shows data from the Bernstein Lab at the Broad Institute. The Bernstein lab is part of the ENCODE consortium. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeRegMarkH3k4me3Nhlf NHLF H3K4Me3 Mark (Often Found Near Promoters) on NHLF Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me3Nhek NHEK H3K4Me3 Mark (Often Found Near Promoters) on NHEK Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me3K562 K562 H3K4Me3 Mark (Often Found Near Promoters) on K562 Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me3Huvec HUVEC H3K4Me3 Mark (Often Found Near Promoters) on HUVEC Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me3Hsmm HSMM H3K4Me3 Mark (Often Found Near Promoters) on HSMM Cells from ENCODE Regulation 
wgEncodeRegMarkH3k4me3H1hesc H1-hESC H3K4Me3 Mark (Often Found Near Promoters) on H1-hESC Cells from ENCODE Regulation 
wgEncodeBroadHistoneGm12878H3k4me3StdSig GM12878 H3K4me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-04 2009-10-04 wgEncodeEH000028 28 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H3K4Me3 Mark (Often Found Near Promoters) on GM12878 Cells from ENCODE Regulation 
spliceAIindelsMasked SpliceAI indels (masked) SpliceAI Indels (masked) Phenotype and Literature Important: The SpliceAI data on the UCSC Genome Browser is directly from Illumina (See Data Access below). However, since SpliceAI refers to the algorithm, and not the computed dataset, the data on the Broad server or other sources may have some differences between them. Description SpliceAI is an open-source deep learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. Such variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms. SpliceAI was developed at Illumina; a lookup tool is provided by the Broad institute. Why are some variants not scored by SpliceAI? SpliceAI only annotates variants within genes defined by the gene annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome ends (5kb on either side), deletions of length greater than twice the input parameter -D, or inconsistent with the reference fasta file. What are the differeneces between masked and unmasked tracks? The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites and weakening unannotated splice sites, which are typically much less pathogenic than weakening annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative splicing analysis and masked tracks for variant interpretation. Display Conventions and Interpretation Variants are colored according to Walker et al. 2023 splicing imact: Predicted impact on splicing: Score &gt;&#61; 0.2 Not informative: Score &lt; 0.2 and &gt; 0.1 No impact on splicing: Score &lt;&#61; 0.1 Mouseover on items shows the variant, gene name, type of change (donor gain/loss, acceptor gain/loss), location of affected cryptic splice, and spliceAI score. Clicking on any item brings up a table with this information. The scores range from 0 to 1 and can be interpreted as the probability of the variant being splice-altering. In the paper, a detailed characterization is provided for 0.2 (high recall), 0.5 (recommended), and 0.8 (high precision) cutoffs. Methods The data were downloaded from Illumina. The spliceAI scores are represented in the VCF INFO field as SpliceAI=G|OR4F5|0.01|0.00|0.00|0.00|-32|49|-40|-31 Here, the pipe-separated fields contain ALT allele Gene name Acceptor gain score Acceptor loss score Donor gain score Donor loss score Relative location of affected cryptic acceptor Relative location of affected acceptor Relative location of affected cryptic donor Relative location of affected donor Since most of the values are 0 or almost 0, we selected only those variants with a score equal to or greater than 0.02. The complete processing of this track can be found in the makedoc. Data Access These data are not available for download from the Genome Browser. The raw data can be found directly on Illumina. See below for a copy of the license restrictions pertaining to these data. License FOR ACADEMIC AND NOT-FOR-PROFIT RESEARCH USE ONLY. The SpliceAI scores are made available by Illumina only for academic or not-for-profit research only. By accessing the SpliceAI data, you acknowledge and agree that you may only use this data for your own personal academic or not-for-profit research only, and not for any other purposes. You may not use this data for any for-profit, clinical, or other commercial purpose without obtaining a commercial license from Illumina, Inc. References Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB et al. Predicting Splicing from Primary Sequence with Deep Learning. Cell. 2019 Jan 24;176(3):535-548.e24. PMID: 30661751 Walker LC, Hoya M, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A et al. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet. 2023 Jul 6;110(7):1046-1067. PMID: 37352859; PMC: PMC10357475 
Total_counts_multiwig Total counts of CAGE reads FANTOM5: Total counts of CAGE reads Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
TotalCounts_Rev Total counts of CAGE reads (rev) Total counts of CAGE reads reverse Regulation 
TotalCounts_Fwd Total counts of CAGE reads (fwd) Total counts of CAGE reads forward Regulation 
wgEncodeRegMarkH3k27ac Layered H3K27Ac H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell lines from ENCODE Regulation Description Chemical modifications (e.g. methylation and acylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. A specific modification of a specific histone protein is called a histone mark. This track shows the levels of enrichment of the H3K27Ac histone mark across the genome as determined by a ChIP-seq assay. The H3K27Ac histone mark is the acetylation of lysine 27 of the H3 histone protein, and it is thought to enhance transcription possibly by blocking the spread of the repressive histone mark H3K27Me3. Additional histone marks and other chromatin associated ChIP-seq data is available at the Broad Histone page. Display conventions By default this track uses a transparent overlay method of displaying data from a number of cell lines in the same vertical space. Each of the cell lines in this track is associated with a particular color, and these cell line colors are consistent across all tracks that are part of the ENCODE Regulation supertrack. These colors are relatively light and saturated so as to work best with the transparent overlay. Unfortunately, outside the ENCODE Regulation tracks, older cell line color conventions are used that don't match the cell line colors used in the ENCODE Regulation tracks. The older colors were not used in the ENCODE Regulation tracks because they were too dark for the transparent overlay. Credits This track shows data from the Bernstein Lab at the Broad Institute. The Bernstein lab is part of the ENCODE consortium. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeRegMarkH3k27acNhlf NHLF H3K27Ac Mark (Often Found Near Regulatory Elements) on NHLF Cells from ENCODE Regulation 
wgEncodeRegMarkH3k27acNhek NHEK H3K27Ac Mark (Often Found Near Regulatory Elements) on NHEK Cells from ENCODE Regulation 
wgEncodeRegMarkH3k27acK562 K562 H3K27Ac Mark (Often Found Near Regulatory Elements) on K562 Cells from ENCODE Regulation 
wgEncodeRegMarkH3k27acHuvec HUVEC H3K27Ac Mark (Often Found Near Regulatory Elements) on HUVEC Cells from ENCODE Regulation 
wgEncodeRegMarkH3k27acHsmm HSMM H3K27Ac Mark (Often Found Near Regulatory Elements) on HSMM Cells from ENCODE Regulation 
wgEncodeRegMarkH3k27acH1hesc H1-hESC H3K27Ac Mark (Often Found Near Regulatory Elements) on H1-hESC Cells from ENCODE Regulation 
wgEncodeRegMarkH3k27acGm12878 GM12878 H3K27Ac Mark (Often Found Near Regulatory Elements) on GM12878 Cells from ENCODE Regulation 
Max_counts_multiwig Max counts of CAGE reads FANTOM5: Max counts of CAGE reads Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
MaxCounts_Rev Max counts of CAGE reads (rev) Max counts of CAGE reads reverse Regulation 
MaxCounts_Fwd Max counts of CAGE reads (fwd) Max counts of CAGE reads forward Regulation 
affyExonArray Affy Exon Array Affymetrix Human Exon Array Probes and Probesets Expression Methods This track shows the genomic locations of the probesets and probes from the Affymetrix Exon array. This array was designed to interrogate every known and putative exon in the human genome. For the design of this array, Affymetrix compiled evidence of expression from sources including well-annotated genes such as RefSeq, genomic alignments of mRNA and EST sequences, gene predictions, exon predictions, and regions that are syntenic to conserved regions in related species. Using this evidence, Affymetrix designed a probeset for each known or putative exon. While some of these regions might never be transcribed, the goal is to obtain a comprehensive measurement of transcription in the human genome. In most cases, this array contains one probeset per exon. However, whenever this design-time evidence suggested that some exon had alternative splice sites, the exon was subdivided into two or more regions, and one probeset was designed for each region (where possible). The array contains no probesets for exons smaller than 25 nucleotides. The exon array supports both gene-level and exon-level expression measurement. When the probesets for a single gene are analyzed together, it yields results for overall gene expression. When the probeset of each exon is contrasted against other exons in the same gene, it yields results for alternative splicing. The probes and probesets on the exon array are divided into five levels or classes, depending mostly on the degree of design-time evidence. Core probes and probesets are supported by the most reliable evidence from RefSeq and full-length mRNA GenBank records containing complete CDS information. Extended probes and probesets are supported by other cDNA evidence beyond what is used to support core probe sets. Extended evidence comes from other Genbank mRNAs not annotated as full-length, EST sequences, ENSEMBL gene collections, syntenically mapped mRNA from Mouse, Rat, or Human, mitoMap mitochondrial genes, microRNA registry genes, vegaGene, and vegaPseudoGene records. Full probes and probesets are supported by computational gene prediction evidence only. They are supported by gene and exon prediction algorithms including GeneID, GenScan, GenScanSubOptimal, exoniphy, RNAGene, sgpGene and Twinscan. Free probes and probesets are supported by annotations which were merged such that no single annotation (or evidence) contains the probe setprobe sets that are supported by annotations which were merged such that no single annotation (or evidence) contains the probe set. Ambiguous probes and probesets cannot be assigned unambiguously to any single gene. All probes and probesets have a two-part label, indicating the transcript cluster ID and probeset ID. The transcript cluster ID is a numeric representation of the gene interrogated by the probeset in question. All probes are labeled with the transcript cluster ID and probeset ID of whatever probeset they belong to. Credits The data for this track were provided by Affymetrix. Further information on the Human Exon Array is available here. 
affyArchive Affy Archive Affymetrix Archive Expression Description This supertrack is a collection of Affymetrix tracks showing the location of the consensus and exemplar sequences used for the selection of probes on the Affymetrix chips. Credits Thanks to Affymetrix for the data underlying these tracks. 
affyExonProbeset Affy Exon Array Affymetrix Human Exon Array Probes and Probesets Expression 
affyExonProbesetAmbiguous Ambiguous PS Affymetrix Human Exon Array Ambiguous Probesets Expression 
affyExonProbesetFree Free PS Affymetrix Human Exon Array Free Probesets Expression 
affyExonProbesetFull Full PS Affymetrix Human Exon Array Full Probesets Expression 
affyExonProbesetExtended Extended PS Affymetrix Human Exon Array Extended Probesets Expression 
affyExonProbesetCore Core PS Affymetrix Human Exon Array Core Probesets Expression 
affyExonProbe Affy Exon Array Affymetrix Human Exon Array Probes and Probesets Expression 
affyExonProbeAmbiguous Ambiguous Probes Affymetrix Human Exon Array Ambiguous Probes Expression 
affyExonProbeFree Free Probes Affymetrix Human Exon Array Free Probes Expression 
affyExonProbeFull Full Probes Affymetrix Human Exon Array Full Probes Expression 
affyExonProbeExtended Extended Probes Affymetrix Human Exon Array Extended Probes Expression 
affyExonProbeCore Core Probes Affymetrix Human Exon Array Core Probes Expression 
FANTOM_CAT FANTOM CAT FANTOM5: atlas of human long non-coding RNAs with accurate 5' ends Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
FANTOM_CATlv4 lv4 stringent FANTOM CAT.lv4 stringent Regulation 
FANTOM_CATlv3 lv3 robust FANTOM CAT.lv3 robust Regulation 
FANTOM_CATlv2 lv2 permissive FANTOM CAT.lv2 permissive Regulation 
FANTOM_CATlv1 lv1 raw FANTOM CAT.lv1 raw Regulation 
wgEncodeRegDnaseClustered DNase Clusters Cluster 2011-10-21 Kent UCSC wgEncodeRegDnaseClustered Element Clusters by Integrative Analysis Kent Kent - UC Santa Cruz DNaseI Hypersensitivity Clusters in 125 cell types from ENCODE (V3) Regulation Description This track shows DNase hypersensitive areas assayed in a large collection of cell types by the ENCODE project. Regulatory regions in general, and promoters in particular, tend to be DNase-sensitive. Additional views of this data and additional documentation on the methods used to identify hypersensitive sites are available from the Uniform DNaseI HS page. The uniform peaks in that track are the basis for the clusters shown here, which combine data from the peaks of the different cell lines. Display Conventions and Configuration A gray box indicates the extent of the hypersensitive region. The darkness is proportional to the maximum signal strength observed in any cell line. The number to the left of the box shows how many cell lines are hypersensitive in the region. The track can be configured to restrict the display to elements above a specified score in the range 100-1000 (where score is based on signal strength). Methods Stringent (FDR 1% thresholded) peaks of DNaseI hypersensitivity from uniform processing by the ENCODE Analysis Working Group (Uniform DNaseI HS) were assigned normalized scores (by UCSC regClusterMakeTableOfTables) in the range 0-1000 based on the narrowPeak signalValue and then clustered on score (by UCSC regCluster) to generate singly-linked clusters. Low-scoring clusters (score &lt;100) were then filtered out. Release Notes This is the third release of this track. It differs from the previous track as it includes clusters having only 1 cell type contributing to the cluster (previously excluded). The previous track is available on the UCSC preview browser as DNase Clusters V2. Credits This track shows data from the University of Washington and Duke ENCODE groups, with uniform processing by the ENCODE Analysis Working Group. The clustering was performed at UCSC. For additional credits and references, see the Uniform DNaseI HS page. Data Release Policy While primary ENCODE data is subject to a restriction period as described in the ENCODE data release policy, this restriction does not apply to the integrative analysis results. The data in this track are freely available. 
encRegTfbsClustered Txn Factr ChIP E3 Transcription Factor ChIP-seq Clusters (338 factors, 130 cell types) from ENCODE 3 Regulation Description This track shows regions of transcription factor binding derived from a large collection of ChIP-seq experiments performed by the ENCODE project between February 2011 and November 2018, spanning the first production phase of ENCODE ("ENCODE 2") through the second full production phase ("ENCODE 3"). Transcription factors (TFs) are proteins that bind to DNA and interact with RNA polymerases to regulate gene expression. Some TFs contain a DNA binding domain and can bind directly to specific short DNA sequences ('motifs'); others bind to DNA indirectly through interactions with TFs containing a DNA binding domain. High-throughput antibody capture and sequencing methods (e.g. chromatin immunoprecipitation followed by sequencing, or 'ChIP-seq') can be used to identify regions of TF binding genome-wide. These regions are commonly called ChIP-seq peaks. ENCODE TF ChIP-seq data were processed using the ENCODE Transcription Factor ChIP-seq Processing Pipeline to generate peaks of TF binding. Peaks from 1264 experiments (1256 in hg38) representing 338 transcription factors (340 in hg38) in 130 cell types (129 in hg38) are combined here into clusters to produce a summary display showing occupancy regions for each factor. The underlying ChIP-seq peak data are available from the ENCODE 3 TF ChIP Peaks tracks ( hg19, hg38) Display Conventions A gray box encloses each peak cluster of transcription factor occupancy, with the darkness of the box being proportional to the maximum signal strength observed in any cell type contributing to the cluster. The HGNC gene name for the transcription factor is shown to the left of each cluster. To the right of the cluster a configurable label can optionally display information about the cell types contributing to the cluster and how many cell types were assayed for the factor (count where detected / count where assayed). For brevity in the display, each cell type is abbreviated to a single letter. The darkness of the letter is proportional to the signal strength observed in the cell line. Abbreviations starting with capital letters designate ENCODE cell types initially identified for intensive study, while those starting with lowercase letters designate cell lines added later in the project. Click on a peak cluster to see more information about the TF/cell assays contributing to the cluster and the cell line abbreviation table. Methods Peaks of transcription factor occupancy ("optimal peak set") from ENCODE ChIP-seq datasets were clustered using the UCSC hgBedsToBedExps tool. Scores were assigned to peaks by multiplying the input signal values by a normalization factor calculated as the ratio of the maximum score value (1000) to the signal value at one standard deviation from the mean, with values exceeding 1000 capped at 1000. This has the effect of distributing scores up to mean plus one 1 standard deviation across the score range, but assigning all above to the maximum score. The cluster score is the highest score for any peak contributing to the cluster. Data Access The raw data for the ENCODE3 TF Clusters track can be accessed from the Table Browser or combined with other datasets through the Data Integrator. This data is stored internally as a BED5+3 MySQL table with additional metadata tables. For automated analysis and download, the encRegTfbsClusteredWithCells.hg38.bed.gz track data file can be downloaded from our downloads server, which has 5 fields of BED data followed by a comma-separated list of cell types. The data can also be queried using the JSON API or the Public SQL server. Credits Thanks to the ENCODE Consortium, the ENCODE ChIP-seq production laboratories, and the ENCODE Data Coordination Center for generating and processing the TF ChIP-seq datasets used here. The ENCODE accession numbers of the constituent datasets are available from the peak details page. Special thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI, at the ENCODE Data Analysis Center (ZLab at UMass Medical Center) for providing the peak datasets, metadata, and guidance developing this track. Please check the ZLab ENCODE Public Hubs for the most updated data. The integrative view presented here was developed by Jim Kent at UCSC. References ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222; PMCID: PMC3079585 ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMCID: PMC3439153 Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT et al. ENCODE data at the ENCODE portal. Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. PMID: 26527727; PMC: PMC4702836 Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100. PMID: 22955619 Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep;22(9):1798-812. PMID: 22955990; PMC: PMC3431495 Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. PMID: 23203885; PMC: PMC3531197 Data Use Policy Users may freely download, analyze and publish results based on any ENCODE data without restrictions. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE production laboratory(s) that generated the datasets used, as described in Citing ENCODE. 
wgEncodeRegTfbsClusteredV3 Txn Factor ChIP Cluster wgEncodeRegTfbsClusteredV3 Element Clusters by Integrative Analysis Transcription Factor ChIP-seq Clusters (161 factors) from ENCODE with Factorbook Motifs Regulation Description This track shows regions of transcription factor binding derived from a large collection of ChIP-seq experiments performed by the ENCODE project, together with DNA binding motifs identified within these regions by the ENCODE Factorbook repository. Transcription factors (TFs) are proteins that bind to DNA and interact with RNA polymerases to regulate gene expression. Some TFs contain a DNA binding domain and can bind directly to specific short DNA sequences ('motifs'); others bind to DNA indirectly through interactions with TFs containing a DNA binding domain. High-throughput antibody capture and sequencing methods (e.g. chromatin immunoprecipitation followed by sequencing, or 'ChIP-seq') can be used to identify regions of TF binding genome-wide. These regions are commonly called ChIP-seq peaks. ENCODE TFBS ChIP-seq data were processed using the computational pipeline developed by the ENCODE Analysis Working Group to generate uniform peaks of TF binding. Peaks for 161 transcription factors in 91 cell types are combined here into clusters to produce a summary display showing occupancy regions for each factor and motif sites within the regions when identified. Additional views of the underlying ChIP-seq data and documentation on the methods used to generate it are available from the ENCODE Uniform TFBS track. Factorbook Motif track shows the complete set of motif locations identified in the uniform ENCODE ChIP-seq peaks. --> Display Conventions A gray box encloses each peak cluster of transcription factor occupancy, with the darkness of the box being proportional to the maximum signal strength observed in any cell line contributing to the cluster. The HGNC gene name for the transcription factor is shown to the left of each cluster. Within a cluster, a green highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the corresponding factor. (NOTE: motif highlights are shown only in browser windows of size 50,000 bp or less, and their display can be suppressed by unchecking the highlight motifs box on the track configuration page). Arrows on the highlight designate the matching strand of the motif. The cell lines where signal was detected for the factor are identified by single-letter abbreviations shown to the right of the cluster. The darkness of each letter is proportional to the signal strength observed in the cell line. Abbreviations starting with capital letters designate ENCODE cell types identified for intensive study - Tier 1 and Tier 2 - while those starting with lowercase letters designate Tier 3 cell lines. Click on a peak cluster to see more information about the TF/cell assays contributing to the cluster, the cell line abbreviation table, and details about the highest scoring canonical motif in the cluster. Methods Peaks of transcription factor occupancy from uniform processing of ENCODE ChIP-seq data by the ENCODE Analysis Working Group were filtered to exclude datasets that did not pass the integrated quality metric (see &quot;Quality Control&quot; section of Uniform TFBS) and then were clustered using the UCSC hgBedsToBedExps tool. Scores were assigned to peaks by multiplying the input signal values by a normalization factor calculated as the ratio of the maximum score value (1000) to the signal value at one standard deviation from the mean, with values exceeding 1000 capped at 1000. This has the effect of distributing scores up to mean plus one 1 standard deviation across the score range, but assigning all above to the maximum score. The cluster score is the highest score for any peak contributing to the cluster. The Factorbook motif discovery and annotation pipeline uses the MEME-ChIP and FIMO tools from the MEME software suite in conjunction with machine learning methods and manual curation to merge discovered motifs with known motifs reported in Jaspar and TransFac. Motif identifications reported in Wang et al. 2012 (below) were supplemented in this track with more recent data (derived from newer ENCODE datasets - Jan 2011 through Mar 2012 freezes), provided by the Factorbook team. Motif identifications from all datasets were merged, with the most significant value (qvalue) reported being picked when motifs were duplicated in multiple cell lines. The scores for the selected best-scoring motif sites were then transformed to -log10. Release Notes Release 4 (February 2014) of this track adds display of the Factorbook motifs. Release 3 (August 2013) added 124 datasets (690 total, vs. 486 in Release 2), representing all ENCODE TF ChIP-seq passing quality assessment through the ENCODE March 2012 data freeze. The peaks used to generate these clusters were called with less stringent thresholds than used during the January 2011 uniform processing shown in Release 2 of this track. The contributing datasets are displayed as individual tracks in the ENCODE Uniform TFBS track, which is available along with the primary data tracks in the ENC TF Binding Supertrack page. The clustering for V3/V4 is based on the transcription factor target, and so differs from V2 where clustering was based on antibody. For the V3/V4 releases, a new track table format, 'factorSource' was used to represent the primary clusters table and downloads file, wgEncodeRegTfbsClusteredV3. This format consists of standard BED5 fields (see File Formats) followed by an experiment count field (expCount) and finally two fields containing comma-separated lists. The first list field (expNums) contains numeric identifiers for experiments, keyed to the wgEncodeRegTfbsClusteredInputsV3 table, which includes such information as the experiment's underlying Uniform TFBS table name, factor targeted, antibody used, cell type, treatment (if any), and laboratory source. The second list field (expScores) contains the scores for the corresponding experiments. For convenience, the file downloads directory for this track also contains a BED file, wgEncodeRegTfbsClusteredWithCellsV3, that lists each cluster with the cluster score followed by a comma-separated list of cell types. The Factorbook motif positions that display as green boxes on the track come from an additional table called factorbookMotifPos, and are supported by additional metadata tables such as factorbookMotifCanonical that connects different terms used for the same factor (RELA &lt;--&gt; NFKB1), and factorbookGeneAlias that connects terms to the the link used at factorbook.org (EGR1 &lt;--&gt; EGR-1), and lastly a position weight matrix table, factorbookMotifPwm, used in building the graphical sequence logo for each motif on the item details page. These tables are available on our public MySQL server and as files on our download server. Credits This track shows ChIP-seq data from the Myers Lab at the HudsonAlpha Institute for Biotechnology and by the labs of Michael Snyder, Mark Gerstein, Sherman Weissman at Yale University, Peggy Farnham at the University of Southern California, Kevin Struhl at Harvard, Kevin White at the University of Chicago, and Vishy Iyer at the University of Texas, Austin. These data were processed into uniform peak calls by the ENCODE Analysis Working Group pipeline developed by Anshul Kundaje The clustering of the uniform peaks was performed by UCSC. The Factorbook motif identifications and localizations (and valuable assistance with interpretation) were provided by Jie Wang, Bong Hyun Kim and Jiali Zhuang of the Zlab (Weng Lab) at UMass Medical School. References Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100. PMID: 22955619 Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep;22(9):1798-812. PMID: 22955990; PMC: PMC3431495 Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. PMID: 23203885; PMC: PMC3531197 Data Release Policy While primary ENCODE data was subject to a restriction period as described in the ENCODE data release policy, this restriction does not apply to the integrative analysis results, and all primary data underlying this track have passed the restriction date. The data in this track are freely available. 
wgEncodeRegTfbsClusteredV2 Txn Fac ChIP V2 Cluster 2011-10-21 Kent UCSC wgEncodeRegTfbsClusteredV2 Element Clusters by Integrative Analysis Kent Kent - UC Santa Cruz Transcription Factor ChIP-seq from ENCODE (V2) Regulation Description This track shows regions where transcription factors, proteins responsible for modulating gene transcription, bind to DNA as assayed by ChIP-seq (chromatin immunoprecipitation with antibodies specific to the transcription factor followed by sequencing of the precipitated DNA). Additional views of this dataset and additional documentation on the methods used for this track are available at the ENC TF Binding Supertrack page. The peaks were computed using a uniform pipeline developed by Anshul Kundaje that uses the variation between the two replicates to develop sensible peak thresholds. This track combines data from many different cell lines and transcription-factor targeting antibodies into a relatively dense display. Display Conventions A gray box encompasses the peaks of transcription factor occupancy. The darkness of the box is proportional to the maximum signal strength observed in any cell line. The name to the left of the box is the transcription factor. The letters to the right represent the cell lines where a signal is detected. The darkness of the letter is proportional to the signal strength in the cell line. Click on an item in the track to see the cell lines spelled out. Release Notes Release 2 (May 2012) of this track fixes a bug that, in some cases, was causing the score values of signals within a cluster to be displayed incorrectly. Credits This track shows data from the Myers Lab at the HudsonAlpha Institute for Biotechnology and by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University; Peggy Farnham at UC Davis; and Kevin Struhl at Harvard. Kevin White at The University of Chicago. Vishy Iyer at The University of Texas Austin. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. The full data release policy for ENCODE is available here. 
affyGnf1h Affy GNF1H Alignments of Affymetrix Consensus/Exemplars from GNF1H Expression Description This track shows the location of the sequences used for the selection of probes on the Affymetrix GNF1H chips. This contains 11406 predicted genes that do not overlap with the Affy U133A chip. Methods The sequences were mapped to the genome using blat followed by pslReps with the parameters: -minCover=0.3 -minAli=0.95 -nearTop=0.005 Credits Thanks to the Genomics Institute of the Novartis Research Foundation (GNF) for the data underlying this track. References Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7. PMID: 15075390; PMC: PMC395923 
cgapSage CGAP SAGE CGAP Long SAGE mRNA and EST Description This track displays genomic mappings for human LongSAGE tags from the The Cancer Genome Anatomy Project. SAGE (Serial Analysis of Gene Expression) [Velculescu 1995] is a quantitative technique for measuring gene expression. For a brief overview of SAGE, see the CGAP SAGE information page. Display Conventions and Configuration Genomic mappings of 17-base LongSAGE tags are displayed. Tag counts are normalized to tags per million (TPM) in each tissue or library. Tags with higher TPM are more darkly shaded. The CATG restriction site before the start of the tag is rendered as a thick line; the 17 bases of the tag are drawn as a thinner line. Thus the thin end of the tag points in the direction of transcription. The track display modes are: dense - Draws locations of mapped tags on a single line. squish - Draws one item per tag per library without labels. pack - Draws one item per tag per tissue with labels. The label includes the number of libraries of each tissue type containing the tag. Clicking on an item lists the libraries containing the tag, with the libraries from the selected tissue in bold. Clicking on a library in the list displays detailed information about that library. full - Draws one item per tag per library. Clicking on an item displays information about the library, along with other libraries containing the tag. The track can be configured to display only tags from a selected tissue. Methods Tag and library data, along with genomic mappers, were obtained from The Cancer Genome Anatomy Project. Information about the various SAGE libraries, data downloads and other tools for exploring and analyzing these data is available from the CGAP SAGE Genie web site. Mapping SAGE tags to the human genome The goal of the SAGE tag mapping is to identify the genomic loci of the associated mRNAs. Since it is impossible to disambiguate tags that map to multiple loci, only unique genomic mappings are kept. To compensate for polypmorphisms between the reference genome and the mRNA libraries, SNPs are considered by the mapping algorithm. For each position in the genome on both strands, all possible 21-mers, given all combinations of SNPs, were considered. The 21-mers beginning with CATG were generated for use in mapping. Only 21-mers that were unique across the genome were used in placing SAGE tags. Only SNPs from dbSNP with the following characteristics were used: single-base maps to a single genomic location reference allele matches reference genome does not occur in a tandem repeat Human embryonic stem cell (ESC) library construction Detailed information regarding the human ESC lines used in this study can be found at https://stemcells.nih.gov and in Hirst et al. 2007. The ESC tags were generated from RNA purified from human ESCs maintained under conditions that promote their maintenance in an undifferentiated state. A complete set of embryonic stem cell LongSAGE tags is available through the CGAP web portal. Credits Many thanks to Martin Hirst of Canada's Michael Smith Genome Sciences Centre for his assistance in developing this track. The LongSAGE data and genomic mappings were provided by the The Cancer Genome Anatomy Project of the National Cancer Institute, U.S. National Institutes of Health. The human embryonic stem cell library was supported by funds from the National Cancer Institute, National Institutes of Health, under Contract No. N01-C0-12400 and by grants from Genome Canada, Genome British Columbia and the Canadian Stem Cell Network. References Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ, Buetow KH, Strausberg RL, De Souza SJ et al. An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11287-92. PMID: 12119410; PMC: PMC123249 Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O'Connor MD, Zeng T, Moksa M, Fichter K, Mah D et al. LongSAGE profiling of nine human embryonic stem cell lines. Genome Biol. 2007;8(6):R113. PMID: 17570852; PMC: PMC2394759 Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K et al. Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res. 2007 Jan;17(1):108-16. PMID: 17135571; PMC: PMC1716260 Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak K et al. A public database for gene expression in human cancers. Cancer Res. 1999 Nov 1;59(21):5403-7. PMID: 10554005 Liang P. SAGE Genie: a suite with panoramic view of gene expression. Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11547-8. PMID: 12195021; PMC: PMC129301 Riggins GJ, Strausberg RL. Genome and genetic resources from the Cancer Genome Anatomy Project. Hum Mol Genet. 2001 Apr;10(7):663-7. PMID: 11257097 Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE. Using the transcriptome to annotate the genome. Nat Biotechnol. 2002 May;20(5):508-12. PMID: 11981567 Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S et al. A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18485-90. PMID: 16352711; PMC: PMC1311911 Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science. 1995 Oct 20;270(5235):484-7. PMID: 7570003 
cons46way Cons 46-Way Vertebrate Multiz Alignment & Conservation (46 Species) Comparative Genomics Description This track shows multiple alignments of 46 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species (vertebrate) and two subsets (primate and placental mammal). The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track. PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites). Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1. Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data, and both were run with the same parameters for each species set (vertebrates, placental mammals, and primates). Thus, in regions in which only primates appear in the alignment, all three sets of scores will be the same, but in regions in which additional species are available, the mammalian and/or vertebrate scores may differ from the primate scores. The alternative plots help to identify sequences that are under different evolutionary pressures in, say, primates and non-primates, or mammals and non-mammals. The species aligned for this track include the reptile, amphibian, bird, and fish clades, as well as marsupial, monotreme (platypus), and placental mammals. Compared to the previous 44-vertebrate alignment (hg18), this track includes 2 new species and 5 species with updated sequence assemblies (Table 1). The new species consist of two assemblies: baboon (papHam1) at 5.3X coverage and wallaby (macEug1) at 2X coverage. The elephant, opossum, rabbit, tetraodon, and zebrafish assemblies have been updated from those used in the previous 44-species alignment. UCSC has repeatmasked and aligned the low-coverage genome assemblies, and provides the sequence for download; however, we do not construct genome browsers for them. Missing sequence in the low-coverage assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see Gap Annotation, below). OrganismSpeciesRelease dateUCSC versionalignment type HumanHomo sapiens Feb. 2009 hg19/GRCh37reference species AlpacaVicugna pacosJul. 2008 vicPac1* Reciprocal Best ArmadilloDasypus novemcinctusJul. 2008 dasNov2* Reciprocal Best BaboonPapio hamadryasNov. 2008 papHam1* Reciprocal Best BushbabyOtolemur garnettiiDec. 2006 otoGar1* Reciprocal Best CatFelis catus Mar. 2006felCat3Reciprocal Best ChickenGallus gallus May 2006galGal3Syntenic Net ChimpPan troglodytes Mar. 2006panTro2Syntenic Net CowBos taurus Oct. 2007bosTau4Syntenic Net DogCanis lupus familiaris May 2005canFam2Syntenic Net DolphinTursiops truncatusFeb. 2008 turTru1* Reciprocal Best ElephantLoxodonta africana Jul. 2009loxAfr3Syntenic Net FuguTakifugu rubripes Oct. 2004fr2MAF Net GorillaGorilla gorilla gorillaOct. 2008 gorGor1* Reciprocal Best Guinea PigCavia porcellus Feb. 2008cavPor3Syntenic Net HedgehogErinaceus europaeusJune 2006 eriEur1* Reciprocal Best HorseEquus caballus Sep. 2007equCab2Syntenic Net Kangaroo ratDipodomys ordiiJul. 2008 dipOrd1* Reciprocal Best LampreyPetromyzon marinus Mar. 2007petMar1MAF Net LizardAnolis carolinensis Feb. 2007anoCar1Syntenic Net MarmosetCallithrix jacchus June 2007calJac1Reciprocal Best MedakaOryzias latipes Oct. 2005oryLat2MAF Net MegabatPteropus vampyrusJul. 2008 pteVam1* Reciprocal Best Little brown batMyotis lucifugusMar. 2006 myoLuc1* Reciprocal Best MouseMus musculus July 2007mm9Syntenic Net Mouse lemurMicrocebus murinusJul. 2007 micMur1* Reciprocal Best OpossumMonodelphis domestica Oct. 2006monDom5Syntenic Net OrangutanPongo pygmaeus abelii July 2007ponAbe2Syntenic Net PikaOchotona princepsJul. 2008 ochPri2* Reciprocal Best PlatypusOrnithorhynchus anatinus Mar. 2007ornAna1Reciprocal Best RabbitOryctolagus cuniculus Apr. 2009oryCun2Syntenic Net RatRattus norvegicus Nov. 2004rn4Syntenic Net RhesusMacaca mulatta Jan. 2006rheMac2Syntenic Net Rock hyraxProcavia capensis Jul. 2008proCap1* Reciprocal Best ShrewSorex araneusJune 2006 sorAra1* Reciprocal Best SlothCholoepus hoffmanniJul. 2008 choHof1* Reciprocal Best SquirrelSpermophilus tridecemlineatusFeb. 2008 speTri1* Reciprocal Best SticklebackGasterosteus aculeatus Feb. 2006gasAcu1MAF Net TarsierTarsier syrichtaAug. 2008 tarSyr1* Reciprocal Best TenrecEchinops telfairiJuly 2005 echTel1* Reciprocal Best TetraodonTetraodon nigroviridis Mar. 2007tetNig2MAF Net Tree ShrewTupaia belangeriDec. 2006 tupBel1* Reciprocal Best WallabyMacropus eugeniiNov. 2007 macEug1* Reciprocal Best X. tropicalisXenopus tropicalis Aug. 2005xenTro2MAF Net Zebra finchTaeniopygia guttata Jul. 2008taeGut1Syntenic Net ZebrafishDanio rerio Dec. 2008danRer6MAF Net Table 1. Genome assemblies included in the 46-way Conservation track. * Data download only, browser not available. Downloads for data in this track are available: Multiz alignments (MAF format), and phylogenetic trees PhyloP conservation (WIG format) PhastCons conservation (WIG format) Display Conventions and Configuration The track configuration options allow the user to display either the vertebrate or placental mammal conservation scores, or both simultaneously. In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options. Pairwise alignments of each species to the human genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons. Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). By default, the following 11 species are included in the pairwise display: rhesus, mouse, dog, horse, armadillo, opossum, platypus, lizard, chicken, X. tropicalis (frog), and stickleback. Note that excluding species from the pairwise display does not alter the the conservation score display. To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment. Gap Annotation The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used: Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the human genome or a lineage-specific deletion between the aligned blocks in the aligning species. Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species. Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species. Genomic Breaks Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows: Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement. Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the human genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence. Base Level When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the human sequence at those alignment positions relative to the longest non-human sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a &quot;*&quot; is displayed; other gap sizes are indicated by &quot;+&quot;. Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes: No codon translation: The gene annotation is not used; the bases are displayed without translation. Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment. Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding. Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation. Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled &quot;None&quot; do not have species-specific reading frames for gene translation. Gene TrackSpecies Known Geneshuman, mouse, rat Ensembl Genes v55 alpaca, armadillo, bush baby, cat, chicken, chimp, cow, dog, dolphin, fugu, gorilla, guinea pig, hedgehog, horse, kangaroo rat, little brown bat, lizard, medaka, megabat, mouse, mouse lemur, opossum, orangutan, pika, platypus, rhesus, rock hyrax, shrew, sloth, squirrel, stickleback, tarsier, tenrec, tetraodon, tree shrew, X. tropicalis, zebra finch, zebrafish Xeno Ref Genesbaboon, elephant, lamprey, marmoset, rabbit, wallaby Table 2. Gene tracks used for codon translation. Methods Pairwise alignments with the human genome were generated for each species using blastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks. An additional filtering step was introduced in the generation of the 46-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query (&quot;reciprocal best&quot;). The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display. Phylogenetic Tree Model Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The vertebrate tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 46way alignment (msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene set, filtered to select single-coverage long transcripts. The placental mammal tree model and primate tree model were extracted from the vertebrate model. PhastCons Conservation The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005. The phastCons parameters were tuned to produce 5% conserved elements in the genome for the vertebrate conservation measurement. This parameter set (expected-length=45, target-coverage=.3, rho=.31) was then used to generate the placental mammal and primate conservation scoring. PhyloP Conservation The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC). Conserved Elements The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full". Credits This track was created using the following programs: Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC). MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC Tree image generator: phyloPng by Galt Barber, UCSC Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community as of March 2007. References Phylo-HMMs, phastCons, and phyloP: Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911 Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823 Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216 Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396 Chain/Net: Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Multiz: Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317 Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007. Blastz: Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 Phylogenetic Tree: Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200 
cons46wayViewalign Multiz Alignments Vertebrate Multiz Alignment & Conservation (46 Species) Comparative Genomics 
multiz46way Multiz Align Multiz Alignments of 46 Vertebrates Comparative Genomics 
cons46wayViewphastcons Element Conservation (phastCons) Vertebrate Multiz Alignment & Conservation (46 Species) Comparative Genomics 
phastCons46way Vertebrate Cons Vertebrate Conservation by PhastCons Comparative Genomics 
phastCons46wayPlacental Mammal Cons Placental Mammal Conservation by PhastCons Comparative Genomics 
phastCons46wayPrimates Primate Cons Primate Conservation by PhastCons Comparative Genomics 
cons46wayViewelements Conserved Elements Vertebrate Multiz Alignment & Conservation (46 Species) Comparative Genomics 
phastConsElements46way Vertebrate El Vertebrate Conserved Elements Comparative Genomics 
phastConsElements46wayPlacental Mammal El Placental Mammal Conserved Elements Comparative Genomics 
phastConsElements46wayPrimates Primate El Primate Conserved Elements Comparative Genomics 
cons46wayViewphyloP Basewise Conservation (phyloP) Vertebrate Multiz Alignment & Conservation (46 Species) Comparative Genomics 
phyloP46wayAll Vertebrate Cons Vertebrate Basewise Conservation by PhyloP Comparative Genomics 
phyloP46wayPlacental Mammal Cons Placental Mammal Basewise Conservation by PhyloP Comparative Genomics 
phyloP46wayPrimates Primate Cons Primate Basewise Conservation by PhyloP Comparative Genomics 
covidHgiGwasR4Pval COVID GWAS v4 COVID risk variants from GWAS meta-analyses by the COVID-19 Host Genetics Initiative (Rel 4, Oct 2020) Phenotype and Literature Description This track set shows the results of the GWAS Data Release 4 (October 2020) from the COVID-19 Host Genetics Initiative (HGI): a collaborative effort to facilitate the generation of meta-analysis across multiple studies contributed by partners world-wide to identify the genetic determinants of SARS-CoV-2 infection susceptibility, disease severity and outcomes. The COVID-19 HGI also aims to provide a platform for study partners to share analytical results in the form of summary statistics and/or individual level data of COVID-19 host genetics research. At the time of this release, a total of 137 studies were registered with this effort. The specific phenotypes studied by the COVID-19 HGI are those that benefit from maximal sample size: primary analysis on disease severity. For the Data Release 4 the number of cases have increased by nearly ten-fold (more than 30,000 COVID-19 cases and 1.47 million controls) by combining data from 34 studies across 16 countries. The four tracks here are based on data from HGI meta-analyses A2, B2, C1, and C2, described here: Severe COVID vars (A2): Cases with very severe respiratory failure confirmed for COVID-19 vs. population (i.e. everybody that is not a case). The increased sample size resulted in strong evidence of seven genomic regions associated with severe COVID-19 and one additional signal associated with COVID-19 partial-susceptibility. Many of these regions were identified by the Genetics of Mortality in Critical Care (GenOMICC) study and are shown below (table adapted from Pairo-Castineira et. al.). SNP Human GRCh37/hg19 Assembly Human GRCh38/hg38 Assembly Risk Allele Alternative Gene nearest to SNP rs73064425 chr3:45901089-45901089 chr3:45859597-45859597 T C LZTFL1 rs9380142 chr6:29798794-29798794 chr6:29831017-29831017 A G HLA-G rs143334143 chr6:31121426-31121426 chr6:31153649-31153649 A G CCHCR1 rs10735079 chr12:113380008-113380008 chr12:112942203-112942203 A G OAS3 rs74956615 chr19:10427721-10427721 chr19:10317045-10317045 A T ICAM5/TYK2 rs2109069 chr19:4719443-4719443 chr19:4719431-4719431 A G DPP9 rs2236757 chr21:34624917-34624917 chr21:33252612-33252612 A G IFNAR2 Hosp COVID vars (B2): Cases hospitalized and confirmed for COVID-19 vs. population (i.e. everybody that is not a case) Tested COVID vars (C1): Cases with laboratory confirmed SARS-CoV-2 infection, or health record/physician-confirmed COVID-19, or self-reported COVID-19 via questionare vs. laboratory /self-reported negative cases All COVID vars (C2): Cases with laboratory confirmed SARS-CoV-2 infection, or health record/physician-confirmed COVID-19, or self-reported COVID-19 vs. population (i.e. everybody that is not a case) Due to privacy concerns, these browser tracks exclude data provided by 23andMe contributed studies in the full analysis results. The actual study and case and control counts for the individual browser tracks are listed in the track labels. Details on all studies can be found here. Display Conventions Displayed items are colored by GWAS effect: red for positive (harmful) effect, blue for negative (protective) effect. The height ('lollipop stem') of the item is based on statistical significance (p-value). For better visualization of the data, only SNPs with p-values smaller than 1e-3 are displayed by default. The color saturation indicates effect size (beta coefficient): values over the median of effect size are brightly colored (bright red &nbsp;&nbsp; , bright blue &nbsp;&nbsp; ), those below the median are paler (light red &nbsp;&nbsp; , light blue &nbsp;&nbsp; ). Each track has separate display controls and data can be filtered according to the number of studies, minimum -log10 p-value, and the effect size (beta coefficient), using the track Configure options. Mouseover on items shows the rs ID (or chrom:pos if none assigned), both the non-effect and effect alleles, the effect size (beta coefficient), the p-value, and the number of studies. Additional information on each variant can be found on the details page by clicking on the item. Methods COVID-19 Host Genetics Initiative (HGI) GWAS meta-analysis round 4 (October 2020) results were used in this study. Each participating study partner submitted GWAS summary statistics for up to four of the COVID-19 phenotype definitions. Data were generated from genome-wide SNP array and whole exome and genome sequencing, leveraging the impact of both common and rare variants. The statistical analysis performed takes into account differences between sex, ancestry, and date of sample collection. Alleles were harmonized across studies and reported allele frequencies are based on gnomAD version 3.0 reference data. Most study partners used the SAIGE GWAS pipeline in order to generate summary statistics used for the COVID-19 HGI meta-analysis. The summary statistics of individual studies were manually examined for inflation, deflation, and excessive number of false positives. Qualifying summary statistics were filtered for INFO > 0.6 and MAF > 0.0001 prior to meta-analyzing the entirety of the data. The meta-analysis was performed using fixed effects inverse variance weighting. The meta-analysis software and workflow are available here. More information about the prospective studies, processing pipeline, results and data sharing can be found here. Data Access The data underlying these tracks and summary statistics results are publicly available in COVID19-hg Release 4 (October 2020). The raw data can be explored interactively with the Table Browser, or the Data Integrator. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Credits Thanks to the COVID-19 Host Genetics Initiative contributors and project leads for making these data available, and in particular to Rachel Liao, Juha Karjalainen, and Kumar Veerapen at the Broad Institute for their review and input during browser track development. References COVID-19 Host Genetics Initiative. The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic. Eur J Hum Genet. 2020 Jun;28(6):715-718. PMID: 32404885; PMC: PMC7220587 Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, Fourman MH, Russell CD et al. Genetic mechanisms of critical illness in Covid-19. Nature. 2020 Dec 11;. PMID: 33307546 
covid COVID Data Container of SARS-CoV-2 data Phenotype and Literature Description This is a container track for all data related to SARS-CoV-2 for hg19 in the UCSC Genome Browser. Click into any of the sub-tracks to see information details on the specific annotations. 
covidHgiGwasR4PvalC2 All COVID vars COVID risk variants from the COVID-19 HGI GWAS Analysis C2 (17965 cases, 33 studies, Rel 4: Oct 2020) Phenotype and Literature 
covidHgiGwasR4PvalC1 Tested COVID vars Tested COVID risk variants from the COVID-19 HGI GWAS Analyis C1 (11085 cases, 20 studies, Rel 4: Oct 2020) Phenotype and Literature 
covidHgiGwasR4PvalB2 Hosp COVID vars Hospitalized COVID risk variants from the COVID-19 HGI GWAS Analysis B2 (7885 cases, 21 studies, Rel 4: Oct 2020) Phenotype and Literature 
covidHgiGwasR4PvalA2 Severe COVID vars Severe respiratory COVID risk variants from the COVID-19 HGI GWAS Analysis A2 (4336 cases, 12 studies, Rel 4: Oct 2020) Phenotype and Literature 
hmc HMC HMC - Homologous Missense Constraint Score on PFAM domains Phenotype and Literature Description The "Constraint scores" container track includes several subtracks showing the results of constraint prediction algorithms. These try to find regions of negative selection, where variations likely have functional impact. The algorithms do not use multi-species alignments to derive evolutionary constraint, but use primarily human variation, usually from variants collected by gnomAD (see the gnomAD V2 or V3 tracks on hg19 and hg38) or TOPMED (contained in our dbSNP tracks and available as a filter). One of the subtracks is based on UK Biobank variants, which are not available publicly, so we have no track with the raw data. The number of human genomes that are used as the input for these scores are 76k, 53k and 110k for gnomAD, TOPMED and UK Biobank, respectively. Note that another important constraint score, gnomAD constraint, is not part of this container track but can be found in the hg38 gnomAD track. The algorithms included in this track are: JARVIS - "Junk" Annotation genome-wide Residual Variation Intolerance Score: JARVIS scores were created by first scanning the entire genome with a sliding-window approach (using a 1-nucleotide step), recording the number of all TOPMED variants and common variants, irrespective of their predicted effect, within each window, to eventually calculate a single-nucleotide resolution genome-wide residual variation intolerance score (gwRVIS). That score, gwRVIS was then combined with primary genomic sequence context, and additional genomic annotations with a multi-module deep learning framework to infer pathogenicity of noncoding regions that still remains naive to existing phylogenetic conservation metrics. The higher the score, the more deleterious the prediction. This score covers the entire genome, except the gaps. HMC - Homologous Missense Constraint: Homologous Missense Constraint (HMC) is a amino acid level measure of genetic intolerance of missense variants within human populations. For all assessable amino-acid positions in Pfam domains, the number of missense substitutions directly observed in gnomAD (Observed) was counted and compared to the expected value under a neutral evolution model (Expected). The upper limit of a 95% confidence interval for the Observed/Expected ratio is defined as the HMC score. Missense variants disrupting the amino-acid positions with HMC&lt;0.8 are predicted to be likely deleterious. This score only covers PFAM domains within coding regions. MetaDome - Tolerance Landscape Score (hg19 only): MetaDome Tolerance Landscape scores are computed as a missense over synonymous variant count ratio, which is calculated in a sliding window (with a size of 21 codons/residues) to provide a per-position indication of regional tolerance to missense variation. The variant database was gnomAD and the score corrected for codon composition. Scores &lt;0.7 are considered intolerant. This score covers only coding regions. MTR - Missense Tolerance Ratio (hg19 only): Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence. It is estimated across sliding windows of 31 codons (default) and uses observed standing variation data from the WES component of gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores were computed using Ensembl v95 release. The number of gnomAD 2 exomes used here is higher than the number of gnomAD 3 samples (125 exoms versus 76k full genomes), but this score only covers coding regions. UK Biobank depletion rank score (hg38 only): Halldorsson et al. tabulated the number of UK Biobank variants in each 500bp window of the genome and compared this number to an expected number given the heptamer nucleotide composition of the window and the fraction of heptamers with a sequence variant across the genome and their mutational classes. A variant depletion score was computed for every overlapping set of 500-bp windows in the genome with a 50-bp step size. They then assigned a rank (depletion rank (DR)) from 0 (most depletion) to 100 (least depletion) for each 500-bp window. Since the windows are overlapping, we plot the value only in the central 50bp of the 500bp window, following advice from the author of the score, Hakon Jonsson, deCODE Genetics. He suggested that the value of the central window, rather than the worst possible score of all overlapping windows, is the most informative for a position. This score covers almost the entire genome, only very few regions were excluded, where the genome sequence had too many gap characters. Display Conventions and Configuration JARVIS JARVIS scores are shown as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The scores were downloaded and converted to a single bigWig file. Move the mouse over the bars to display the exact values. A horizontal line is shown at the 0.733 value which signifies the 90th percentile. See hg19 makeDoc and hg38 makeDoc. Interpretation: The authors offer a suggested guideline of > 0.9998 for identifying higher confidence calls and minimizing false positives. In addition to that strict threshold, the following two more relaxed cutoffs can be used to explore additional hits. Note that these thresholds are offered as guidelines and are not necessarily representative of pathogenicity. PercentileJARVIS score threshold 99th0.9998 95th0.9826 90th0.7338 HMC HMC scores are displayed as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The highly-constrained cutoff of 0.8 is indicated with a line. Interpretation: A protein residue with HMC score &lt;1 indicates that missense variants affecting the homologous residues are significantly under negative selection (P-value &lt; 0.05) and likely to be deleterious. A more stringent score threshold of HMC&lt;0.8 is recommended to prioritize predicted disease-associated variants. MetaDome MetaDome data can be found on two tracks, MetaDome and MetaDome All Data. The MetaDome track should be used by default for data exploration. In this track the raw data containing the MetaDome tolerance scores were converted into a signal ("wiggle") track. Since this data was computed on the proteome, there was a small amount of coordinate overlap, roughly 0.42%. In these regions the lowest possible score was chosen for display in the track to maintain sensitivity. For this reason, if a protein variant is being evaluated, the MetaDome All Data track can be used to validate the score. More information on this data can be found in the MetaDome FAQ. Interpretation: The authors suggest the following guidelines for evaluating intolerance. By default, the MetaDome track displays a horizontal line at 0.7 which signifies the first intolerant bin. For more information see the MetaDome publication. ClassificationMetaDome Tolerance Score Highly intolerant&le; 0.175 Intolerant&le; 0.525 Slightly intolerant&le; 0.7 MTR MTR data can be found on two tracks, MTR All data and MTR Scores. In the MTR Scores track the data has been converted into 4 separate signal tracks representing each base pair mutation, with the lowest possible score shown when multiple transcripts overlap at a position. Overlaps can happen since this score is derived from transcripts and multiple transcripts can overlap. A horizontal line is drawn on the 0.8 score line to roughly represent the 25th percentile, meaning the items below may be of particular interest. It is recommended that the data be explored using this version of the track, as it condenses the information substantially while retaining the magnitude of the data. Any specific point mutations of interest can then be researched in the MTR All data track. This track contains all of the information from MTRV2 including more than 3 possible scores per base when transcripts overlap. A mouse-over on this track shows the ref and alt allele, as well as the MTR score and the MTR score percentile. Filters are available for MTR score, False Discovery Rate (FDR), MTR percentile, and variant consequence. By default, only items in the bottom 25 percentile are shown. Items in the track are colored according to their MTR percentile: Green items MTR percentiles over 75 Black items MTR percentiles between 25 and 75 Red items MTR percentiles below 25 Blue items No MTR score Interpretation: Regions with low MTR scores were seen to be enriched with pathogenic variants. For example, ClinVar pathogenic variants were seen to have an average score of 0.77 whereas ClinVar benign variants had an average score of 0.92. Further validation using the FATHMM cancer-associated training dataset saw that scores less than 0.5 contained 8.6% of the pathogenic variants while only containing 0.9% of neutral variants. In summary, lower scores are more likely to represent pathogenic variants whereas higher scores could be pathogenic, but have a higher chance to be a false positive. For more information see the MTR-Viewer publication. Methods JARVIS Scores were downloaded and converted to a single bigWig file. See the hg19 makeDoc and the hg38 makeDoc for more info. HMC Scores were downloaded and converted to .bedGraph files with a custom Python script. The bedGraph files were then converted to bigWig files, as documented in our makeDoc hg19 build log. MetaDome The authors provided a bed file containing codon coordinates along with the scores. This file was parsed with a python script to create the two tracks. For the first track the scores were aggregated for each coordinate, then the lowest score chosen for any overlaps and the result written out to bedGraph format. The file was then converted to bigWig with the bedGraphToBigWig utility. For the second track the file was reorganized into a bed 4+3 and conveted to bigBed with the bedToBigBed utility. See the hg19 makeDoc for details including the build script. The raw MetaDome data can also be accessed via their Zenodo handle. MTR V2 file was downloaded and columns were reshuffled as well as itemRgb added for the MTR All data track. For the MTR Scores track the file was parsed with a python script to pull out the highest possible MTR score for each of the 3 possible mutations at each base pair and 4 tracks built out of these values representing each mutation. See the hg19 makeDoc entry on MTR for more info. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/hmc/hmc.bw stdout Please refer to our Data Access FAQ for more information. Credits Thanks to Jean-Madeleine Desainteagathe (APHP Paris, France) for suggesting the JARVIS, MTR, HMC tracks. Thanks to Xialei Zhang for providing the HMC data file and to Dimitrios Vitsios and Slave Petrovski for helping clean up the hg38 JARVIS files for providing guidance on interpretation. Additional thanks to Laurens van de Wiel for providing the MetaDome data as well as guidance on the track development and interpretation. References Vitsios D, Dhindsa RS, Middleton L, Gussow AB, Petrovski S. Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. Nat Commun. 2021 Mar 8;12(1):1504. PMID: 33686085; PMC: PMC7940646 Xiaolei Zhang, Pantazis I. Theotokis, Nicholas Li, the SHaRe Investigators, Caroline F. Wright, Kaitlin E. Samocha, Nicola Whiffin, James S. Ware Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery. Medrxiv 2022.02.16.22271023 Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat. 2019 Aug;40(8):1030-1038. PMID: 31116477; PMC: PMC6772141 Silk M, Petrovski S, Ascher DB. MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 2019 Jul 2;47(W1):W121-W126. PMID: 31170280; PMC: PMC6602522 Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO et al. The sequences of 150,119 genomes in the UK Biobank. Nature. 2022 Jul;607(7920):732-740. PMID: 35859178; PMC: PMC9329122 
refSeqComposite NCBI RefSeq RefSeq genes from NCBI Genes and Gene Predictions Description The NCBI RefSeq Genes composite track shows human protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use coordinates provided by RefSeq, except for the UCSC RefSeq track, which UCSC produces by realigning the RefSeq RNAs to the genome. This realignment may result in occasional differences between the annotation coordinates provided by UCSC and NCBI. See the Methods section for more details about how the different tracks were created. Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track is a composite track that contains differing data sets. To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to hide. Note: Not all subtracts are available on all assemblies. The possible subtracks include: RefSeq aligned annotations and UCSC alignment of RefSeq annotations RefSeq All &ndash; all curated and predicted annotations provided by RefSeq. RefSeq Curated &ndash; subset of RefSeq All that includes only those transcripts whose accessions begin with NM, NR, NP or YP. (NP and YP are used only for protein-coding genes on the mitochondrion; YP is used for human only.) These were manually curated by the NCBI RefSeq group, based on publications describing transcripts and manual reviews of evidence which includes EST and full-length cDNA alignments, protein sequences, splice sites and any other evidence available in databases or the scientific literature. The resulting sequences can differ from the genome, they exist independently from a particular human genome build, and so must be aligned to the genome to create a track. The "RefSeq Curated" track is NCBI's mapping of curated transcripts to the genome. For transcripts where researchers are interested in an alternative alignment, the "UCSC RefSeq" track can be used, it shows a BLAT alignment of curated RefSeq transcripts (see "UCSC RefSeq" below and also the FAQ). RefSeq Predicted &ndash; subset of RefSeq All that includes those annotations whose accessions begin with XM or XR. They were predicted based on protein, cDNA, EST and RNA-seq alignments to the genome assembly by the NCBI Gnomon prediction software. RefSeq Other &ndash; all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the RefSeq Curated or the RefSeq Predicted tracks. Examples are untranscribed pseudogenes or gene clusters, such as HOX or protocadherin alpha. They were manually curated from publications or databases but are not typical transcribed genes. RefSeq Alignments &ndash; alignments of RefSeq RNAs to the human genome provided by the RefSeq group, following the display conventions for PSL tracks. RefSeq Diffs &ndash; alignment differences between the human reference genome(s) and RefSeq transcripts. (Track not currently available for every assembly.) UCSC RefSeq &ndash; annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the human genome. This track was previously known as the &quot;RefSeq Genes&quot; track. Because this track shows all possible top-scoring alignments, it can contain duplicated transcripts. See our FAQ for details. RefSeq Select &ndash; Subset of RefSeq Curated, transcripts marked as part of the RefSeq Select dataset. A single Select transcript is chosen as representative for each protein-coding gene. See NCBI RefSeq Select. RefSeq HGMD (subset) &ndash; Subset of RefSeq Curated, transcripts annotated by the Human Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. It is the most restricted RefSeq subset, targeting clinical diagnostics. The RefSeq All, RefSeq Curated, RefSeq Predicted, RefSeq HGMD, RefSeq Select and UCSC RefSeq tracks follow the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by RefSeq. Color Level of review Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information. Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff. Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted. The item labels and codon display properties for features within this track can be configured through the check-box controls at the top of the track description page. To adjust the settings for an individual subtrack, click the wrench icon next to the track name in the subtrack list . Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name or OMIM identifier instead of the gene name, show all or a subset of these labels including the gene name, OMIM identifier and accession names, or turn off the label completely. Codon coloring: This track has an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. The RefSeq Diffs track contains five different types of inconsistency between the reference genome sequence and the RefSeq transcript sequences. The five types of differences are as follows: mismatch &ndash; aligned but mismatching bases, plus HGVS g. to show the genomic change required to match the transcript and HGVS c./n. to show the transcript change required to match the genome. short gap &ndash; genomic gaps that are too small to be introns (arbitrary cutoff of &lt; 45 bp), most likely insertions/deletion variants or errors, with HGVS g. and c./n. showing differences. shift gap &ndash; shortGap items whose placement could be shifted left and/or right on the genome due to repetitive sequence, with HGVS c./n. position range of ambiguous region in transcript. Here, thin and thick lines are used -- the thin line shows the span of the repetitive sequence, and the thick line shows the rightmost shifted gap. double gap &ndash; genomic gaps that are long enough to be introns but that skip over transcript sequence (invisible in default setting), with HGVS c./n. deletion. skipped &ndash; sequence at the beginning or end of a transcript that is not aligned to the genome (invisible in default setting), with HGVS c./n. deletion HGVS Terminology (Human Genome Variation Society): g. = genomic sequence ; c. = coding DNA sequence ; n. = non-coding RNA reference sequence. When reporting HGVS with RefSeq sequences, to make sure that results from research articles can be mapped to the genome unambiguously, please specify the RefSeq annotation release displayed on the transcript's Genome Browser details page and also the RefSeq transcript ID with version (e.g. NM_012309.4 not NM_012309). Methods Tracks contained in the RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using data from the NCBI RefSeq project. Data files were downloaded from RefSeq in GFF file format and converted to the genePred and PSL table formats for display in the Genome Browser. Information about the NCBI annotation pipeline can be found here. The RefSeq Diffs track is generated by UCSC using NCBI's RefSeq RNA alignments. The UCSC RefSeq Genes track is constructed using the same methods as previous RefSeq Genes tracks. RefSeq RNAs were aligned against the human genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. Data Access The raw data for these tracks can be accessed in multiple ways. It can be explored interactively using the REST API, Table Browser or using the Table Browser or Data Integrator. The tables can also be accessed programmatically through our public MySQL server or downloaded from our downloads server for local processing. The previous track versions are available in the archives of our downloads server. You can also access any RefSeq table entries in JSON format through our JSON API. The data in the RefSeq Other and RefSeq Diffs tracks are organized in bigBed file format; more information about accessing the information in this bigBed file can be found below. The other subtracks are associated with database tables as follows: genePred format: RefSeq All - ncbiRefSeq RefSeq Curated - ncbiRefSeqCurated RefSeq Predicted - ncbiRefSeqPredicted RefSeq HGMD - ncbiRefSeqHgmd RefSeq Select - ncbiRefSeqSelect UCSC RefSeq - refGene PSL format: RefSeq Alignments - ncbiRefSeqPsl The first column of each of these tables is &quot;bin&quot;. This column is designed to speed up access for display in the Genome Browser, but can be safely ignored in downstream analysis. You can read more about the bin indexing system here. The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed files, which can be obtained from our downloads server here, ncbiRefSeqOther.bb and ncbiRefSeqDiffs.bb. Individual regions or the whole set of genome-wide annotations can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system from the utilities directory linked below. For example, to extract only annotations in a given region, you could use the following command: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/ncbiRefSeq/ncbiRefSeqOther.bb -chrom=chr16 -start=34990190 -end=36727467 stdout You can download a GTF format version of the RefSeq All table from the GTF downloads directory. The genePred format tracks can also be converted to GTF format using the genePredToGtf utility, available from the utilities directory on the UCSC downloads server. The utility can be run from the command line like so: genePredToGtf hg19 ncbiRefSeqPredicted ncbiRefSeqPredicted.gtf Note that using genePredToGtf in this manner accesses our public MySQL server, and you therefore must set up your hg.conf as described on the MySQL page linked near the beginning of the Data Access section. A file containing the RNA sequences in FASTA format for all items in the RefSeq All, RefSeq Curated, and RefSeq Predicted tracks can be found on our downloads server here. Please refer to our mailing list archives for questions. Credits This track was produced at UCSC from data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
ncbiRefSeqHgmd RefSeq HGMD NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD Genes and Gene Predictions 
ncbiRefSeqSelect RefSeq Select and MANE NCBI RefSeq Select and MANE subset: A single representative transcript Genes and Gene Predictions 
refGene UCSC RefSeq UCSC annotations of RefSeq RNAs (NM_* and NR_*) Genes and Gene Predictions Description The RefSeq Genes track shows known human protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly. Please visit the Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark). The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely. Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box. Methods RefSeq RNAs were aligned against the human genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
ncbiRefSeqGenomicDiff RefSeq Diffs Differences between NCBI RefSeq Transcripts and the Reference Genome Genes and Gene Predictions 
ncbiRefSeqPsl RefSeq Alignments RefSeq Alignments of RNAs Genes and Gene Predictions 
ncbiRefSeqOther RefSeq Other NCBI RefSeq Other Annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) Genes and Gene Predictions 
ncbiRefSeqCurated RefSeq Curated NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) Genes and Gene Predictions 
ncbiRefSeq RefSeq All NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*) Genes and Gene Predictions 
omimGene2 OMIM Genes OMIM Gene Phenotypes - Dark Green Can Be Disease-causing Phenotype and Literature Description NOTE: OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the OMIM database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. Further, please be sure to click through to omim.org for the very latest, as they are continually updating data. NOTE ABOUT DOWNLOADS: OMIM is the property of Johns Hopkins University and is not available for download or mirroring by any third party without their permission. Please see OMIM for downloads. OMIM is a compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known Mendelian disorders and over 12,000 genes. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. This database was initiated in the early 1960s by Dr. Victor A. McKusick as a catalog of Mendelian traits and disorders, entitled Mendelian Inheritance in Man (MIM). The OMIM data are separated into three separate tracks: OMIM Alellic Variant Phenotypes (OMIM Alleles) &nbsp;&nbsp;&nbsp;&nbsp;Variants in the OMIM database that have associated dbSNP identifiers. OMIM Gene Phenotypes (OMIM Genes) &nbsp;&nbsp;&nbsp;&nbsp;The genomic positions of gene entries in the OMIM database. The coloring indicates the associated OMIM phenotype map key. OMIM Cytogenetic Loci Phenotypes - Gene Unknown (OMIM Cyto Loci) &nbsp;&nbsp;&nbsp;&nbsp;Regions known to be associated with a phenotype, but for which no specific gene is known to be causative. This track also includes known multi-gene syndromes. This track shows the genomic positions of all gene entries in the Online Mendelian Inheritance in Man (OMIM) database. Display Conventions and Configuration Genomic locations of OMIM gene entries are displayed as solid blocks. The entries are colored according to the associated OMIM phenotype map key (if any): Lighter Green for phenotype map key 1 OMIM records - the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known. Light Green for phenotype map key 2 OMIM records - the disorder has been placed on the map by linkage; no mutation has been found. Dark Green for phenotype map key 3 OMIM records - the molecular basis for the disorder is known; a mutation has been found in the gene. Purple for phenotype map key 4 OMIM records - a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype. Light Gray for Others - no associated OMIM phenotype map key info available. Gene symbol, phenotype, and inheritance information, when available, are displayed on the details page for an item, and links to related RefSeq Genes and UCSC Genes are given. The descriptions of the OMIM entries are shown on the main browser display when mousing over each entry. Mode of Inheritance Abbreviation Autosomal Dominant AD Autosomal Recessive AR Digenic Dominant DD Digenic Recessive DR Isolated Cases IC Mitochondrial Mi Multifactorial Mu Pseudoautosomal Dominant PADom Pseudoautosomal Recessive PARec Somatic Mosaicism SomMos Somatic Mutation SMu X-Linked XL X-Linked Dominant XLD X-Linked Recessive XLR Y-Linked YL Brackets, "[ ]", before the phenotype name indicate "nondiseases," mainly genetic variations that lead to apparently abnormal laboratory test values (e.g., dysalbuminemic euthyroidal hyperthyroxinemia). Braces, "{ }", indicate mutations that contribute to susceptibility to multifactorial disorders (e.g., diabetes, asthma) or to susceptibility to infection (e.g., malaria). Question marks, "?", indicate that the relationship between the phenotype and gene is provisional. More details about this relationship are provided in the comment field of the map and in the gene and phenotype OMIM entries. Methods The mappings displayed in this track are based on OMIM gene entries, their Entrez Gene IDs, and the corresponding RefSeq Gene locations: The data file genemap.txt from OMIM was loaded into the MySQL table omimGeneMap. The data file mim2gene.txt from OMIM was processed and loaded into the MySQL table omim2gene. Entries in genemap.txt having disorder info were parsed and loaded into the omimPhenotype table. For each OMIM gene in the omim2gene table, the Entrez Gene ID was used to get the corresponding RefSeq Gene ID via the refLink table, and the RefSeq ID was used to get the genomic location from the refGene table.* The OMIM gene IDs and corresponding RefSeq Gene locations were loaded into the omimGene2 table, the primary table for this track. *The locations in the refGene table are from alignments of RefSeq Genes to the reference genome using BLAT. Data Updates This track is automatically updated once a week from OMIM data. The most recent update time is shown at the top of the track documentation page. Data Access Because OMIM has only allowed Data queries within individual chromosomes, no download files are available from the Genome Browser. Full genome datasets can be downloaded directly from the OMIM Downloads page. All genome-wide downloads are freely available from OMIM after registration. If you need the OMIM data in exactly the format of the UCSC Genome Browser, for example if you are running a UCSC Genome Browser local installation (a partial &quot;mirror&quot;), please create a user account on omim.org and contact OMIM via https://omim.org/contact. Send them your OMIM account name and request access to the UCSC Genome Browser &quot;entitlement&quot;. They will then grant you access to a MySQL/MariaDB data dump that contains all UCSC Genome Browser OMIM tables. UCSC offers queries within chromosomes from Table Browser that include a variety of filtering options and cross-referencing other datasets using our Data Integrator tool. UCSC also has an API that can be used to retrieve data in JSON format from a particular chromosome range. Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information. Example: Retrieve phenotype, Mode of Inheritance, and other OMIM data within a range Go to Table Browser, make sure the right dataset is selected: group: Phenotype and Literature, track: OMIM Genes, table: omimGene2. Define region of interest by entering coordinates or a gene symbol into the &quot;Position&quot; textbox, such as chr1:11,166,591-11,322,608 or MTOR, or upload a list. Format your data by setting the &quot;Output format&quot; dropdown to &quot;selected fields from primary and related Tables&quot; and click get output. This brings up the data field and linked table selection page. Select chrom, chromStart, chromEnd, and name from omimGene2 table. Then select the related tables omim2gene and omimPhenotype and click allow selection from check tables. This brings up the fields of the linked tables, where you can select approvedGeneSymbol, omimID, description, omimPhenotypeMapKey, and inhMode. Click on the get output to proceed to the results page: chr1 11166591 11322608 601231 Gene: MTOR, Synonyms: FRAP1, SKS, Phenotypes: Smith-Kingsmore syndrome, AD, 3; Focal cortical dysplasia, type II, somatic, 3 For a quick link to pre-fill these options, click this session link. Credits Thanks to OMIM and NCBI for the use of their data. This track was constructed by Fan Hsu, Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group. References Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. PMID: 18842627; PMC: PMC2686440 Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7. PMID: 15608251; PMC: PMC539987 
TSS_activity_read_counts TSS activity - read counts FANTOM5: TSS activity per sample read counts Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
VeinAdult_CNhs12844_ctss_rev VeinAdult- vein, adult_CNhs12844_10191-103E2_reverse Regulation 
VeinAdult_CNhs12844_ctss_fwd VeinAdult+ vein, adult_CNhs12844_10191-103E2_forward Regulation 
VaginaAdult_CNhs12854_ctss_rev VaginaAdult- vagina, adult_CNhs12854_10204-103F6_reverse Regulation 
VaginaAdult_CNhs12854_ctss_fwd VaginaAdult+ vagina, adult_CNhs12854_10204-103F6_forward Regulation 
UterusFetalDonor1_CNhs11763_ctss_rev UterusFetalD1- uterus, fetal, donor1_CNhs11763_10055-101H1_reverse Regulation 
UterusFetalDonor1_CNhs11763_ctss_fwd UterusFetalD1+ uterus, fetal, donor1_CNhs11763_10055-101H1_forward Regulation 
UterusAdultPool1_CNhs11676_ctss_rev UterusAdultPl1- uterus, adult, pool1_CNhs11676_10100-102D1_reverse Regulation 
UterusAdultPool1_CNhs11676_ctss_fwd UterusAdultPl1+ uterus, adult, pool1_CNhs11676_10100-102D1_forward Regulation 
UrethraDonor2_CNhs13464_ctss_rev UrethraD2- Urethra, donor2_CNhs13464_10319-105A4_reverse Regulation 
UrethraDonor2_CNhs13464_ctss_fwd UrethraD2+ Urethra, donor2_CNhs13464_10319-105A4_forward Regulation 
UniversalRNAHumanNormalTissuesBiochainPool1_CNhs10612_ctss_rev UniversalRnaNormalTissuesBiochainPl1- Universal RNA - Human Normal Tissues Biochain, pool1_CNhs10612_10007-101B4_reverse Regulation 
UniversalRNAHumanNormalTissuesBiochainPool1_CNhs10612_ctss_fwd UniversalRnaNormalTissuesBiochainPl1+ Universal RNA - Human Normal Tissues Biochain, pool1_CNhs10612_10007-101B4_forward Regulation 
UmbilicalCordFetalDonor1_CNhs11765_ctss_rev UmbilicalCordFetalD1- umbilical cord, fetal, donor1_CNhs11765_10057-101H3_reverse Regulation 
UmbilicalCordFetalDonor1_CNhs11765_ctss_fwd UmbilicalCordFetalD1+ umbilical cord, fetal, donor1_CNhs11765_10057-101H3_forward Regulation 
TracheaFetalDonor1_CNhs11766_ctss_rev TracheaFetalD1- trachea, fetal, donor1_CNhs11766_10058-101H4_reverse Regulation 
TracheaFetalDonor1_CNhs11766_ctss_fwd TracheaFetalD1+ trachea, fetal, donor1_CNhs11766_10058-101H4_forward Regulation 
TracheaAdultPool1_CNhs10635_ctss_rev TracheaAdultPl1- trachea, adult, pool1_CNhs10635_10029-101E2_reverse Regulation 
TracheaAdultPool1_CNhs10635_ctss_fwd TracheaAdultPl1+ trachea, adult, pool1_CNhs10635_10029-101E2_forward Regulation 
TonsilAdultPool1_CNhs10654_ctss_rev TonsilAdultPl1- tonsil, adult, pool1_CNhs10654_10047-101G2_reverse Regulation 
TonsilAdultPool1_CNhs10654_ctss_fwd TonsilAdultPl1+ tonsil, adult, pool1_CNhs10654_10047-101G2_forward Regulation 
TongueFetalDonor1_CNhs11768_ctss_rev TongueFetalD1- tongue, fetal, donor1_CNhs11768_10059-101H5_reverse Regulation 
TongueFetalDonor1_CNhs11768_ctss_fwd TongueFetalD1+ tongue, fetal, donor1_CNhs11768_10059-101H5_forward Regulation 
TongueEpidermisFungiformPapillaeDonor1_CNhs13460_ctss_rev TongueEpidermisD1- tongue epidermis (fungiform papillae), donor1_CNhs13460_10288-104F9_reverse Regulation 
TongueEpidermisFungiformPapillaeDonor1_CNhs13460_ctss_fwd TongueEpidermisD1+ tongue epidermis (fungiform papillae), donor1_CNhs13460_10288-104F9_forward Regulation 
TongueAdult_CNhs12853_ctss_rev TongueAdult- tongue, adult_CNhs12853_10203-103F5_reverse Regulation 
TongueAdult_CNhs12853_ctss_fwd TongueAdult+ tongue, adult_CNhs12853_10203-103F5_forward Regulation 
ThyroidFetalDonor1_CNhs11769_ctss_rev ThyroidFetalD1- thyroid, fetal, donor1_CNhs11769_10060-101H6_reverse Regulation 
ThyroidFetalDonor1_CNhs11769_ctss_fwd ThyroidFetalD1+ thyroid, fetal, donor1_CNhs11769_10060-101H6_forward Regulation 
ThyroidAdultPool1_CNhs10634_ctss_rev ThyroidAdultPl1- thyroid, adult, pool1_CNhs10634_10028-101E1_reverse Regulation 
ThyroidAdultPool1_CNhs10634_ctss_fwd ThyroidAdultPl1+ thyroid, adult, pool1_CNhs10634_10028-101E1_forward Regulation 
ThymusFetalPool1_CNhs10650_ctss_rev ThymusFetalPl1- thymus, fetal, pool1_CNhs10650_10043-101F7_reverse Regulation 
ThymusFetalPool1_CNhs10650_ctss_fwd ThymusFetalPl1+ thymus, fetal, pool1_CNhs10650_10043-101F7_forward Regulation 
ThymusAdultPool1_CNhs10633_ctss_rev ThymusAdultPl1- thymus, adult, pool1_CNhs10633_10027-101D9_reverse Regulation 
ThymusAdultPool1_CNhs10633_ctss_fwd ThymusAdultPl1+ thymus, adult, pool1_CNhs10633_10027-101D9_forward Regulation 
ThroatFetalDonor1_CNhs11770_ctss_rev ThroatFetalD1- throat, fetal, donor1_CNhs11770_10061-101H7_reverse Regulation 
ThroatFetalDonor1_CNhs11770_ctss_fwd ThroatFetalD1+ throat, fetal, donor1_CNhs11770_10061-101H7_forward Regulation 
ThroatAdult_CNhs12858_ctss_rev ThroatAdult- throat, adult_CNhs12858_10209-103G2_reverse Regulation 
ThroatAdult_CNhs12858_ctss_fwd ThroatAdult+ throat, adult_CNhs12858_10209-103G2_forward Regulation 
ThalamusNewbornDonor10223_CNhs14084_ctss_rev ThalamusNbD10223- thalamus, newborn, donor10223_CNhs14084_10366-105F6_reverse Regulation 
ThalamusNewbornDonor10223_CNhs14084_ctss_fwd ThalamusNbD10223+ thalamus, newborn, donor10223_CNhs14084_10366-105F6_forward Regulation 
ThalamusAdultDonor10258TechRep2_CNhs14551_ctss_rev ThalamusAdultD10258Tr2- thalamus, adult, donor10258, tech_rep2_CNhs14551_10370-105G1_reverse Regulation 
ThalamusAdultDonor10258TechRep2_CNhs14551_ctss_fwd ThalamusAdultD10258Tr2+ thalamus, adult, donor10258, tech_rep2_CNhs14551_10370-105G1_forward Regulation 
ThalamusAdultDonor10258TechRep1_CNhs14223_ctss_rev ThalamusAdultD10258Tr1- thalamus, adult, donor10258, tech_rep1_CNhs14223_10370-105G1_reverse Regulation 
ThalamusAdultDonor10258TechRep1_CNhs14223_ctss_fwd ThalamusAdultD10258Tr1+ thalamus, adult, donor10258, tech_rep1_CNhs14223_10370-105G1_forward Regulation 
ThalamusAdultDonor10252_CNhs12314_ctss_rev ThalamusAdultD10252- thalamus, adult, donor10252_CNhs12314_10154-103A1_reverse Regulation 
ThalamusAdultDonor10252_CNhs12314_ctss_fwd ThalamusAdultD10252+ thalamus, adult, donor10252_CNhs12314_10154-103A1_forward Regulation 
ThalamusAdultDonor10196_CNhs13794_ctss_rev ThalamusAdultD10196- thalamus - adult, donor10196_CNhs13794_10168-103B6_reverse Regulation 
ThalamusAdultDonor10196_CNhs13794_ctss_fwd ThalamusAdultD10196+ thalamus - adult, donor10196_CNhs13794_10168-103B6_forward Regulation 
TestisAdultPool2_CNhs12998_ctss_rev TestisAdultPl2- testis, adult, pool2_CNhs12998_10096-102C6_reverse Regulation 
TestisAdultPool2_CNhs12998_ctss_fwd TestisAdultPl2+ testis, adult, pool2_CNhs12998_10096-102C6_forward Regulation 
TestisAdultPool1_CNhs10632_ctss_rev TestisAdultPl1- testis, adult, pool1_CNhs10632_10026-101D8_reverse Regulation 
TestisAdultPool1_CNhs10632_ctss_fwd TestisAdultPl1+ testis, adult, pool1_CNhs10632_10026-101D8_forward Regulation 
TemporalLobeFetalDonor1TechRep2_CNhs12996_ctss_rev TemporalLobeFetalD1Tr2- temporal lobe, fetal, donor1, tech_rep2_CNhs12996_10063-101H9_reverse Regulation 
TemporalLobeFetalDonor1TechRep2_CNhs12996_ctss_fwd TemporalLobeFetalD1Tr2+ temporal lobe, fetal, donor1, tech_rep2_CNhs12996_10063-101H9_forward Regulation 
TemporalLobeFetalDonor1TechRep1_CNhs11772_ctss_rev TemporalLobeFetalD1Tr1- temporal lobe, fetal, donor1, tech_rep1_CNhs11772_10063-101H9_reverse Regulation 
TemporalLobeFetalDonor1TechRep1_CNhs11772_ctss_fwd TemporalLobeFetalD1Tr1+ temporal lobe, fetal, donor1, tech_rep1_CNhs11772_10063-101H9_forward Regulation 
TemporalLobeAdultPool1_CNhs10637_ctss_rev TemporalLobeAdultPl1- temporal lobe, adult, pool1_CNhs10637_10031-101E4_reverse Regulation 
TemporalLobeAdultPool1_CNhs10637_ctss_fwd TemporalLobeAdultPl1+ temporal lobe, adult, pool1_CNhs10637_10031-101E4_forward Regulation 
SubstantiaNigraNewbornDonor10223_CNhs14076_ctss_rev SubstantiaNigraNbD10223- substantia nigra, newborn, donor10223_CNhs14076_10358-105E7_reverse Regulation 
SubstantiaNigraNewbornDonor10223_CNhs14076_ctss_fwd SubstantiaNigraNbD10223+ substantia nigra, newborn, donor10223_CNhs14076_10358-105E7_forward Regulation 
SubstantiaNigraAdultDonor10258_CNhs14224_ctss_rev SubstantiaNigraAdultD10258- substantia nigra, adult, donor10258_CNhs14224_10371-105G2_reverse Regulation 
SubstantiaNigraAdultDonor10258_CNhs14224_ctss_fwd SubstantiaNigraAdultD10258+ substantia nigra, adult, donor10258_CNhs14224_10371-105G2_forward Regulation 
SubstantiaNigraAdultDonor10252_CNhs12318_ctss_rev SubstantiaNigraAdultD10252- substantia nigra, adult, donor10252_CNhs12318_10158-103A5_reverse Regulation 
SubstantiaNigraAdultDonor10252_CNhs12318_ctss_fwd SubstantiaNigraAdultD10252+ substantia nigra, adult, donor10252_CNhs12318_10158-103A5_forward Regulation 
SubstantiaNigraAdultDonor10196_CNhs13803_ctss_rev SubstantiaNigraAdultD10196- substantia nigra - adult, donor10196_CNhs13803_10178-103C7_reverse Regulation 
SubstantiaNigraAdultDonor10196_CNhs13803_ctss_fwd SubstantiaNigraAdultD10196+ substantia nigra - adult, donor10196_CNhs13803_10178-103C7_forward Regulation 
SubmaxillaryGlandAdult_CNhs12852_ctss_rev SubmaxillaryGlandAdult- submaxillary gland, adult_CNhs12852_10202-103F4_reverse Regulation 
SubmaxillaryGlandAdult_CNhs12852_ctss_fwd SubmaxillaryGlandAdult+ submaxillary gland, adult_CNhs12852_10202-103F4_forward Regulation 
StomachFetalDonor1_CNhs11771_ctss_rev StomachFetalD1- stomach, fetal, donor1_CNhs11771_10062-101H8_reverse Regulation 
StomachFetalDonor1_CNhs11771_ctss_fwd StomachFetalD1+ stomach, fetal, donor1_CNhs11771_10062-101H8_forward Regulation 
SpleenFetalPool1_CNhs10651_ctss_rev SpleenFetalPl1- spleen, fetal, pool1_CNhs10651_10044-101F8_reverse Regulation 
SpleenFetalPool1_CNhs10651_ctss_fwd SpleenFetalPl1+ spleen, fetal, pool1_CNhs10651_10044-101F8_forward Regulation 
SpleenAdultPool1_CNhs10631_ctss_rev SpleenAdultPl1- spleen, adult, pool1_CNhs10631_10025-101D7_reverse Regulation 
SpleenAdultPool1_CNhs10631_ctss_fwd SpleenAdultPl1+ spleen, adult, pool1_CNhs10631_10025-101D7_forward Regulation 
SpinalCordNewbornDonor10223_CNhs14077_ctss_rev SpinalCordNbD10223- spinal cord, newborn, donor10223_CNhs14077_10359-105E8_reverse Regulation 
SpinalCordNewbornDonor10223_CNhs14077_ctss_fwd SpinalCordNbD10223+ spinal cord, newborn, donor10223_CNhs14077_10359-105E8_forward Regulation 
SpinalCordFetalDonor1_CNhs11764_ctss_rev SpinalCordFetalD1- spinal cord, fetal, donor1_CNhs11764_10056-101H2_reverse Regulation 
SpinalCordFetalDonor1_CNhs11764_ctss_fwd SpinalCordFetalD1+ spinal cord, fetal, donor1_CNhs11764_10056-101H2_forward Regulation 
SpinalCordAdultDonor10258_CNhs14222_ctss_rev SpinalCordAdultD10258- spinal cord, adult, donor10258_CNhs14222_10369-105F9_reverse Regulation 
SpinalCordAdultDonor10258_CNhs14222_ctss_fwd SpinalCordAdultD10258+ spinal cord, adult, donor10258_CNhs14222_10369-105F9_forward Regulation 
SpinalCordAdultDonor10252_CNhs12227_ctss_rev SpinalCordAdultD10252- spinal cord, adult, donor10252_CNhs12227_10159-103A6_reverse Regulation 
SpinalCordAdultDonor10252_CNhs12227_ctss_fwd SpinalCordAdultD10252+ spinal cord, adult, donor10252_CNhs12227_10159-103A6_forward Regulation 
SpinalCordAdultDonor10196_CNhs13807_ctss_rev SpinalCordAdultD10196- spinal cord - adult, donor10196_CNhs13807_10181-103D1_reverse Regulation 
SpinalCordAdultDonor10196_CNhs13807_ctss_fwd SpinalCordAdultD10196+ spinal cord - adult, donor10196_CNhs13807_10181-103D1_forward Regulation 
SmoothMuscleAdultPool1_CNhs11755_ctss_rev SmoothMuscleAdultPl1- smooth muscle, adult, pool1_CNhs11755_10048-101G3_reverse Regulation 
SmoothMuscleAdultPool1_CNhs11755_ctss_fwd SmoothMuscleAdultPl1+ smooth muscle, adult, pool1_CNhs11755_10048-101G3_forward Regulation 
SmallIntestineFetalDonor1_CNhs11773_ctss_rev SmallIntestineFetalD1- small intestine, fetal, donor1_CNhs11773_10064-101I1_reverse Regulation 
SmallIntestineFetalDonor1_CNhs11773_ctss_fwd SmallIntestineFetalD1+ small intestine, fetal, donor1_CNhs11773_10064-101I1_forward Regulation 
SmallIntestineAdultPool1_CNhs10630_ctss_rev SmallIntestineAdultPl1- small intestine, adult, pool1_CNhs10630_10024-101D6_reverse Regulation 
SmallIntestineAdultPool1_CNhs10630_ctss_fwd SmallIntestineAdultPl1+ small intestine, adult, pool1_CNhs10630_10024-101D6_forward Regulation 
SkinPalmDonor1_CNhs13458_ctss_rev SkinPalmD1- Skin - palm, donor1_CNhs13458_10286-104F7_reverse Regulation 
SkinPalmDonor1_CNhs13458_ctss_fwd SkinPalmD1+ Skin - palm, donor1_CNhs13458_10286-104F7_forward Regulation 
SkinFetalDonor1_CNhs11774_ctss_rev SkinFetalD1- skin, fetal, donor1_CNhs11774_10065-101I2_reverse Regulation 
SkinFetalDonor1_CNhs11774_ctss_fwd SkinFetalD1+ skin, fetal, donor1_CNhs11774_10065-101I2_forward Regulation 
SkinAdultDonor1_CNhs11785_ctss_rev SkinAdultD1- skin, adult, donor1_CNhs11785_10074-102A2_reverse Regulation 
SkinAdultDonor1_CNhs11785_ctss_fwd SkinAdultD1+ skin, adult, donor1_CNhs11785_10074-102A2_forward Regulation 
SkeletalMuscleSoleusMuscleDonor1_CNhs13454_ctss_rev SkeletalMuscleSoleusMuscleD1- skeletal muscle - soleus muscle, donor1_CNhs13454_10282-104F3_reverse Regulation 
SkeletalMuscleSoleusMuscleDonor1_CNhs13454_ctss_fwd SkeletalMuscleSoleusMuscleD1+ skeletal muscle - soleus muscle, donor1_CNhs13454_10282-104F3_forward Regulation 
SkeletalMuscleFetalDonor1_CNhs11776_ctss_rev SkeletalMuscleFetalD1- skeletal muscle, fetal, donor1_CNhs11776_10066-101I3_reverse Regulation 
SkeletalMuscleFetalDonor1_CNhs11776_ctss_fwd SkeletalMuscleFetalD1+ skeletal muscle, fetal, donor1_CNhs11776_10066-101I3_forward Regulation 
SkeletalMuscleAdultPool1_CNhs10629_ctss_rev SkeletalMuscleAdultPl1- skeletal muscle, adult, pool1_CNhs10629_10023-101D5_reverse Regulation 
SkeletalMuscleAdultPool1_CNhs10629_ctss_fwd SkeletalMuscleAdultPl1+ skeletal muscle, adult, pool1_CNhs10629_10023-101D5_forward Regulation 
SeminalVesicleAdult_CNhs12851_ctss_rev SeminalVesicleAdult- seminal vesicle, adult_CNhs12851_10201-103F3_reverse Regulation 
SeminalVesicleAdult_CNhs12851_ctss_fwd SeminalVesicleAdult+ seminal vesicle, adult_CNhs12851_10201-103F3_forward Regulation 
SalivaryGlandAdultPool1_CNhs11677_ctss_rev SalivaryGlandAdultPl1- salivary gland, adult, pool1_CNhs11677_10093-102C3_reverse Regulation 
SalivaryGlandAdultPool1_CNhs11677_ctss_fwd SalivaryGlandAdultPl1+ salivary gland, adult, pool1_CNhs11677_10093-102C3_forward Regulation 
SABiosciencesXpressRefHumanUniversalTotalRNAPool1_CNhs10610_ctss_rev SabiosciencesXpressrefUniversalPl1- SABiosciences XpressRef Human Universal Total RNA, pool1_CNhs10610_10002-101A5_reverse Regulation 
SABiosciencesXpressRefHumanUniversalTotalRNAPool1_CNhs10610_ctss_fwd SabiosciencesXpressrefUniversalPl1+ SABiosciences XpressRef Human Universal Total RNA, pool1_CNhs10610_10002-101A5_forward Regulation 
RetinaAdultPool1_CNhs10636_ctss_rev RetinaAdultPl1- retina, adult, pool1_CNhs10636_10030-101E3_reverse Regulation 
RetinaAdultPool1_CNhs10636_ctss_fwd RetinaAdultPl1+ retina, adult, pool1_CNhs10636_10030-101E3_forward Regulation 
RectumFetalDonor1_CNhs11777_ctss_rev RectumFetalD1- rectum, fetal, donor1_CNhs11777_10067-101I4_reverse Regulation 
RectumFetalDonor1_CNhs11777_ctss_fwd RectumFetalD1+ rectum, fetal, donor1_CNhs11777_10067-101I4_forward Regulation 
PutamenNewbornDonor10223_CNhs14083_ctss_rev PutamenNbD10223- putamen, newborn, donor10223_CNhs14083_10365-105F5_reverse Regulation 
PutamenNewbornDonor10223_CNhs14083_ctss_fwd PutamenNbD10223+ putamen, newborn, donor10223_CNhs14083_10365-105F5_forward Regulation 
PutamenAdultDonor10258TechRep2_CNhs14618_ctss_rev PutamenAdultD10258Tr2- putamen, adult, donor10258, tech_rep2_CNhs14618_10372-105G3_reverse Regulation 
PutamenAdultDonor10258TechRep2_CNhs14618_ctss_fwd PutamenAdultD10258Tr2+ putamen, adult, donor10258, tech_rep2_CNhs14618_10372-105G3_forward Regulation 
PutamenAdultDonor10258TechRep1_CNhs14225_ctss_rev PutamenAdultD10258Tr1- putamen, adult, donor10258, tech_rep1_CNhs14225_10372-105G3_reverse Regulation 
PutamenAdultDonor10258TechRep1_CNhs14225_ctss_fwd PutamenAdultD10258Tr1+ putamen, adult, donor10258, tech_rep1_CNhs14225_10372-105G3_forward Regulation 
PutamenAdultDonor10252_CNhs13912_ctss_rev PutamenAdultD10252- putamen, adult, donor10252_CNhs13912_10152-102I8_reverse Regulation 
PutamenAdultDonor10252_CNhs13912_ctss_fwd PutamenAdultD10252+ putamen, adult, donor10252_CNhs13912_10152-102I8_forward Regulation 
PutamenAdultDonor10196_CNhs12324_ctss_rev PutamenAdultD10196- putamen, adult, donor10196_CNhs12324_10176-103C5_reverse Regulation 
PutamenAdultDonor10196_CNhs12324_ctss_fwd PutamenAdultD10196+ putamen, adult, donor10196_CNhs12324_10176-103C5_forward Regulation 
ProstateAdultPool1_CNhs10628_ctss_rev ProstateAdultPl1- prostate, adult, pool1_CNhs10628_10022-101D4_reverse Regulation 
ProstateAdultPool1_CNhs10628_ctss_fwd ProstateAdultPl1+ prostate, adult, pool1_CNhs10628_10022-101D4_forward Regulation 
PostcentralGyrusAdultPool1_CNhs10638_ctss_rev PostcentralGyrusAdultPl1- postcentral gyrus, adult, pool1_CNhs10638_10032-101E5_reverse Regulation 
PostcentralGyrusAdultPool1_CNhs10638_ctss_fwd PostcentralGyrusAdultPl1+ postcentral gyrus, adult, pool1_CNhs10638_10032-101E5_forward Regulation 
PonsAdultPool1_CNhs10640_ctss_rev PonsAdultPl1- pons, adult, pool1_CNhs10640_10033-101E6_reverse Regulation 
PonsAdultPool1_CNhs10640_ctss_fwd PonsAdultPl1+ pons, adult, pool1_CNhs10640_10033-101E6_forward Regulation 
PlacentaAdultPool1_CNhs10627_ctss_rev PlacentaAdultPl1- placenta, adult, pool1_CNhs10627_10021-101D3_reverse Regulation 
PlacentaAdultPool1_CNhs10627_ctss_fwd PlacentaAdultPl1+ placenta, adult, pool1_CNhs10627_10021-101D3_forward Regulation 
PituitaryGlandAdultDonor10258_CNhs14231_ctss_rev PituitaryGlandAdultD10258- pituitary gland, adult, donor10258_CNhs14231_10378-105G9_reverse Regulation 
PituitaryGlandAdultDonor10258_CNhs14231_ctss_fwd PituitaryGlandAdultD10258+ pituitary gland, adult, donor10258_CNhs14231_10378-105G9_forward Regulation 
PituitaryGlandAdultDonor10252_CNhs12229_ctss_rev PituitaryGlandAdultD10252- pituitary gland, adult, donor10252_CNhs12229_10162-103A9_reverse Regulation 
PituitaryGlandAdultDonor10252_CNhs12229_ctss_fwd PituitaryGlandAdultD10252+ pituitary gland, adult, donor10252_CNhs12229_10162-103A9_forward Regulation 
PituitaryGlandAdultDonor10196_CNhs13805_ctss_rev PituitaryGlandAdultD10196- pituitary gland - adult, donor10196_CNhs13805_10180-103C9_reverse Regulation 
PituitaryGlandAdultDonor10196_CNhs13805_ctss_fwd PituitaryGlandAdultD10196+ pituitary gland - adult, donor10196_CNhs13805_10180-103C9_forward Regulation 
PinealGlandAdultDonor10258_CNhs14230_ctss_rev PinealGlandAdultD10258- pineal gland, adult, donor10258_CNhs14230_10377-105G8_reverse Regulation 
PinealGlandAdultDonor10258_CNhs14230_ctss_fwd PinealGlandAdultD10258+ pineal gland, adult, donor10258_CNhs14230_10377-105G8_forward Regulation 
PinealGlandAdultDonor10252_CNhs12228_ctss_rev PinealGlandAdultD10252- pineal gland, adult, donor10252_CNhs12228_10160-103A7_reverse Regulation 
PinealGlandAdultDonor10252_CNhs12228_ctss_fwd PinealGlandAdultD10252+ pineal gland, adult, donor10252_CNhs12228_10160-103A7_forward Regulation 
PinealGlandAdultDonor10196_CNhs13804_ctss_rev PinealGlandAdultD10196- pineal gland - adult, donor10196_CNhs13804_10179-103C8_reverse Regulation 
PinealGlandAdultDonor10196_CNhs13804_ctss_fwd PinealGlandAdultD10196+ pineal gland - adult, donor10196_CNhs13804_10179-103C8_forward Regulation 
PenisAdult_CNhs12850_ctss_rev PenisAdult- penis, adult_CNhs12850_10200-103F2_reverse Regulation 
PenisAdult_CNhs12850_ctss_fwd PenisAdult+ penis, adult_CNhs12850_10200-103F2_forward Regulation 
ParotidGlandAdult_CNhs12849_ctss_rev ParotidGlandAdult- parotid gland, adult_CNhs12849_10199-103F1_reverse Regulation 
ParotidGlandAdult_CNhs12849_ctss_fwd ParotidGlandAdult+ parotid gland, adult_CNhs12849_10199-103F1_forward Regulation 
ParietalLobeNewbornDonor10223_CNhs14074_ctss_rev ParietalLobeNbD10223- parietal lobe, newborn, donor10223_CNhs14074_10356-105E5_reverse Regulation 
ParietalLobeNewbornDonor10223_CNhs14074_ctss_fwd ParietalLobeNbD10223+ parietal lobe, newborn, donor10223_CNhs14074_10356-105E5_forward Regulation 
ParietalLobeFetalDonor1_CNhs11782_ctss_rev ParietalLobeFetalD1- parietal lobe, fetal, donor1_CNhs11782_10072-101I9_reverse Regulation 
ParietalLobeFetalDonor1_CNhs11782_ctss_fwd ParietalLobeFetalD1+ parietal lobe, fetal, donor1_CNhs11782_10072-101I9_forward Regulation 
ParietalLobeAdultPool1_CNhs10641_ctss_rev ParietalLobeAdultPl1- parietal lobe, adult, pool1_CNhs10641_10034-101E7_reverse Regulation 
ParietalLobeAdultPool1_CNhs10641_ctss_fwd ParietalLobeAdultPl1+ parietal lobe, adult, pool1_CNhs10641_10034-101E7_forward Regulation 
ParietalLobeAdultDonor10252_CNhs12317_ctss_rev ParietalLobeAdultD10252- parietal lobe, adult, donor10252_CNhs12317_10157-103A4_reverse Regulation 
ParietalLobeAdultDonor10252_CNhs12317_ctss_fwd ParietalLobeAdultD10252+ parietal lobe, adult, donor10252_CNhs12317_10157-103A4_forward Regulation 
ParietalLobeAdultDonor10196_CNhs13797_ctss_rev ParietalLobeAdultD10196- parietal lobe - adult, donor10196_CNhs13797_10171-103B9_reverse Regulation 
ParietalLobeAdultDonor10196_CNhs13797_ctss_fwd ParietalLobeAdultD10196+ parietal lobe - adult, donor10196_CNhs13797_10171-103B9_forward Regulation 
ParietalCortexAdultDonor10258_CNhs14226_ctss_rev ParietalCortexAdultD10258- parietal cortex, adult, donor10258_CNhs14226_10373-105G4_reverse Regulation 
ParietalCortexAdultDonor10258_CNhs14226_ctss_fwd ParietalCortexAdultD10258+ parietal cortex, adult, donor10258_CNhs14226_10373-105G4_forward Regulation 
ParacentralGyrusAdultPool1_CNhs10642_ctss_rev ParacentralGyrusAdultPl1- paracentral gyrus, adult, pool1_CNhs10642_10035-101E8_reverse Regulation 
ParacentralGyrusAdultPool1_CNhs10642_ctss_fwd ParacentralGyrusAdultPl1+ paracentral gyrus, adult, pool1_CNhs10642_10035-101E8_forward Regulation 
PancreasAdultDonor1_CNhs11756_ctss_rev PancreasAdultD1- pancreas, adult, donor1_CNhs11756_10049-101G4_reverse Regulation 
PancreasAdultDonor1_CNhs11756_ctss_fwd PancreasAdultD1+ pancreas, adult, donor1_CNhs11756_10049-101G4_forward Regulation 
OvaryAdultPool1_CNhs10626_ctss_rev OvaryAdultPl1- ovary, adult, pool1_CNhs10626_10020-101D2_reverse Regulation 
OvaryAdultPool1_CNhs10626_ctss_fwd OvaryAdultPl1+ ovary, adult, pool1_CNhs10626_10020-101D2_forward Regulation 
OpticNerveDonor1_CNhs13449_ctss_rev OpticNerveD1- optic nerve, donor1_CNhs13449_10277-104E7_reverse Regulation 
OpticNerveDonor1_CNhs13449_ctss_fwd OpticNerveD1+ optic nerve, donor1_CNhs13449_10277-104E7_forward Regulation 
OlfactoryRegionAdult_CNhs12611_ctss_rev OlfactoryRegionAdult- olfactory region, adult_CNhs12611_10195-103E6_reverse Regulation 
OlfactoryRegionAdult_CNhs12611_ctss_fwd OlfactoryRegionAdult+ olfactory region, adult_CNhs12611_10195-103E6_forward Regulation 
OccipitalPoleAdultPool1_CNhs10643_ctss_rev OccipitalPoleAdultPl1- occipital pole, adult, pool1_CNhs10643_10036-101E9_reverse Regulation 
OccipitalPoleAdultPool1_CNhs10643_ctss_fwd OccipitalPoleAdultPl1+ occipital pole, adult, pool1_CNhs10643_10036-101E9_forward Regulation 
OccipitalLobeFetalDonor1_CNhs11784_ctss_rev OccipitalLobeFetalD1- occipital lobe, fetal, donor1_CNhs11784_10073-102A1_reverse Regulation 
OccipitalLobeFetalDonor1_CNhs11784_ctss_fwd OccipitalLobeFetalD1+ occipital lobe, fetal, donor1_CNhs11784_10073-102A1_forward Regulation 
OccipitalLobeAdultDonor1_CNhs11787_ctss_rev OccipitalLobeAdultD1- occipital lobe, adult, donor1_CNhs11787_10076-102A4_reverse Regulation 
OccipitalLobeAdultDonor1_CNhs11787_ctss_fwd OccipitalLobeAdultD1+ occipital lobe, adult, donor1_CNhs11787_10076-102A4_forward Regulation 
OccipitalCortexNewbornDonor10223_CNhs14073_ctss_rev OccipitalCortexNbD10223- occipital cortex, newborn, donor10223_CNhs14073_10355-105E4_reverse Regulation 
OccipitalCortexNewbornDonor10223_CNhs14073_ctss_fwd OccipitalCortexNbD10223+ occipital cortex, newborn, donor10223_CNhs14073_10355-105E4_forward Regulation 
OccipitalCortexAdultDonor10252_CNhs12320_ctss_rev OccipitalCortexAdultD10252- occipital cortex, adult, donor10252_CNhs12320_10163-103B1_reverse Regulation 
OccipitalCortexAdultDonor10252_CNhs12320_ctss_fwd OccipitalCortexAdultD10252+ occipital cortex, adult, donor10252_CNhs12320_10163-103B1_forward Regulation 
OccipitalCortexAdultDonor10196_CNhs13798_ctss_rev OccipitalCortexAdultD10196- occipital cortex - adult, donor10196_CNhs13798_10172-103C1_reverse Regulation 
OccipitalCortexAdultDonor10196_CNhs13798_ctss_fwd OccipitalCortexAdultD10196+ occipital cortex - adult, donor10196_CNhs13798_10172-103C1_forward Regulation 
NucleusAccumbensAdultPool1_CNhs10644_ctss_rev NucleusAccumbensAdultPl1- nucleus accumbens, adult, pool1_CNhs10644_10037-101F1_reverse Regulation 
NucleusAccumbensAdultPool1_CNhs10644_ctss_fwd NucleusAccumbensAdultPl1+ nucleus accumbens, adult, pool1_CNhs10644_10037-101F1_forward Regulation 
MedullaOblongataNewbornDonor10223_CNhs14079_ctss_rev MedullaOblongataNbD10223- medulla oblongata, newborn, donor10223_CNhs14079_10361-105F1_reverse Regulation 
MedullaOblongataNewbornDonor10223_CNhs14079_ctss_fwd MedullaOblongataNbD10223+ medulla oblongata, newborn, donor10223_CNhs14079_10361-105F1_forward Regulation 
MedullaOblongataAdultPool1_CNhs10645_ctss_rev MedullaOblongataAdultPl1- medulla oblongata, adult, pool1_CNhs10645_10038-101F2_reverse Regulation 
MedullaOblongataAdultPool1_CNhs10645_ctss_fwd MedullaOblongataAdultPl1+ medulla oblongata, adult, pool1_CNhs10645_10038-101F2_forward Regulation 
MedullaOblongataAdultDonor10252_CNhs12315_ctss_rev MedullaOblongataAdultD10252- medulla oblongata, adult, donor10252_CNhs12315_10155-103A2_reverse Regulation 
MedullaOblongataAdultDonor10252_CNhs12315_ctss_fwd MedullaOblongataAdultD10252+ medulla oblongata, adult, donor10252_CNhs12315_10155-103A2_forward Regulation 
MedullaOblongataAdultDonor10196_CNhs13800_ctss_rev MedullaOblongataAdultD10196- medulla oblongata - adult, donor10196_CNhs13800_10174-103C3_reverse Regulation 
MedullaOblongataAdultDonor10196_CNhs13800_ctss_fwd MedullaOblongataAdultD10196+ medulla oblongata - adult, donor10196_CNhs13800_10174-103C3_forward Regulation 
MedialTemporalGyrusNewbornDonor10223_CNhs14070_ctss_rev MedialTemporalGyrusNbD10223- medial temporal gyrus, newborn, donor10223_CNhs14070_10353-105E2_reverse Regulation 
MedialTemporalGyrusNewbornDonor10223_CNhs14070_ctss_fwd MedialTemporalGyrusNbD10223+ medial temporal gyrus, newborn, donor10223_CNhs14070_10353-105E2_forward Regulation 
MedialTemporalGyrusAdultDonor10258TechRep2_CNhs14552_ctss_rev MedialTemporalGyrusAdultD10258Tr2- medial temporal gyrus, adult, donor10258, tech_rep2_CNhs14552_10376-105G7_reverse Regulation 
MedialTemporalGyrusAdultDonor10258TechRep2_CNhs14552_ctss_fwd MedialTemporalGyrusAdultD10258Tr2+ medial temporal gyrus, adult, donor10258, tech_rep2_CNhs14552_10376-105G7_forward Regulation 
MedialTemporalGyrusAdultDonor10258TechRep1_CNhs14229_ctss_rev MedialTemporalGyrusAdultD10258Tr1- medial temporal gyrus, adult, donor10258, tech_rep1_CNhs14229_10376-105G7_reverse Regulation 
MedialTemporalGyrusAdultDonor10258TechRep1_CNhs14229_ctss_fwd MedialTemporalGyrusAdultD10258Tr1+ medial temporal gyrus, adult, donor10258, tech_rep1_CNhs14229_10376-105G7_forward Regulation 
MedialTemporalGyrusAdultDonor10252_CNhs12316_ctss_rev MedialTemporalGyrusAdultD10252- medial temporal gyrus, adult, donor10252_CNhs12316_10156-103A3_reverse Regulation 
MedialTemporalGyrusAdultDonor10252_CNhs12316_ctss_fwd MedialTemporalGyrusAdultD10252+ medial temporal gyrus, adult, donor10252_CNhs12316_10156-103A3_forward Regulation 
MedialTemporalGyrusAdultDonor10196_CNhs13809_ctss_rev MedialTemporalGyrusAdultD10196- medial temporal gyrus - adult, donor10196_CNhs13809_10183-103D3_reverse Regulation 
MedialTemporalGyrusAdultDonor10196_CNhs13809_ctss_fwd MedialTemporalGyrusAdultD10196+ medial temporal gyrus - adult, donor10196_CNhs13809_10183-103D3_forward Regulation 
MedialFrontalGyrusNewbornDonor10223_CNhs14069_ctss_rev MedialFrontalGyrusNbD10223- medial frontal gyrus, newborn, donor10223_CNhs14069_10352-105E1_reverse Regulation 
MedialFrontalGyrusNewbornDonor10223_CNhs14069_ctss_fwd MedialFrontalGyrusNbD10223+ medial frontal gyrus, newborn, donor10223_CNhs14069_10352-105E1_forward Regulation 
MedialFrontalGyrusAdultDonor10258_CNhs14221_ctss_rev MedialFrontalGyrusAdultD10258- medial frontal gyrus, adult, donor10258_CNhs14221_10368-105F8_reverse Regulation 
MedialFrontalGyrusAdultDonor10258_CNhs14221_ctss_fwd MedialFrontalGyrusAdultD10258+ medial frontal gyrus, adult, donor10258_CNhs14221_10368-105F8_forward Regulation 
MedialFrontalGyrusAdultDonor10252_CNhs12310_ctss_rev MedialFrontalGyrusAdultD10252- medial frontal gyrus, adult, donor10252_CNhs12310_10150-102I6_reverse Regulation 
MedialFrontalGyrusAdultDonor10252_CNhs12310_ctss_fwd MedialFrontalGyrusAdultD10252+ medial frontal gyrus, adult, donor10252_CNhs12310_10150-102I6_forward Regulation 
MedialFrontalGyrusAdultDonor10196_CNhs13796_ctss_rev MedialFrontalGyrusAdultD10196- medial frontal gyrus - adult, donor10196_CNhs13796_10170-103B8_reverse Regulation 
MedialFrontalGyrusAdultDonor10196_CNhs13796_ctss_fwd MedialFrontalGyrusAdultD10196+ medial frontal gyrus - adult, donor10196_CNhs13796_10170-103B8_forward Regulation 
LymphNodeAdultDonor1_CNhs11788_ctss_rev LymphNodeAdultD1- lymph node, adult, donor1_CNhs11788_10077-102A5_reverse Regulation 
LymphNodeAdultDonor1_CNhs11788_ctss_fwd LymphNodeAdultD1+ lymph node, adult, donor1_CNhs11788_10077-102A5_forward Regulation 
LungRightLowerLobeAdultDonor1_CNhs11786_ctss_rev LungRightLowerLobeAdultD1- lung, right lower lobe, adult, donor1_CNhs11786_10075-102A3_reverse Regulation 
LungRightLowerLobeAdultDonor1_CNhs11786_ctss_fwd LungRightLowerLobeAdultD1+ lung, right lower lobe, adult, donor1_CNhs11786_10075-102A3_forward Regulation 
LungFetalDonor1_CNhs11680_ctss_rev LungFetalD1- lung, fetal, donor1_CNhs11680_10068-101I5_reverse Regulation 
LungFetalDonor1_CNhs11680_ctss_fwd LungFetalD1+ lung, fetal, donor1_CNhs11680_10068-101I5_forward Regulation 
LungAdultPool1_CNhs10625_ctss_rev LungAdultPl1- lung, adult, pool1_CNhs10625_10019-101D1_reverse Regulation 
LungAdultPool1_CNhs10625_ctss_fwd LungAdultPl1+ lung, adult, pool1_CNhs10625_10019-101D1_forward Regulation 
LocusCoeruleusNewbornDonor10223_CNhs14080_ctss_rev LocusCoeruleusNbD10223- locus coeruleus, newborn, donor10223_CNhs14080_10362-105F2_reverse Regulation 
LocusCoeruleusNewbornDonor10223_CNhs14080_ctss_fwd LocusCoeruleusNbD10223+ locus coeruleus, newborn, donor10223_CNhs14080_10362-105F2_forward Regulation 
LocusCoeruleusAdultDonor10258_CNhs14550_ctss_rev LocusCoeruleusAdultD10258- locus coeruleus, adult, donor10258_CNhs14550_10375-105G6_reverse Regulation 
LocusCoeruleusAdultDonor10258_CNhs14550_ctss_fwd LocusCoeruleusAdultD10258+ locus coeruleus, adult, donor10258_CNhs14550_10375-105G6_forward Regulation 
LocusCoeruleusAdultDonor10252_CNhs12322_ctss_rev LocusCoeruleusAdultD10252- locus coeruleus, adult, donor10252_CNhs12322_10165-103B3_reverse Regulation 
LocusCoeruleusAdultDonor10252_CNhs12322_ctss_fwd LocusCoeruleusAdultD10252+ locus coeruleus, adult, donor10252_CNhs12322_10165-103B3_forward Regulation 
LocusCoeruleusAdultDonor10196_CNhs13808_ctss_rev LocusCoeruleusAdultD10196- locus coeruleus - adult, donor10196_CNhs13808_10182-103D2_reverse Regulation 
LocusCoeruleusAdultDonor10196_CNhs13808_ctss_fwd LocusCoeruleusAdultD10196+ locus coeruleus - adult, donor10196_CNhs13808_10182-103D2_forward Regulation 
LiverFetalPool1_CNhs11798_ctss_rev LiverFetalPl1- liver, fetal, pool1_CNhs11798_10086-102B5_reverse Regulation 
LiverFetalPool1_CNhs11798_ctss_fwd LiverFetalPl1+ liver, fetal, pool1_CNhs11798_10086-102B5_forward Regulation 
LiverAdultPool1_CNhs10624_ctss_rev LiverAdultPl1- liver, adult, pool1_CNhs10624_10018-101C9_reverse Regulation 
LiverAdultPool1_CNhs10624_ctss_fwd LiverAdultPl1+ liver, adult, pool1_CNhs10624_10018-101C9_forward Regulation 
LeftVentricleAdultDonor1_CNhs11789_ctss_rev LeftVentricleAdultD1- left ventricle, adult, donor1_CNhs11789_10078-102A6_reverse Regulation 
LeftVentricleAdultDonor1_CNhs11789_ctss_fwd LeftVentricleAdultD1+ left ventricle, adult, donor1_CNhs11789_10078-102A6_forward Regulation 
LeftAtriumAdultDonor1_CNhs11790_ctss_rev LeftAtriumAdultD1- left atrium, adult, donor1_CNhs11790_10079-102A7_reverse Regulation 
LeftAtriumAdultDonor1_CNhs11790_ctss_fwd LeftAtriumAdultD1+ left atrium, adult, donor1_CNhs11790_10079-102A7_forward Regulation 
KidneyFetalPool1_CNhs10652_ctss_rev KidneyFetalPl1- kidney, fetal, pool1_CNhs10652_10045-101F9_reverse Regulation 
KidneyFetalPool1_CNhs10652_ctss_fwd KidneyFetalPl1+ kidney, fetal, pool1_CNhs10652_10045-101F9_forward Regulation 
KidneyAdultPool1_CNhs10622_ctss_rev KidneyAdultPl1- kidney, adult, pool1_CNhs10622_10017-101C8_reverse Regulation 
KidneyAdultPool1_CNhs10622_ctss_fwd KidneyAdultPl1+ kidney, adult, pool1_CNhs10622_10017-101C8_forward Regulation 
InsulaAdultPool1_CNhs10646_ctss_rev InsulaAdultPl1- insula, adult, pool1_CNhs10646_10039-101F3_reverse Regulation 
InsulaAdultPool1_CNhs10646_ctss_fwd InsulaAdultPl1+ insula, adult, pool1_CNhs10646_10039-101F3_forward Regulation 
HippocampusNewbornDonor10223_CNhs14081_ctss_rev HippocampusNbD10223- hippocampus, newborn, donor10223_CNhs14081_10363-105F3_reverse Regulation 
HippocampusNewbornDonor10223_CNhs14081_ctss_fwd HippocampusNbD10223+ hippocampus, newborn, donor10223_CNhs14081_10363-105F3_forward Regulation 
HippocampusAdultDonor10258_CNhs14227_ctss_rev HippocampusAdultD10258- hippocampus, adult, donor10258_CNhs14227_10374-105G5_reverse Regulation 
HippocampusAdultDonor10258_CNhs14227_ctss_fwd HippocampusAdultD10258+ hippocampus, adult, donor10258_CNhs14227_10374-105G5_forward Regulation 
HippocampusAdultDonor10252_CNhs12312_ctss_rev HippocampusAdultD10252- hippocampus, adult, donor10252_CNhs12312_10153-102I9_reverse Regulation 
HippocampusAdultDonor10252_CNhs12312_ctss_fwd HippocampusAdultD10252+ hippocampus, adult, donor10252_CNhs12312_10153-102I9_forward Regulation 
HippocampusAdultDonor10196_CNhs13795_ctss_rev HippocampusAdultD10196- hippocampus - adult, donor10196_CNhs13795_10169-103B7_reverse Regulation 
HippocampusAdultDonor10196_CNhs13795_ctss_fwd HippocampusAdultD10196+ hippocampus - adult, donor10196_CNhs13795_10169-103B7_forward Regulation 
HeartTricuspidValveAdult_CNhs12857_ctss_rev HeartTricuspidValveAdult- heart - tricuspid valve, adult_CNhs12857_10207-103F9_reverse Regulation 
HeartTricuspidValveAdult_CNhs12857_ctss_fwd HeartTricuspidValveAdult+ heart - tricuspid valve, adult_CNhs12857_10207-103F9_forward Regulation 
HeartPulmonicValveAdult_CNhs12856_ctss_rev HeartPulmonicValveAdult- heart - pulmonic valve, adult_CNhs12856_10206-103F8_reverse Regulation 
HeartPulmonicValveAdult_CNhs12856_ctss_fwd HeartPulmonicValveAdult+ heart - pulmonic valve, adult_CNhs12856_10206-103F8_forward Regulation 
HeartMitralValveAdult_CNhs12855_ctss_rev HeartMitralValveAdult- heart - mitral valve, adult_CNhs12855_10205-103F7_reverse Regulation 
HeartMitralValveAdult_CNhs12855_ctss_fwd HeartMitralValveAdult+ heart - mitral valve, adult_CNhs12855_10205-103F7_forward Regulation 
HeartFetalPool1_CNhs10653_ctss_rev HeartFetalPl1- heart, fetal, pool1_CNhs10653_10046-101G1_reverse Regulation 
HeartFetalPool1_CNhs10653_ctss_fwd HeartFetalPl1+ heart, fetal, pool1_CNhs10653_10046-101G1_forward Regulation 
HeartAdultPool1_CNhs10621_ctss_rev HeartAdultPl1- heart, adult, pool1_CNhs10621_10016-101C7_reverse Regulation 
HeartAdultPool1_CNhs10621_ctss_fwd HeartAdultPl1+ heart, adult, pool1_CNhs10621_10016-101C7_forward Regulation 
HeartAdultDiseasedPostinfarctionDonor1_CNhs11757_ctss_rev HeartAdultDiseasedPost-infarctionD1- heart, adult, diseased post-infarction, donor1_CNhs11757_10050-101G5_reverse Regulation 
HeartAdultDiseasedPostinfarctionDonor1_CNhs11757_ctss_fwd HeartAdultDiseasedPost-infarctionD1+ heart, adult, diseased post-infarction, donor1_CNhs11757_10050-101G5_forward Regulation 
HeartAdultDiseasedDonor1_CNhs11758_ctss_rev HeartAdultDiseasedD1- heart, adult, diseased, donor1_CNhs11758_10051-101G6_reverse Regulation 
HeartAdultDiseasedDonor1_CNhs11758_ctss_fwd HeartAdultDiseasedD1+ heart, adult, diseased, donor1_CNhs11758_10051-101G6_forward Regulation 
GlobusPallidusNewbornDonor10223_CNhs14082_ctss_rev GlobusPallidusNbD10223- globus pallidus, newborn, donor10223_CNhs14082_10364-105F4_reverse Regulation 
GlobusPallidusNewbornDonor10223_CNhs14082_ctss_fwd GlobusPallidusNbD10223+ globus pallidus, newborn, donor10223_CNhs14082_10364-105F4_forward Regulation 
GlobusPallidusAdultDonor10258_CNhs14549_ctss_rev GlobusPallidusAdultD10258- globus pallidus, adult, donor10258_CNhs14549_10367-105F7_reverse Regulation 
GlobusPallidusAdultDonor10258_CNhs14549_ctss_fwd GlobusPallidusAdultD10258+ globus pallidus, adult, donor10258_CNhs14549_10367-105F7_forward Regulation 
GlobusPallidusAdultDonor10252_CNhs12319_ctss_rev GlobusPallidusAdultD10252- globus pallidus, adult, donor10252_CNhs12319_10161-103A8_reverse Regulation 
GlobusPallidusAdultDonor10252_CNhs12319_ctss_fwd GlobusPallidusAdultD10252+ globus pallidus, adult, donor10252_CNhs12319_10161-103A8_forward Regulation 
GlobusPallidusAdultDonor10196_CNhs13801_ctss_rev GlobusPallidusAdultD10196- globus pallidus - adult, donor10196_CNhs13801_10175-103C4_reverse Regulation 
GlobusPallidusAdultDonor10196_CNhs13801_ctss_fwd GlobusPallidusAdultD10196+ globus pallidus - adult, donor10196_CNhs13801_10175-103C4_forward Regulation 
GallBladderAdult_CNhs12848_ctss_rev GallBladderAdult- gall bladder, adult_CNhs12848_10198-103E9_reverse Regulation 
GallBladderAdult_CNhs12848_ctss_fwd GallBladderAdult+ gall bladder, adult_CNhs12848_10198-103E9_forward Regulation 
FrontalLobeAdultPool1_CNhs10647_ctss_rev FrontalLobeAdultPl1- frontal lobe, adult, pool1_CNhs10647_10040-101F4_reverse Regulation 
FrontalLobeAdultPool1_CNhs10647_ctss_fwd FrontalLobeAdultPl1+ frontal lobe, adult, pool1_CNhs10647_10040-101F4_forward Regulation 
FingernailIncludingNailPlateEponychiumAndHyponychiumDonor2_CNhs13445_ctss_rev FingernailD2- Fingernail (including nail plate, eponychium and hyponychium), donor2_CNhs13445_10301-104H4_reverse Regulation 
FingernailIncludingNailPlateEponychiumAndHyponychiumDonor2_CNhs13445_ctss_fwd FingernailD2+ Fingernail (including nail plate, eponychium and hyponychium), donor2_CNhs13445_10301-104H4_forward Regulation 
EyeVitreousHumorDonor1_CNhs13440_ctss_rev EyeVitreousHumorD1- eye - vitreous humor, donor1_CNhs13440_10268-104D7_reverse Regulation 
EyeVitreousHumorDonor1_CNhs13440_ctss_fwd EyeVitreousHumorD1+ eye - vitreous humor, donor1_CNhs13440_10268-104D7_forward Regulation 
EyeMuscleSuperiorDonor2_CNhs13441_ctss_rev EyeMuscleSuperiorD2- eye - muscle superior, donor2_CNhs13441_10297-104G9_reverse Regulation 
EyeMuscleSuperiorDonor2_CNhs13441_ctss_fwd EyeMuscleSuperiorD2+ eye - muscle superior, donor2_CNhs13441_10297-104G9_forward Regulation 
EyeMuscleMedialDonor2_CNhs13443_ctss_rev EyeMuscleMedialD2- eye - muscle medial, donor2_CNhs13443_10299-104H2_reverse Regulation 
EyeMuscleMedialDonor2_CNhs13443_ctss_fwd EyeMuscleMedialD2+ eye - muscle medial, donor2_CNhs13443_10299-104H2_forward Regulation 
EyeMuscleLateralDonor2_CNhs13442_ctss_rev EyeMuscleLateralD2- eye - muscle lateral, donor2_CNhs13442_10298-104H1_reverse Regulation 
EyeMuscleLateralDonor2_CNhs13442_ctss_fwd EyeMuscleLateralD2+ eye - muscle lateral, donor2_CNhs13442_10298-104H1_forward Regulation 
EyeMuscleInferiorRectusDonor1_CNhs13444_ctss_rev EyeMuscleInferiorRectusD1- eye - muscle inferior rectus, donor1_CNhs13444_10272-104E2_reverse Regulation 
EyeMuscleInferiorRectusDonor1_CNhs13444_ctss_fwd EyeMuscleInferiorRectusD1+ eye - muscle inferior rectus, donor1_CNhs13444_10272-104E2_forward Regulation 
EyeFetalDonor1_CNhs11762_ctss_rev EyeFetalD1- eye, fetal, donor1_CNhs11762_10054-101G9_reverse Regulation 
EyeFetalDonor1_CNhs11762_ctss_fwd EyeFetalD1+ eye, fetal, donor1_CNhs11762_10054-101G9_forward Regulation 
EsophagusAdultPool1_CNhs10620_ctss_rev EsophagusAdultPl1- esophagus, adult, pool1_CNhs10620_10015-101C6_reverse Regulation 
EsophagusAdultPool1_CNhs10620_ctss_fwd EsophagusAdultPl1+ esophagus, adult, pool1_CNhs10620_10015-101C6_forward Regulation 
EpididymisAdult_CNhs12847_ctss_rev EpididymisAdult- epididymis, adult_CNhs12847_10197-103E8_reverse Regulation 
EpididymisAdult_CNhs12847_ctss_fwd EpididymisAdult+ epididymis, adult_CNhs12847_10197-103E8_forward Regulation 
DuraMaterAdultDonor1_CNhs10648_ctss_rev DuraMaterAdultD1- dura mater, adult, donor1_CNhs10648_10041-101F5_reverse Regulation 
DuraMaterAdultDonor1_CNhs10648_ctss_fwd DuraMaterAdultD1+ dura mater, adult, donor1_CNhs10648_10041-101F5_forward Regulation 
DuodenumFetalDonor1TechRep2_CNhs12997_ctss_rev DuodenumFetalD1Tr2- duodenum, fetal, donor1, tech_rep2_CNhs12997_10071-101I8_reverse Regulation 
DuodenumFetalDonor1TechRep2_CNhs12997_ctss_fwd DuodenumFetalD1Tr2+ duodenum, fetal, donor1, tech_rep2_CNhs12997_10071-101I8_forward Regulation 
DuodenumFetalDonor1TechRep1_CNhs11781_ctss_rev DuodenumFetalD1Tr1- duodenum, fetal, donor1, tech_rep1_CNhs11781_10071-101I8_reverse Regulation 
DuodenumFetalDonor1TechRep1_CNhs11781_ctss_fwd DuodenumFetalD1Tr1+ duodenum, fetal, donor1, tech_rep1_CNhs11781_10071-101I8_forward Regulation 
DuctusDeferensAdult_CNhs12846_ctss_rev DuctusDeferensAdult- ductus deferens, adult_CNhs12846_10196-103E7_reverse Regulation 
DuctusDeferensAdult_CNhs12846_ctss_fwd DuctusDeferensAdult+ ductus deferens, adult_CNhs12846_10196-103E7_forward Regulation 
DiencephalonAdult_CNhs12610_ctss_rev DiencephalonAdult- diencephalon, adult_CNhs12610_10193-103E4_reverse Regulation 
DiencephalonAdult_CNhs12610_ctss_fwd DiencephalonAdult+ diencephalon, adult_CNhs12610_10193-103E4_forward Regulation 
DiaphragmFetalDonor1_CNhs11779_ctss_rev DiaphragmFetalD1- diaphragm, fetal, donor1_CNhs11779_10069-101I6_reverse Regulation 
DiaphragmFetalDonor1_CNhs11779_ctss_fwd DiaphragmFetalD1+ diaphragm, fetal, donor1_CNhs11779_10069-101I6_forward Regulation 
CruciateLigamentDonor2_CNhs13439_ctss_rev CruciateLigamentD2- cruciate ligament, donor2_CNhs13439_10295-104G7_reverse Regulation 
CruciateLigamentDonor2_CNhs13439_ctss_fwd CruciateLigamentD2+ cruciate ligament, donor2_CNhs13439_10295-104G7_forward Regulation 
CorpusCallosumAdultPool1_CNhs10649_ctss_rev CorpusCallosumAdultPl1- corpus callosum, adult, pool1_CNhs10649_10042-101F6_reverse Regulation 
CorpusCallosumAdultPool1_CNhs10649_ctss_fwd CorpusCallosumAdultPl1+ corpus callosum, adult, pool1_CNhs10649_10042-101F6_forward Regulation 
ColonFetalDonor1_CNhs11780_ctss_rev ColonFetalD1- colon, fetal, donor1_CNhs11780_10070-101I7_reverse Regulation 
ColonFetalDonor1_CNhs11780_ctss_fwd ColonFetalD1+ colon, fetal, donor1_CNhs11780_10070-101I7_forward Regulation 
ColonAdultPool1_CNhs10619_ctss_rev ColonAdultPl1- colon, adult, pool1_CNhs10619_10014-101C5_reverse Regulation 
ColonAdultPool1_CNhs10619_ctss_fwd ColonAdultPl1+ colon, adult, pool1_CNhs10619_10014-101C5_forward Regulation 
ColonAdultDonor1_CNhs11794_ctss_rev ColonAdultD1- colon, adult, donor1_CNhs11794_10082-102B1_reverse Regulation 
ColonAdultDonor1_CNhs11794_ctss_fwd ColonAdultD1+ colon, adult, donor1_CNhs11794_10082-102B1_forward Regulation 
ClontechHumanUniversalReferenceTotalRNAPool1_CNhs10608_ctss_rev ClontechUniversalReferencePl1- Clontech Human Universal Reference Total RNA, pool1_CNhs10608_10000-101A1_reverse Regulation 
ClontechHumanUniversalReferenceTotalRNAPool1_CNhs10608_ctss_fwd ClontechUniversalReferencePl1+ Clontech Human Universal Reference Total RNA, pool1_CNhs10608_10000-101A1_forward Regulation 
CervixAdultPool1_CNhs10618_ctss_rev CervixAdultPl1- cervix, adult, pool1_CNhs10618_10013-101C4_reverse Regulation 
CervixAdultPool1_CNhs10618_ctss_fwd CervixAdultPl1+ cervix, adult, pool1_CNhs10618_10013-101C4_forward Regulation 
CerebrospinalFluidDonor2_CNhs13437_ctss_rev CerebrospinalFluidD2- cerebrospinal fluid, donor2_CNhs13437_10294-104G6_reverse Regulation 
CerebrospinalFluidDonor2_CNhs13437_ctss_fwd CerebrospinalFluidD2+ cerebrospinal fluid, donor2_CNhs13437_10294-104G6_forward Regulation 
CerebralMeningesAdult_CNhs12840_ctss_rev CerebralMeningesAdult- cerebral meninges, adult_CNhs12840_10188-103D8_reverse Regulation 
CerebralMeningesAdult_CNhs12840_ctss_fwd CerebralMeningesAdult+ cerebral meninges, adult_CNhs12840_10188-103D8_forward Regulation 
CerebellumNewbornDonor10223_CNhs14075_ctss_rev CerebellumNbD10223- cerebellum, newborn, donor10223_CNhs14075_10357-105E6_reverse Regulation 
CerebellumNewbornDonor10223_CNhs14075_ctss_fwd CerebellumNbD10223+ cerebellum, newborn, donor10223_CNhs14075_10357-105E6_forward Regulation 
CerebellumAdultPool1_CNhs11795_ctss_rev CerebellumAdultPl1- cerebellum, adult, pool1_CNhs11795_10083-102B2_reverse Regulation 
CerebellumAdultPool1_CNhs11795_ctss_fwd CerebellumAdultPl1+ cerebellum, adult, pool1_CNhs11795_10083-102B2_forward Regulation 
CerebellumAdultDonor10252_CNhs12323_ctss_rev CerebellumAdultD10252- cerebellum, adult, donor10252_CNhs12323_10166-103B4_reverse Regulation 
CerebellumAdultDonor10252_CNhs12323_ctss_fwd CerebellumAdultD10252+ cerebellum, adult, donor10252_CNhs12323_10166-103B4_forward Regulation 
CerebellumAdultDonor10196_CNhs13799_ctss_rev CerebellumAdultD10196- cerebellum - adult, donor10196_CNhs13799_10173-103C2_reverse Regulation 
CerebellumAdultDonor10196_CNhs13799_ctss_fwd CerebellumAdultD10196+ cerebellum - adult, donor10196_CNhs13799_10173-103C2_forward Regulation 
CaudateNucleusNewbornDonor10223_CNhs14071_ctss_rev CaudateNucleusNbD10223- caudate nucleus, newborn, donor10223_CNhs14071_10354-105E3_reverse Regulation 
CaudateNucleusNewbornDonor10223_CNhs14071_ctss_fwd CaudateNucleusNbD10223+ caudate nucleus, newborn, donor10223_CNhs14071_10354-105E3_forward Regulation 
CaudateNucleusAdultDonor10258_CNhs14232_ctss_rev CaudateNucleusAdultD10258- caudate nucleus, adult, donor10258_CNhs14232_10379-105H1_reverse Regulation 
CaudateNucleusAdultDonor10258_CNhs14232_ctss_fwd CaudateNucleusAdultD10258+ caudate nucleus, adult, donor10258_CNhs14232_10379-105H1_forward Regulation 
CaudateNucleusAdultDonor10252_CNhs12321_ctss_rev CaudateNucleusAdultD10252- caudate nucleus, adult, donor10252_CNhs12321_10164-103B2_reverse Regulation 
CaudateNucleusAdultDonor10252_CNhs12321_ctss_fwd CaudateNucleusAdultD10252+ caudate nucleus, adult, donor10252_CNhs12321_10164-103B2_forward Regulation 
CaudateNucleusAdultDonor10196_CNhs13802_ctss_rev CaudateNucleusAdultD10196- caudate nucleus - adult, donor10196_CNhs13802_10177-103C6_reverse Regulation 
CaudateNucleusAdultDonor10196_CNhs13802_ctss_fwd CaudateNucleusAdultD10196+ caudate nucleus - adult, donor10196_CNhs13802_10177-103C6_forward Regulation 
BreastAdultDonor1_CNhs11792_ctss_rev BreastAdultD1- breast, adult, donor1_CNhs11792_10080-102A8_reverse Regulation 
BreastAdultDonor1_CNhs11792_ctss_fwd BreastAdultD1+ breast, adult, donor1_CNhs11792_10080-102A8_forward Regulation 
BrainFetalPool1_CNhs11797_ctss_rev BrainFetalPl1- brain, fetal, pool1_CNhs11797_10085-102B4_reverse Regulation 
BrainFetalPool1_CNhs11797_ctss_fwd BrainFetalPl1+ brain, fetal, pool1_CNhs11797_10085-102B4_forward Regulation 
BrainAdultPool1_CNhs10617_ctss_rev BrainAdultPl1- brain, adult, pool1_CNhs10617_10012-101C3_reverse Regulation 
BrainAdultPool1_CNhs10617_ctss_fwd BrainAdultPl1+ brain, adult, pool1_CNhs10617_10012-101C3_forward Regulation 
BrainAdultDonor1_CNhs11796_ctss_rev BrainAdultD1- brain, adult, donor1_CNhs11796_10084-102B3_reverse Regulation 
BrainAdultDonor1_CNhs11796_ctss_fwd BrainAdultD1+ brain, adult, donor1_CNhs11796_10084-102B3_forward Regulation 
BoneMarrowAdult_CNhs12845_ctss_rev BoneMarrowAdult- bone marrow, adult_CNhs12845_10192-103E3_reverse Regulation 
BoneMarrowAdult_CNhs12845_ctss_fwd BoneMarrowAdult+ bone marrow, adult_CNhs12845_10192-103E3_forward Regulation 
BloodAdultPool1_CNhs11761_ctss_rev BloodAdultPl1- blood, adult, pool1_CNhs11761_10053-101G8_reverse Regulation 
BloodAdultPool1_CNhs11761_ctss_fwd BloodAdultPl1+ blood, adult, pool1_CNhs11761_10053-101G8_forward Regulation 
BladderAdultPool1_CNhs10616_ctss_rev BladderAdultPl1- bladder, adult, pool1_CNhs10616_10011-101C2_reverse Regulation 
BladderAdultPool1_CNhs10616_ctss_fwd BladderAdultPl1+ bladder, adult, pool1_CNhs10616_10011-101C2_forward Regulation 
ArteryAdult_CNhs12843_ctss_rev ArteryAdult- artery, adult_CNhs12843_10190-103E1_reverse Regulation 
ArteryAdult_CNhs12843_ctss_fwd ArteryAdult+ artery, adult_CNhs12843_10190-103E1_forward Regulation 
AppendixAdult_CNhs12842_ctss_rev AppendixAdult- appendix, adult_CNhs12842_10189-103D9_reverse Regulation 
AppendixAdult_CNhs12842_ctss_fwd AppendixAdult+ appendix, adult_CNhs12842_10189-103D9_forward Regulation 
AortaAdultPool1_CNhs11760_ctss_rev AortaAdultPl1- aorta, adult, pool1_CNhs11760_10052-101G7_reverse Regulation 
AortaAdultPool1_CNhs11760_ctss_fwd AortaAdultPl1+ aorta, adult, pool1_CNhs11760_10052-101G7_forward Regulation 
AmygdalaNewbornDonor10223_CNhs14078_ctss_rev AmygdalaNbD1D10223- amygdala, newborn, donor10223_CNhs14078_10360-105E9_reverse Regulation 
AmygdalaNewbornDonor10223_CNhs14078_ctss_fwd AmygdalaNbD1D10223+ amygdala, newborn, donor10223_CNhs14078_10360-105E9_forward Regulation 
AmygdalaAdultDonor10252_CNhs12311_ctss_rev AmygdalaAdultD10252- amygdala, adult, donor10252_CNhs12311_10151-102I7_reverse Regulation 
AmygdalaAdultDonor10252_CNhs12311_ctss_fwd AmygdalaAdultD10252+ amygdala, adult, donor10252_CNhs12311_10151-102I7_forward Regulation 
AmygdalaAdultDonor10196_CNhs13793_ctss_rev AmygdalaAdultD10196- amygdala - adult, donor10196_CNhs13793_10167-103B5_reverse Regulation 
AmygdalaAdultDonor10196_CNhs13793_ctss_fwd AmygdalaAdultD10196+ amygdala - adult, donor10196_CNhs13793_10167-103B5_forward Regulation 
AdrenalGlandAdultPool1_CNhs11793_ctss_rev AdrenalGlandAdultPl1- adrenal gland, adult, pool1_CNhs11793_10081-102A9_reverse Regulation 
AdrenalGlandAdultPool1_CNhs11793_ctss_fwd AdrenalGlandAdultPl1+ adrenal gland, adult, pool1_CNhs11793_10081-102A9_forward Regulation 
AdiposeTissueAdultPool1_CNhs10615_ctss_rev AdiposeTissueAdultPl1- adipose tissue, adult, pool1_CNhs10615_10010-101C1_reverse Regulation 
AdiposeTissueAdultPool1_CNhs10615_ctss_fwd AdiposeTissueAdultPl1+ adipose tissue, adult, pool1_CNhs10615_10010-101C1_forward Regulation 
AdiposeDonor4_CNhs13975_ctss_rev AdiposeD4- adipose, donor4_CNhs13975_10187-103D7_reverse Regulation 
AdiposeDonor4_CNhs13975_ctss_fwd AdiposeD4+ adipose, donor4_CNhs13975_10187-103D7_forward Regulation 
AdiposeDonor3_CNhs13974_ctss_rev AdiposeD3- adipose, donor3_CNhs13974_10186-103D6_reverse Regulation 
AdiposeDonor3_CNhs13974_ctss_fwd AdiposeD3+ adipose, donor3_CNhs13974_10186-103D6_forward Regulation 
AdiposeDonor2_CNhs13973_ctss_rev AdiposeD2- adipose, donor2_CNhs13973_10185-103D5_reverse Regulation 
AdiposeDonor2_CNhs13973_ctss_fwd AdiposeD2+ adipose, donor2_CNhs13973_10185-103D5_forward Regulation 
AdiposeDonor1_CNhs13972_ctss_rev AdiposeD1- adipose, donor1_CNhs13972_10184-103D4_reverse Regulation 
AdiposeDonor1_CNhs13972_ctss_fwd AdiposeD1+ adipose, donor1_CNhs13972_10184-103D4_forward Regulation 
AchillesTendonDonor2_CNhs13435_ctss_rev AchillesTendonD2- achilles tendon, donor2_CNhs13435_10292-104G4_reverse Regulation 
AchillesTendonDonor2_CNhs13435_ctss_fwd AchillesTendonD2+ achilles tendon, donor2_CNhs13435_10292-104G4_forward Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep3B3T17_CNhs14196_ctss_rev Tc:Saos-2Untreated_Day28Br3- Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep3 (B3 T17)_CNhs14196_12893-137H4_reverse Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep3B3T17_CNhs14196_ctss_fwd Tc:Saos-2Untreated_Day28Br3+ Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep3 (B3 T17)_CNhs14196_12893-137H4_forward Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep2B2T17_CNhs14195_ctss_rev Tc:Saos-2Untreated_Day28Br2- Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep2 (B2 T17)_CNhs14195_12795-136F5_reverse Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep2B2T17_CNhs14195_ctss_fwd Tc:Saos-2Untreated_Day28Br2+ Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep2 (B2 T17)_CNhs14195_12795-136F5_forward Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep1B1T17_CNhs14194_ctss_rev Tc:Saos-2Untreated_Day28Br1- Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep1 (B1 T17)_CNhs14194_12697-135D6_reverse Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep1B1T17_CNhs14194_ctss_fwd Tc:Saos-2Untreated_Day28Br1+ Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep1 (B1 T17)_CNhs14194_12697-135D6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep3_CNhs13634_ctss_rev Tc:MscToAdiposeUndiffBr3- mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep3_CNhs13634_13282-142F6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep3_CNhs13634_ctss_fwd Tc:MscToAdiposeUndiffBr3+ mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep3_CNhs13634_13282-142F6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep2_CNhs13633_ctss_rev Tc:MscToAdiposeUndiffBr2- mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep2_CNhs13633_13281-142F5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep2_CNhs13633_ctss_fwd Tc:MscToAdiposeUndiffBr2+ mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep2_CNhs13633_13281-142F5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep1_CNhs13692_ctss_rev Tc:MscToAdiposeUndiffBr1- mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep1_CNhs13692_13280-142F4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep1_CNhs13692_ctss_fwd Tc:MscToAdiposeUndiffBr1+ mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep1_CNhs13692_13280-142F4_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor1868_121MI_0h_CNhs13637_ctss_rev Tc:MdmToMock_00hr00minD1- Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor1 (868_121:MI_0h)_CNhs13637_13304-142I1_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor1868_121MI_0h_CNhs13637_ctss_fwd Tc:MdmToMock_00hr00minD1+ Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor1 (868_121:MI_0h)_CNhs13637_13304-142I1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor1T20Subject1_CNhs12930_ctss_rev Tc:MdmToLps_16hrD1- Monocyte-derived macrophages response to LPS, 16hr, donor1 (t20 Subject1)_CNhs12930_12717-135F8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor1T20Subject1_CNhs12930_ctss_fwd Tc:MdmToLps_16hrD1+ Monocyte-derived macrophages response to LPS, 16hr, donor1 (t20 Subject1)_CNhs12930_12717-135F8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor1T17Subject1_CNhs12928_ctss_rev Tc:MdmToLps_10hrD1- Monocyte-derived macrophages response to LPS, 10hr, donor1 (t17 Subject1)_CNhs12928_12714-135F5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor1T17Subject1_CNhs12928_ctss_fwd Tc:MdmToLps_10hrD1+ Monocyte-derived macrophages response to LPS, 10hr, donor1 (t17 Subject1)_CNhs12928_12714-135F5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor3T15Subject3_CNhs13325_ctss_rev Tc:MdmToLps_07hrD3- Monocyte-derived macrophages response to LPS, 07hr, donor3 (t15 Subject3)_CNhs13325_12908-138A1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor3T15Subject3_CNhs13325_ctss_fwd Tc:MdmToLps_07hrD3+ Monocyte-derived macrophages response to LPS, 07hr, donor3 (t15 Subject3)_CNhs13325_12908-138A1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor2T15Subject2_CNhs13394_ctss_rev Tc:MdmToLps_07hrD2- Monocyte-derived macrophages response to LPS, 07hr, donor2 (t15 Subject2)_CNhs13394_12810-136H2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor2T15Subject2_CNhs13394_ctss_fwd Tc:MdmToLps_07hrD2+ Monocyte-derived macrophages response to LPS, 07hr, donor2 (t15 Subject2)_CNhs13394_12810-136H2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor1T15Subject1_CNhs12926_ctss_rev Tc:MdmToLps_07hrD1- Monocyte-derived macrophages response to LPS, 07hr, donor1 (t15 Subject1)_CNhs12926_12712-135F3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor1T15Subject1_CNhs12926_ctss_fwd Tc:MdmToLps_07hrD1+ Monocyte-derived macrophages response to LPS, 07hr, donor1 (t15 Subject1)_CNhs12926_12712-135F3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor3T14Subject3_CNhs13187_ctss_rev Tc:MdmToLps_06hrD3- Monocyte-derived macrophages response to LPS, 06hr, donor3 (t14 Subject3)_CNhs13187_12907-137I9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor3T14Subject3_CNhs13187_ctss_fwd Tc:MdmToLps_06hrD3+ Monocyte-derived macrophages response to LPS, 06hr, donor3 (t14 Subject3)_CNhs13187_12907-137I9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor2T14Subject2_CNhs13393_ctss_rev Tc:MdmToLps_06hrD2- Monocyte-derived macrophages response to LPS, 06hr, donor2 (t14 Subject2)_CNhs13393_12809-136H1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor2T14Subject2_CNhs13393_ctss_fwd Tc:MdmToLps_06hrD2+ Monocyte-derived macrophages response to LPS, 06hr, donor2 (t14 Subject2)_CNhs13393_12809-136H1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor1T14Subject1_CNhs12925_ctss_rev Tc:MdmToLps_06hrD1- Monocyte-derived macrophages response to LPS, 06hr, donor1 (t14 Subject1)_CNhs12925_12711-135F2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor1T14Subject1_CNhs12925_ctss_fwd Tc:MdmToLps_06hrD1+ Monocyte-derived macrophages response to LPS, 06hr, donor1 (t14 Subject1)_CNhs12925_12711-135F2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor1T12Subject1_CNhs13154_ctss_rev Tc:MdmToLps_04hrD1- Monocyte-derived macrophages response to LPS, 04hr, donor1 (t12 Subject1)_CNhs13154_12709-135E9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor1T12Subject1_CNhs13154_ctss_fwd Tc:MdmToLps_04hrD1+ Monocyte-derived macrophages response to LPS, 04hr, donor1 (t12 Subject1)_CNhs13154_12709-135E9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor1T11Subject1_CNhs13153_ctss_rev Tc:MdmToLps_03hr30minD1- Monocyte-derived macrophages response to LPS, 03hr30min, donor1 (t11 Subject1)_CNhs13153_12708-135E8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor1T11Subject1_CNhs13153_ctss_fwd Tc:MdmToLps_03hr30minD1+ Monocyte-derived macrophages response to LPS, 03hr30min, donor1 (t11 Subject1)_CNhs13153_12708-135E8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor1T8Subject1_CNhs13151_ctss_rev Tc:MdmToLps_02hr00minD1- Monocyte-derived macrophages response to LPS, 02hr00min, donor1 (t8 Subject1)_CNhs13151_12705-135E5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor1T8Subject1_CNhs13151_ctss_fwd Tc:MdmToLps_02hr00minD1+ Monocyte-derived macrophages response to LPS, 02hr00min, donor1 (t8 Subject1)_CNhs13151_12705-135E5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor3T7Subject3_CNhs13180_ctss_rev Tc:MdmToLps_01hr40minD3- Monocyte-derived macrophages response to LPS, 01hr40min, donor3 (t7 Subject3)_CNhs13180_12900-137I2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor3T7Subject3_CNhs13180_ctss_fwd Tc:MdmToLps_01hr40minD3+ Monocyte-derived macrophages response to LPS, 01hr40min, donor3 (t7 Subject3)_CNhs13180_12900-137I2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor2T7Subject2_CNhs13385_ctss_rev Tc:MdmToLps_01hr40minD2- Monocyte-derived macrophages response to LPS, 01hr40min, donor2 (t7 Subject2)_CNhs13385_12802-136G3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor2T7Subject2_CNhs13385_ctss_fwd Tc:MdmToLps_01hr40minD2+ Monocyte-derived macrophages response to LPS, 01hr40min, donor2 (t7 Subject2)_CNhs13385_12802-136G3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor1T7Subject1_CNhs13150_ctss_rev Tc:MdmToLps_01hr40minD1- Monocyte-derived macrophages response to LPS, 01hr40min, donor1 (t7 Subject1)_CNhs13150_12704-135E4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor1T7Subject1_CNhs13150_ctss_fwd Tc:MdmToLps_01hr40minD1+ Monocyte-derived macrophages response to LPS, 01hr40min, donor1 (t7 Subject1)_CNhs13150_12704-135E4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor1T6Subject1_CNhs13149_ctss_rev Tc:MdmToLps_01hr20minD1- Monocyte-derived macrophages response to LPS, 01hr20min, donor1 (t6 Subject1)_CNhs13149_12703-135E3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor1T6Subject1_CNhs13149_ctss_fwd Tc:MdmToLps_01hr20minD1+ Monocyte-derived macrophages response to LPS, 01hr20min, donor1 (t6 Subject1)_CNhs13149_12703-135E3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor1T5Subject1_CNhs13148_ctss_rev Tc:MdmToLps_01hr00minD1- Monocyte-derived macrophages response to LPS, 01hr00min, donor1 (t5 Subject1)_CNhs13148_12702-135E2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor1T5Subject1_CNhs13148_ctss_fwd Tc:MdmToLps_01hr00minD1+ Monocyte-derived macrophages response to LPS, 01hr00min, donor1 (t5 Subject1)_CNhs13148_12702-135E2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor1T4Subject1_CNhs13147_ctss_rev Tc:MdmToLps_00hr45minD1- Monocyte-derived macrophages response to LPS, 00hr45min, donor1 (t4 Subject1)_CNhs13147_12701-135E1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor1T4Subject1_CNhs13147_ctss_fwd Tc:MdmToLps_00hr45minD1+ Monocyte-derived macrophages response to LPS, 00hr45min, donor1 (t4 Subject1)_CNhs13147_12701-135E1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor1T3Subject1_CNhs13146_ctss_rev Tc:MdmToLps_00hr30minD1- Monocyte-derived macrophages response to LPS, 00hr30min, donor1 (t3 Subject1)_CNhs13146_12700-135D9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor1T3Subject1_CNhs13146_ctss_fwd Tc:MdmToLps_00hr30minD1+ Monocyte-derived macrophages response to LPS, 00hr30min, donor1 (t3 Subject1)_CNhs13146_12700-135D9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor1T2Subject1_CNhs13145_ctss_rev Tc:MdmToLps_00hr15minD1- Monocyte-derived macrophages response to LPS, 00hr15min, donor1 (t2 Subject1)_CNhs13145_12699-135D8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor1T2Subject1_CNhs13145_ctss_fwd Tc:MdmToLps_00hr15minD1+ Monocyte-derived macrophages response to LPS, 00hr15min, donor1 (t2 Subject1)_CNhs13145_12699-135D8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep3_CNhs12804_ctss_rev Tc:K562ToHemin_Day04Br3- K562 erythroblastic leukemia response to hemin, day04, biol_rep3_CNhs12804_13228-141I6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep3_CNhs12804_ctss_fwd Tc:K562ToHemin_Day04Br3+ K562 erythroblastic leukemia response to hemin, day04, biol_rep3_CNhs12804_13228-141I6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep2_CNhs12702_ctss_rev Tc:K562ToHemin_Day04Br2- K562 erythroblastic leukemia response to hemin, day04, biol_rep2_CNhs12702_13162-141B3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep2_CNhs12702_ctss_fwd Tc:K562ToHemin_Day04Br2+ K562 erythroblastic leukemia response to hemin, day04, biol_rep2_CNhs12702_13162-141B3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep1_CNhs12474_ctss_rev Tc:K562ToHemin_Day04Br1- K562 erythroblastic leukemia response to hemin, day04, biol_rep1_CNhs12474_13096-140C9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep1_CNhs12474_ctss_fwd Tc:K562ToHemin_Day04Br1+ K562 erythroblastic leukemia response to hemin, day04, biol_rep1_CNhs12474_13096-140C9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep3_CNhs12803_ctss_rev Tc:K562ToHemin_Day03Br3- K562 erythroblastic leukemia response to hemin, day03, biol_rep3_CNhs12803_13227-141I5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep3_CNhs12803_ctss_fwd Tc:K562ToHemin_Day03Br3+ K562 erythroblastic leukemia response to hemin, day03, biol_rep3_CNhs12803_13227-141I5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep2_CNhs12701_ctss_rev Tc:K562ToHemin_Day03Br2- K562 erythroblastic leukemia response to hemin, day03, biol_rep2_CNhs12701_13161-141B2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep2_CNhs12701_ctss_fwd Tc:K562ToHemin_Day03Br2+ K562 erythroblastic leukemia response to hemin, day03, biol_rep2_CNhs12701_13161-141B2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep1_CNhs12473_ctss_rev Tc:K562ToHemin_Day03Br1- K562 erythroblastic leukemia response to hemin, day03, biol_rep1_CNhs12473_13095-140C8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep1_CNhs12473_ctss_fwd Tc:K562ToHemin_Day03Br1+ K562 erythroblastic leukemia response to hemin, day03, biol_rep1_CNhs12473_13095-140C8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep3_CNhs12802_ctss_rev Tc:K562ToHemin_Day02Br3- K562 erythroblastic leukemia response to hemin, day02, biol_rep3_CNhs12802_13226-141I4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep3_CNhs12802_ctss_fwd Tc:K562ToHemin_Day02Br3+ K562 erythroblastic leukemia response to hemin, day02, biol_rep3_CNhs12802_13226-141I4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep2_CNhs12700_ctss_rev Tc:K562ToHemin_Day02Br2- K562 erythroblastic leukemia response to hemin, day02, biol_rep2_CNhs12700_13160-141B1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep2_CNhs12700_ctss_fwd Tc:K562ToHemin_Day02Br2+ K562 erythroblastic leukemia response to hemin, day02, biol_rep2_CNhs12700_13160-141B1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep1_CNhs12472_ctss_rev Tc:K562ToHemin_Day02Br1- K562 erythroblastic leukemia response to hemin, day02, biol_rep1_CNhs12472_13094-140C7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep1_CNhs12472_ctss_fwd Tc:K562ToHemin_Day02Br1+ K562 erythroblastic leukemia response to hemin, day02, biol_rep1_CNhs12472_13094-140C7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep3_CNhs12801_ctss_rev Tc:K562ToHemin_24hrBr3- K562 erythroblastic leukemia response to hemin, 24hr, biol_rep3_CNhs12801_13225-141I3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep3_CNhs12801_ctss_fwd Tc:K562ToHemin_24hrBr3+ K562 erythroblastic leukemia response to hemin, 24hr, biol_rep3_CNhs12801_13225-141I3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep2_CNhs12699_ctss_rev Tc:K562ToHemin_24hrBr2- K562 erythroblastic leukemia response to hemin, 24hr, biol_rep2_CNhs12699_13159-141A9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep2_CNhs12699_ctss_fwd Tc:K562ToHemin_24hrBr2+ K562 erythroblastic leukemia response to hemin, 24hr, biol_rep2_CNhs12699_13159-141A9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep1_CNhs12471_ctss_rev Tc:K562ToHemin_24hrBr1- K562 erythroblastic leukemia response to hemin, 24hr, biol_rep1_CNhs12471_13093-140C6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep1_CNhs12471_ctss_fwd Tc:K562ToHemin_24hrBr1+ K562 erythroblastic leukemia response to hemin, 24hr, biol_rep1_CNhs12471_13093-140C6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep3_CNhs12800_ctss_rev Tc:K562ToHemin_12hrBr3- K562 erythroblastic leukemia response to hemin, 12hr, biol_rep3_CNhs12800_13224-141I2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep3_CNhs12800_ctss_fwd Tc:K562ToHemin_12hrBr3+ K562 erythroblastic leukemia response to hemin, 12hr, biol_rep3_CNhs12800_13224-141I2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep2_CNhs12698_ctss_rev Tc:K562ToHemin_12hrBr2- K562 erythroblastic leukemia response to hemin, 12hr, biol_rep2_CNhs12698_13158-141A8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep2_CNhs12698_ctss_fwd Tc:K562ToHemin_12hrBr2+ K562 erythroblastic leukemia response to hemin, 12hr, biol_rep2_CNhs12698_13158-141A8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep1_CNhs12470_ctss_rev Tc:K562ToHemin_12hrBr1- K562 erythroblastic leukemia response to hemin, 12hr, biol_rep1_CNhs12470_13092-140C5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep1_CNhs12470_ctss_fwd Tc:K562ToHemin_12hrBr1+ K562 erythroblastic leukemia response to hemin, 12hr, biol_rep1_CNhs12470_13092-140C5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep3_CNhs12799_ctss_rev Tc:K562ToHemin_06hrBr3- K562 erythroblastic leukemia response to hemin, 06hr, biol_rep3_CNhs12799_13223-141I1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep3_CNhs12799_ctss_fwd Tc:K562ToHemin_06hrBr3+ K562 erythroblastic leukemia response to hemin, 06hr, biol_rep3_CNhs12799_13223-141I1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep2_CNhs12697_ctss_rev Tc:K562ToHemin_06hrBr2- K562 erythroblastic leukemia response to hemin, 06hr, biol_rep2_CNhs12697_13157-141A7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep2_CNhs12697_ctss_fwd Tc:K562ToHemin_06hrBr2+ K562 erythroblastic leukemia response to hemin, 06hr, biol_rep2_CNhs12697_13157-141A7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep1_CNhs12469_ctss_rev Tc:K562ToHemin_06hrBr1- K562 erythroblastic leukemia response to hemin, 06hr, biol_rep1_CNhs12469_13091-140C4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep1_CNhs12469_ctss_fwd Tc:K562ToHemin_06hrBr1+ K562 erythroblastic leukemia response to hemin, 06hr, biol_rep1_CNhs12469_13091-140C4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep3_CNhs12798_ctss_rev Tc:K562ToHemin_04hrBr3- K562 erythroblastic leukemia response to hemin, 04hr, biol_rep3_CNhs12798_13222-141H9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep3_CNhs12798_ctss_fwd Tc:K562ToHemin_04hrBr3+ K562 erythroblastic leukemia response to hemin, 04hr, biol_rep3_CNhs12798_13222-141H9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep2_CNhs12696_ctss_rev Tc:K562ToHemin_04hrBr2- K562 erythroblastic leukemia response to hemin, 04hr, biol_rep2_CNhs12696_13156-141A6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep2_CNhs12696_ctss_fwd Tc:K562ToHemin_04hrBr2+ K562 erythroblastic leukemia response to hemin, 04hr, biol_rep2_CNhs12696_13156-141A6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep1_CNhs12468_ctss_rev Tc:K562ToHemin_04hrBr1- K562 erythroblastic leukemia response to hemin, 04hr, biol_rep1_CNhs12468_13090-140C3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep1_CNhs12468_ctss_fwd Tc:K562ToHemin_04hrBr1+ K562 erythroblastic leukemia response to hemin, 04hr, biol_rep1_CNhs12468_13090-140C3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep3_CNhs12797_ctss_rev Tc:K562ToHemin_03hr30minBr3- K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep3_CNhs12797_13221-141H8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep3_CNhs12797_ctss_fwd Tc:K562ToHemin_03hr30minBr3+ K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep3_CNhs12797_13221-141H8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep2_CNhs12695_ctss_rev Tc:K562ToHemin_03hr30minBr2- K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep2_CNhs12695_13155-141A5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep2_CNhs12695_ctss_fwd Tc:K562ToHemin_03hr30minBr2+ K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep2_CNhs12695_13155-141A5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep1_CNhs12467_ctss_rev Tc:K562ToHemin_03hr30minBr1- K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep1_CNhs12467_13089-140C2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep1_CNhs12467_ctss_fwd Tc:K562ToHemin_03hr30minBr1+ K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep1_CNhs12467_13089-140C2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep3_CNhs12796_ctss_rev Tc:K562ToHemin_03hr00minBr3- K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep3_CNhs12796_13220-141H7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep3_CNhs12796_ctss_fwd Tc:K562ToHemin_03hr00minBr3+ K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep3_CNhs12796_13220-141H7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep2_CNhs12694_ctss_rev Tc:K562ToHemin_03hr00minBr2- K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep2_CNhs12694_13154-141A4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep2_CNhs12694_ctss_fwd Tc:K562ToHemin_03hr00minBr2+ K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep2_CNhs12694_13154-141A4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep1_CNhs12466_ctss_rev Tc:K562ToHemin_03hr00minBr1- K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep1_CNhs12466_13088-140C1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep1_CNhs12466_ctss_fwd Tc:K562ToHemin_03hr00minBr1+ K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep1_CNhs12466_13088-140C1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep3_CNhs12795_ctss_rev Tc:K562ToHemin_02hr30minBr3- K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep3_CNhs12795_13219-141H6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep3_CNhs12795_ctss_fwd Tc:K562ToHemin_02hr30minBr3+ K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep3_CNhs12795_13219-141H6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep2_CNhs12693_ctss_rev Tc:K562ToHemin_02hr30minBr2- K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep2_CNhs12693_13153-141A3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep2_CNhs12693_ctss_fwd Tc:K562ToHemin_02hr30minBr2+ K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep2_CNhs12693_13153-141A3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep1_CNhs12465_ctss_rev Tc:K562ToHemin_02hr30minBr1- K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep1_CNhs12465_13087-140B9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep1_CNhs12465_ctss_fwd Tc:K562ToHemin_02hr30minBr1+ K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep1_CNhs12465_13087-140B9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep3_CNhs12794_ctss_rev Tc:K562ToHemin_02hr00minBr3- K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep3_CNhs12794_13218-141H5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep3_CNhs12794_ctss_fwd Tc:K562ToHemin_02hr00minBr3+ K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep3_CNhs12794_13218-141H5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep2_CNhs12692_ctss_rev Tc:K562ToHemin_02hr00minBr2- K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep2_CNhs12692_13152-141A2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep2_CNhs12692_ctss_fwd Tc:K562ToHemin_02hr00minBr2+ K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep2_CNhs12692_13152-141A2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep1_CNhs12737_ctss_rev Tc:K562ToHemin_02hr00minBr1- K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep1_CNhs12737_13086-140B8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep1_CNhs12737_ctss_fwd Tc:K562ToHemin_02hr00minBr1+ K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep1_CNhs12737_13086-140B8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep3_CNhs12792_ctss_rev Tc:K562ToHemin_01hr40minBr3- K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep3_CNhs12792_13217-141H4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep3_CNhs12792_ctss_fwd Tc:K562ToHemin_01hr40minBr3+ K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep3_CNhs12792_13217-141H4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep2_CNhs12691_ctss_rev Tc:K562ToHemin_01hr40minBr2- K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep2_CNhs12691_13151-141A1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep2_CNhs12691_ctss_fwd Tc:K562ToHemin_01hr40minBr2+ K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep2_CNhs12691_13151-141A1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep1_CNhs12464_ctss_rev Tc:K562ToHemin_01hr40minBr1- K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep1_CNhs12464_13085-140B7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep1_CNhs12464_ctss_fwd Tc:K562ToHemin_01hr40minBr1+ K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep1_CNhs12464_13085-140B7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep3_CNhs12791_ctss_rev Tc:K562ToHemin_01hr20minBr3- K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep3_CNhs12791_13216-141H3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep3_CNhs12791_ctss_fwd Tc:K562ToHemin_01hr20minBr3+ K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep3_CNhs12791_13216-141H3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep2_CNhs12690_ctss_rev Tc:K562ToHemin_01hr20minBr2- K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep2_CNhs12690_13150-140I9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep2_CNhs12690_ctss_fwd Tc:K562ToHemin_01hr20minBr2+ K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep2_CNhs12690_13150-140I9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep1_CNhs12463_ctss_rev Tc:K562ToHemin_01hr20minBr1- K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep1_CNhs12463_13084-140B6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep1_CNhs12463_ctss_fwd Tc:K562ToHemin_01hr20minBr1+ K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep1_CNhs12463_13084-140B6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep3_CNhs12790_ctss_rev Tc:K562ToHemin_01hr00minBr3- K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep3_CNhs12790_13215-141H2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep3_CNhs12790_ctss_fwd Tc:K562ToHemin_01hr00minBr3+ K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep3_CNhs12790_13215-141H2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep2_CNhs12689_ctss_rev Tc:K562ToHemin_01hr00minBr2- K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep2_CNhs12689_13149-140I8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep2_CNhs12689_ctss_fwd Tc:K562ToHemin_01hr00minBr2+ K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep2_CNhs12689_13149-140I8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep1_CNhs12462_ctss_rev Tc:K562ToHemin_01hr00minBr1- K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep1_CNhs12462_13083-140B5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep1_CNhs12462_ctss_fwd Tc:K562ToHemin_01hr00minBr1+ K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep1_CNhs12462_13083-140B5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep3_CNhs12789_ctss_rev Tc:K562ToHemin_00hr45minBr3- K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep3_CNhs12789_13214-141H1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep3_CNhs12789_ctss_fwd Tc:K562ToHemin_00hr45minBr3+ K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep3_CNhs12789_13214-141H1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep2_CNhs12688_ctss_rev Tc:K562ToHemin_00hr45minBr2- K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep2_CNhs12688_13148-140I7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep2_CNhs12688_ctss_fwd Tc:K562ToHemin_00hr45minBr2+ K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep2_CNhs12688_13148-140I7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep1_CNhs12461_ctss_rev Tc:K562ToHemin_00hr45minBr1- K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep1_CNhs12461_13082-140B4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep1_CNhs12461_ctss_fwd Tc:K562ToHemin_00hr45minBr1+ K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep1_CNhs12461_13082-140B4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep3_CNhs12788_ctss_rev Tc:K562ToHemin_00hr30minBr3- K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep3_CNhs12788_13213-141G9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep3_CNhs12788_ctss_fwd Tc:K562ToHemin_00hr30minBr3+ K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep3_CNhs12788_13213-141G9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep2_CNhs12687_ctss_rev Tc:K562ToHemin_00hr30minBr2- K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep2_CNhs12687_13147-140I6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep2_CNhs12687_ctss_fwd Tc:K562ToHemin_00hr30minBr2+ K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep2_CNhs12687_13147-140I6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep1_CNhs12460_ctss_rev Tc:K562ToHemin_00hr30minBr1- K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep1_CNhs12460_13081-140B3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep1_CNhs12460_ctss_fwd Tc:K562ToHemin_00hr30minBr1+ K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep1_CNhs12460_13081-140B3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep3_CNhs12787_ctss_rev Tc:K562ToHemin_00hr15minBr3- K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep3_CNhs12787_13212-141G8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep3_CNhs12787_ctss_fwd Tc:K562ToHemin_00hr15minBr3+ K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep3_CNhs12787_13212-141G8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep2_CNhs12686_ctss_rev Tc:K562ToHemin_00hr15minBr2- K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep2_CNhs12686_13146-140I5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep2_CNhs12686_ctss_fwd Tc:K562ToHemin_00hr15minBr2+ K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep2_CNhs12686_13146-140I5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep1_CNhs12459_ctss_rev Tc:K562ToHemin_00hr15minBr1- K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep1_CNhs12459_13080-140B2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep1_CNhs12459_ctss_fwd Tc:K562ToHemin_00hr15minBr1+ K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep1_CNhs12459_13080-140B2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep3_CNhs12786_ctss_rev Tc:K562ToHemin_00hr00minBr3- K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep3_CNhs12786_13211-141G7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep3_CNhs12786_ctss_fwd Tc:K562ToHemin_00hr00minBr3+ K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep3_CNhs12786_13211-141G7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep2_CNhs12684_ctss_rev Tc:K562ToHemin_00hr00minBr2- K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep2_CNhs12684_13145-140I4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep2_CNhs12684_ctss_fwd Tc:K562ToHemin_00hr00minBr2+ K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep2_CNhs12684_13145-140I4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep1_CNhs12458_ctss_rev Tc:K562ToHemin_00hr00minBr1- K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep1_CNhs12458_13079-140B1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep1_CNhs12458_ctss_fwd Tc:K562ToHemin_00hr00minBr1+ K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep1_CNhs12458_13079-140B1_forward Regulation 
HIPSBiolRep3_CNhs14216_ctss_rev Tc:hIPSBr3- hIPS, biol_rep3_CNhs14216_14382-156B8_reverse Regulation 
HIPSBiolRep3_CNhs14216_ctss_fwd Tc:hIPSBr3+ hIPS, biol_rep3_CNhs14216_14382-156B8_forward Regulation 
HIPSBiolRep2_CNhs14215_ctss_rev Tc:hIPSBr2- hIPS, biol_rep2_CNhs14215_14381-156B7_reverse Regulation 
HIPSBiolRep2_CNhs14215_ctss_fwd Tc:hIPSBr2+ hIPS, biol_rep2_CNhs14215_14381-156B7_forward Regulation 
HIPSBiolRep1_CNhs14214_ctss_rev Tc:hIPSBr1- hIPS, biol_rep1_CNhs14214_14380-156B6_reverse Regulation 
HIPSBiolRep1_CNhs14214_ctss_fwd Tc:hIPSBr1+ hIPS, biol_rep1_CNhs14214_14380-156B6_forward Regulation 
HIPSCCl2BiolRep3_CNhs14219_ctss_rev Tc:hIPS+CCl2Br3- hIPS +CCl2, biol_rep3_CNhs14219_14385-156C2_reverse Regulation 
HIPSCCl2BiolRep3_CNhs14219_ctss_fwd Tc:hIPS+CCl2Br3+ hIPS +CCl2, biol_rep3_CNhs14219_14385-156C2_forward Regulation 
HIPSCCl2BiolRep2_CNhs14218_ctss_rev Tc:hIPS+CCl2Br2- hIPS +CCl2, biol_rep2_CNhs14218_14384-156C1_reverse Regulation 
HIPSCCl2BiolRep2_CNhs14218_ctss_fwd Tc:hIPS+CCl2Br2+ hIPS +CCl2, biol_rep2_CNhs14218_14384-156C1_forward Regulation 
HIPSCCl2BiolRep1_CNhs14217_ctss_rev Tc:hIPS+CCl2Br1- hIPS +CCl2, biol_rep1_CNhs14217_14383-156B9_reverse Regulation 
HIPSCCl2BiolRep1_CNhs14217_ctss_fwd Tc:hIPS+CCl2Br1+ hIPS +CCl2, biol_rep1_CNhs14217_14383-156B9_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep3_CNhs13971_ctss_rev Tc:H1ToHsc_Day09Br3- H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep3_CNhs13971_13531-145G3_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep3_CNhs13971_ctss_fwd Tc:H1ToHsc_Day09Br3+ H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep3_CNhs13971_13531-145G3_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep2_CNhs13970_ctss_rev Tc:H1ToHsc_Day09Br2- H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep2_CNhs13970_13530-145G2_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep2_CNhs13970_ctss_fwd Tc:H1ToHsc_Day09Br2+ H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep2_CNhs13970_13530-145G2_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep1_CNhs13969_ctss_rev Tc:H1ToHsc_Day09Br1- H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep1_CNhs13969_13529-145G1_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep1_CNhs13969_ctss_fwd Tc:H1ToHsc_Day09Br1+ H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep1_CNhs13969_13529-145G1_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep3_CNhs13968_ctss_rev Tc:H1ToHsc_Day03Br3- H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep3_CNhs13968_13528-145F9_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep3_CNhs13968_ctss_fwd Tc:H1ToHsc_Day03Br3+ H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep3_CNhs13968_13528-145F9_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep2_CNhs13966_ctss_rev Tc:H1ToHsc_Day03Br2- H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep2_CNhs13966_13527-145F8_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep2_CNhs13966_ctss_fwd Tc:H1ToHsc_Day03Br2+ H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep2_CNhs13966_13527-145F8_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep1_CNhs13965_ctss_rev Tc:H1ToHsc_Day03Br1- H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep1_CNhs13965_13526-145F7_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep1_CNhs13965_ctss_fwd Tc:H1ToHsc_Day03Br1+ H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep1_CNhs13965_13526-145F7_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep3_CNhs13964_ctss_rev Tc:H1ToHsc_Day00Br3- H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep3_CNhs13964_13525-145F6_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep3_CNhs13964_ctss_fwd Tc:H1ToHsc_Day00Br3+ H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep3_CNhs13964_13525-145F6_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep2_CNhs14068_ctss_rev Tc:H1ToHsc_Day00Br2- H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep2_CNhs14068_13524-145F5_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep2_CNhs14068_ctss_fwd Tc:H1ToHsc_Day00Br2+ H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep2_CNhs14068_13524-145F5_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep1_CNhs14067_ctss_rev Tc:H1ToHsc_Day00Br1- H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep1_CNhs14067_13523-145F4_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep1_CNhs14067_ctss_fwd Tc:H1ToHsc_Day00Br1+ H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep1_CNhs14067_13523-145F4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep2_CNhs14536_ctss_rev Tc:ARPE-19Emt_24hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep2_CNhs14536_13680-147E8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep2_CNhs14536_ctss_fwd Tc:ARPE-19Emt_24hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep2_CNhs14536_13680-147E8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep2_CNhs14520_ctss_rev Tc:ARPE-19Emt_06hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep2_CNhs14520_13665-147D2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep2_CNhs14520_ctss_fwd Tc:ARPE-19Emt_06hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep2_CNhs14520_13665-147D2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor3_CNhs14584_ctss_rev MyoblastToMyotubes_Day10D3- Myoblast differentiation to myotubes, day10, control donor3_CNhs14584_13494-145C2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor3_CNhs14584_ctss_fwd MyoblastToMyotubes_Day10D3+ Myoblast differentiation to myotubes, day10, control donor3_CNhs14584_13494-145C2_forward Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor2_CNhs14601_ctss_rev MyoblastToMyotubes_Day06D2- Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor2_CNhs14601_13510-145D9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor2_CNhs14601_ctss_fwd MyoblastToMyotubes_Day06D2+ Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor2_CNhs14601_13510-145D9_forward Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor2_CNhs14568_ctss_rev MyoblastToMyotubes_Day01D2- Myoblast differentiation to myotubes, day01, control donor2_CNhs14568_13479-145A5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor2_CNhs14568_ctss_fwd MyoblastToMyotubes_Day01D2+ Myoblast differentiation to myotubes, day01, control donor2_CNhs14568_13479-145A5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep2_CNhs13631_ctss_rev MscAdipogenicInduction_Day14Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep2_CNhs13631_13278-142F2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep2_CNhs13631_ctss_fwd MscAdipogenicInduction_Day14Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep2_CNhs13631_13278-142F2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep2_CNhs13623_ctss_rev MscAdipogenicInduction_Day04Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep2_CNhs13623_13269-142E2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep2_CNhs13623_ctss_fwd MscAdipogenicInduction_Day04Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep2_CNhs13623_13269-142E2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep1_CNhs13615_ctss_rev MscAdipogenicInduction_Day01Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep1_CNhs13615_13262-142D4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep1_CNhs13615_ctss_fwd MscAdipogenicInduction_Day01Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep1_CNhs13615_13262-142D4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep3_CNhs13614_ctss_rev MscAdipogenicInduction_12hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep3_CNhs13614_13261-142D3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep3_CNhs13614_ctss_fwd MscAdipogenicInduction_12hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep3_CNhs13614_13261-142D3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep2_CNhs13613_ctss_rev MscAdipogenicInduction_12hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep2_CNhs13613_13260-142D2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep2_CNhs13613_ctss_fwd MscAdipogenicInduction_12hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep2_CNhs13613_13260-142D2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep1_CNhs13612_ctss_rev MscAdipogenicInduction_12hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep1_CNhs13612_13259-142D1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep1_CNhs13612_ctss_fwd MscAdipogenicInduction_12hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep1_CNhs13612_13259-142D1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep2_CNhs13610_ctss_rev MscAdipogenicInduction_03hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep2_CNhs13610_13257-142C8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep2_CNhs13610_ctss_fwd MscAdipogenicInduction_03hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep2_CNhs13610_13257-142C8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep2_CNhs13607_ctss_rev MscAdipogenicInduction_02hr30minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep2_CNhs13607_13254-142C5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep2_CNhs13607_ctss_fwd MscAdipogenicInduction_02hr30minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep2_CNhs13607_13254-142C5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep3_CNhs13605_ctss_rev MscAdipogenicInduction_02hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep3_CNhs13605_13252-142C3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep3_CNhs13605_ctss_fwd MscAdipogenicInduction_02hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep3_CNhs13605_13252-142C3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep3_CNhs13599_ctss_rev MscAdipogenicInduction_01hr20minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep3_CNhs13599_13246-142B6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep3_CNhs13599_ctss_fwd MscAdipogenicInduction_01hr20minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep3_CNhs13599_13246-142B6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep2_CNhs13598_ctss_rev MscAdipogenicInduction_01hr20minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep2_CNhs13598_13245-142B5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep2_CNhs13598_ctss_fwd MscAdipogenicInduction_01hr20minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep2_CNhs13598_13245-142B5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep1_CNhs13434_ctss_rev MscAdipogenicInduction_01hr20minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep1_CNhs13434_13244-142B4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep1_CNhs13434_ctss_fwd MscAdipogenicInduction_01hr20minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep1_CNhs13434_13244-142B4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep3_CNhs13427_ctss_rev MscAdipogenicInduction_00hr30minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep3_CNhs13427_13237-142A6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep3_CNhs13427_ctss_fwd MscAdipogenicInduction_00hr30minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep3_CNhs13427_13237-142A6_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor4227_121Ud_24h_CNhs13643_ctss_rev MonocyteMacrophageUdornInfluenza_24hr00minD4- Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor4 (227_121:Ud_24h)_CNhs13643_13314-143A2_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor4227_121Ud_24h_CNhs13643_ctss_fwd MonocyteMacrophageUdornInfluenza_24hr00minD4+ Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor4 (227_121:Ud_24h)_CNhs13643_13314-143A2_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor2150_120Ud_2h_CNhs13647_ctss_rev MonocyteMacrophageUdornInfluenza_02hr00minD2- Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor2 (150_120:Ud_2h)_CNhs13647_13318-143A6_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor2150_120Ud_2h_CNhs13647_ctss_fwd MonocyteMacrophageUdornInfluenza_02hr00minD2+ Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor2 (150_120:Ud_2h)_CNhs13647_13318-143A6_forward Regulation 
MelanocyteDonor3MC3_CNhs13406_ctss_rev MelanocyteD3- Melanocyte, donor3 (MC+3)_CNhs13406_12837-137B2_reverse Regulation 
MelanocyteDonor3MC3_CNhs13406_ctss_fwd MelanocyteD3+ Melanocyte, donor3 (MC+3)_CNhs13406_12837-137B2_forward Regulation 
MelanocyteDonor2MC2_CNhs13156_ctss_rev MelanocyteD2- Melanocyte, donor2 (MC+2)_CNhs13156_12739-135I3_reverse Regulation 
MelanocyteDonor2MC2_CNhs13156_ctss_fwd MelanocyteD2+ Melanocyte, donor2 (MC+2)_CNhs13156_12739-135I3_forward Regulation 
MelanocyteDonor1MC1_CNhs12816_ctss_rev MelanocyteD1- Melanocyte, donor1 (MC+1)_CNhs12816_12641-134G4_reverse Regulation 
MelanocyteDonor1MC1_CNhs12816_ctss_fwd MelanocyteD1+ Melanocyte, donor1 (MC+1)_CNhs12816_12641-134G4_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep1_CNhs13659_ctss_rev Hes3-gfpCardiomyocyticInduction_Day07Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep1_CNhs13659_13334-143C4_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep1_CNhs13659_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day07Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep1_CNhs13659_13334-143C4_forward Regulation 
H9EmbryonicStemCellsBiolRep3H9ES3_CNhs12837_ctss_rev H9EmbryonicStemCellsBr3- H9 Embryonic Stem cells, biol_rep3 (H9ES-3)_CNhs12837_12822-136I5_reverse Regulation 
H9EmbryonicStemCellsBiolRep3H9ES3_CNhs12837_ctss_fwd H9EmbryonicStemCellsBr3+ H9 Embryonic Stem cells, biol_rep3 (H9ES-3)_CNhs12837_12822-136I5_forward Regulation 
H9EmbryonicStemCellsBiolRep2H9ES2_CNhs12824_ctss_rev H9EmbryonicStemCellsBr2- H9 Embryonic Stem cells, biol_rep2 (H9ES-2)_CNhs12824_12724-135G6_reverse Regulation 
H9EmbryonicStemCellsBiolRep2H9ES2_CNhs12824_ctss_fwd H9EmbryonicStemCellsBr2+ H9 Embryonic Stem cells, biol_rep2 (H9ES-2)_CNhs12824_12724-135G6_forward Regulation 
H9EmbryonicStemCellsBiolRep1H9ES1_CNhs11917_ctss_rev H9EmbryonicStemCellsBr1- H9 Embryonic Stem cells, biol_rep1 (H9ES-1)_CNhs11917_12626-134E7_reverse Regulation 
H9EmbryonicStemCellsBiolRep1H9ES1_CNhs11917_ctss_fwd H9EmbryonicStemCellsBr1+ H9 Embryonic Stem cells, biol_rep1 (H9ES-1)_CNhs11917_12626-134E7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep3LK57_CNhs13585_ctss_rev AorticSmsToIL1b_05hrBr3- Aortic smooth muscle cell response to IL1b, 05hr, biol_rep3 (LK57)_CNhs13585_12856-137D3_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep3LK57_CNhs13585_ctss_fwd AorticSmsToIL1b_05hrBr3+ Aortic smooth muscle cell response to IL1b, 05hr, biol_rep3 (LK57)_CNhs13585_12856-137D3_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep3LK51_CNhs13583_ctss_rev AorticSmsToIL1b_03hrBr3- Aortic smooth muscle cell response to IL1b, 03hr, biol_rep3 (LK51)_CNhs13583_12854-137D1_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep3LK51_CNhs13583_ctss_fwd AorticSmsToIL1b_03hrBr3+ Aortic smooth muscle cell response to IL1b, 03hr, biol_rep3 (LK51)_CNhs13583_12854-137D1_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep1LK46_CNhs13354_ctss_rev AorticSmsToIL1b_02hrBr1- Aortic smooth muscle cell response to IL1b, 02hr, biol_rep1 (LK46)_CNhs13354_12657-134I2_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep1LK46_CNhs13354_ctss_fwd AorticSmsToIL1b_02hrBr1+ Aortic smooth muscle cell response to IL1b, 02hr, biol_rep1 (LK46)_CNhs13354_12657-134I2_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep3LK45_CNhs13581_ctss_rev AorticSmsToIL1b_01hrBr3- Aortic smooth muscle cell response to IL1b, 01hr, biol_rep3 (LK45)_CNhs13581_12852-137C8_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep3LK45_CNhs13581_ctss_fwd AorticSmsToIL1b_01hrBr3+ Aortic smooth muscle cell response to IL1b, 01hr, biol_rep3 (LK45)_CNhs13581_12852-137C8_forward Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep3LK24_CNhs13574_ctss_rev AorticSmsToFgf2_04hrBr3- Aortic smooth muscle cell response to FGF2, 04hr, biol_rep3 (LK24)_CNhs13574_12845-137C1_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep3LK24_CNhs13574_ctss_fwd AorticSmsToFgf2_04hrBr3+ Aortic smooth muscle cell response to FGF2, 04hr, biol_rep3 (LK24)_CNhs13574_12845-137C1_forward Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep2LK23_CNhs13365_ctss_rev AorticSmsToFgf2_04hrBr2- Aortic smooth muscle cell response to FGF2, 04hr, biol_rep2 (LK23)_CNhs13365_12747-136A2_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep2LK23_CNhs13365_ctss_fwd AorticSmsToFgf2_04hrBr2+ Aortic smooth muscle cell response to FGF2, 04hr, biol_rep2 (LK23)_CNhs13365_12747-136A2_forward Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep1LK22_CNhs13346_ctss_rev AorticSmsToFgf2_04hrBr1- Aortic smooth muscle cell response to FGF2, 04hr, biol_rep1 (LK22)_CNhs13346_12649-134H3_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep1LK22_CNhs13346_ctss_fwd AorticSmsToFgf2_04hrBr1+ Aortic smooth muscle cell response to FGF2, 04hr, biol_rep1 (LK22)_CNhs13346_12649-134H3_forward Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep2LK14_CNhs13362_ctss_rev AorticSmsToFgf2_01hrBr2- Aortic smooth muscle cell response to FGF2, 01hr, biol_rep2 (LK14)_CNhs13362_12744-135I8_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep2LK14_CNhs13362_ctss_fwd AorticSmsToFgf2_01hrBr2+ Aortic smooth muscle cell response to FGF2, 01hr, biol_rep2 (LK14)_CNhs13362_12744-135I8_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep3LK3_CNhs13567_ctss_rev AorticSmsToFgf2_00hr00minBr3- Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep3 (LK3)_CNhs13567_12838-137B3_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep3LK3_CNhs13567_ctss_fwd AorticSmsToFgf2_00hr00minBr3+ Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep3 (LK3)_CNhs13567_12838-137B3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep1_CNhs12564_ctss_rev Mcf7ToEgf1_00hr00minBr1- MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep1_CNhs12564_13031-139E7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep1_CNhs12564_ctss_fwd Mcf7ToEgf1_00hr00minBr1+ MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep1_CNhs12564_13031-139E7_forward Regulation 
WholeBloodRibopureDonor090612Donation3_CNhs11949_ctss_rev WholeBloodD090612Dn3- Whole blood (ribopure), donor090612, donation3_CNhs11949_12184-129A6_reverse Regulation 
WholeBloodRibopureDonor090612Donation3_CNhs11949_ctss_fwd WholeBloodD090612Dn3+ Whole blood (ribopure), donor090612, donation3_CNhs11949_12184-129A6_forward Regulation 
WholeBloodRibopureDonor090612Donation2_CNhs11673_ctss_rev WholeBloodD090612Dn2- Whole blood (ribopure), donor090612, donation2_CNhs11673_12183-129A5_reverse Regulation 
WholeBloodRibopureDonor090612Donation2_CNhs11673_ctss_fwd WholeBloodD090612Dn2+ Whole blood (ribopure), donor090612, donation2_CNhs11673_12183-129A5_forward Regulation 
WholeBloodRibopureDonor090612Donation1_CNhs11672_ctss_rev WholeBloodD090612Dn1- Whole blood (ribopure), donor090612, donation1_CNhs11672_12182-129A4_reverse Regulation 
WholeBloodRibopureDonor090612Donation1_CNhs11672_ctss_fwd WholeBloodD090612Dn1+ Whole blood (ribopure), donor090612, donation1_CNhs11672_12182-129A4_forward Regulation 
WholeBloodRibopureDonor090325Donation2_CNhs11076_ctss_rev WholeBloodD090325Dn2- Whole blood (ribopure), donor090325, donation2_CNhs11076_12177-128I8_reverse Regulation 
WholeBloodRibopureDonor090325Donation2_CNhs11076_ctss_fwd WholeBloodD090325Dn2+ Whole blood (ribopure), donor090325, donation2_CNhs11076_12177-128I8_forward Regulation 
WholeBloodRibopureDonor090325Donation1_CNhs11075_ctss_rev WholeBloodD090325Dn1- Whole blood (ribopure), donor090325, donation1_CNhs11075_12176-128I7_reverse Regulation 
WholeBloodRibopureDonor090325Donation1_CNhs11075_ctss_fwd WholeBloodD090325Dn1+ Whole blood (ribopure), donor090325, donation1_CNhs11075_12176-128I7_forward Regulation 
WholeBloodRibopureDonor090309Donation3_CNhs11948_ctss_rev WholeBloodD090309Dn3- Whole blood (ribopure), donor090309, donation3_CNhs11948_12181-129A3_reverse Regulation 
WholeBloodRibopureDonor090309Donation3_CNhs11948_ctss_fwd WholeBloodD090309Dn3+ Whole blood (ribopure), donor090309, donation3_CNhs11948_12181-129A3_forward Regulation 
WholeBloodRibopureDonor090309Donation2_CNhs11671_ctss_rev WholeBloodD090309Dn2- Whole blood (ribopure), donor090309, donation2_CNhs11671_12180-129A2_reverse Regulation 
WholeBloodRibopureDonor090309Donation2_CNhs11671_ctss_fwd WholeBloodD090309Dn2+ Whole blood (ribopure), donor090309, donation2_CNhs11671_12180-129A2_forward Regulation 
WholeBloodRibopureDonor090309Donation1_CNhs11675_ctss_rev WholeBloodD090309Dn1- Whole blood (ribopure), donor090309, donation1_CNhs11675_12179-129A1_reverse Regulation 
WholeBloodRibopureDonor090309Donation1_CNhs11675_ctss_fwd WholeBloodD090309Dn1+ Whole blood (ribopure), donor090309, donation1_CNhs11675_12179-129A1_forward Regulation 
UrothelialCellsDonor3_CNhs12122_ctss_rev UrothelialCellsD3- Urothelial Cells, donor3_CNhs12122_11681-122H7_reverse Regulation 
UrothelialCellsDonor3_CNhs12122_ctss_fwd UrothelialCellsD3+ Urothelial Cells, donor3_CNhs12122_11681-122H7_forward Regulation 
UrothelialCellsDonor2_CNhs12091_ctss_rev UrothelialCellsD2- Urothelial Cells, donor2_CNhs12091_11600-120H7_reverse Regulation 
UrothelialCellsDonor2_CNhs12091_ctss_fwd UrothelialCellsD2+ Urothelial Cells, donor2_CNhs12091_11600-120H7_forward Regulation 
UrothelialCellsDonor1_CNhs11334_ctss_rev UrothelialCellsD1- Urothelial Cells, donor1_CNhs11334_11520-119H8_reverse Regulation 
UrothelialCellsDonor1_CNhs11334_ctss_fwd UrothelialCellsD1+ Urothelial Cells, donor1_CNhs11334_11520-119H8_forward Regulation 
UrothelialCellsDonor0_CNhs10843_ctss_rev UrothelialCellsD0- Urothelial cells, donor0_CNhs10843_11216-116B1_reverse Regulation 
UrothelialCellsDonor0_CNhs10843_ctss_fwd UrothelialCellsD0+ Urothelial cells, donor0_CNhs10843_11216-116B1_forward Regulation 
TrachealEpithelialCellsDonor3_CNhs12051_ctss_rev TrachealEpithelialCellsD3- Tracheal Epithelial Cells, donor3_CNhs12051_11441-118I1_reverse Regulation 
TrachealEpithelialCellsDonor3_CNhs12051_ctss_fwd TrachealEpithelialCellsD3+ Tracheal Epithelial Cells, donor3_CNhs12051_11441-118I1_forward Regulation 
TrachealEpithelialCellsDonor2_CNhs11993_ctss_rev TrachealEpithelialCellsD2- Tracheal Epithelial Cells, donor2_CNhs11993_11369-118A1_reverse Regulation 
TrachealEpithelialCellsDonor2_CNhs11993_ctss_fwd TrachealEpithelialCellsD2+ Tracheal Epithelial Cells, donor2_CNhs11993_11369-118A1_forward Regulation 
TrachealEpithelialCellsDonor1_CNhs11092_ctss_rev TrachealEpithelialCellsD1- Tracheal Epithelial Cells, donor1_CNhs11092_11292-117A5_reverse Regulation 
TrachealEpithelialCellsDonor1_CNhs11092_ctss_fwd TrachealEpithelialCellsD1+ Tracheal Epithelial Cells, donor1_CNhs11092_11292-117A5_forward Regulation 
TrabecularMeshworkCellsDonor3_CNhs12124_ctss_rev TrabecularMeshworkCellsD3- Trabecular Meshwork Cells, donor3_CNhs12124_11693-123A1_reverse Regulation 
TrabecularMeshworkCellsDonor3_CNhs12124_ctss_fwd TrabecularMeshworkCellsD3+ Trabecular Meshwork Cells, donor3_CNhs12124_11693-123A1_forward Regulation 
TrabecularMeshworkCellsDonor2_CNhs12097_ctss_rev TrabecularMeshworkCellsD2- Trabecular Meshwork Cells, donor2_CNhs12097_11612-122A1_reverse Regulation 
TrabecularMeshworkCellsDonor2_CNhs12097_ctss_fwd TrabecularMeshworkCellsD2+ Trabecular Meshwork Cells, donor2_CNhs12097_11612-122A1_forward Regulation 
TrabecularMeshworkCellsDonor1_CNhs11340_ctss_rev TrabecularMeshworkCellsD1- Trabecular Meshwork Cells, donor1_CNhs11340_11532-120A2_reverse Regulation 
TrabecularMeshworkCellsDonor1_CNhs11340_ctss_fwd TrabecularMeshworkCellsD1+ Trabecular Meshwork Cells, donor1_CNhs11340_11532-120A2_forward Regulation 
TenocyteDonor3_CNhs12641_ctss_rev TenocyteD3- tenocyte, donor3_CNhs12641_11768-123I4_reverse Regulation 
TenocyteDonor3_CNhs12641_ctss_fwd TenocyteD3+ tenocyte, donor3_CNhs12641_11768-123I4_forward Regulation 
TenocyteDonor2_CNhs12640_ctss_rev TenocyteD2- tenocyte, donor2_CNhs12640_11765-123I1_reverse Regulation 
TenocyteDonor2_CNhs12640_ctss_fwd TenocyteD2+ tenocyte, donor2_CNhs12640_11765-123I1_forward Regulation 
TenocyteDonor1_CNhs12639_ctss_rev TenocyteD1- tenocyte, donor1_CNhs12639_11763-123H8_reverse Regulation 
TenocyteDonor1_CNhs12639_ctss_fwd TenocyteD1+ tenocyte, donor1_CNhs12639_11763-123H8_forward Regulation 
SynoviocyteDonor3_CNhs12050_ctss_rev SynoviocyteD3- Synoviocyte, donor3_CNhs12050_11440-118H9_reverse Regulation 
SynoviocyteDonor3_CNhs12050_ctss_fwd SynoviocyteD3+ Synoviocyte, donor3_CNhs12050_11440-118H9_forward Regulation 
SynoviocyteDonor2_CNhs11992_ctss_rev SynoviocyteD2- Synoviocyte, donor2_CNhs11992_11368-117I9_reverse Regulation 
SynoviocyteDonor2_CNhs11992_ctss_fwd SynoviocyteD2+ Synoviocyte, donor2_CNhs11992_11368-117I9_forward Regulation 
SynoviocyteDonor1_CNhs11068_ctss_rev SynoviocyteD1- Synoviocyte, donor1_CNhs11068_11291-117A4_reverse Regulation 
SynoviocyteDonor1_CNhs11068_ctss_fwd SynoviocyteD1+ Synoviocyte, donor1_CNhs11068_11291-117A4_forward Regulation 
SmoothMuscleCellsUterineDonor3_CNhs11927_ctss_rev SmcUterineD3- Smooth Muscle Cells - Uterine, donor3_CNhs11927_11466-119B8_reverse Regulation 
SmoothMuscleCellsUterineDonor3_CNhs11927_ctss_fwd SmcUterineD3+ Smooth Muscle Cells - Uterine, donor3_CNhs11927_11466-119B8_forward Regulation 
SmoothMuscleCellsUterineDonor1_CNhs11921_ctss_rev SmcUterineD1- Smooth Muscle Cells - Uterine, donor1_CNhs11921_11258-116F7_reverse Regulation 
SmoothMuscleCellsUterineDonor1_CNhs11921_ctss_fwd SmcUterineD1+ Smooth Muscle Cells - Uterine, donor1_CNhs11921_11258-116F7_forward Regulation 
SmoothMuscleCellsUmbilicalVeinDonor3_CNhs13076_ctss_rev SmcUmbilicalVeinD3- Smooth Muscle Cells - Umbilical Vein, donor3_CNhs13076_11702-123B1_reverse Regulation 
SmoothMuscleCellsUmbilicalVeinDonor3_CNhs13076_ctss_fwd SmcUmbilicalVeinD3+ Smooth Muscle Cells - Umbilical Vein, donor3_CNhs13076_11702-123B1_forward Regulation 
SmoothMuscleCellsUmbilicalVeinDonor2_CNhs12569_ctss_rev SmcUmbilicalVeinD2- Smooth Muscle Cells - Umbilical Vein, donor2_CNhs12569_11621-122B1_reverse Regulation 
SmoothMuscleCellsUmbilicalVeinDonor2_CNhs12569_ctss_fwd SmcUmbilicalVeinD2+ Smooth Muscle Cells - Umbilical Vein, donor2_CNhs12569_11621-122B1_forward Regulation 
SmoothMuscleCellsUmbilicalVeinDonor1_CNhs12597_ctss_rev SmcUmbilicalVeinD1- Smooth Muscle Cells - Umbilical Vein, donor1_CNhs12597_11541-120B2_reverse Regulation 
SmoothMuscleCellsUmbilicalVeinDonor1_CNhs12597_ctss_fwd SmcUmbilicalVeinD1+ Smooth Muscle Cells - Umbilical Vein, donor1_CNhs12597_11541-120B2_forward Regulation 
SmoothMuscleCellsUmbilicalArteryDonor3_CNhs12049_ctss_rev SmcUmbilicalArteryD3- Smooth Muscle Cells - Umbilical Artery, donor3_CNhs12049_11439-118H8_reverse Regulation 
SmoothMuscleCellsUmbilicalArteryDonor3_CNhs12049_ctss_fwd SmcUmbilicalArteryD3+ Smooth Muscle Cells - Umbilical Artery, donor3_CNhs12049_11439-118H8_forward Regulation 
SmoothMuscleCellsUmbilicalArteryDonor2_CNhs11991_ctss_rev SmcUmbilicalArteryD2- Smooth Muscle Cells - Umbilical Artery, donor2_CNhs11991_11367-117I8_reverse Regulation 
SmoothMuscleCellsUmbilicalArteryDonor2_CNhs11991_ctss_fwd SmcUmbilicalArteryD2+ Smooth Muscle Cells - Umbilical Artery, donor2_CNhs11991_11367-117I8_forward Regulation 
SmoothMuscleCellsUmbilicalArteryDonor1_CNhs11091_ctss_rev SmcUmbilicalArteryD1- Smooth Muscle Cells - Umbilical Artery, donor1_CNhs11091_11290-117A3_reverse Regulation 
SmoothMuscleCellsUmbilicalArteryDonor1_CNhs11091_ctss_fwd SmcUmbilicalArteryD1+ Smooth Muscle Cells - Umbilical Artery, donor1_CNhs11091_11290-117A3_forward Regulation 
SmoothMuscleCellsUmbilicalArteryDonor0_CNhs10839_ctss_rev SmcUmbilicalArteryD0- Smooth Muscle Cells - Umbilical artery, donor0_CNhs10839_11212-116A6_reverse Regulation 
SmoothMuscleCellsUmbilicalArteryDonor0_CNhs10839_ctss_fwd SmcUmbilicalArteryD0+ Smooth Muscle Cells - Umbilical artery, donor0_CNhs10839_11212-116A6_forward Regulation 
SmoothMuscleCellsTrachealDonor3_CNhs12894_ctss_rev SmcTrachealD3- Smooth Muscle Cells - Tracheal, donor3_CNhs12894_11674-122G9_reverse Regulation 
SmoothMuscleCellsTrachealDonor3_CNhs12894_ctss_fwd SmcTrachealD3+ Smooth Muscle Cells - Tracheal, donor3_CNhs12894_11674-122G9_forward Regulation 
SmoothMuscleCellsTrachealDonor2_CNhs12567_ctss_rev SmcTrachealD2- Smooth Muscle Cells - Tracheal, donor2_CNhs12567_11593-120G9_reverse Regulation 
SmoothMuscleCellsTrachealDonor2_CNhs12567_ctss_fwd SmcTrachealD2+ Smooth Muscle Cells - Tracheal, donor2_CNhs12567_11593-120G9_forward Regulation 
SmoothMuscleCellsTrachealDonor1_CNhs11329_ctss_rev SmcTrachealD1- Smooth Muscle Cells - Tracheal, donor1_CNhs11329_11513-119H1_reverse Regulation 
SmoothMuscleCellsTrachealDonor1_CNhs11329_ctss_fwd SmcTrachealD1+ Smooth Muscle Cells - Tracheal, donor1_CNhs11329_11513-119H1_forward Regulation 
SmoothMuscleCellsSubclavianArteryDonor3_CNhs12048_ctss_rev SmcSubclavianArteryD3- Smooth Muscle Cells - Subclavian Artery, donor3_CNhs12048_11438-118H7_reverse Regulation 
SmoothMuscleCellsSubclavianArteryDonor3_CNhs12048_ctss_fwd SmcSubclavianArteryD3+ Smooth Muscle Cells - Subclavian Artery, donor3_CNhs12048_11438-118H7_forward Regulation 
SmoothMuscleCellsSubclavianArteryDonor2_CNhs11990_ctss_rev SmcSubclavianArteryD2- Smooth Muscle Cells - Subclavian Artery, donor2_CNhs11990_11366-117I7_reverse Regulation 
SmoothMuscleCellsSubclavianArteryDonor2_CNhs11990_ctss_fwd SmcSubclavianArteryD2+ Smooth Muscle Cells - Subclavian Artery, donor2_CNhs11990_11366-117I7_forward Regulation 
SmoothMuscleCellsSubclavianArteryDonor1_CNhs11090_ctss_rev SmcSubclavianArteryD1- Smooth Muscle Cells - Subclavian Artery, donor1_CNhs11090_11289-117A2_reverse Regulation 
SmoothMuscleCellsSubclavianArteryDonor1_CNhs11090_ctss_fwd SmcSubclavianArteryD1+ Smooth Muscle Cells - Subclavian Artery, donor1_CNhs11090_11289-117A2_forward Regulation 
SmoothMuscleCellsPulmonaryArteryDonor3_CNhs12047_ctss_rev SmcPulmonaryArteryD3- Smooth Muscle Cells - Pulmonary Artery, donor3_CNhs12047_11437-118H6_reverse Regulation 
SmoothMuscleCellsPulmonaryArteryDonor3_CNhs12047_ctss_fwd SmcPulmonaryArteryD3+ Smooth Muscle Cells - Pulmonary Artery, donor3_CNhs12047_11437-118H6_forward Regulation 
SmoothMuscleCellsPulmonaryArteryDonor2_CNhs11989_ctss_rev SmcPulmonaryArteryD2- Smooth Muscle Cells - Pulmonary Artery, donor2_CNhs11989_11365-117I6_reverse Regulation 
SmoothMuscleCellsPulmonaryArteryDonor2_CNhs11989_ctss_fwd SmcPulmonaryArteryD2+ Smooth Muscle Cells - Pulmonary Artery, donor2_CNhs11989_11365-117I6_forward Regulation 
SmoothMuscleCellsPulmonaryArteryDonor1_CNhs11089_ctss_rev SmcPulmonaryArteryD1- Smooth Muscle Cells - Pulmonary Artery, donor1_CNhs11089_11288-117A1_reverse Regulation 
SmoothMuscleCellsPulmonaryArteryDonor1_CNhs11089_ctss_fwd SmcPulmonaryArteryD1+ Smooth Muscle Cells - Pulmonary Artery, donor1_CNhs11089_11288-117A1_forward Regulation 
SmoothMuscleCellsProstateDonor3_CNhs11910_ctss_rev SmcProstateD3- Smooth Muscle Cells - Prostate, donor3_CNhs11910_11465-119B7_reverse Regulation 
SmoothMuscleCellsProstateDonor3_CNhs11910_ctss_fwd SmcProstateD3+ Smooth Muscle Cells - Prostate, donor3_CNhs11910_11465-119B7_forward Regulation 
SmoothMuscleCellsProstateDonor2_CNhs11976_ctss_rev SmcProstateD2- Smooth Muscle Cells - Prostate, donor2_CNhs11976_11335-117F3_reverse Regulation 
SmoothMuscleCellsProstateDonor2_CNhs11976_ctss_fwd SmcProstateD2+ Smooth Muscle Cells - Prostate, donor2_CNhs11976_11335-117F3_forward Regulation 
SmoothMuscleCellsProstateDonor1_CNhs11920_ctss_rev SmcProstateD1- Smooth Muscle Cells - Prostate, donor1_CNhs11920_11257-116F6_reverse Regulation 
SmoothMuscleCellsProstateDonor1_CNhs11920_ctss_fwd SmcProstateD1+ Smooth Muscle Cells - Prostate, donor1_CNhs11920_11257-116F6_forward Regulation 
SmoothMuscleCellsIntestinalDonor1_CNhs12595_ctss_rev SmcIntestinalD1- Smooth Muscle Cells - Intestinal, donor1_CNhs12595_11509-119G6_reverse Regulation 
SmoothMuscleCellsIntestinalDonor1_CNhs12595_ctss_fwd SmcIntestinalD1+ Smooth Muscle Cells - Intestinal, donor1_CNhs12595_11509-119G6_forward Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor3_CNhs12046_ctss_rev SmcInternalThoracicArteryD3- Smooth Muscle Cells - Internal Thoracic Artery, donor3_CNhs12046_11436-118H5_reverse Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor3_CNhs12046_ctss_fwd SmcInternalThoracicArteryD3+ Smooth Muscle Cells - Internal Thoracic Artery, donor3_CNhs12046_11436-118H5_forward Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor2_CNhs11988_ctss_rev SmcInternalThoracicArteryD2- Smooth Muscle Cells - Internal Thoracic Artery, donor2_CNhs11988_11364-117I5_reverse Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor2_CNhs11988_ctss_fwd SmcInternalThoracicArteryD2+ Smooth Muscle Cells - Internal Thoracic Artery, donor2_CNhs11988_11364-117I5_forward Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor1_CNhs11067_ctss_rev SmcInternalThoracicArteryD1- Smooth Muscle Cells - Internal Thoracic Artery, donor1_CNhs11067_11287-116I9_reverse Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor1_CNhs11067_ctss_fwd SmcInternalThoracicArteryD1+ Smooth Muscle Cells - Internal Thoracic Artery, donor1_CNhs11067_11287-116I9_forward Regulation 
SmoothMuscleCellsEsophagealDonor2_CNhs12727_ctss_rev SmcEsophagealD2- Smooth Muscle Cells - Esophageal, donor2_CNhs12727_11588-120G4_reverse Regulation 
SmoothMuscleCellsEsophagealDonor2_CNhs12727_ctss_fwd SmcEsophagealD2+ Smooth Muscle Cells - Esophageal, donor2_CNhs12727_11588-120G4_forward Regulation 
SmoothMuscleCellsEsophagealDonor1_CNhs11324_ctss_rev SmcEsophagealD1- Smooth Muscle Cells - Esophageal, donor1_CNhs11324_11508-119G5_reverse Regulation 
SmoothMuscleCellsEsophagealDonor1_CNhs11324_ctss_fwd SmcEsophagealD1+ Smooth Muscle Cells - Esophageal, donor1_CNhs11324_11508-119G5_forward Regulation 
SmoothMuscleCellsCoronaryArteryDonor3_CNhs12045_ctss_rev SmcCoronaryArteryD3- Smooth Muscle Cells - Coronary Artery, donor3_CNhs12045_11435-118H4_reverse Regulation 
SmoothMuscleCellsCoronaryArteryDonor3_CNhs12045_ctss_fwd SmcCoronaryArteryD3+ Smooth Muscle Cells - Coronary Artery, donor3_CNhs12045_11435-118H4_forward Regulation 
SmoothMuscleCellsCoronaryArteryDonor2_CNhs11987_ctss_rev SmcCoronaryArteryD2- Smooth Muscle Cells - Coronary Artery, donor2_CNhs11987_11363-117I4_reverse Regulation 
SmoothMuscleCellsCoronaryArteryDonor2_CNhs11987_ctss_fwd SmcCoronaryArteryD2+ Smooth Muscle Cells - Coronary Artery, donor2_CNhs11987_11363-117I4_forward Regulation 
SmoothMuscleCellsCoronaryArteryDonor1_CNhs11088_ctss_rev SmcCoronaryArteryD1- Smooth Muscle Cells - Coronary Artery, donor1_CNhs11088_11286-116I8_reverse Regulation 
SmoothMuscleCellsCoronaryArteryDonor1_CNhs11088_ctss_fwd SmcCoronaryArteryD1+ Smooth Muscle Cells - Coronary Artery, donor1_CNhs11088_11286-116I8_forward Regulation 
SmoothMuscleCellsColonicDonor3_CNhs12007_ctss_rev SmcColonicD3- Smooth Muscle Cells - Colonic, donor3_CNhs12007_11396-118D1_reverse Regulation 
SmoothMuscleCellsColonicDonor3_CNhs12007_ctss_fwd SmcColonicD3+ Smooth Muscle Cells - Colonic, donor3_CNhs12007_11396-118D1_forward Regulation 
SmoothMuscleCellsColonicDonor2_CNhs11963_ctss_rev SmcColonicD2- Smooth Muscle Cells - Colonic, donor2_CNhs11963_11320-117D6_reverse Regulation 
SmoothMuscleCellsColonicDonor2_CNhs11963_ctss_fwd SmcColonicD2+ Smooth Muscle Cells - Colonic, donor2_CNhs11963_11320-117D6_forward Regulation 
SmoothMuscleCellsColonicDonor1_CNhs10868_ctss_rev SmcColonicD1- Smooth Muscle Cells - Colonic, donor1_CNhs10868_11239-116D6_reverse Regulation 
SmoothMuscleCellsColonicDonor1_CNhs10868_ctss_fwd SmcColonicD1+ Smooth Muscle Cells - Colonic, donor1_CNhs10868_11239-116D6_forward Regulation 
SmoothMuscleCellsCarotidDonor3_CNhs12044_ctss_rev SmcCarotidD3- Smooth Muscle Cells - Carotid, donor3_CNhs12044_11434-118H3_reverse Regulation 
SmoothMuscleCellsCarotidDonor3_CNhs12044_ctss_fwd SmcCarotidD3+ Smooth Muscle Cells - Carotid, donor3_CNhs12044_11434-118H3_forward Regulation 
SmoothMuscleCellsCarotidDonor2_CNhs11986_ctss_rev SmcCarotidD2- Smooth Muscle Cells - Carotid, donor2_CNhs11986_11362-117I3_reverse Regulation 
SmoothMuscleCellsCarotidDonor2_CNhs11986_ctss_fwd SmcCarotidD2+ Smooth Muscle Cells - Carotid, donor2_CNhs11986_11362-117I3_forward Regulation 
SmoothMuscleCellsCarotidDonor1_CNhs11087_ctss_rev SmcCarotidD1- Smooth Muscle Cells - Carotid, donor1_CNhs11087_11285-116I7_reverse Regulation 
SmoothMuscleCellsCarotidDonor1_CNhs11087_ctss_fwd SmcCarotidD1+ Smooth Muscle Cells - Carotid, donor1_CNhs11087_11285-116I7_forward Regulation 
SmoothMuscleCellsBronchialDonor2_CNhs12348_ctss_rev SmcBronchialD2- Smooth Muscle Cells - Bronchial, donor2_CNhs12348_11592-120G8_reverse Regulation 
SmoothMuscleCellsBronchialDonor2_CNhs12348_ctss_fwd SmcBronchialD2+ Smooth Muscle Cells - Bronchial, donor2_CNhs12348_11592-120G8_forward Regulation 
SmoothMuscleCellsBronchialDonor1_CNhs11328_ctss_rev SmcBronchialD1- Smooth Muscle Cells - Bronchial, donor1_CNhs11328_11512-119G9_reverse Regulation 
SmoothMuscleCellsBronchialDonor1_CNhs11328_ctss_fwd SmcBronchialD1+ Smooth Muscle Cells - Bronchial, donor1_CNhs11328_11512-119G9_forward Regulation 
SmoothMuscleCellsBrainVascularDonor3_CNhs12004_ctss_rev SmcBrainVascularD3- Smooth Muscle Cells - Brain Vascular, donor3_CNhs12004_11391-118C5_reverse Regulation 
SmoothMuscleCellsBrainVascularDonor3_CNhs12004_ctss_fwd SmcBrainVascularD3+ Smooth Muscle Cells - Brain Vascular, donor3_CNhs12004_11391-118C5_forward Regulation 
SmoothMuscleCellsBrainVascularDonor2_CNhs11900_ctss_rev SmcBrainVascularD2- Smooth Muscle Cells - Brain Vascular, donor2_CNhs11900_11315-117D1_reverse Regulation 
SmoothMuscleCellsBrainVascularDonor2_CNhs11900_ctss_fwd SmcBrainVascularD2+ Smooth Muscle Cells - Brain Vascular, donor2_CNhs11900_11315-117D1_forward Regulation 
SmoothMuscleCellsBrainVascularDonor1_CNhs10863_ctss_rev SmcBrainVascularD1- Smooth Muscle Cells - Brain Vascular, donor1_CNhs10863_11234-116D1_reverse Regulation 
SmoothMuscleCellsBrainVascularDonor1_CNhs10863_ctss_fwd SmcBrainVascularD1+ Smooth Muscle Cells - Brain Vascular, donor1_CNhs10863_11234-116D1_forward Regulation 
SmoothMuscleCellsBrachiocephalicDonor3_CNhs12043_ctss_rev SmcBrachiocephalicD3- Smooth Muscle Cells - Brachiocephalic, donor3_CNhs12043_11433-118H2_reverse Regulation 
SmoothMuscleCellsBrachiocephalicDonor3_CNhs12043_ctss_fwd SmcBrachiocephalicD3+ Smooth Muscle Cells - Brachiocephalic, donor3_CNhs12043_11433-118H2_forward Regulation 
SmoothMuscleCellsBrachiocephalicDonor2_CNhs11985_ctss_rev SmcBrachiocephalicD2- Smooth Muscle Cells - Brachiocephalic, donor2_CNhs11985_11361-117I2_reverse Regulation 
SmoothMuscleCellsBrachiocephalicDonor2_CNhs11985_ctss_fwd SmcBrachiocephalicD2+ Smooth Muscle Cells - Brachiocephalic, donor2_CNhs11985_11361-117I2_forward Regulation 
SmoothMuscleCellsBrachiocephalicDonor1_CNhs11086_ctss_rev SmcBrachiocephalicD1- Smooth Muscle Cells - Brachiocephalic, donor1_CNhs11086_11284-116I6_reverse Regulation 
SmoothMuscleCellsBrachiocephalicDonor1_CNhs11086_ctss_fwd SmcBrachiocephalicD1+ Smooth Muscle Cells - Brachiocephalic, donor1_CNhs11086_11284-116I6_forward Regulation 
SmoothMuscleCellsBladderDonor1_CNhs12893_ctss_rev SmcBladderD1- Smooth Muscle Cells - Bladder, donor1_CNhs12893_11519-119H7_reverse Regulation 
SmoothMuscleCellsBladderDonor1_CNhs12893_ctss_fwd SmcBladderD1+ Smooth Muscle Cells - Bladder, donor1_CNhs12893_11519-119H7_forward Regulation 
SmoothMuscleCellsAorticDonor3_CNhs11309_ctss_rev SmcAorticCytofracD3- Smooth Muscle Cells - Aortic, donor3_CNhs11309_11432-118H1_reverse Regulation 
SmoothMuscleCellsAorticDonor3_CNhs11309_ctss_fwd SmcAorticCytofracD3+ Smooth Muscle Cells - Aortic, donor3_CNhs11309_11432-118H1_forward Regulation 
SmoothMuscleCellsAorticDonor2_CNhs11305_ctss_rev SmcAorticCytofracD2- Smooth Muscle Cells - Aortic, donor2_CNhs11305_11360-117I1_reverse Regulation 
SmoothMuscleCellsAorticDonor2_CNhs11305_ctss_fwd SmcAorticCytofracD2+ Smooth Muscle Cells - Aortic, donor2_CNhs11305_11360-117I1_forward Regulation 
SmoothMuscleCellsAorticDonor1_CNhs11085_ctss_rev SmcAorticCytofracD1- Smooth Muscle Cells - Aortic, donor1_CNhs11085_11283-116I5_reverse Regulation 
SmoothMuscleCellsAorticDonor1_CNhs11085_ctss_fwd SmcAorticCytofracD1+ Smooth Muscle Cells - Aortic, donor1_CNhs11085_11283-116I5_forward Regulation 
SmoothMuscleCellsAorticDonor0_CNhs10838_ctss_rev SmcAorticCytofracD0- Smooth Muscle Cells - Aortic, donor0_CNhs10838_11210-116A4_reverse Regulation 
SmoothMuscleCellsAorticDonor0_CNhs10838_ctss_fwd SmcAorticCytofracD0+ Smooth Muscle Cells - Aortic, donor0_CNhs10838_11210-116A4_forward Regulation 
SmoothMuscleCellsAirwayControlDonor4_CNhs14193_ctss_rev SmcAirwayControlD4- Smooth muscle cells - airway, control, donor4_CNhs14193_11969-126D7_reverse Regulation 
SmoothMuscleCellsAirwayControlDonor4_CNhs14193_ctss_fwd SmcAirwayControlD4+ Smooth muscle cells - airway, control, donor4_CNhs14193_11969-126D7_forward Regulation 
SmoothMuscleCellsAirwayControlDonor3_CNhs14192_ctss_rev SmcAirwayControlD3- Smooth muscle cells - airway, control, donor3_CNhs14192_11968-126D6_reverse Regulation 
SmoothMuscleCellsAirwayControlDonor3_CNhs14192_ctss_fwd SmcAirwayControlD3+ Smooth muscle cells - airway, control, donor3_CNhs14192_11968-126D6_forward Regulation 
SmoothMuscleCellsAirwayControlDonor2_CNhs14191_ctss_rev SmcAirwayControlD2- Smooth muscle cells - airway, control, donor2_CNhs14191_11967-126D5_reverse Regulation 
SmoothMuscleCellsAirwayControlDonor2_CNhs14191_ctss_fwd SmcAirwayControlD2+ Smooth muscle cells - airway, control, donor2_CNhs14191_11967-126D5_forward Regulation 
SmoothMuscleCellsAirwayControlDonor1_CNhs14190_ctss_rev SmcAirwayControlD1- Smooth muscle cells - airway, control, donor1_CNhs14190_11966-126D4_reverse Regulation 
SmoothMuscleCellsAirwayControlDonor1_CNhs14190_ctss_fwd SmcAirwayControlD1+ Smooth muscle cells - airway, control, donor1_CNhs14190_11966-126D4_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor6_CNhs14189_ctss_rev SmcAirwayAsthmaD6- Smooth muscle cells - airway, asthmatic, donor6_CNhs14189_11965-126D3_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor6_CNhs14189_ctss_fwd SmcAirwayAsthmaD6+ Smooth muscle cells - airway, asthmatic, donor6_CNhs14189_11965-126D3_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor5_CNhs14188_ctss_rev SmcAirwayAsthmaD5- Smooth muscle cells - airway, asthmatic, donor5_CNhs14188_11964-126D2_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor5_CNhs14188_ctss_fwd SmcAirwayAsthmaD5+ Smooth muscle cells - airway, asthmatic, donor5_CNhs14188_11964-126D2_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor4_CNhs14187_ctss_rev SmcAirwayAsthmaD4- Smooth muscle cells - airway, asthmatic, donor4_CNhs14187_11963-126D1_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor4_CNhs14187_ctss_fwd SmcAirwayAsthmaD4+ Smooth muscle cells - airway, asthmatic, donor4_CNhs14187_11963-126D1_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor3_CNhs14186_ctss_rev SmcAirwayAsthmaD3- Smooth muscle cells - airway, asthmatic, donor3_CNhs14186_11962-126C9_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor3_CNhs14186_ctss_fwd SmcAirwayAsthmaD3+ Smooth muscle cells - airway, asthmatic, donor3_CNhs14186_11962-126C9_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor2_CNhs14184_ctss_rev SmcAirwayAsthmaD2- Smooth muscle cells - airway, asthmatic, donor2_CNhs14184_11961-126C8_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor2_CNhs14184_ctss_fwd SmcAirwayAsthmaD2+ Smooth muscle cells - airway, asthmatic, donor2_CNhs14184_11961-126C8_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor1_CNhs14183_ctss_rev SmcAirwayAsthmaD1- Smooth muscle cells - airway, asthmatic, donor1_CNhs14183_11960-126C7_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor1_CNhs14183_ctss_fwd SmcAirwayAsthmaD1+ Smooth muscle cells - airway, asthmatic, donor1_CNhs14183_11960-126C7_forward Regulation 
SmallAirwayEpithelialCellsDonor3_CNhs12016_ctss_rev SmallAirwayEpithelialCellsD3- Small Airway Epithelial Cells, donor3_CNhs12016_11406-118E2_reverse Regulation 
SmallAirwayEpithelialCellsDonor3_CNhs12016_ctss_fwd SmallAirwayEpithelialCellsD3+ Small Airway Epithelial Cells, donor3_CNhs12016_11406-118E2_forward Regulation 
SmallAirwayEpithelialCellsDonor2_CNhs11975_ctss_rev SmallAirwayEpithelialCellsD2- Small Airway Epithelial Cells, donor2_CNhs11975_11334-117F2_reverse Regulation 
SmallAirwayEpithelialCellsDonor2_CNhs11975_ctss_fwd SmallAirwayEpithelialCellsD2+ Small Airway Epithelial Cells, donor2_CNhs11975_11334-117F2_forward Regulation 
SmallAirwayEpithelialCellsDonor1_CNhs10884_ctss_rev SmallAirwayEpithelialCellsD1- Small Airway Epithelial Cells, donor1_CNhs10884_11256-116F5_reverse Regulation 
SmallAirwayEpithelialCellsDonor1_CNhs10884_ctss_fwd SmallAirwayEpithelialCellsD1+ Small Airway Epithelial Cells, donor1_CNhs10884_11256-116F5_forward Regulation 
SkeletalMuscleSatelliteCellsDonor3_CNhs12008_ctss_rev SkeletalMuscleSatelliteCellsD3- Skeletal Muscle Satellite Cells, donor3_CNhs12008_11397-118D2_reverse Regulation 
SkeletalMuscleSatelliteCellsDonor3_CNhs12008_ctss_fwd SkeletalMuscleSatelliteCellsD3+ Skeletal Muscle Satellite Cells, donor3_CNhs12008_11397-118D2_forward Regulation 
SkeletalMuscleSatelliteCellsDonor2_CNhs11964_ctss_rev SkeletalMuscleSatelliteCellsD2- Skeletal Muscle Satellite Cells, donor2_CNhs11964_11321-117D7_reverse Regulation 
SkeletalMuscleSatelliteCellsDonor2_CNhs11964_ctss_fwd SkeletalMuscleSatelliteCellsD2+ Skeletal Muscle Satellite Cells, donor2_CNhs11964_11321-117D7_forward Regulation 
SkeletalMuscleSatelliteCellsDonor1_CNhs10869_ctss_rev SkeletalMuscleSatelliteCellsD1- Skeletal Muscle Satellite Cells, donor1_CNhs10869_11240-116D7_reverse Regulation 
SkeletalMuscleSatelliteCellsDonor1_CNhs10869_ctss_fwd SkeletalMuscleSatelliteCellsD1+ Skeletal Muscle Satellite Cells, donor1_CNhs10869_11240-116D7_forward Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor3_CNhs12041_ctss_rev SkeletalMuscleCellsIntoMyotubesD3- Skeletal muscle cells differentiated into Myotubes - multinucleated, donor3_CNhs12041_11431-118G9_reverse Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor3_CNhs12041_ctss_fwd SkeletalMuscleCellsIntoMyotubesD3+ Skeletal muscle cells differentiated into Myotubes - multinucleated, donor3_CNhs12041_11431-118G9_forward Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor2_CNhs11984_ctss_rev SkeletalMuscleCellsIntoMyotubesD2- Skeletal muscle cells differentiated into Myotubes - multinucleated, donor2_CNhs11984_11359-117H9_reverse Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor2_CNhs11984_ctss_fwd SkeletalMuscleCellsIntoMyotubesD2+ Skeletal muscle cells differentiated into Myotubes - multinucleated, donor2_CNhs11984_11359-117H9_forward Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor1_CNhs11084_ctss_rev SkeletalMuscleCellsIntoMyotubesD1- Skeletal muscle cells differentiated into Myotubes - multinucleated, donor1_CNhs11084_11282-116I4_reverse Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor1_CNhs11084_ctss_fwd SkeletalMuscleCellsIntoMyotubesD1+ Skeletal muscle cells differentiated into Myotubes - multinucleated, donor1_CNhs11084_11282-116I4_forward Regulation 
SkeletalMuscleCellsDonor6_CNhs12060_ctss_rev SkeletalMuscleCellsD6- Skeletal Muscle Cells, donor6_CNhs12060_11459-119B1_reverse Regulation 
SkeletalMuscleCellsDonor6_CNhs12060_ctss_fwd SkeletalMuscleCellsD6+ Skeletal Muscle Cells, donor6_CNhs12060_11459-119B1_forward Regulation 
SkeletalMuscleCellsDonor5_CNhs12056_ctss_rev SkeletalMuscleCellsD5- Skeletal Muscle Cells, donor5_CNhs12056_11455-119A6_reverse Regulation 
SkeletalMuscleCellsDonor5_CNhs12056_ctss_fwd SkeletalMuscleCellsD5+ Skeletal Muscle Cells, donor5_CNhs12056_11455-119A6_forward Regulation 
SkeletalMuscleCellsDonor4_CNhs12053_ctss_rev SkeletalMuscleCellsD4- Skeletal Muscle Cells, donor4_CNhs12053_11451-119A2_reverse Regulation 
SkeletalMuscleCellsDonor4_CNhs12053_ctss_fwd SkeletalMuscleCellsD4+ Skeletal Muscle Cells, donor4_CNhs12053_11451-119A2_forward Regulation 
SkeletalMuscleCellsDonor3_CNhs12040_ctss_rev SkeletalMuscleCellsD3- Skeletal Muscle Cells, donor3_CNhs12040_11430-118G8_reverse Regulation 
SkeletalMuscleCellsDonor3_CNhs12040_ctss_fwd SkeletalMuscleCellsD3+ Skeletal Muscle Cells, donor3_CNhs12040_11430-118G8_forward Regulation 
SkeletalMuscleCellsDonor2_CNhs11983_ctss_rev SkeletalMuscleCellsD2- Skeletal Muscle Cells, donor2_CNhs11983_11358-117H8_reverse Regulation 
SkeletalMuscleCellsDonor2_CNhs11983_ctss_fwd SkeletalMuscleCellsD2+ Skeletal Muscle Cells, donor2_CNhs11983_11358-117H8_forward Regulation 
SkeletalMuscleCellsDonor1_CNhs11083_ctss_rev SkeletalMuscleCellsD1- Skeletal Muscle Cells, donor1_CNhs11083_11281-116I3_reverse Regulation 
SkeletalMuscleCellsDonor1_CNhs11083_ctss_fwd SkeletalMuscleCellsD1+ Skeletal Muscle Cells, donor1_CNhs11083_11281-116I3_forward Regulation 
SertoliCellsDonor2_CNhs11974_ctss_rev SertoliCellsD2- Sertoli Cells, donor2_CNhs11974_11333-117F1_reverse Regulation 
SertoliCellsDonor2_CNhs11974_ctss_fwd SertoliCellsD2+ Sertoli Cells, donor2_CNhs11974_11333-117F1_forward Regulation 
SertoliCellsDonor1_CNhs10851_ctss_rev SertoliCellsD1- Sertoli Cells, donor1_CNhs10851_11255-116F4_reverse Regulation 
SertoliCellsDonor1_CNhs10851_ctss_fwd SertoliCellsD1+ Sertoli Cells, donor1_CNhs10851_11255-116F4_forward Regulation 
SebocyteDonor3_CNhs11995_ctss_rev SebocyteD3- Sebocyte, donor3_CNhs11995_11378-118B1_reverse Regulation 
SebocyteDonor3_CNhs11995_ctss_fwd SebocyteD3+ Sebocyte, donor3_CNhs11995_11378-118B1_forward Regulation 
SebocyteDonor2_CNhs11951_ctss_rev SebocyteD2- Sebocyte, donor2_CNhs11951_11301-117B5_reverse Regulation 
SebocyteDonor2_CNhs11951_ctss_fwd SebocyteD2+ Sebocyte, donor2_CNhs11951_11301-117B5_forward Regulation 
SebocyteDonor1_CNhs10847_ctss_rev SebocyteD1- Sebocyte, donor1_CNhs10847_11220-116B5_reverse Regulation 
SebocyteDonor1_CNhs10847_ctss_fwd SebocyteD1+ Sebocyte, donor1_CNhs10847_11220-116B5_forward Regulation 
SchwannCellsDonor3_CNhs12621_ctss_rev SchwannCellsD3- Schwann Cells, donor3_CNhs12621_11659-122F3_reverse Regulation 
SchwannCellsDonor3_CNhs12621_ctss_fwd SchwannCellsD3+ Schwann Cells, donor3_CNhs12621_11659-122F3_forward Regulation 
SchwannCellsDonor2_CNhs12345_ctss_rev SchwannCellsD2- Schwann Cells, donor2_CNhs12345_11578-120F3_reverse Regulation 
SchwannCellsDonor2_CNhs12345_ctss_fwd SchwannCellsD2+ Schwann Cells, donor2_CNhs12345_11578-120F3_forward Regulation 
SchwannCellsDonor1_CNhs12073_ctss_rev SchwannCellsD1- Schwann Cells, donor1_CNhs12073_11498-119F4_reverse Regulation 
SchwannCellsDonor1_CNhs12073_ctss_fwd SchwannCellsD1+ Schwann Cells, donor1_CNhs12073_11498-119F4_forward Regulation 
SalivaryAcinarCellsDonor3_CNhs12812_ctss_rev SalivaryAcinarCellsD3- salivary acinar cells, donor3_CNhs12812_11773-123I9_reverse Regulation 
SalivaryAcinarCellsDonor3_CNhs12812_ctss_fwd SalivaryAcinarCellsD3+ salivary acinar cells, donor3_CNhs12812_11773-123I9_forward Regulation 
SalivaryAcinarCellsDonor2_CNhs12811_ctss_rev SalivaryAcinarCellsD2- salivary acinar cells, donor2_CNhs12811_11772-123I8_reverse Regulation 
SalivaryAcinarCellsDonor2_CNhs12811_ctss_fwd SalivaryAcinarCellsD2+ salivary acinar cells, donor2_CNhs12811_11772-123I8_forward Regulation 
SalivaryAcinarCellsDonor1_CNhs12810_ctss_rev SalivaryAcinarCellsD1- salivary acinar cells, donor1_CNhs12810_11771-123I7_reverse Regulation 
SalivaryAcinarCellsDonor1_CNhs12810_ctss_fwd SalivaryAcinarCellsD1+ salivary acinar cells, donor1_CNhs12810_11771-123I7_forward Regulation 
RenalProximalTubularEpithelialCellDonor3_CNhs12120_ctss_rev RptecD3- Renal Proximal Tubular Epithelial Cell, donor3_CNhs12120_11676-122H2_reverse Regulation 
RenalProximalTubularEpithelialCellDonor3_CNhs12120_ctss_fwd RptecD3+ Renal Proximal Tubular Epithelial Cell, donor3_CNhs12120_11676-122H2_forward Regulation 
RenalProximalTubularEpithelialCellDonor2_CNhs12087_ctss_rev RptecD2- Renal Proximal Tubular Epithelial Cell, donor2_CNhs12087_11595-120H2_reverse Regulation 
RenalProximalTubularEpithelialCellDonor2_CNhs12087_ctss_fwd RptecD2+ Renal Proximal Tubular Epithelial Cell, donor2_CNhs12087_11595-120H2_forward Regulation 
RenalProximalTubularEpithelialCellDonor1_CNhs11330_ctss_rev RptecD1- Renal Proximal Tubular Epithelial Cell, donor1_CNhs11330_11515-119H3_reverse Regulation 
RenalProximalTubularEpithelialCellDonor1_CNhs11330_ctss_fwd RptecD1+ Renal Proximal Tubular Epithelial Cell, donor1_CNhs11330_11515-119H3_forward Regulation 
RetinalPigmentEpithelialCellsDonor3_CNhs12733_ctss_rev RpecD3- Retinal Pigment Epithelial Cells, donor3_CNhs12733_11689-122I6_reverse Regulation 
RetinalPigmentEpithelialCellsDonor3_CNhs12733_ctss_fwd RpecD3+ Retinal Pigment Epithelial Cells, donor3_CNhs12733_11689-122I6_forward Regulation 
RetinalPigmentEpithelialCellsDonor2_CNhs12096_ctss_rev RpecD2- Retinal Pigment Epithelial Cells, donor2_CNhs12096_11608-120I6_reverse Regulation 
RetinalPigmentEpithelialCellsDonor2_CNhs12096_ctss_fwd RpecD2+ Retinal Pigment Epithelial Cells, donor2_CNhs12096_11608-120I6_forward Regulation 
RetinalPigmentEpithelialCellsDonor1_CNhs11338_ctss_rev RpecD1- Retinal Pigment Epithelial Cells, donor1_CNhs11338_11528-119I7_reverse Regulation 
RetinalPigmentEpithelialCellsDonor1_CNhs11338_ctss_fwd RpecD1+ Retinal Pigment Epithelial Cells, donor1_CNhs11338_11528-119I7_forward Regulation 
RetinalPigmentEpithelialCellsDonor0_CNhs10842_ctss_rev RpecD0- Retinal Pigment Epithelial Cells, donor0_CNhs10842_11215-116A9_reverse Regulation 
RetinalPigmentEpithelialCellsDonor0_CNhs10842_ctss_fwd RpecD0+ Retinal Pigment Epithelial Cells, donor0_CNhs10842_11215-116A9_forward Regulation 
RenalGlomerularEndothelialCellsDonor4_CNhs13080_ctss_rev RgecD4- Renal Glomerular Endothelial Cells, donor4_CNhs13080_11783-124B1_reverse Regulation 
RenalGlomerularEndothelialCellsDonor4_CNhs13080_ctss_fwd RgecD4+ Renal Glomerular Endothelial Cells, donor4_CNhs13080_11783-124B1_forward Regulation 
RenalGlomerularEndothelialCellsDonor3_CNhs12624_ctss_rev RgecD3- Renal Glomerular Endothelial Cells, donor3_CNhs12624_11675-122H1_reverse Regulation 
RenalGlomerularEndothelialCellsDonor3_CNhs12624_ctss_fwd RgecD3+ Renal Glomerular Endothelial Cells, donor3_CNhs12624_11675-122H1_forward Regulation 
RenalGlomerularEndothelialCellsDonor2_CNhs12086_ctss_rev RgecD2- Renal Glomerular Endothelial Cells, donor2_CNhs12086_11594-120H1_reverse Regulation 
RenalGlomerularEndothelialCellsDonor2_CNhs12086_ctss_fwd RgecD2+ Renal Glomerular Endothelial Cells, donor2_CNhs12086_11594-120H1_forward Regulation 
RenalGlomerularEndothelialCellsDonor1_CNhs12074_ctss_rev RgecD1- Renal Glomerular Endothelial Cells, donor1_CNhs12074_11514-119H2_reverse Regulation 
RenalGlomerularEndothelialCellsDonor1_CNhs12074_ctss_fwd RgecD1+ Renal Glomerular Endothelial Cells, donor1_CNhs12074_11514-119H2_forward Regulation 
RenalMesangialCellsDonor3_CNhs12121_ctss_rev RenalMesangialCellsD3- Renal Mesangial Cells, donor3_CNhs12121_11679-122H5_reverse Regulation 
RenalMesangialCellsDonor3_CNhs12121_ctss_fwd RenalMesangialCellsD3+ Renal Mesangial Cells, donor3_CNhs12121_11679-122H5_forward Regulation 
RenalMesangialCellsDonor2_CNhs12089_ctss_rev RenalMesangialCellsD2- Renal Mesangial Cells, donor2_CNhs12089_11598-120H5_reverse Regulation 
RenalMesangialCellsDonor2_CNhs12089_ctss_fwd RenalMesangialCellsD2+ Renal Mesangial Cells, donor2_CNhs12089_11598-120H5_forward Regulation 
RenalMesangialCellsDonor1_CNhs11333_ctss_rev RenalMesangialCellsD1- Renal Mesangial Cells, donor1_CNhs11333_11518-119H6_reverse Regulation 
RenalMesangialCellsDonor1_CNhs11333_ctss_fwd RenalMesangialCellsD1+ Renal Mesangial Cells, donor1_CNhs11333_11518-119H6_forward Regulation 
RenalEpithelialCellsDonor3_CNhs12732_ctss_rev RenalEpithelialCellsD3- Renal Epithelial Cells, donor3_CNhs12732_11678-122H4_reverse Regulation 
RenalEpithelialCellsDonor3_CNhs12732_ctss_fwd RenalEpithelialCellsD3+ Renal Epithelial Cells, donor3_CNhs12732_11678-122H4_forward Regulation 
RenalEpithelialCellsDonor2_CNhs12088_ctss_rev RenalEpithelialCellsD2- Renal Epithelial Cells, donor2_CNhs12088_11597-120H4_reverse Regulation 
RenalEpithelialCellsDonor2_CNhs12088_ctss_fwd RenalEpithelialCellsD2+ Renal Epithelial Cells, donor2_CNhs12088_11597-120H4_forward Regulation 
RenalEpithelialCellsDonor1_CNhs11332_ctss_rev RenalEpithelialCellsD1- Renal Epithelial Cells, donor1_CNhs11332_11517-119H5_reverse Regulation 
RenalEpithelialCellsDonor1_CNhs11332_ctss_fwd RenalEpithelialCellsD1+ Renal Epithelial Cells, donor1_CNhs11332_11517-119H5_forward Regulation 
RenalCorticalEpithelialCellsDonor2_CNhs12728_ctss_rev RcecD2- Renal Cortical Epithelial Cells, donor2_CNhs12728_11596-120H3_reverse Regulation 
RenalCorticalEpithelialCellsDonor2_CNhs12728_ctss_fwd RcecD2+ Renal Cortical Epithelial Cells, donor2_CNhs12728_11596-120H3_forward Regulation 
RenalCorticalEpithelialCellsDonor1_CNhs11331_ctss_rev RcecD1- Renal Cortical Epithelial Cells, donor1_CNhs11331_11516-119H4_reverse Regulation 
RenalCorticalEpithelialCellsDonor1_CNhs11331_ctss_fwd RcecD1+ Renal Cortical Epithelial Cells, donor1_CNhs11331_11516-119H4_forward Regulation 
ProstateStromalCellsDonor3_CNhs12015_ctss_rev ProstateStromalCellsD3- Prostate Stromal Cells, donor3_CNhs12015_11405-118E1_reverse Regulation 
ProstateStromalCellsDonor3_CNhs12015_ctss_fwd ProstateStromalCellsD3+ Prostate Stromal Cells, donor3_CNhs12015_11405-118E1_forward Regulation 
ProstateStromalCellsDonor2_CNhs11973_ctss_rev ProstateStromalCellsD2- Prostate Stromal Cells, donor2_CNhs11973_11332-117E9_reverse Regulation 
ProstateStromalCellsDonor2_CNhs11973_ctss_fwd ProstateStromalCellsD2+ Prostate Stromal Cells, donor2_CNhs11973_11332-117E9_forward Regulation 
ProstateStromalCellsDonor1_CNhs10883_ctss_rev ProstateStromalCellsD1- Prostate Stromal Cells, donor1_CNhs10883_11254-116F3_reverse Regulation 
ProstateStromalCellsDonor1_CNhs10883_ctss_fwd ProstateStromalCellsD1+ Prostate Stromal Cells, donor1_CNhs10883_11254-116F3_forward Regulation 
ProstateEpithelialCellsDonor3_CNhs12014_ctss_rev ProstateEpithelialCellsD3- Prostate Epithelial Cells, donor3_CNhs12014_11404-118D9_reverse Regulation 
ProstateEpithelialCellsDonor3_CNhs12014_ctss_fwd ProstateEpithelialCellsD3+ Prostate Epithelial Cells, donor3_CNhs12014_11404-118D9_forward Regulation 
ProstateEpithelialCellsDonor2_CNhs11972_ctss_rev ProstateEpithelialCellsD2- Prostate Epithelial Cells, donor2_CNhs11972_11331-117E8_reverse Regulation 
ProstateEpithelialCellsDonor2_CNhs11972_ctss_fwd ProstateEpithelialCellsD2+ Prostate Epithelial Cells, donor2_CNhs11972_11331-117E8_forward Regulation 
ProstateEpithelialCellsPolarizedDonor1_CNhs10882_ctss_rev ProstateEpithelialCellsD1- Prostate Epithelial Cells (polarized), donor1_CNhs10882_11253-116F2_reverse Regulation 
ProstateEpithelialCellsPolarizedDonor1_CNhs10882_ctss_fwd ProstateEpithelialCellsD1+ Prostate Epithelial Cells (polarized), donor1_CNhs10882_11253-116F2_forward Regulation 
PreadipocyteVisceralDonor3_CNhs12039_ctss_rev PreadipocyteVisceralD3- Preadipocyte - visceral, donor3_CNhs12039_11429-118G7_reverse Regulation 
PreadipocyteVisceralDonor3_CNhs12039_ctss_fwd PreadipocyteVisceralD3+ Preadipocyte - visceral, donor3_CNhs12039_11429-118G7_forward Regulation 
PreadipocyteVisceralDonor2_CNhs11982_ctss_rev PreadipocyteVisceralD2- Preadipocyte - visceral, donor2_CNhs11982_11357-117H7_reverse Regulation 
PreadipocyteVisceralDonor2_CNhs11982_ctss_fwd PreadipocyteVisceralD2+ Preadipocyte - visceral, donor2_CNhs11982_11357-117H7_forward Regulation 
PreadipocyteVisceralDonor1_CNhs11082_ctss_rev PreadipocyteVisceralD1- Preadipocyte - visceral, donor1_CNhs11082_11280-116I2_reverse Regulation 
PreadipocyteVisceralDonor1_CNhs11082_ctss_fwd PreadipocyteVisceralD1+ Preadipocyte - visceral, donor1_CNhs11082_11280-116I2_forward Regulation 
PreadipocyteSubcutaneousDonor3_CNhs12038_ctss_rev PreadipocyteSubcutaneousD3- Preadipocyte - subcutaneous, donor3_CNhs12038_11428-118G6_reverse Regulation 
PreadipocyteSubcutaneousDonor3_CNhs12038_ctss_fwd PreadipocyteSubcutaneousD3+ Preadipocyte - subcutaneous, donor3_CNhs12038_11428-118G6_forward Regulation 
PreadipocyteSubcutaneousDonor2_CNhs11981_ctss_rev PreadipocyteSubcutaneousD2- Preadipocyte - subcutaneous, donor2_CNhs11981_11356-117H6_reverse Regulation 
PreadipocyteSubcutaneousDonor2_CNhs11981_ctss_fwd PreadipocyteSubcutaneousD2+ Preadipocyte - subcutaneous, donor2_CNhs11981_11356-117H6_forward Regulation 
PreadipocyteSubcutaneousDonor1_CNhs11081_ctss_rev PreadipocyteSubcutaneousD1- Preadipocyte - subcutaneous, donor1_CNhs11081_11279-116I1_reverse Regulation 
PreadipocyteSubcutaneousDonor1_CNhs11081_ctss_fwd PreadipocyteSubcutaneousD1+ Preadipocyte - subcutaneous, donor1_CNhs11081_11279-116I1_forward Regulation 
PreadipocytePerirenalDonor1_CNhs12065_ctss_rev PreadipocytePerirenalD1- Preadipocyte - perirenal, donor1_CNhs12065_11469-119C2_reverse Regulation 
PreadipocytePerirenalDonor1_CNhs12065_ctss_fwd PreadipocytePerirenalD1+ Preadipocyte - perirenal, donor1_CNhs12065_11469-119C2_forward Regulation 
PreadipocyteOmentalDonor3_CNhs12013_ctss_rev PreadipocyteOmentalD3- Preadipocyte - omental, donor3_CNhs12013_11403-118D8_reverse Regulation 
PreadipocyteOmentalDonor3_CNhs12013_ctss_fwd PreadipocyteOmentalD3+ Preadipocyte - omental, donor3_CNhs12013_11403-118D8_forward Regulation 
PreadipocyteOmentalDonor2_CNhs11902_ctss_rev PreadipocyteOmentalD2- Preadipocyte - omental, donor2_CNhs11902_11329-117E6_reverse Regulation 
PreadipocyteOmentalDonor2_CNhs11902_ctss_fwd PreadipocyteOmentalD2+ Preadipocyte - omental, donor2_CNhs11902_11329-117E6_forward Regulation 
PreadipocyteOmentalDonor1_CNhs11065_ctss_rev PreadipocyteOmentalD1- Preadipocyte - omental, donor1_CNhs11065_11468-119C1_reverse Regulation 
PreadipocyteOmentalDonor1_CNhs11065_ctss_fwd PreadipocyteOmentalD1+ Preadipocyte - omental, donor1_CNhs11065_11468-119C1_forward Regulation 
PreadipocyteBreastDonor2_CNhs11971_ctss_rev PreadipocyteBreastD2- Preadipocyte - breast, donor2_CNhs11971_11328-117E5_reverse Regulation 
PreadipocyteBreastDonor2_CNhs11971_ctss_fwd PreadipocyteBreastD2+ Preadipocyte - breast, donor2_CNhs11971_11328-117E5_forward Regulation 
PreadipocyteBreastDonor1_CNhs11052_ctss_rev PreadipocyteBreastD1- Preadipocyte - breast, donor1_CNhs11052_11467-119B9_reverse Regulation 
PreadipocyteBreastDonor1_CNhs11052_ctss_fwd PreadipocyteBreastD1+ Preadipocyte - breast, donor1_CNhs11052_11467-119B9_forward Regulation 
PlacentalEpithelialCellsDonor3_CNhs12037_ctss_rev PlacentalEpithelialCellsD3- Placental Epithelial Cells, donor3_CNhs12037_11427-118G5_reverse Regulation 
PlacentalEpithelialCellsDonor3_CNhs12037_ctss_fwd PlacentalEpithelialCellsD3+ Placental Epithelial Cells, donor3_CNhs12037_11427-118G5_forward Regulation 
PlacentalEpithelialCellsDonor2_CNhs11386_ctss_rev PlacentalEpithelialCellsD2- Placental Epithelial Cells, donor2_CNhs11386_11355-117H5_reverse Regulation 
PlacentalEpithelialCellsDonor2_CNhs11386_ctss_fwd PlacentalEpithelialCellsD2+ Placental Epithelial Cells, donor2_CNhs11386_11355-117H5_forward Regulation 
PlacentalEpithelialCellsDonor1_CNhs11079_ctss_rev PlacentalEpithelialCellsD1- Placental Epithelial Cells, donor1_CNhs11079_11278-116H9_reverse Regulation 
PlacentalEpithelialCellsDonor1_CNhs11079_ctss_fwd PlacentalEpithelialCellsD1+ Placental Epithelial Cells, donor1_CNhs11079_11278-116H9_forward Regulation 
PeripheralBloodMononuclearCellsDonor3_CNhs12002_ctss_rev PeripheralBloodMononuclearCellsD3- Peripheral Blood Mononuclear Cells, donor3_CNhs12002_11388-118C2_reverse Regulation 
PeripheralBloodMononuclearCellsDonor3_CNhs12002_ctss_fwd PeripheralBloodMononuclearCellsD3+ Peripheral Blood Mononuclear Cells, donor3_CNhs12002_11388-118C2_forward Regulation 
PeripheralBloodMononuclearCellsDonor2_CNhs11958_ctss_rev PeripheralBloodMononuclearCellsD2- Peripheral Blood Mononuclear Cells, donor2_CNhs11958_11312-117C7_reverse Regulation 
PeripheralBloodMononuclearCellsDonor2_CNhs11958_ctss_fwd PeripheralBloodMononuclearCellsD2+ Peripheral Blood Mononuclear Cells, donor2_CNhs11958_11312-117C7_forward Regulation 
PeripheralBloodMononuclearCellsDonor1_CNhs10860_ctss_rev PeripheralBloodMononuclearCellsD1- Peripheral Blood Mononuclear Cells, donor1_CNhs10860_11231-116C7_reverse Regulation 
PeripheralBloodMononuclearCellsDonor1_CNhs10860_ctss_fwd PeripheralBloodMononuclearCellsD1+ Peripheral Blood Mononuclear Cells, donor1_CNhs10860_11231-116C7_forward Regulation 
PerineurialCellsDonor2_CNhs12590_ctss_rev PerineurialCellsD2- Perineurial Cells, donor2_CNhs12590_11579-120F4_reverse Regulation 
PerineurialCellsDonor2_CNhs12590_ctss_fwd PerineurialCellsD2+ Perineurial Cells, donor2_CNhs12590_11579-120F4_forward Regulation 
PerineurialCellsDonor1_CNhs12587_ctss_rev PerineurialCellsD1- Perineurial Cells, donor1_CNhs12587_11499-119F5_reverse Regulation 
PerineurialCellsDonor1_CNhs12587_ctss_fwd PerineurialCellsD1+ Perineurial Cells, donor1_CNhs12587_11499-119F5_forward Regulation 
PericytesDonor3_CNhs12116_ctss_rev PericytesD3- Pericytes, donor3_CNhs12116_11652-122E5_reverse Regulation 
PericytesDonor3_CNhs12116_ctss_fwd PericytesD3+ Pericytes, donor3_CNhs12116_11652-122E5_forward Regulation 
PericytesDonor2_CNhs12079_ctss_rev PericytesD2- Pericytes, donor2_CNhs12079_11571-120E5_reverse Regulation 
PericytesDonor2_CNhs12079_ctss_fwd PericytesD2+ Pericytes, donor2_CNhs12079_11571-120E5_forward Regulation 
PericytesDonor1_CNhs11317_ctss_rev PericytesD1- Pericytes, donor1_CNhs11317_11491-119E6_reverse Regulation 
PericytesDonor1_CNhs11317_ctss_fwd PericytesD1+ Pericytes, donor1_CNhs11317_11491-119E6_forward Regulation 
PancreaticStromalCellsDonor1_CNhs10877_ctss_rev PancreaticStromalCellsD1- Pancreatic stromal cells, donor1_CNhs10877_11249-116E7_reverse Regulation 
PancreaticStromalCellsDonor1_CNhs10877_ctss_fwd PancreaticStromalCellsD1+ Pancreatic stromal cells, donor1_CNhs10877_11249-116E7_forward Regulation 
OsteoblastDifferentiatedDonor3_CNhs12035_ctss_rev OsteoblastDifferentiatedD3- Osteoblast - differentiated, donor3_CNhs12035_11425-118G3_reverse Regulation 
OsteoblastDifferentiatedDonor3_CNhs12035_ctss_fwd OsteoblastDifferentiatedD3+ Osteoblast - differentiated, donor3_CNhs12035_11425-118G3_forward Regulation 
OsteoblastDifferentiatedDonor2_CNhs11980_ctss_rev OsteoblastDifferentiatedD2- Osteoblast - differentiated, donor2_CNhs11980_11353-117H3_reverse Regulation 
OsteoblastDifferentiatedDonor2_CNhs11980_ctss_fwd OsteoblastDifferentiatedD2+ Osteoblast - differentiated, donor2_CNhs11980_11353-117H3_forward Regulation 
OsteoblastDifferentiatedDonor1_CNhs11311_ctss_rev OsteoblastDifferentiatedD1- Osteoblast - differentiated, donor1_CNhs11311_11276-116H7_reverse Regulation 
OsteoblastDifferentiatedDonor1_CNhs11311_ctss_fwd OsteoblastDifferentiatedD1+ Osteoblast - differentiated, donor1_CNhs11311_11276-116H7_forward Regulation 
OsteoblastDonor3_CNhs12036_ctss_rev OsteoblastD3- Osteoblast, donor3_CNhs12036_11426-118G4_reverse Regulation 
OsteoblastDonor3_CNhs12036_ctss_fwd OsteoblastD3+ Osteoblast, donor3_CNhs12036_11426-118G4_forward Regulation 
OsteoblastDonor2_CNhs11385_ctss_rev OsteoblastD2- Osteoblast, donor2_CNhs11385_11354-117H4_reverse Regulation 
OsteoblastDonor2_CNhs11385_ctss_fwd OsteoblastD2+ Osteoblast, donor2_CNhs11385_11354-117H4_forward Regulation 
OsteoblastDonor1_CNhs11078_ctss_rev OsteoblastD1- Osteoblast, donor1_CNhs11078_11277-116H8_reverse Regulation 
OsteoblastDonor1_CNhs11078_ctss_fwd OsteoblastD1+ Osteoblast, donor1_CNhs11078_11277-116H8_forward Regulation 
OligodendrocytePrecursorsDonor1_CNhs12586_ctss_rev OligodendrocytePrecursorsD1- Oligodendrocyte - precursors, donor1_CNhs12586_11496-119F2_reverse Regulation 
OligodendrocytePrecursorsDonor1_CNhs12586_ctss_fwd OligodendrocytePrecursorsD1+ Oligodendrocyte - precursors, donor1_CNhs12586_11496-119F2_forward Regulation 
OlfactoryEpithelialCellsDonor4_CNhs13819_ctss_rev OlfactoryEpithelialCellsD4- Olfactory epithelial cells, donor4_CNhs13819_11936-126A1_reverse Regulation 
OlfactoryEpithelialCellsDonor4_CNhs13819_ctss_fwd OlfactoryEpithelialCellsD4+ Olfactory epithelial cells, donor4_CNhs13819_11936-126A1_forward Regulation 
OlfactoryEpithelialCellsDonor3_CNhs13818_ctss_rev OlfactoryEpithelialCellsD3- Olfactory epithelial cells, donor3_CNhs13818_11935-125I9_reverse Regulation 
OlfactoryEpithelialCellsDonor3_CNhs13818_ctss_fwd OlfactoryEpithelialCellsD3+ Olfactory epithelial cells, donor3_CNhs13818_11935-125I9_forward Regulation 
OlfactoryEpithelialCellsDonor2_CNhs13817_ctss_rev OlfactoryEpithelialCellsD2- Olfactory epithelial cells, donor2_CNhs13817_11934-125I8_reverse Regulation 
OlfactoryEpithelialCellsDonor2_CNhs13817_ctss_fwd OlfactoryEpithelialCellsD2+ Olfactory epithelial cells, donor2_CNhs13817_11934-125I8_forward Regulation 
OlfactoryEpithelialCellsDonor1_CNhs13816_ctss_rev OlfactoryEpithelialCellsD1- Olfactory epithelial cells, donor1_CNhs13816_11933-125I7_reverse Regulation 
OlfactoryEpithelialCellsDonor1_CNhs13816_ctss_fwd OlfactoryEpithelialCellsD1+ Olfactory epithelial cells, donor1_CNhs13816_11933-125I7_forward Regulation 
NucleusPulposusCellDonor3_CNhs12063_ctss_rev NucleusPulposusCellD3- Nucleus Pulposus Cell, donor3_CNhs12063_11462-119B4_reverse Regulation 
NucleusPulposusCellDonor3_CNhs12063_ctss_fwd NucleusPulposusCellD3+ Nucleus Pulposus Cell, donor3_CNhs12063_11462-119B4_forward Regulation 
NucleusPulposusCellDonor2_CNhs12019_ctss_rev NucleusPulposusCellD2- Nucleus Pulposus Cell, donor2_CNhs12019_11409-118E5_reverse Regulation 
NucleusPulposusCellDonor2_CNhs12019_ctss_fwd NucleusPulposusCellD2+ Nucleus Pulposus Cell, donor2_CNhs12019_11409-118E5_forward Regulation 
NucleusPulposusCellDonor1_CNhs10881_ctss_rev NucleusPulposusCellD1- Nucleus Pulposus Cell, donor1_CNhs10881_11252-116F1_reverse Regulation 
NucleusPulposusCellDonor1_CNhs10881_ctss_fwd NucleusPulposusCellD1+ Nucleus Pulposus Cell, donor1_CNhs10881_11252-116F1_forward Regulation 
NeutrophilsDonor3_CNhs11905_ctss_rev NeutrophilsD3- Neutrophils, donor3_CNhs11905_11390-118C4_reverse Regulation 
NeutrophilsDonor3_CNhs11905_ctss_fwd NeutrophilsD3+ Neutrophils, donor3_CNhs11905_11390-118C4_forward Regulation 
NeutrophilsDonor2_CNhs11959_ctss_rev NeutrophilsD2- Neutrophils, donor2_CNhs11959_11314-117C9_reverse Regulation 
NeutrophilsDonor2_CNhs11959_ctss_fwd NeutrophilsD2+ Neutrophils, donor2_CNhs11959_11314-117C9_forward Regulation 
NeutrophilsDonor1_CNhs10862_ctss_rev NeutrophilsD1- Neutrophils, donor1_CNhs10862_11233-116C9_reverse Regulation 
NeutrophilsDonor1_CNhs10862_ctss_fwd NeutrophilsD1+ Neutrophils, donor1_CNhs10862_11233-116C9_forward Regulation 
NeuronsDonor3_CNhs13815_ctss_rev NeuronsD3- Neurons, donor3_CNhs13815_11655-122E8_reverse Regulation 
NeuronsDonor3_CNhs13815_ctss_fwd NeuronsD3+ Neurons, donor3_CNhs13815_11655-122E8_forward Regulation 
NeuronsDonor2_CNhs12726_ctss_rev NeuronsD2- Neurons, donor2_CNhs12726_11574-120E8_reverse Regulation 
NeuronsDonor2_CNhs12726_ctss_fwd NeuronsD2+ Neurons, donor2_CNhs12726_11574-120E8_forward Regulation 
NeuronsDonor1_CNhs12338_ctss_rev NeuronsD1- Neurons, donor1_CNhs12338_11494-119E9_reverse Regulation 
NeuronsDonor1_CNhs12338_ctss_fwd NeuronsD1+ Neurons, donor1_CNhs12338_11494-119E9_forward Regulation 
NeuralStemCellsDonor2_CNhs11384_ctss_rev NeuralStemCellsD2- Neural stem cells, donor2_CNhs11384_11352-117H2_reverse Regulation 
NeuralStemCellsDonor2_CNhs11384_ctss_fwd NeuralStemCellsD2+ Neural stem cells, donor2_CNhs11384_11352-117H2_forward Regulation 
NeuralStemCellsDonor1_CNhs11063_ctss_rev NeuralStemCellsD1- Neural stem cells, donor1_CNhs11063_11275-116H6_reverse Regulation 
NeuralStemCellsDonor1_CNhs11063_ctss_fwd NeuralStemCellsD1+ Neural stem cells, donor1_CNhs11063_11275-116H6_forward Regulation 
NaturalKillerCellsDonor3_CNhs12001_ctss_rev NaturalKillerCellsD3- Natural Killer Cells, donor3_CNhs12001_11387-118C1_reverse Regulation 
NaturalKillerCellsDonor3_CNhs12001_ctss_fwd NaturalKillerCellsD3+ Natural Killer Cells, donor3_CNhs12001_11387-118C1_forward Regulation 
NaturalKillerCellsDonor2_CNhs11957_ctss_rev NaturalKillerCellsD2- Natural Killer Cells, donor2_CNhs11957_11311-117C6_reverse Regulation 
NaturalKillerCellsDonor2_CNhs11957_ctss_fwd NaturalKillerCellsD2+ Natural Killer Cells, donor2_CNhs11957_11311-117C6_forward Regulation 
NaturalKillerCellsDonor1_CNhs10859_ctss_rev NaturalKillerCellsD1- Natural Killer Cells, donor1_CNhs10859_11230-116C6_reverse Regulation 
NaturalKillerCellsDonor1_CNhs10859_ctss_fwd NaturalKillerCellsD1+ Natural Killer Cells, donor1_CNhs10859_11230-116C6_forward Regulation 
NasalEpithelialCellsDonor2_CNhs12574_ctss_rev NasalEpithelialCellsD2- nasal epithelial cells, donor2_CNhs12574_12227-129F4_reverse Regulation 
NasalEpithelialCellsDonor2_CNhs12574_ctss_fwd NasalEpithelialCellsD2+ nasal epithelial cells, donor2_CNhs12574_12227-129F4_forward Regulation 
NasalEpithelialCellsDonor1TechRep1_CNhs12589_ctss_rev NasalEpithelialCellsD1Tr1- nasal epithelial cells, donor1, tech_rep1_CNhs12589_12226-129F3_reverse Regulation 
NasalEpithelialCellsDonor1TechRep1_CNhs12589_ctss_fwd NasalEpithelialCellsD1Tr1+ nasal epithelial cells, donor1, tech_rep1_CNhs12589_12226-129F3_forward Regulation 
MyoblastDonor3_CNhs11908_ctss_rev MyoblastD3- Myoblast, donor3_CNhs11908_11398-118D3_reverse Regulation 
MyoblastDonor3_CNhs11908_ctss_fwd MyoblastD3+ Myoblast, donor3_CNhs11908_11398-118D3_forward Regulation 
MyoblastDonor2_CNhs11965_ctss_rev MyoblastD2- Myoblast, donor2_CNhs11965_11322-117D8_reverse Regulation 
MyoblastDonor2_CNhs11965_ctss_fwd MyoblastD2+ Myoblast, donor2_CNhs11965_11322-117D8_forward Regulation 
MyoblastDonor1_CNhs10870_ctss_rev MyoblastD1- Myoblast, donor1_CNhs10870_11241-116D8_reverse Regulation 
MyoblastDonor1_CNhs10870_ctss_fwd MyoblastD1+ Myoblast, donor1_CNhs10870_11241-116D8_forward Regulation 
MesenchymalStemCellsWhartonsJellyDonor1_CNhs11057_ctss_rev MscWharton'sJellyD1- Mesenchymal Stem Cells - Wharton's Jelly, donor1_CNhs11057_11548-120B9_reverse Regulation 
MesenchymalStemCellsWhartonsJellyDonor1_CNhs11057_ctss_fwd MscWharton'sJellyD1+ Mesenchymal Stem Cells - Wharton's Jelly, donor1_CNhs11057_11548-120B9_forward Regulation 
MesenchymalStemCellsVertebralDonor1_CNhs10846_ctss_rev MscVertebralD1- Mesenchymal Stem Cells - Vertebral, donor1_CNhs10846_11219-116B4_reverse Regulation 
MesenchymalStemCellsVertebralDonor1_CNhs10846_ctss_fwd MscVertebralD1+ Mesenchymal Stem Cells - Vertebral, donor1_CNhs10846_11219-116B4_forward Regulation 
MesenchymalStemCellsUmbilicalDonor3_CNhs12127_ctss_rev MscUmbilicalD3- Mesenchymal Stem Cells - umbilical, donor3_CNhs12127_11700-123A8_reverse Regulation 
MesenchymalStemCellsUmbilicalDonor3_CNhs12127_ctss_fwd MscUmbilicalD3+ Mesenchymal Stem Cells - umbilical, donor3_CNhs12127_11700-123A8_forward Regulation 
MesenchymalStemCellsUmbilicalDonor2_CNhs12102_ctss_rev MscUmbilicalD2- Mesenchymal Stem Cells - umbilical, donor2_CNhs12102_11619-122A8_reverse Regulation 
MesenchymalStemCellsUmbilicalDonor2_CNhs12102_ctss_fwd MscUmbilicalD2+ Mesenchymal Stem Cells - umbilical, donor2_CNhs12102_11619-122A8_forward Regulation 
MesenchymalStemCellsUmbilicalDonor1_CNhs11347_ctss_rev MscUmbilicalD1- Mesenchymal Stem Cells - umbilical, donor1_CNhs11347_11539-120A9_reverse Regulation 
MesenchymalStemCellsUmbilicalDonor1_CNhs11347_ctss_fwd MscUmbilicalD1+ Mesenchymal Stem Cells - umbilical, donor1_CNhs11347_11539-120A9_forward Regulation 
MesenchymalStemCellsUmbilicalDonor0_CNhs12492_ctss_rev MscUmbilicalD0- Mesenchymal stem cells - umbilical, donor0_CNhs12492_11214-116A8_reverse Regulation 
MesenchymalStemCellsUmbilicalDonor0_CNhs12492_ctss_fwd MscUmbilicalD0+ Mesenchymal stem cells - umbilical, donor0_CNhs12492_11214-116A8_forward Regulation 
MesenchymalStemCellsHepaticDonor2_CNhs12730_ctss_rev MscHepaticD2- Mesenchymal Stem Cells - hepatic, donor2_CNhs12730_11618-122A7_reverse Regulation 
MesenchymalStemCellsHepaticDonor2_CNhs12730_ctss_fwd MscHepaticD2+ Mesenchymal Stem Cells - hepatic, donor2_CNhs12730_11618-122A7_forward Regulation 
MesenchymalStemCellsHepaticDonor1_CNhs11346_ctss_rev MscHepaticD1- Mesenchymal Stem Cells - hepatic, donor1_CNhs11346_11538-120A8_reverse Regulation 
MesenchymalStemCellsHepaticDonor1_CNhs11346_ctss_fwd MscHepaticD1+ Mesenchymal Stem Cells - hepatic, donor1_CNhs11346_11538-120A8_forward Regulation 
MesenchymalStemCellsHepaticDonor0_CNhs10845_ctss_rev MscHepaticD0- Mesenchymal stem cells - hepatic, donor0_CNhs10845_11218-116B3_reverse Regulation 
MesenchymalStemCellsHepaticDonor0_CNhs10845_ctss_fwd MscHepaticD0+ Mesenchymal stem cells - hepatic, donor0_CNhs10845_11218-116B3_forward Regulation 
MesenchymalStemCellsBoneMarrowDonor4_CNhs11316_ctss_rev MscBoneMarrowD4- Mesenchymal Stem Cells - bone marrow, donor4_CNhs11316_11464-119B6_reverse Regulation 
MesenchymalStemCellsBoneMarrowDonor4_CNhs11316_ctss_fwd MscBoneMarrowD4+ Mesenchymal Stem Cells - bone marrow, donor4_CNhs11316_11464-119B6_forward Regulation 
MesenchymalStemCellsBoneMarrowDonor3_CNhs12126_ctss_rev MscBoneMarrowD3- Mesenchymal Stem Cells - bone marrow, donor3_CNhs12126_11697-123A5_reverse Regulation 
MesenchymalStemCellsBoneMarrowDonor3_CNhs12126_ctss_fwd MscBoneMarrowD3+ Mesenchymal Stem Cells - bone marrow, donor3_CNhs12126_11697-123A5_forward Regulation 
MesenchymalStemCellsBoneMarrowDonor2_CNhs12100_ctss_rev MscBoneMarrowD2- Mesenchymal Stem Cells - bone marrow, donor2_CNhs12100_11616-122A5_reverse Regulation 
MesenchymalStemCellsBoneMarrowDonor2_CNhs12100_ctss_fwd MscBoneMarrowD2+ Mesenchymal Stem Cells - bone marrow, donor2_CNhs12100_11616-122A5_forward Regulation 
MesenchymalStemCellsBoneMarrowDonor1_CNhs11344_ctss_rev MscBoneMarrowD1- Mesenchymal Stem Cells - bone marrow, donor1_CNhs11344_11536-120A6_reverse Regulation 
MesenchymalStemCellsBoneMarrowDonor1_CNhs11344_ctss_fwd MscBoneMarrowD1+ Mesenchymal Stem Cells - bone marrow, donor1_CNhs11344_11536-120A6_forward Regulation 
MesenchymalStemCellsAmnioticMembraneDonor2_CNhs12104_ctss_rev MscAmnioticMembraneD2- Mesenchymal Stem Cells - amniotic membrane, donor2_CNhs12104_11627-122B7_reverse Regulation 
MesenchymalStemCellsAmnioticMembraneDonor2_CNhs12104_ctss_fwd MscAmnioticMembraneD2+ Mesenchymal Stem Cells - amniotic membrane, donor2_CNhs12104_11627-122B7_forward Regulation 
MesenchymalStemCellsAmnioticMembraneDonor1_CNhs11349_ctss_rev MscAmnioticMembraneD1- Mesenchymal Stem Cells - amniotic membrane, donor1_CNhs11349_11547-120B8_reverse Regulation 
MesenchymalStemCellsAmnioticMembraneDonor1_CNhs11349_ctss_fwd MscAmnioticMembraneD1+ Mesenchymal Stem Cells - amniotic membrane, donor1_CNhs11349_11547-120B8_forward Regulation 
MesenchymalStemCellsAdiposeDonor3_CNhs12922_ctss_rev MscAdiposeD3- Mesenchymal Stem Cells - adipose, donor3_CNhs12922_11698-123A6_reverse Regulation 
MesenchymalStemCellsAdiposeDonor3_CNhs12922_ctss_fwd MscAdiposeD3+ Mesenchymal Stem Cells - adipose, donor3_CNhs12922_11698-123A6_forward Regulation 
MesenchymalStemCellsAdiposeDonor2_CNhs12101_ctss_rev MscAdiposeD2- Mesenchymal Stem Cells - adipose, donor2_CNhs12101_11617-122A6_reverse Regulation 
MesenchymalStemCellsAdiposeDonor2_CNhs12101_ctss_fwd MscAdiposeD2+ Mesenchymal Stem Cells - adipose, donor2_CNhs12101_11617-122A6_forward Regulation 
MesenchymalStemCellsAdiposeDonor1_CNhs11345_ctss_rev MscAdiposeD1- Mesenchymal Stem Cells - adipose, donor1_CNhs11345_11537-120A7_reverse Regulation 
MesenchymalStemCellsAdiposeDonor1_CNhs11345_ctss_fwd MscAdiposeD1+ Mesenchymal Stem Cells - adipose, donor1_CNhs11345_11537-120A7_forward Regulation 
MesenchymalStemCellsAdiposeDonor0_CNhs10844_ctss_rev MscAdiposeD0- Mesenchymal stem cells - adipose, donor0_CNhs10844_11217-116B2_reverse Regulation 
MesenchymalStemCellsAdiposeDonor0_CNhs10844_ctss_fwd MscAdiposeD0+ Mesenchymal stem cells - adipose, donor0_CNhs10844_11217-116B2_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor4_CNhs13096_ctss_rev MpcOvarianCancerRightOvaryD4- mesenchymal precursor cell - ovarian cancer right ovary, donor4_CNhs13096_11837-124H1_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor4_CNhs13096_ctss_fwd MpcOvarianCancerRightOvaryD4+ mesenchymal precursor cell - ovarian cancer right ovary, donor4_CNhs13096_11837-124H1_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor3SOC5702_CNhs12377_ctss_rev MpcOvarianCancerRightOvaryD3- mesenchymal precursor cell - ovarian cancer right ovary, donor3 (SOC-57-02)_CNhs12377_11761-123H6_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor3SOC5702G_CNhs13507_ctss_rev MpcOvarianCancerRightOvaryD3- mesenchymal precursor cell - ovarian cancer right ovary, donor3 (SOC-57-02-G)_CNhs13507_11842-124H6_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor3SOC5702_CNhs12377_ctss_fwd MpcOvarianCancerRightOvaryD3+ mesenchymal precursor cell - ovarian cancer right ovary, donor3 (SOC-57-02)_CNhs12377_11761-123H6_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor3SOC5702G_CNhs13507_ctss_fwd MpcOvarianCancerRightOvaryD3+ mesenchymal precursor cell - ovarian cancer right ovary, donor3 (SOC-57-02-G)_CNhs13507_11842-124H6_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor2_CNhs12375_ctss_rev MpcOvarianCancerRightOvaryD2- mesenchymal precursor cell - ovarian cancer right ovary, donor2_CNhs12375_11759-123H4_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor2_CNhs12375_ctss_fwd MpcOvarianCancerRightOvaryD2+ mesenchymal precursor cell - ovarian cancer right ovary, donor2_CNhs12375_11759-123H4_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor1_CNhs12373_ctss_rev MpcOvarianCancerRightOvaryD1- mesenchymal precursor cell - ovarian cancer right ovary, donor1_CNhs12373_11757-123H2_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor1_CNhs12373_ctss_fwd MpcOvarianCancerRightOvaryD1+ mesenchymal precursor cell - ovarian cancer right ovary, donor1_CNhs12373_11757-123H2_forward Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor4_CNhs13097_ctss_rev MpcOvarianCancerMetastasisD4- mesenchymal precursor cell - ovarian cancer metastasis, donor4_CNhs13097_11838-124H2_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor4_CNhs13097_ctss_fwd MpcOvarianCancerMetastasisD4+ mesenchymal precursor cell - ovarian cancer metastasis, donor4_CNhs13097_11838-124H2_forward Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor3_CNhs12378_ctss_rev MpcOvarianCancerMetastasisD3- mesenchymal precursor cell - ovarian cancer metastasis, donor3_CNhs12378_11762-123H7_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor3_CNhs12378_ctss_fwd MpcOvarianCancerMetastasisD3+ mesenchymal precursor cell - ovarian cancer metastasis, donor3_CNhs12378_11762-123H7_forward Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor2_CNhs13093_ctss_rev MpcOvarianCancerMetastasisD2- mesenchymal precursor cell - ovarian cancer metastasis, donor2_CNhs13093_11835-124G8_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor2_CNhs13093_ctss_fwd MpcOvarianCancerMetastasisD2+ mesenchymal precursor cell - ovarian cancer metastasis, donor2_CNhs13093_11835-124G8_forward Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor1_CNhs12374_ctss_rev MpcOvarianCancerMetastasisD1- mesenchymal precursor cell - ovarian cancer metastasis, donor1_CNhs12374_11758-123H3_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor1_CNhs12374_ctss_fwd MpcOvarianCancerMetastasisD1+ mesenchymal precursor cell - ovarian cancer metastasis, donor1_CNhs12374_11758-123H3_forward Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor4_CNhs13094_ctss_rev MpcOvarianCancerLeftOvaryD4- mesenchymal precursor cell - ovarian cancer left ovary, donor4_CNhs13094_11836-124G9_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor4_CNhs13094_ctss_fwd MpcOvarianCancerLeftOvaryD4+ mesenchymal precursor cell - ovarian cancer left ovary, donor4_CNhs13094_11836-124G9_forward Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor3_CNhs12376_ctss_rev MpcOvarianCancerLeftOvaryD3- mesenchymal precursor cell - ovarian cancer left ovary, donor3_CNhs12376_11760-123H5_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor3_CNhs12376_ctss_fwd MpcOvarianCancerLeftOvaryD3+ mesenchymal precursor cell - ovarian cancer left ovary, donor3_CNhs12376_11760-123H5_forward Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor2_CNhs13092_ctss_rev MpcOvarianCancerLeftOvaryD2- mesenchymal precursor cell - ovarian cancer left ovary, donor2_CNhs13092_11833-124G6_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor2_CNhs13092_ctss_fwd MpcOvarianCancerLeftOvaryD2+ mesenchymal precursor cell - ovarian cancer left ovary, donor2_CNhs13092_11833-124G6_forward Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor1_CNhs12372_ctss_rev MpcOvarianCancerLeftOvaryD1- mesenchymal precursor cell - ovarian cancer left ovary, donor1_CNhs12372_11756-123H1_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor1_CNhs12372_ctss_fwd MpcOvarianCancerLeftOvaryD1+ mesenchymal precursor cell - ovarian cancer left ovary, donor1_CNhs12372_11756-123H1_forward Regulation 
MesenchymalPrecursorCellCardiacDonor4_CNhs12371_ctss_rev MpcCardiacD4- mesenchymal precursor cell - cardiac, donor4_CNhs12371_11755-123G9_reverse Regulation 
MesenchymalPrecursorCellCardiacDonor4_CNhs12371_ctss_fwd MpcCardiacD4+ mesenchymal precursor cell - cardiac, donor4_CNhs12371_11755-123G9_forward Regulation 
MesenchymalPrecursorCellCardiacDonor3_CNhs12370_ctss_rev MpcCardiacD3- mesenchymal precursor cell - cardiac, donor3_CNhs12370_11754-123G8_reverse Regulation 
MesenchymalPrecursorCellCardiacDonor3_CNhs12370_ctss_fwd MpcCardiacD3+ mesenchymal precursor cell - cardiac, donor3_CNhs12370_11754-123G8_forward Regulation 
MesenchymalPrecursorCellCardiacDonor2_CNhs12369_ctss_rev MpcCardiacD2- mesenchymal precursor cell - cardiac, donor2_CNhs12369_11753-123G7_reverse Regulation 
MesenchymalPrecursorCellCardiacDonor2_CNhs12369_ctss_fwd MpcCardiacD2+ mesenchymal precursor cell - cardiac, donor2_CNhs12369_11753-123G7_forward Regulation 
MesenchymalPrecursorCellCardiacDonor1_CNhs12368_ctss_rev MpcCardiacD1- mesenchymal precursor cell - cardiac, donor1_CNhs12368_11752-123G6_reverse Regulation 
MesenchymalPrecursorCellCardiacDonor1_CNhs12368_ctss_fwd MpcCardiacD1+ mesenchymal precursor cell - cardiac, donor1_CNhs12368_11752-123G6_forward Regulation 
MesenchymalPrecursorCellBoneMarrowDonor3_CNhs13098_ctss_rev MpcBoneMarrowD3- mesenchymal precursor cell - bone marrow, donor3_CNhs13098_11840-124H4_reverse Regulation 
MesenchymalPrecursorCellBoneMarrowDonor3_CNhs13098_ctss_fwd MpcBoneMarrowD3+ mesenchymal precursor cell - bone marrow, donor3_CNhs13098_11840-124H4_forward Regulation 
MesenchymalPrecursorCellBoneMarrowDonor2_CNhs12367_ctss_rev MpcBoneMarrowD2- mesenchymal precursor cell - bone marrow, donor2_CNhs12367_11751-123G5_reverse Regulation 
MesenchymalPrecursorCellBoneMarrowDonor2_CNhs12367_ctss_fwd MpcBoneMarrowD2+ mesenchymal precursor cell - bone marrow, donor2_CNhs12367_11751-123G5_forward Regulation 
MesenchymalPrecursorCellBoneMarrowDonor1_CNhs12366_ctss_rev MpcBoneMarrowD1- mesenchymal precursor cell - bone marrow, donor1_CNhs12366_11750-123G4_reverse Regulation 
MesenchymalPrecursorCellBoneMarrowDonor1_CNhs12366_ctss_fwd MpcBoneMarrowD1+ mesenchymal precursor cell - bone marrow, donor1_CNhs12366_11750-123G4_forward Regulation 
MesenchymalPrecursorCellAdiposeDonor3_CNhs12365_ctss_rev MpcAdiposeD3- mesenchymal precursor cell - adipose, donor3_CNhs12365_11749-123G3_reverse Regulation 
MesenchymalPrecursorCellAdiposeDonor3_CNhs12365_ctss_fwd MpcAdiposeD3+ mesenchymal precursor cell - adipose, donor3_CNhs12365_11749-123G3_forward Regulation 
MesenchymalPrecursorCellAdiposeDonor2_CNhs12364_ctss_rev MpcAdiposeD2- mesenchymal precursor cell - adipose, donor2_CNhs12364_11748-123G2_reverse Regulation 
MesenchymalPrecursorCellAdiposeDonor2_CNhs12364_ctss_fwd MpcAdiposeD2+ mesenchymal precursor cell - adipose, donor2_CNhs12364_11748-123G2_forward Regulation 
MesenchymalPrecursorCellAdiposeDonor1_CNhs12363_ctss_rev MpcAdiposeD1- mesenchymal precursor cell - adipose, donor1_CNhs12363_11747-123G1_reverse Regulation 
MesenchymalPrecursorCellAdiposeDonor1_CNhs12363_ctss_fwd MpcAdiposeD1+ mesenchymal precursor cell - adipose, donor1_CNhs12363_11747-123G1_forward Regulation 
MigratoryLangerhansCellsDonor3_CNhs13547_ctss_rev MigratoryLangerhansCellsD3- migratory langerhans cells, donor3_CNhs13547_11903-125F4_reverse Regulation 
MigratoryLangerhansCellsDonor3_CNhs13547_ctss_fwd MigratoryLangerhansCellsD3+ migratory langerhans cells, donor3_CNhs13547_11903-125F4_forward Regulation 
MigratoryLangerhansCellsDonor2_CNhs13536_ctss_rev MigratoryLangerhansCellsD2- migratory langerhans cells, donor2_CNhs13536_11902-125F3_reverse Regulation 
MigratoryLangerhansCellsDonor2_CNhs13536_ctss_fwd MigratoryLangerhansCellsD2+ migratory langerhans cells, donor2_CNhs13536_11902-125F3_forward Regulation 
MigratoryLangerhansCellsDonor1_CNhs13535_ctss_rev MigratoryLangerhansCellsD1- migratory langerhans cells, donor1_CNhs13535_11901-125F2_reverse Regulation 
MigratoryLangerhansCellsDonor1_CNhs13535_ctss_fwd MigratoryLangerhansCellsD1+ migratory langerhans cells, donor1_CNhs13535_11901-125F2_forward Regulation 
MesothelialCellsDonor3_CNhs12012_ctss_rev MesothelialCellsD3- Mesothelial Cells, donor3_CNhs12012_11402-118D7_reverse Regulation 
MesothelialCellsDonor3_CNhs12012_ctss_fwd MesothelialCellsD3+ Mesothelial Cells, donor3_CNhs12012_11402-118D7_forward Regulation 
MesothelialCellsDonor1_CNhs10850_ctss_rev MesothelialCellsD1- Mesothelial Cells, donor1_CNhs10850_11247-116E5_reverse Regulation 
MesothelialCellsDonor1_CNhs10850_ctss_fwd MesothelialCellsD1+ Mesothelial Cells, donor1_CNhs10850_11247-116E5_forward Regulation 
MeningealCellsDonor3_CNhs12731_ctss_rev MeningealCellsD3- Meningeal Cells, donor3_CNhs12731_11654-122E7_reverse Regulation 
MeningealCellsDonor3_CNhs12731_ctss_fwd MeningealCellsD3+ Meningeal Cells, donor3_CNhs12731_11654-122E7_forward Regulation 
MeningealCellsDonor2_CNhs12080_ctss_rev MeningealCellsD2- Meningeal Cells, donor2_CNhs12080_11573-120E7_reverse Regulation 
MeningealCellsDonor2_CNhs12080_ctss_fwd MeningealCellsD2+ Meningeal Cells, donor2_CNhs12080_11573-120E7_forward Regulation 
MeningealCellsDonor1_CNhs11320_ctss_rev MeningealCellsD1- Meningeal Cells, donor1_CNhs11320_11493-119E8_reverse Regulation 
MeningealCellsDonor1_CNhs11320_ctss_fwd MeningealCellsD1+ Meningeal Cells, donor1_CNhs11320_11493-119E8_forward Regulation 
MelanocyteLightDonor3_CNhs12033_ctss_rev MelanocyteLightD3- Melanocyte - light, donor3_CNhs12033_11423-118G1_reverse Regulation 
MelanocyteLightDonor3_CNhs12033_ctss_fwd MelanocyteLightD3+ Melanocyte - light, donor3_CNhs12033_11423-118G1_forward Regulation 
MelanocyteLightDonor2_CNhs11383_ctss_rev MelanocyteLightD2- Melanocyte - light, donor2_CNhs11383_11351-117H1_reverse Regulation 
MelanocyteLightDonor2_CNhs11383_ctss_fwd MelanocyteLightD2+ Melanocyte - light, donor2_CNhs11383_11351-117H1_forward Regulation 
MelanocyteLightDonor1_CNhs11303_ctss_rev MelanocyteLightD1- Melanocyte - light, donor1_CNhs11303_11274-116H5_reverse Regulation 
MelanocyteLightDonor1_CNhs11303_ctss_fwd MelanocyteLightD1+ Melanocyte - light, donor1_CNhs11303_11274-116H5_forward Regulation 
MelanocyteDarkDonor3_CNhs12570_ctss_rev MelanocyteDarkD3- Melanocyte - dark, donor3_CNhs12570_11663-122F7_reverse Regulation 
MelanocyteDarkDonor3_CNhs12570_ctss_fwd MelanocyteDarkD3+ Melanocyte - dark, donor3_CNhs12570_11663-122F7_forward Regulation 
MelanocyteDarkDonor2_CNhs12346_ctss_rev MelanocyteDarkD2- Melanocyte - dark, donor2_CNhs12346_11582-120F7_reverse Regulation 
MelanocyteDarkDonor2_CNhs12346_ctss_fwd MelanocyteDarkD2+ Melanocyte - dark, donor2_CNhs12346_11582-120F7_forward Regulation 
MelanocyteDarkDonor1_CNhs12591_ctss_rev MelanocyteDarkD1- Melanocyte - dark, donor1_CNhs12591_11502-119F8_reverse Regulation 
MelanocyteDarkDonor1_CNhs12591_ctss_fwd MelanocyteDarkD1+ Melanocyte - dark, donor1_CNhs12591_11502-119F8_forward Regulation 
MastCellStimulatedDonor1_CNhs11073_ctss_rev MastCellStimulatedD1- Mast cell - stimulated, donor1_CNhs11073_11487-119E2_reverse Regulation 
MastCellStimulatedDonor1_CNhs11073_ctss_fwd MastCellStimulatedD1+ Mast cell - stimulated, donor1_CNhs11073_11487-119E2_forward Regulation 
MastCellExpandedAndStimulatedDonor8_CNhs13927_ctss_rev MastCellExpD8- Mast cell, expanded and stimulated, donor8_CNhs13927_11942-126A7_reverse Regulation 
MastCellExpandedDonor8_CNhs13926_ctss_rev MastCellExpD8- Mast cell, expanded, donor8_CNhs13926_11941-126A6_reverse Regulation 
MastCellExpandedAndStimulatedDonor8_CNhs13927_ctss_fwd MastCellExpD8+ Mast cell, expanded and stimulated, donor8_CNhs13927_11942-126A7_forward Regulation 
MastCellExpandedDonor8_CNhs13926_ctss_fwd MastCellExpD8+ Mast cell, expanded, donor8_CNhs13926_11941-126A6_forward Regulation 
MastCellExpandedDonor5_CNhs13924_ctss_rev MastCellExpD5- Mast cell, expanded, donor5_CNhs13924_11939-126A4_reverse Regulation 
MastCellExpandedAndStimulatedDonor5_CNhs13925_ctss_rev MastCellExpD5- Mast cell, expanded and stimulated, donor5_CNhs13925_11940-126A5_reverse Regulation 
MastCellExpandedDonor5_CNhs13924_ctss_fwd MastCellExpD5+ Mast cell, expanded, donor5_CNhs13924_11939-126A4_forward Regulation 
MastCellExpandedAndStimulatedDonor5_CNhs13925_ctss_fwd MastCellExpD5+ Mast cell, expanded and stimulated, donor5_CNhs13925_11940-126A5_forward Regulation 
MastCellDonor4_CNhs12592_ctss_rev MastCellD4- Mast cell, donor4_CNhs12592_11567-120E1_reverse Regulation 
MastCellDonor4_CNhs12592_ctss_fwd MastCellD4+ Mast cell, donor4_CNhs12592_11567-120E1_forward Regulation 
MastCellDonor3_CNhs12593_ctss_rev MastCellD3- Mast cell, donor3_CNhs12593_11566-120D9_reverse Regulation 
MastCellDonor3_CNhs12593_ctss_fwd MastCellD3+ Mast cell, donor3_CNhs12593_11566-120D9_forward Regulation 
MastCellDonor2_CNhs12594_ctss_rev MastCellD2- Mast cell, donor2_CNhs12594_11565-120D8_reverse Regulation 
MastCellDonor2_CNhs12594_ctss_fwd MastCellD2+ Mast cell, donor2_CNhs12594_11565-120D8_forward Regulation 
MastCellDonor1_CNhs12566_ctss_rev MastCellD1- Mast cell, donor1_CNhs12566_11563-120D6_reverse Regulation 
MastCellDonor1_CNhs12566_ctss_fwd MastCellD1+ Mast cell, donor1_CNhs12566_11563-120D6_forward Regulation 
MammaryEpithelialCellDonor3_CNhs12032_ctss_rev MammaryEpithelialCellD3- Mammary Epithelial Cell, donor3_CNhs12032_11422-118F9_reverse Regulation 
MammaryEpithelialCellDonor3_CNhs12032_ctss_fwd MammaryEpithelialCellD3+ Mammary Epithelial Cell, donor3_CNhs12032_11422-118F9_forward Regulation 
MammaryEpithelialCellDonor2_CNhs11382_ctss_rev MammaryEpithelialCellD2- Mammary Epithelial Cell, donor2_CNhs11382_11350-117G9_reverse Regulation 
MammaryEpithelialCellDonor2_CNhs11382_ctss_fwd MammaryEpithelialCellD2+ Mammary Epithelial Cell, donor2_CNhs11382_11350-117G9_forward Regulation 
MammaryEpithelialCellDonor1_CNhs11077_ctss_rev MammaryEpithelialCellD1- Mammary Epithelial Cell, donor1_CNhs11077_11273-116H4_reverse Regulation 
MammaryEpithelialCellDonor1_CNhs11077_ctss_fwd MammaryEpithelialCellD1+ Mammary Epithelial Cell, donor1_CNhs11077_11273-116H4_forward Regulation 
MallassezderivedCellsDonor3_CNhs13551_ctss_rev MallassezCellsD3- Mallassez-derived cells, donor3_CNhs13551_11930-125I4_reverse Regulation 
MallassezderivedCellsDonor3_CNhs13551_ctss_fwd MallassezCellsD3+ Mallassez-derived cells, donor3_CNhs13551_11930-125I4_forward Regulation 
MallassezderivedCellsDonor2_CNhs13550_ctss_rev MallassezCellsD2- Mallassez-derived cells, donor2_CNhs13550_11929-125I3_reverse Regulation 
MallassezderivedCellsDonor2_CNhs13550_ctss_fwd MallassezCellsD2+ Mallassez-derived cells, donor2_CNhs13550_11929-125I3_forward Regulation 
MacrophageMonocyteDerivedDonor3_CNhs12003_ctss_rev MacrophageMonocyteD3- Macrophage - monocyte derived, donor3_CNhs12003_11389-118C3_reverse Regulation 
MacrophageMonocyteDerivedDonor3_CNhs12003_ctss_fwd MacrophageMonocyteD3+ Macrophage - monocyte derived, donor3_CNhs12003_11389-118C3_forward Regulation 
MacrophageMonocyteDerivedDonor2_CNhs11899_ctss_rev MacrophageMonocyteD2- Macrophage - monocyte derived, donor2_CNhs11899_11313-117C8_reverse Regulation 
MacrophageMonocyteDerivedDonor2_CNhs11899_ctss_fwd MacrophageMonocyteD2+ Macrophage - monocyte derived, donor2_CNhs11899_11313-117C8_forward Regulation 
MacrophageMonocyteDerivedDonor1_CNhs10861_ctss_rev MacrophageMonocyteD1- Macrophage - monocyte derived, donor1_CNhs10861_11232-116C8_reverse Regulation 
MacrophageMonocyteDerivedDonor1_CNhs10861_ctss_fwd MacrophageMonocyteD1+ Macrophage - monocyte derived, donor1_CNhs10861_11232-116C8_forward Regulation 
LensEpithelialCellsDonor3_CNhs12572_ctss_rev LensEpithelialCellsD3- Lens Epithelial Cells, donor3_CNhs12572_11690-122I7_reverse Regulation 
LensEpithelialCellsDonor3_CNhs12572_ctss_fwd LensEpithelialCellsD3+ Lens Epithelial Cells, donor3_CNhs12572_11690-122I7_forward Regulation 
LensEpithelialCellsDonor2_CNhs12568_ctss_rev LensEpithelialCellsD2- Lens Epithelial Cells, donor2_CNhs12568_11609-120I7_reverse Regulation 
LensEpithelialCellsDonor2_CNhs12568_ctss_fwd LensEpithelialCellsD2+ Lens Epithelial Cells, donor2_CNhs12568_11609-120I7_forward Regulation 
LensEpithelialCellsDonor1_CNhs12342_ctss_rev LensEpithelialCellsD1- Lens Epithelial Cells, donor1_CNhs12342_11529-119I8_reverse Regulation 
LensEpithelialCellsDonor1_CNhs12342_ctss_fwd LensEpithelialCellsD1+ Lens Epithelial Cells, donor1_CNhs12342_11529-119I8_forward Regulation 
KeratocytesDonor3_CNhs12921_ctss_rev KeratocytesD3- Keratocytes, donor3_CNhs12921_11688-122I5_reverse Regulation 
KeratocytesDonor3_CNhs12921_ctss_fwd KeratocytesD3+ Keratocytes, donor3_CNhs12921_11688-122I5_forward Regulation 
KeratocytesDonor2_CNhs12095_ctss_rev KeratocytesD2- Keratocytes, donor2_CNhs12095_11607-120I5_reverse Regulation 
KeratocytesDonor2_CNhs12095_ctss_fwd KeratocytesD2+ Keratocytes, donor2_CNhs12095_11607-120I5_forward Regulation 
KeratocytesDonor1_CNhs11337_ctss_rev KeratocytesD1- Keratocytes, donor1_CNhs11337_11527-119I6_reverse Regulation 
KeratocytesDonor1_CNhs11337_ctss_fwd KeratocytesD1+ Keratocytes, donor1_CNhs11337_11527-119I6_forward Regulation 
KeratinocyteOralDonor1_CNhs10879_ctss_rev KeratinocyteOralD1- Keratinocyte - oral, donor1_CNhs10879_11251-116E9_reverse Regulation 
KeratinocyteOralDonor1_CNhs10879_ctss_fwd KeratinocyteOralD1+ Keratinocyte - oral, donor1_CNhs10879_11251-116E9_forward Regulation 
KeratinocyteEpidermalDonor3_CNhs12031_ctss_rev KeratinocyteEpidermalD3- Keratinocyte - epidermal, donor3_CNhs12031_11421-118F8_reverse Regulation 
KeratinocyteEpidermalDonor3_CNhs12031_ctss_fwd KeratinocyteEpidermalD3+ Keratinocyte - epidermal, donor3_CNhs12031_11421-118F8_forward Regulation 
KeratinocyteEpidermalDonor2_CNhs11381_ctss_rev KeratinocyteEpidermalD2- Keratinocyte - epidermal, donor2_CNhs11381_11349-117G8_reverse Regulation 
KeratinocyteEpidermalDonor2_CNhs11381_ctss_fwd KeratinocyteEpidermalD2+ Keratinocyte - epidermal, donor2_CNhs11381_11349-117G8_forward Regulation 
KeratinocyteEpidermalDonor1_CNhs11064_ctss_rev KeratinocyteEpidermalD1- Keratinocyte - epidermal, donor1_CNhs11064_11272-116H3_reverse Regulation 
KeratinocyteEpidermalDonor1_CNhs11064_ctss_fwd KeratinocyteEpidermalD1+ Keratinocyte - epidermal, donor1_CNhs11064_11272-116H3_forward Regulation 
IrisPigmentEpithelialCellsDonor1_CNhs12596_ctss_rev IrisPigmentEpithelialCellsD1- Iris Pigment Epithelial Cells, donor1_CNhs12596_11530-119I9_reverse Regulation 
IrisPigmentEpithelialCellsDonor1_CNhs12596_ctss_fwd IrisPigmentEpithelialCellsD1+ Iris Pigment Epithelial Cells, donor1_CNhs12596_11530-119I9_forward Regulation 
IntestinalEpithelialCellsPolarizedDonor1_CNhs10875_ctss_rev IntestinalEpithelialCellsD1- Intestinal epithelial cells (polarized), donor1_CNhs10875_11246-116E4_reverse Regulation 
IntestinalEpithelialCellsPolarizedDonor1_CNhs10875_ctss_fwd IntestinalEpithelialCellsD1+ Intestinal epithelial cells (polarized), donor1_CNhs10875_11246-116E4_forward Regulation 
ImmatureLangerhansCellsDonor2_CNhs13480_ctss_rev ImmatureLangerhansCellsD2- immature langerhans cells, donor2_CNhs13480_11905-125F6_reverse Regulation 
ImmatureLangerhansCellsDonor2_CNhs13480_ctss_fwd ImmatureLangerhansCellsD2+ immature langerhans cells, donor2_CNhs13480_11905-125F6_forward Regulation 
ImmatureLangerhansCellsDonor1_CNhs13537_ctss_rev ImmatureLangerhansCellsD1- immature langerhans cells, donor1_CNhs13537_11904-125F5_reverse Regulation 
ImmatureLangerhansCellsDonor1_CNhs13537_ctss_fwd ImmatureLangerhansCellsD1+ immature langerhans cells, donor1_CNhs13537_11904-125F5_forward Regulation 
HepatocyteDonor3_CNhs12626_ctss_rev HepatocyteD3- Hepatocyte, donor3_CNhs12626_11684-122I1_reverse Regulation 
HepatocyteDonor3_CNhs12626_ctss_fwd HepatocyteD3+ Hepatocyte, donor3_CNhs12626_11684-122I1_forward Regulation 
HepatocyteDonor2_CNhs12349_ctss_rev HepatocyteD2- Hepatocyte, donor2_CNhs12349_11603-120I1_reverse Regulation 
HepatocyteDonor2_CNhs12349_ctss_fwd HepatocyteD2+ Hepatocyte, donor2_CNhs12349_11603-120I1_forward Regulation 
HepatocyteDonor1_CNhs12340_ctss_rev HepatocyteD1- Hepatocyte, donor1_CNhs12340_11523-119I2_reverse Regulation 
HepatocyteDonor1_CNhs12340_ctss_fwd HepatocyteD1+ Hepatocyte, donor1_CNhs12340_11523-119I2_forward Regulation 
HepaticStellateCellsLipocyteDonor3_CNhs12627_ctss_rev HepaticStellateCellsD3- Hepatic Stellate Cells (lipocyte), donor3_CNhs12627_11685-122I2_reverse Regulation 
HepaticStellateCellsLipocyteDonor3_CNhs12627_ctss_fwd HepaticStellateCellsD3+ Hepatic Stellate Cells (lipocyte), donor3_CNhs12627_11685-122I2_forward Regulation 
HepaticStellateCellsLipocyteDonor2_CNhs12093_ctss_rev HepaticStellateCellsD2- Hepatic Stellate Cells (lipocyte), donor2_CNhs12093_11604-120I2_reverse Regulation 
HepaticStellateCellsLipocyteDonor2_CNhs12093_ctss_fwd HepaticStellateCellsD2+ Hepatic Stellate Cells (lipocyte), donor2_CNhs12093_11604-120I2_forward Regulation 
HepaticStellateCellsLipocyteDonor1_CNhs11335_ctss_rev HepaticStellateCellsD1- Hepatic Stellate Cells (lipocyte), donor1_CNhs11335_11524-119I3_reverse Regulation 
HepaticStellateCellsLipocyteDonor1_CNhs11335_ctss_fwd HepaticStellateCellsD1+ Hepatic Stellate Cells (lipocyte), donor1_CNhs11335_11524-119I3_forward Regulation 
HepaticSinusoidalEndothelialCellsDonor3_CNhs12625_ctss_rev HepaticSinusoidalEndothelialCellsD3- Hepatic Sinusoidal Endothelial Cells, donor3_CNhs12625_11682-122H8_reverse Regulation 
HepaticSinusoidalEndothelialCellsDonor3_CNhs12625_ctss_fwd HepaticSinusoidalEndothelialCellsD3+ Hepatic Sinusoidal Endothelial Cells, donor3_CNhs12625_11682-122H8_forward Regulation 
HepaticSinusoidalEndothelialCellsDonor2_CNhs12092_ctss_rev HepaticSinusoidalEndothelialCellsD2- Hepatic Sinusoidal Endothelial Cells, donor2_CNhs12092_11601-120H8_reverse Regulation 
HepaticSinusoidalEndothelialCellsDonor2_CNhs12092_ctss_fwd HepaticSinusoidalEndothelialCellsD2+ Hepatic Sinusoidal Endothelial Cells, donor2_CNhs12092_11601-120H8_forward Regulation 
HepaticSinusoidalEndothelialCellsDonor1_CNhs12075_ctss_rev HepaticSinusoidalEndothelialCellsD1- Hepatic Sinusoidal Endothelial Cells, donor1_CNhs12075_11521-119H9_reverse Regulation 
HepaticSinusoidalEndothelialCellsDonor1_CNhs12075_ctss_fwd HepaticSinusoidalEndothelialCellsD1+ Hepatic Sinusoidal Endothelial Cells, donor1_CNhs12075_11521-119H9_forward Regulation 
HairFollicleOuterRootSheathCellsDonor2_CNhs12347_ctss_rev HairFollicleOuterRootSheathCellsD2- Hair Follicle Outer Root Sheath Cells, donor2_CNhs12347_11584-120F9_reverse Regulation 
HairFollicleOuterRootSheathCellsDonor2_CNhs12347_ctss_fwd HairFollicleOuterRootSheathCellsD2+ Hair Follicle Outer Root Sheath Cells, donor2_CNhs12347_11584-120F9_forward Regulation 
HairFollicleOuterRootSheathCellsDonor1_CNhs12339_ctss_rev HairFollicleOuterRootSheathCellsD1- Hair Follicle Outer Root Sheath Cells, donor1_CNhs12339_11504-119G1_reverse Regulation 
HairFollicleOuterRootSheathCellsDonor1_CNhs12339_ctss_fwd HairFollicleOuterRootSheathCellsD1+ Hair Follicle Outer Root Sheath Cells, donor1_CNhs12339_11504-119G1_forward Regulation 
HairFollicleDermalPapillaCellsDonor3_CNhs12030_ctss_rev HairFollicleDermalPapillaCellsD3- Hair Follicle Dermal Papilla Cells, donor3_CNhs12030_11420-118F7_reverse Regulation 
HairFollicleDermalPapillaCellsDonor3_CNhs12030_ctss_fwd HairFollicleDermalPapillaCellsD3+ Hair Follicle Dermal Papilla Cells, donor3_CNhs12030_11420-118F7_forward Regulation 
HairFollicleDermalPapillaCellsDonor2_CNhs11979_ctss_rev HairFollicleDermalPapillaCellsD2- Hair Follicle Dermal Papilla Cells, donor2_CNhs11979_11348-117G7_reverse Regulation 
HairFollicleDermalPapillaCellsDonor2_CNhs11979_ctss_fwd HairFollicleDermalPapillaCellsD2+ Hair Follicle Dermal Papilla Cells, donor2_CNhs11979_11348-117G7_forward Regulation 
HairFollicleDermalPapillaCellsDonor1_CNhs12501_ctss_rev HairFollicleDermalPapillaCellsD1- Hair Follicle Dermal Papilla Cells, donor1_CNhs12501_11271-116H2_reverse Regulation 
HairFollicleDermalPapillaCellsDonor1_CNhs12501_ctss_fwd HairFollicleDermalPapillaCellsD1+ Hair Follicle Dermal Papilla Cells, donor1_CNhs12501_11271-116H2_forward Regulation 
GingivalEpithelialCellsDonor3GEA15_CNhs11903_ctss_rev GingivalEpithelialCellsD3- Gingival epithelial cells, donor3 (GEA15)_CNhs11903_11379-118B2_reverse Regulation 
GingivalEpithelialCellsDonor3GEA15_CNhs11903_ctss_fwd GingivalEpithelialCellsD3+ Gingival epithelial cells, donor3 (GEA15)_CNhs11903_11379-118B2_forward Regulation 
GingivalEpithelialCellsDonor2GEA14_CNhs11896_ctss_rev GingivalEpithelialCellsD2- Gingival epithelial cells, donor2 (GEA14)_CNhs11896_11302-117B6_reverse Regulation 
GingivalEpithelialCellsDonor2GEA14_CNhs11896_ctss_fwd GingivalEpithelialCellsD2+ Gingival epithelial cells, donor2 (GEA14)_CNhs11896_11302-117B6_forward Regulation 
GingivalEpithelialCellsDonor1GEA11_CNhs11061_ctss_rev GingivalEpithelialCellsD1- Gingival epithelial cells, donor1 (GEA11)_CNhs11061_11221-116B6_reverse Regulation 
GingivalEpithelialCellsDonor1GEA11_CNhs11061_ctss_fwd GingivalEpithelialCellsD1+ Gingival epithelial cells, donor1 (GEA11)_CNhs11061_11221-116B6_forward Regulation 
GammaDeltaPositiveTCellsDonor2_CNhs13915_ctss_rev GammaDeltaTcellsD2- gamma delta positive T cells, donor2_CNhs13915_11938-126A3_reverse Regulation 
GammaDeltaPositiveTCellsDonor2_CNhs13915_ctss_fwd GammaDeltaTcellsD2+ gamma delta positive T cells, donor2_CNhs13915_11938-126A3_forward Regulation 
GammaDeltaPositiveTCellsDonor1_CNhs13914_ctss_rev GammaDeltaTcellsD1- gamma delta positive T cells, donor1_CNhs13914_11937-126A2_reverse Regulation 
GammaDeltaPositiveTCellsDonor1_CNhs13914_ctss_fwd GammaDeltaTcellsD1+ gamma delta positive T cells, donor1_CNhs13914_11937-126A2_forward Regulation 
FibroblastVillousMesenchymalDonor3_CNhs12920_ctss_rev FibroVillousMesenchymalD3- Fibroblast - Villous Mesenchymal, donor3_CNhs12920_11696-123A4_reverse Regulation 
FibroblastVillousMesenchymalDonor3_CNhs12920_ctss_fwd FibroVillousMesenchymalD3+ Fibroblast - Villous Mesenchymal, donor3_CNhs12920_11696-123A4_forward Regulation 
FibroblastVillousMesenchymalDonor2_CNhs12099_ctss_rev FibroVillousMesenchymalD2- Fibroblast - Villous Mesenchymal, donor2_CNhs12099_11615-122A4_reverse Regulation 
FibroblastVillousMesenchymalDonor2_CNhs12099_ctss_fwd FibroVillousMesenchymalD2+ Fibroblast - Villous Mesenchymal, donor2_CNhs12099_11615-122A4_forward Regulation 
FibroblastVillousMesenchymalDonor1_CNhs11343_ctss_rev FibroVillousMesenchymalD1- Fibroblast - Villous Mesenchymal, donor1_CNhs11343_11535-120A5_reverse Regulation 
FibroblastVillousMesenchymalDonor1_CNhs11343_ctss_fwd FibroVillousMesenchymalD1+ Fibroblast - Villous Mesenchymal, donor1_CNhs11343_11535-120A5_forward Regulation 
FibroblastSkinWalkerWarburgDonor1_CNhs11352_ctss_rev FibroSkinWalkerWarburgD1- Fibroblast - skin walker warburg, donor1_CNhs11352_11554-120C6_reverse Regulation 
FibroblastSkinWalkerWarburgDonor1_CNhs11352_ctss_fwd FibroSkinWalkerWarburgD1+ Fibroblast - skin walker warburg, donor1_CNhs11352_11554-120C6_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor3_CNhs11912_ctss_rev FibroSkinSpinalMuscularAtrophyNucfracD3- Fibroblast - skin spinal muscular atrophy, donor3_CNhs11912_11559-120D2_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor3_CNhs11912_ctss_fwd FibroSkinSpinalMuscularAtrophyNucfracD3+ Fibroblast - skin spinal muscular atrophy, donor3_CNhs11912_11559-120D2_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor2_CNhs11911_ctss_rev FibroSkinSpinalMuscularAtrophyNucfracD2- Fibroblast - skin spinal muscular atrophy, donor2_CNhs11911_11558-120D1_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor2_CNhs11911_ctss_fwd FibroSkinSpinalMuscularAtrophyNucfracD2+ Fibroblast - skin spinal muscular atrophy, donor2_CNhs11911_11558-120D1_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor1_CNhs11074_ctss_rev FibroSkinSpinalMuscularAtrophyNucfracD1- Fibroblast - skin spinal muscular atrophy, donor1_CNhs11074_11555-120C7_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor1_CNhs11074_ctss_fwd FibroSkinSpinalMuscularAtrophyNucfracD1+ Fibroblast - skin spinal muscular atrophy, donor1_CNhs11074_11555-120C7_forward Regulation 
FibroblastSkinNormalDonor2_CNhs11914_ctss_rev FibroSkinNormalNucfracD2- Fibroblast - skin normal, donor2_CNhs11914_11561-120D4_reverse Regulation 
FibroblastSkinNormalDonor2_CNhs11914_ctss_fwd FibroSkinNormalNucfracD2+ Fibroblast - skin normal, donor2_CNhs11914_11561-120D4_forward Regulation 
FibroblastSkinNormalDonor1_CNhs11351_ctss_rev FibroSkinNormalNucfracD1- Fibroblast - skin normal, donor1_CNhs11351_11553-120C5_reverse Regulation 
FibroblastSkinNormalDonor1_CNhs11351_ctss_fwd FibroSkinNormalNucfracD1+ Fibroblast - skin normal, donor1_CNhs11351_11553-120C5_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor3_CNhs11913_ctss_rev FibroSkinDystrophiaMyotonicaNucfracD3- Fibroblast - skin dystrophia myotonica, donor3_CNhs11913_11560-120D3_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor3_CNhs11913_ctss_fwd FibroSkinDystrophiaMyotonicaNucfracD3+ Fibroblast - skin dystrophia myotonica, donor3_CNhs11913_11560-120D3_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor2_CNhs11354_ctss_rev FibroSkinDystrophiaMyotonicaNucfracD2- Fibroblast - skin dystrophia myotonica, donor2_CNhs11354_11557-120C9_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor2_CNhs11354_ctss_fwd FibroSkinDystrophiaMyotonicaNucfracD2+ Fibroblast - skin dystrophia myotonica, donor2_CNhs11354_11557-120C9_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor1_CNhs11353_ctss_rev FibroSkinDystrophiaMyotonicaNucfracD1- Fibroblast - skin dystrophia myotonica, donor1_CNhs11353_11556-120C8_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor1_CNhs11353_ctss_fwd FibroSkinDystrophiaMyotonicaNucfracD1+ Fibroblast - skin dystrophia myotonica, donor1_CNhs11353_11556-120C8_forward Regulation 
FibroblastPulmonaryArteryDonor1_CNhs10878_ctss_rev FibroPulmonaryArteryD1- Fibroblast - Pulmonary Artery, donor1_CNhs10878_11250-116E8_reverse Regulation 
FibroblastPulmonaryArteryDonor1_CNhs10878_ctss_fwd FibroPulmonaryArteryD1+ Fibroblast - Pulmonary Artery, donor1_CNhs10878_11250-116E8_forward Regulation 
FibroblastPeriodontalLigamentDonor6PLH3_CNhs11996_ctss_rev FibroPeriodontalLigamentD6- Fibroblast - Periodontal Ligament, donor6 (PLH3)_CNhs11996_11380-118B3_reverse Regulation 
FibroblastPeriodontalLigamentDonor6PLH3_CNhs11996_ctss_fwd FibroPeriodontalLigamentD6+ Fibroblast - Periodontal Ligament, donor6 (PLH3)_CNhs11996_11380-118B3_forward Regulation 
FibroblastPeriodontalLigamentDonor5PL30_CNhs11953_ctss_rev FibroPeriodontalLigamentD5- Fibroblast - Periodontal Ligament, donor5 (PL30)_CNhs11953_11304-117B8_reverse Regulation 
FibroblastPeriodontalLigamentDonor5PL30_CNhs11953_ctss_fwd FibroPeriodontalLigamentD5+ Fibroblast - Periodontal Ligament, donor5 (PL30)_CNhs11953_11304-117B8_forward Regulation 
FibroblastPeriodontalLigamentDonor4PL29_CNhs12493_ctss_rev FibroPeriodontalLigamentD4- Fibroblast - Periodontal Ligament, donor4 (PL29)_CNhs12493_11223-116B8_reverse Regulation 
FibroblastPeriodontalLigamentDonor4PL29_CNhs12493_ctss_fwd FibroPeriodontalLigamentD4+ Fibroblast - Periodontal Ligament, donor4 (PL29)_CNhs12493_11223-116B8_forward Regulation 
FibroblastPeriodontalLigamentDonor3_CNhs11907_ctss_rev FibroPeriodontalLigamentD3- Fibroblast - Periodontal Ligament, donor3_CNhs11907_11395-118C9_reverse Regulation 
FibroblastPeriodontalLigamentDonor3_CNhs11907_ctss_fwd FibroPeriodontalLigamentD3+ Fibroblast - Periodontal Ligament, donor3_CNhs11907_11395-118C9_forward Regulation 
FibroblastPeriodontalLigamentDonor2_CNhs11962_ctss_rev FibroPeriodontalLigamentD2- Fibroblast - Periodontal Ligament, donor2_CNhs11962_11319-117D5_reverse Regulation 
FibroblastPeriodontalLigamentDonor2_CNhs11962_ctss_fwd FibroPeriodontalLigamentD2+ Fibroblast - Periodontal Ligament, donor2_CNhs11962_11319-117D5_forward Regulation 
FibroblastPeriodontalLigamentDonor1_CNhs10867_ctss_rev FibroPeriodontalLigamentD1- Fibroblast - Periodontal Ligament, donor1_CNhs10867_11238-116D5_reverse Regulation 
FibroblastPeriodontalLigamentDonor1_CNhs10867_ctss_fwd FibroPeriodontalLigamentD1+ Fibroblast - Periodontal Ligament, donor1_CNhs10867_11238-116D5_forward Regulation 
FibroblastMammaryDonor3_CNhs12128_ctss_rev FibroMammaryD3- Fibroblast - Mammary, donor3_CNhs12128_11701-123A9_reverse Regulation 
FibroblastMammaryDonor3_CNhs12128_ctss_fwd FibroMammaryD3+ Fibroblast - Mammary, donor3_CNhs12128_11701-123A9_forward Regulation 
FibroblastMammaryDonor2_CNhs12103_ctss_rev FibroMammaryD2- Fibroblast - Mammary, donor2_CNhs12103_11620-122A9_reverse Regulation 
FibroblastMammaryDonor2_CNhs12103_ctss_fwd FibroMammaryD2+ Fibroblast - Mammary, donor2_CNhs12103_11620-122A9_forward Regulation 
FibroblastMammaryDonor1_CNhs11348_ctss_rev FibroMammaryD1- Fibroblast - Mammary, donor1_CNhs11348_11540-120B1_reverse Regulation 
FibroblastMammaryDonor1_CNhs11348_ctss_fwd FibroMammaryD1+ Fibroblast - Mammary, donor1_CNhs11348_11540-120B1_forward Regulation 
FibroblastLymphaticDonor3_CNhs12118_ctss_rev FibroLymphaticD3- Fibroblast - Lymphatic, donor3_CNhs12118_11667-122G2_reverse Regulation 
FibroblastLymphaticDonor3_CNhs12118_ctss_fwd FibroLymphaticD3+ Fibroblast - Lymphatic, donor3_CNhs12118_11667-122G2_forward Regulation 
FibroblastLymphaticDonor2_CNhs12082_ctss_rev FibroLymphaticD2- Fibroblast - Lymphatic, donor2_CNhs12082_11586-120G2_reverse Regulation 
FibroblastLymphaticDonor2_CNhs12082_ctss_fwd FibroLymphaticD2+ Fibroblast - Lymphatic, donor2_CNhs12082_11586-120G2_forward Regulation 
FibroblastLymphaticDonor1_CNhs11322_ctss_rev FibroLymphaticD1- Fibroblast - Lymphatic, donor1_CNhs11322_11506-119G3_reverse Regulation 
FibroblastLymphaticDonor1_CNhs11322_ctss_fwd FibroLymphaticD1+ Fibroblast - Lymphatic, donor1_CNhs11322_11506-119G3_forward Regulation 
FibroblastLungDonor3_CNhs12029_ctss_rev FibroLungD3- Fibroblast - Lung, donor3_CNhs12029_11419-118F6_reverse Regulation 
FibroblastLungDonor3_CNhs12029_ctss_fwd FibroLungD3+ Fibroblast - Lung, donor3_CNhs12029_11419-118F6_forward Regulation 
FibroblastLungDonor2_CNhs11380_ctss_rev FibroLungD2- Fibroblast - Lung, donor2_CNhs11380_11347-117G6_reverse Regulation 
FibroblastLungDonor2_CNhs11380_ctss_fwd FibroLungD2+ Fibroblast - Lung, donor2_CNhs11380_11347-117G6_forward Regulation 
FibroblastLungDonor1_CNhs12500_ctss_rev FibroLungD1- Fibroblast - Lung, donor1_CNhs12500_11270-116H1_reverse Regulation 
FibroblastLungDonor1_CNhs12500_ctss_fwd FibroLungD1+ Fibroblast - Lung, donor1_CNhs12500_11270-116H1_forward Regulation 
FibroblastGingivalDonor9Control_CNhs14134_ctss_rev FibroGingivalD9- Fibroblast - Gingival, donor9 (control)_CNhs14134_11927-125I1_reverse Regulation 
FibroblastGingivalDonor9Control_CNhs14134_ctss_fwd FibroGingivalD9+ Fibroblast - Gingival, donor9 (control)_CNhs14134_11927-125I1_forward Regulation 
FibroblastGingivalDonor8Control_CNhs14133_ctss_rev FibroGingivalD8- Fibroblast - Gingival, donor8 (control)_CNhs14133_11926-125H9_reverse Regulation 
FibroblastGingivalDonor8ChronicPeriodontitis_CNhs14132_ctss_rev FibroGingivalD8- Fibroblast - Gingival, donor8 (chronic periodontitis)_CNhs14132_11925-125H8_reverse Regulation 
FibroblastGingivalDonor8Control_CNhs14133_ctss_fwd FibroGingivalD8+ Fibroblast - Gingival, donor8 (control)_CNhs14133_11926-125H9_forward Regulation 
FibroblastGingivalDonor8ChronicPeriodontitis_CNhs14132_ctss_fwd FibroGingivalD8+ Fibroblast - Gingival, donor8 (chronic periodontitis)_CNhs14132_11925-125H8_forward Regulation 
FibroblastGingivalDonor7AggressivePeriodontitis_CNhs14130_ctss_rev FibroGingivalD7- Fibroblast - Gingival, donor7 (aggressive periodontitis)_CNhs14130_11923-125H6_reverse Regulation 
FibroblastGingivalDonor7Control_CNhs14131_ctss_rev FibroGingivalD7- Fibroblast - Gingival, donor7 (control)_CNhs14131_11924-125H7_reverse Regulation 
FibroblastGingivalDonor7AggressivePeriodontitis_CNhs14130_ctss_fwd FibroGingivalD7+ Fibroblast - Gingival, donor7 (aggressive periodontitis)_CNhs14130_11923-125H6_forward Regulation 
FibroblastGingivalDonor7Control_CNhs14131_ctss_fwd FibroGingivalD7+ Fibroblast - Gingival, donor7 (control)_CNhs14131_11924-125H7_forward Regulation 
FibroblastGingivalDonor6AggressivePeriodontitis_CNhs14128_ctss_rev FibroGingivalD6- Fibroblast - Gingival, donor6 (aggressive periodontitis)_CNhs14128_11921-125H4_reverse Regulation 
FibroblastGingivalDonor6Control_CNhs14129_ctss_rev FibroGingivalD6- Fibroblast - Gingival, donor6 (control)_CNhs14129_11922-125H5_reverse Regulation 
FibroblastGingivalDonor6Control_CNhs14129_ctss_fwd FibroGingivalD6+ Fibroblast - Gingival, donor6 (control)_CNhs14129_11922-125H5_forward Regulation 
FibroblastGingivalDonor6AggressivePeriodontitis_CNhs14128_ctss_fwd FibroGingivalD6+ Fibroblast - Gingival, donor6 (aggressive periodontitis)_CNhs14128_11921-125H4_forward Regulation 
FibroblastGingivalDonor5GFH3_CNhs11952_ctss_rev FibroGingivalD5- Fibroblast - Gingival, donor5 (GFH3)_CNhs11952_11303-117B7_reverse Regulation 
FibroblastGingivalDonor5GFH3_CNhs11952_ctss_fwd FibroGingivalD5+ Fibroblast - Gingival, donor5 (GFH3)_CNhs11952_11303-117B7_forward Regulation 
FibroblastGingivalDonor4GFH2_CNhs10848_ctss_rev FibroGingivalD4- Fibroblast - Gingival, donor4 (GFH2)_CNhs10848_11222-116B7_reverse Regulation 
FibroblastGingivalDonor4GFH2_CNhs10848_ctss_fwd FibroGingivalD4+ Fibroblast - Gingival, donor4 (GFH2)_CNhs10848_11222-116B7_forward Regulation 
FibroblastGingivalDonor3_CNhs12006_ctss_rev FibroGingivalD3- Fibroblast - Gingival, donor3_CNhs12006_11394-118C8_reverse Regulation 
FibroblastGingivalDonor3_CNhs12006_ctss_fwd FibroGingivalD3+ Fibroblast - Gingival, donor3_CNhs12006_11394-118C8_forward Regulation 
FibroblastGingivalDonor2_CNhs11961_ctss_rev FibroGingivalD2- Fibroblast - Gingival, donor2_CNhs11961_11318-117D4_reverse Regulation 
FibroblastGingivalDonor2_CNhs11961_ctss_fwd FibroGingivalD2+ Fibroblast - Gingival, donor2_CNhs11961_11318-117D4_forward Regulation 
FibroblastGingivalDonor10Periodontitis_CNhs14135_ctss_rev FibroGingivalD10 (p- Fibroblast - Gingival, donor10 (periodontitis)_CNhs14135_11928-125I2_reverse Regulation 
FibroblastGingivalDonor10Periodontitis_CNhs14135_ctss_fwd FibroGingivalD10 (p+ Fibroblast - Gingival, donor10 (periodontitis)_CNhs14135_11928-125I2_forward Regulation 
FibroblastGingivalDonor1_CNhs10866_ctss_rev FibroGingivalD1- Fibroblast - Gingival, donor1_CNhs10866_11237-116D4_reverse Regulation 
FibroblastGingivalDonor1_CNhs10866_ctss_fwd FibroGingivalD1+ Fibroblast - Gingival, donor1_CNhs10866_11237-116D4_forward Regulation 
FibroblastDermalDonor6_CNhs12059_ctss_rev FibroDermalD6- Fibroblast - Dermal, donor6_CNhs12059_11458-119A9_reverse Regulation 
FibroblastDermalDonor6_CNhs12059_ctss_fwd FibroDermalD6+ Fibroblast - Dermal, donor6_CNhs12059_11458-119A9_forward Regulation 
FibroblastDermalDonor5_CNhs12055_ctss_rev FibroDermalD5- Fibroblast - Dermal, donor5_CNhs12055_11454-119A5_reverse Regulation 
FibroblastDermalDonor5_CNhs12055_ctss_fwd FibroDermalD5+ Fibroblast - Dermal, donor5_CNhs12055_11454-119A5_forward Regulation 
FibroblastDermalDonor4_CNhs12052_ctss_rev FibroDermalD4- Fibroblast - Dermal, donor4_CNhs12052_11450-119A1_reverse Regulation 
FibroblastDermalDonor4_CNhs12052_ctss_fwd FibroDermalD4+ Fibroblast - Dermal, donor4_CNhs12052_11450-119A1_forward Regulation 
FibroblastDermalDonor3_CNhs12028_ctss_rev FibroDermalD3- Fibroblast - Dermal, donor3_CNhs12028_11418-118F5_reverse Regulation 
FibroblastDermalDonor3_CNhs12028_ctss_fwd FibroDermalD3+ Fibroblast - Dermal, donor3_CNhs12028_11418-118F5_forward Regulation 
FibroblastDermalDonor2_CNhs11379_ctss_rev FibroDermalD2- Fibroblast - Dermal, donor2_CNhs11379_11346-117G5_reverse Regulation 
FibroblastDermalDonor2_CNhs11379_ctss_fwd FibroDermalD2+ Fibroblast - Dermal, donor2_CNhs11379_11346-117G5_forward Regulation 
FibroblastDermalDonor1_CNhs12499_ctss_rev FibroDermalD1- Fibroblast - Dermal, donor1_CNhs12499_11269-116G9_reverse Regulation 
FibroblastDermalDonor1_CNhs12499_ctss_fwd FibroDermalD1+ Fibroblast - Dermal, donor1_CNhs12499_11269-116G9_forward Regulation 
FibroblastConjunctivalDonor3_CNhs12734_ctss_rev FibroConjunctivalD3- Fibroblast - Conjunctival, donor3_CNhs12734_11692-122I9_reverse Regulation 
FibroblastConjunctivalDonor3_CNhs12734_ctss_fwd FibroConjunctivalD3+ Fibroblast - Conjunctival, donor3_CNhs12734_11692-122I9_forward Regulation 
FibroblastConjunctivalDonor1_CNhs11339_ctss_rev FibroConjunctivalD1- Fibroblast - Conjunctival, donor1_CNhs11339_11531-120A1_reverse Regulation 
FibroblastConjunctivalDonor1_CNhs11339_ctss_fwd FibroConjunctivalD1+ Fibroblast - Conjunctival, donor1_CNhs11339_11531-120A1_forward Regulation 
FibroblastChoroidPlexusDonor3_CNhs12620_ctss_rev FibroChoroidPlexusD3- Fibroblast - Choroid Plexus, donor3_CNhs12620_11653-122E6_reverse Regulation 
FibroblastChoroidPlexusDonor3_CNhs12620_ctss_fwd FibroChoroidPlexusD3+ Fibroblast - Choroid Plexus, donor3_CNhs12620_11653-122E6_forward Regulation 
FibroblastChoroidPlexusDonor2_CNhs12344_ctss_rev FibroChoroidPlexusD2- Fibroblast - Choroid Plexus, donor2_CNhs12344_11572-120E6_reverse Regulation 
FibroblastChoroidPlexusDonor2_CNhs12344_ctss_fwd FibroChoroidPlexusD2+ Fibroblast - Choroid Plexus, donor2_CNhs12344_11572-120E6_forward Regulation 
FibroblastChoroidPlexusDonor1_CNhs11319_ctss_rev FibroChoroidPlexusD1- Fibroblast - Choroid Plexus, donor1_CNhs11319_11492-119E7_reverse Regulation 
FibroblastChoroidPlexusDonor1_CNhs11319_ctss_fwd FibroChoroidPlexusD1+ Fibroblast - Choroid Plexus, donor1_CNhs11319_11492-119E7_forward Regulation 
FibroblastCardiacDonor6_CNhs12061_ctss_rev FibroCardiacD6- Fibroblast - Cardiac, donor6_CNhs12061_11460-119B2_reverse Regulation 
FibroblastCardiacDonor6_CNhs12061_ctss_fwd FibroCardiacD6+ Fibroblast - Cardiac, donor6_CNhs12061_11460-119B2_forward Regulation 
FibroblastCardiacDonor5_CNhs12057_ctss_rev FibroCardiacD5- Fibroblast - Cardiac, donor5_CNhs12057_11456-119A7_reverse Regulation 
FibroblastCardiacDonor5_CNhs12057_ctss_fwd FibroCardiacD5+ Fibroblast - Cardiac, donor5_CNhs12057_11456-119A7_forward Regulation 
FibroblastCardiacDonor4_CNhs11909_ctss_rev FibroCardiacD4- Fibroblast - Cardiac, donor4_CNhs11909_11452-119A3_reverse Regulation 
FibroblastCardiacDonor4_CNhs11909_ctss_fwd FibroCardiacD4+ Fibroblast - Cardiac, donor4_CNhs11909_11452-119A3_forward Regulation 
FibroblastCardiacDonor3_CNhs12027_ctss_rev FibroCardiacD3- Fibroblast - Cardiac, donor3_CNhs12027_11417-118F4_reverse Regulation 
FibroblastCardiacDonor3_CNhs12027_ctss_fwd FibroCardiacD3+ Fibroblast - Cardiac, donor3_CNhs12027_11417-118F4_forward Regulation 
FibroblastCardiacDonor2_CNhs11378_ctss_rev FibroCardiacD2- Fibroblast - Cardiac, donor2_CNhs11378_11345-117G4_reverse Regulation 
FibroblastCardiacDonor2_CNhs11378_ctss_fwd FibroCardiacD2+ Fibroblast - Cardiac, donor2_CNhs11378_11345-117G4_forward Regulation 
FibroblastCardiacDonor1_CNhs12498_ctss_rev FibroCardiacD1- Fibroblast - Cardiac, donor1_CNhs12498_11268-116G8_reverse Regulation 
FibroblastCardiacDonor1_CNhs12498_ctss_fwd FibroCardiacD1+ Fibroblast - Cardiac, donor1_CNhs12498_11268-116G8_forward Regulation 
FibroblastAorticAdventitialDonor3_CNhs12011_ctss_rev FibroAorticAdventitialD3- Fibroblast - Aortic Adventitial, donor3_CNhs12011_11401-118D6_reverse Regulation 
FibroblastAorticAdventitialDonor3_CNhs12011_ctss_fwd FibroAorticAdventitialD3+ Fibroblast - Aortic Adventitial, donor3_CNhs12011_11401-118D6_forward Regulation 
FibroblastAorticAdventitialDonor2_CNhs11968_ctss_rev FibroAorticAdventitialD2- Fibroblast - Aortic Adventitial, donor2_CNhs11968_11326-117E3_reverse Regulation 
FibroblastAorticAdventitialDonor2_CNhs11968_ctss_fwd FibroAorticAdventitialD2+ Fibroblast - Aortic Adventitial, donor2_CNhs11968_11326-117E3_forward Regulation 
FibroblastAorticAdventitialDonor1_CNhs10874_ctss_rev FibroAorticAdventitialD1- Fibroblast - Aortic Adventitial, donor1_CNhs10874_11245-116E3_reverse Regulation 
FibroblastAorticAdventitialDonor1_CNhs10874_ctss_fwd FibroAorticAdventitialD1+ Fibroblast - Aortic Adventitial, donor1_CNhs10874_11245-116E3_forward Regulation 
EsophagealEpithelialCellsDonor3_CNhs12622_ctss_rev EsophagealEpithelialCellsD3- Esophageal Epithelial Cells, donor3_CNhs12622_11668-122G3_reverse Regulation 
EsophagealEpithelialCellsDonor3_CNhs12622_ctss_fwd EsophagealEpithelialCellsD3+ Esophageal Epithelial Cells, donor3_CNhs12622_11668-122G3_forward Regulation 
EsophagealEpithelialCellsDonor2_CNhs12083_ctss_rev EsophagealEpithelialCellsD2- Esophageal Epithelial Cells, donor2_CNhs12083_11587-120G3_reverse Regulation 
EsophagealEpithelialCellsDonor2_CNhs12083_ctss_fwd EsophagealEpithelialCellsD2+ Esophageal Epithelial Cells, donor2_CNhs12083_11587-120G3_forward Regulation 
EsophagealEpithelialCellsDonor1_CNhs11323_ctss_rev EsophagealEpithelialCellsD1- Esophageal Epithelial Cells, donor1_CNhs11323_11507-119G4_reverse Regulation 
EsophagealEpithelialCellsDonor1_CNhs11323_ctss_fwd EsophagealEpithelialCellsD1+ Esophageal Epithelial Cells, donor1_CNhs11323_11507-119G4_forward Regulation 
EndothelialCellsVeinDonor3_CNhs12026_ctss_rev EndothelialCellsVeinD3- Endothelial Cells - Vein, donor3_CNhs12026_11416-118F3_reverse Regulation 
EndothelialCellsVeinDonor3_CNhs12026_ctss_fwd EndothelialCellsVeinD3+ Endothelial Cells - Vein, donor3_CNhs12026_11416-118F3_forward Regulation 
EndothelialCellsVeinDonor2_CNhs11377_ctss_rev EndothelialCellsVeinD2- Endothelial Cells - Vein, donor2_CNhs11377_11344-117G3_reverse Regulation 
EndothelialCellsVeinDonor2_CNhs11377_ctss_fwd EndothelialCellsVeinD2+ Endothelial Cells - Vein, donor2_CNhs11377_11344-117G3_forward Regulation 
EndothelialCellsVeinDonor1_CNhs12497_ctss_rev EndothelialCellsVeinD1- Endothelial Cells - Vein, donor1_CNhs12497_11267-116G7_reverse Regulation 
EndothelialCellsVeinDonor1_CNhs12497_ctss_fwd EndothelialCellsVeinD1+ Endothelial Cells - Vein, donor1_CNhs12497_11267-116G7_forward Regulation 
EndothelialCellsUmbilicalVeinDonor3_CNhs12010_ctss_rev EndothelialCellsUmbilicalVeinD3- Endothelial Cells - Umbilical vein, donor3_CNhs12010_11400-118D5_reverse Regulation 
EndothelialCellsUmbilicalVeinDonor3_CNhs12010_ctss_fwd EndothelialCellsUmbilicalVeinD3+ Endothelial Cells - Umbilical vein, donor3_CNhs12010_11400-118D5_forward Regulation 
EndothelialCellsUmbilicalVeinDonor2_CNhs11967_ctss_rev EndothelialCellsUmbilicalVeinD2- Endothelial Cells - Umbilical vein, donor2_CNhs11967_11324-117E1_reverse Regulation 
EndothelialCellsUmbilicalVeinDonor2_CNhs11967_ctss_fwd EndothelialCellsUmbilicalVeinD2+ Endothelial Cells - Umbilical vein, donor2_CNhs11967_11324-117E1_forward Regulation 
EndothelialCellsUmbilicalVeinDonor1_CNhs10872_ctss_rev EndothelialCellsUmbilicalVeinD1- Endothelial Cells - Umbilical vein, donor1_CNhs10872_11243-116E1_reverse Regulation 
EndothelialCellsUmbilicalVeinDonor1_CNhs10872_ctss_fwd EndothelialCellsUmbilicalVeinD1+ Endothelial Cells - Umbilical vein, donor1_CNhs10872_11243-116E1_forward Regulation 
EndothelialCellsThoracicDonor2_CNhs11978_ctss_rev EndothelialCellsThoracicD2- Endothelial Cells - Thoracic, donor2_CNhs11978_11343-117G2_reverse Regulation 
EndothelialCellsThoracicDonor2_CNhs11978_ctss_fwd EndothelialCellsThoracicD2+ Endothelial Cells - Thoracic, donor2_CNhs11978_11343-117G2_forward Regulation 
EndothelialCellsThoracicDonor1_CNhs11926_ctss_rev EndothelialCellsThoracicD1- Endothelial Cells - Thoracic, donor1_CNhs11926_11266-116G6_reverse Regulation 
EndothelialCellsThoracicDonor1_CNhs11926_ctss_fwd EndothelialCellsThoracicD1+ Endothelial Cells - Thoracic, donor1_CNhs11926_11266-116G6_forward Regulation 
EndothelialCellsMicrovascularDonor3_CNhs12024_ctss_rev EndothelialCellsMicrovascularD3- Endothelial Cells - Microvascular, donor3_CNhs12024_11414-118F1_reverse Regulation 
EndothelialCellsMicrovascularDonor3_CNhs12024_ctss_fwd EndothelialCellsMicrovascularD3+ Endothelial Cells - Microvascular, donor3_CNhs12024_11414-118F1_forward Regulation 
EndothelialCellsMicrovascularDonor2_CNhs11376_ctss_rev EndothelialCellsMicrovascularD2- Endothelial Cells - Microvascular, donor2_CNhs11376_11342-117G1_reverse Regulation 
EndothelialCellsMicrovascularDonor2_CNhs11376_ctss_fwd EndothelialCellsMicrovascularD2+ Endothelial Cells - Microvascular, donor2_CNhs11376_11342-117G1_forward Regulation 
EndothelialCellsMicrovascularDonor1_CNhs11925_ctss_rev EndothelialCellsMicrovascularD1- Endothelial Cells - Microvascular, donor1_CNhs11925_11265-116G5_reverse Regulation 
EndothelialCellsMicrovascularDonor1_CNhs11925_ctss_fwd EndothelialCellsMicrovascularD1+ Endothelial Cells - Microvascular, donor1_CNhs11925_11265-116G5_forward Regulation 
EndothelialCellsLymphaticDonor3_CNhs11906_ctss_rev EndothelialCellsLymphaticD3- Endothelial Cells - Lymphatic, donor3_CNhs11906_11393-118C7_reverse Regulation 
EndothelialCellsLymphaticDonor3_CNhs11906_ctss_fwd EndothelialCellsLymphaticD3+ Endothelial Cells - Lymphatic, donor3_CNhs11906_11393-118C7_forward Regulation 
EndothelialCellsLymphaticDonor2_CNhs11901_ctss_rev EndothelialCellsLymphaticD2- Endothelial Cells - Lymphatic, donor2_CNhs11901_11317-117D3_reverse Regulation 
EndothelialCellsLymphaticDonor2_CNhs11901_ctss_fwd EndothelialCellsLymphaticD2+ Endothelial Cells - Lymphatic, donor2_CNhs11901_11317-117D3_forward Regulation 
EndothelialCellsLymphaticDonor1_CNhs10865_ctss_rev EndothelialCellsLymphaticD1- Endothelial Cells - Lymphatic, donor1_CNhs10865_11236-116D3_reverse Regulation 
EndothelialCellsLymphaticDonor1_CNhs10865_ctss_fwd EndothelialCellsLymphaticD1+ Endothelial Cells - Lymphatic, donor1_CNhs10865_11236-116D3_forward Regulation 
EndothelialCellsArteryDonor3_CNhs12023_ctss_rev EndothelialCellsArteryD3- Endothelial Cells - Artery, donor3_CNhs12023_11413-118E9_reverse Regulation 
EndothelialCellsArteryDonor3_CNhs12023_ctss_fwd EndothelialCellsArteryD3+ Endothelial Cells - Artery, donor3_CNhs12023_11413-118E9_forward Regulation 
EndothelialCellsArteryDonor2_CNhs11977_ctss_rev EndothelialCellsArteryD2- Endothelial Cells - Artery, donor2_CNhs11977_11341-117F9_reverse Regulation 
EndothelialCellsArteryDonor2_CNhs11977_ctss_fwd EndothelialCellsArteryD2+ Endothelial Cells - Artery, donor2_CNhs11977_11341-117F9_forward Regulation 
EndothelialCellsArteryDonor1_CNhs12496_ctss_rev EndothelialCellsArteryD1- Endothelial Cells - Artery, donor1_CNhs12496_11264-116G4_reverse Regulation 
EndothelialCellsArteryDonor1_CNhs12496_ctss_fwd EndothelialCellsArteryD1+ Endothelial Cells - Artery, donor1_CNhs12496_11264-116G4_forward Regulation 
EndothelialCellsAorticDonor3_CNhs12022_ctss_rev EndothelialCellsAorticD3- Endothelial Cells - Aortic, donor3_CNhs12022_11412-118E8_reverse Regulation 
EndothelialCellsAorticDonor3_CNhs12022_ctss_fwd EndothelialCellsAorticD3+ Endothelial Cells - Aortic, donor3_CNhs12022_11412-118E8_forward Regulation 
EndothelialCellsAorticDonor2_CNhs11375_ctss_rev EndothelialCellsAorticD2- Endothelial Cells - Aortic, donor2_CNhs11375_11340-117F8_reverse Regulation 
EndothelialCellsAorticDonor2_CNhs11375_ctss_fwd EndothelialCellsAorticD2+ Endothelial Cells - Aortic, donor2_CNhs11375_11340-117F8_forward Regulation 
EndothelialCellsAorticDonor1_CNhs12495_ctss_rev EndothelialCellsAorticD1- Endothelial Cells - Aortic, donor1_CNhs12495_11263-116G3_reverse Regulation 
EndothelialCellsAorticDonor1_CNhs12495_ctss_fwd EndothelialCellsAorticD1+ Endothelial Cells - Aortic, donor1_CNhs12495_11263-116G3_forward Regulation 
EndothelialCellsAorticDonor0_CNhs10837_ctss_rev EndothelialCellsAorticD0- Endothelial Cells - Aortic, donor0_CNhs10837_11207-116A1_reverse Regulation 
EndothelialCellsAorticDonor0_CNhs10837_ctss_fwd EndothelialCellsAorticD0+ Endothelial Cells - Aortic, donor0_CNhs10837_11207-116A1_forward Regulation 
DendriticCellsPlasmacytoidDonor1_CNhs10857_ctss_rev DendriticCellsPlasmacytoidD1- Dendritic Cells - plasmacytoid, donor1_CNhs10857_11228-116C4_reverse Regulation 
DendriticCellsPlasmacytoidDonor1_CNhs10857_ctss_fwd DendriticCellsPlasmacytoidD1+ Dendritic Cells - plasmacytoid, donor1_CNhs10857_11228-116C4_forward Regulation 
DendriticCellsMonocyteImmatureDerivedDonor3_CNhs12000_ctss_rev DendriticCellsMonocyteImmatureD3- Dendritic Cells - monocyte immature derived, donor3_CNhs12000_11384-118B7_reverse Regulation 
DendriticCellsMonocyteImmatureDerivedDonor3_CNhs12000_ctss_fwd DendriticCellsMonocyteImmatureD3+ Dendritic Cells - monocyte immature derived, donor3_CNhs12000_11384-118B7_forward Regulation 
DendriticCellsMonocyteImmatureDerivedDonor1TechRep2_CNhs11062_ctss_rev DendriticCellsMonocyteImmatureD1Tr2- Dendritic Cells - monocyte immature derived, donor1, tech_rep2_CNhs11062_11227-116C3_reverse Regulation 
DendriticCellsMonocyteImmatureDerivedDonor1TechRep2_CNhs11062_ctss_fwd DendriticCellsMonocyteImmatureD1Tr2+ Dendritic Cells - monocyte immature derived, donor1, tech_rep2_CNhs11062_11227-116C3_forward Regulation 
DendriticCellsMonocyteImmatureDerivedDonor1TechRep1_CNhs10855_ctss_rev DendriticCellsMonocyteImmatureD1Tr1- Dendritic Cells - monocyte immature derived, donor1, tech_rep1_CNhs10855_11227-116C3_reverse Regulation 
DendriticCellsMonocyteImmatureDerivedDonor1TechRep1_CNhs10855_ctss_fwd DendriticCellsMonocyteImmatureD1Tr1+ Dendritic Cells - monocyte immature derived, donor1, tech_rep1_CNhs10855_11227-116C3_forward Regulation 
CornealEpithelialCellsDonor3_CNhs12123_ctss_rev CornealEpithelialCellsD3- Corneal Epithelial Cells, donor3_CNhs12123_11687-122I4_reverse Regulation 
CornealEpithelialCellsDonor3_CNhs12123_ctss_fwd CornealEpithelialCellsD3+ Corneal Epithelial Cells, donor3_CNhs12123_11687-122I4_forward Regulation 
CornealEpithelialCellsDonor2_CNhs12094_ctss_rev CornealEpithelialCellsD2- Corneal Epithelial Cells, donor2_CNhs12094_11606-120I4_reverse Regulation 
CornealEpithelialCellsDonor2_CNhs12094_ctss_fwd CornealEpithelialCellsD2+ Corneal Epithelial Cells, donor2_CNhs12094_11606-120I4_forward Regulation 
CornealEpithelialCellsDonor1_CNhs11336_ctss_rev CornealEpithelialCellsD1- Corneal Epithelial Cells, donor1_CNhs11336_11526-119I5_reverse Regulation 
CornealEpithelialCellsDonor1_CNhs11336_ctss_fwd CornealEpithelialCellsD1+ Corneal Epithelial Cells, donor1_CNhs11336_11526-119I5_forward Regulation 
CiliaryEpithelialCellsDonor3_CNhs12009_ctss_rev CiliaryEpithelialCellsD3- Ciliary Epithelial Cells, donor3_CNhs12009_11399-118D4_reverse Regulation 
CiliaryEpithelialCellsDonor3_CNhs12009_ctss_fwd CiliaryEpithelialCellsD3+ Ciliary Epithelial Cells, donor3_CNhs12009_11399-118D4_forward Regulation 
CiliaryEpithelialCellsDonor2_CNhs11966_ctss_rev CiliaryEpithelialCellsD2- Ciliary Epithelial Cells, donor2_CNhs11966_11323-117D9_reverse Regulation 
CiliaryEpithelialCellsDonor2_CNhs11966_ctss_fwd CiliaryEpithelialCellsD2+ Ciliary Epithelial Cells, donor2_CNhs11966_11323-117D9_forward Regulation 
CiliaryEpithelialCellsDonor1_CNhs10871_ctss_rev CiliaryEpithelialCellsD1- Ciliary Epithelial Cells, donor1_CNhs10871_11242-116D9_reverse Regulation 
CiliaryEpithelialCellsDonor1_CNhs10871_ctss_fwd CiliaryEpithelialCellsD1+ Ciliary Epithelial Cells, donor1_CNhs10871_11242-116D9_forward Regulation 
ChorionicMembraneCellsDonor3_CNhs12380_ctss_rev ChorionicMembraneCellsD3- chorionic membrane cells, donor3_CNhs12380_12240-129G8_reverse Regulation 
ChorionicMembraneCellsDonor3_CNhs12380_ctss_fwd ChorionicMembraneCellsD3+ chorionic membrane cells, donor3_CNhs12380_12240-129G8_forward Regulation 
ChorionicMembraneCellsDonor2_CNhs12506_ctss_rev ChorionicMembraneCellsD2- chorionic membrane cells, donor2_CNhs12506_12239-129G7_reverse Regulation 
ChorionicMembraneCellsDonor2_CNhs12506_ctss_fwd ChorionicMembraneCellsD2+ chorionic membrane cells, donor2_CNhs12506_12239-129G7_forward Regulation 
ChorionicMembraneCellsDonor1_CNhs12504_ctss_rev ChorionicMembraneCellsD1- chorionic membrane cells, donor1_CNhs12504_12238-129G6_reverse Regulation 
ChorionicMembraneCellsDonor1_CNhs12504_ctss_fwd ChorionicMembraneCellsD1+ chorionic membrane cells, donor1_CNhs12504_12238-129G6_forward Regulation 
ChondrocyteReDiffDonor3_CNhs12021_ctss_rev ChondrocyteReDiffD3- Chondrocyte - re diff, donor3_CNhs12021_11411-118E7_reverse Regulation 
ChondrocyteReDiffDonor3_CNhs12021_ctss_fwd ChondrocyteReDiffD3+ Chondrocyte - re diff, donor3_CNhs12021_11411-118E7_forward Regulation 
ChondrocyteReDiffDonor2_CNhs11373_ctss_rev ChondrocyteReDiffD2- Chondrocyte - re diff, donor2_CNhs11373_11339-117F7_reverse Regulation 
ChondrocyteReDiffDonor2_CNhs11373_ctss_fwd ChondrocyteReDiffD2+ Chondrocyte - re diff, donor2_CNhs11373_11339-117F7_forward Regulation 
ChondrocyteDeDiffDonor3_CNhs12020_ctss_rev ChondrocyteDeDiffD3- Chondrocyte - de diff, donor3_CNhs12020_11410-118E6_reverse Regulation 
ChondrocyteDeDiffDonor3_CNhs12020_ctss_fwd ChondrocyteDeDiffD3+ Chondrocyte - de diff, donor3_CNhs12020_11410-118E6_forward Regulation 
ChondrocyteDeDiffDonor2_CNhs11372_ctss_rev ChondrocyteDeDiffD2- Chondrocyte - de diff, donor2_CNhs11372_11338-117F6_reverse Regulation 
ChondrocyteDeDiffDonor2_CNhs11372_ctss_fwd ChondrocyteDeDiffD2+ Chondrocyte - de diff, donor2_CNhs11372_11338-117F6_forward Regulation 
ChondrocyteDeDiffDonor1_CNhs11923_ctss_rev ChondrocyteDeDiffD1- Chondrocyte - de diff, donor1_CNhs11923_11261-116G1_reverse Regulation 
ChondrocyteDeDiffDonor1_CNhs11923_ctss_fwd ChondrocyteDeDiffD1+ Chondrocyte - de diff, donor1_CNhs11923_11261-116G1_forward Regulation 
CD8TCellsDonor3_CNhs11999_ctss_rev Cd8+TCellsD3- CD8+ T Cells, donor3_CNhs11999_11383-118B6_reverse Regulation 
CD8TCellsDonor3_CNhs11999_ctss_fwd Cd8+TCellsD3+ CD8+ T Cells, donor3_CNhs11999_11383-118B6_forward Regulation 
CD8TCellsDonor2_CNhs11956_ctss_rev Cd8+TCellsD2- CD8+ T Cells, donor2_CNhs11956_11307-117C2_reverse Regulation 
CD8TCellsDonor2_CNhs11956_ctss_fwd Cd8+TCellsD2+ CD8+ T Cells, donor2_CNhs11956_11307-117C2_forward Regulation 
CD8TCellsDonor1_CNhs10854_ctss_rev Cd8+TCellsD1- CD8+ T Cells, donor1_CNhs10854_11226-116C2_reverse Regulation 
CD8TCellsDonor1_CNhs10854_ctss_fwd Cd8+TCellsD1+ CD8+ T Cells, donor1_CNhs10854_11226-116C2_forward Regulation 
CD4TCellsDonor3_CNhs11998_ctss_rev Cd4+TCellsD3- CD4+ T Cells, donor3_CNhs11998_11382-118B5_reverse Regulation 
CD4TCellsDonor3_CNhs11998_ctss_fwd Cd4+TCellsD3+ CD4+ T Cells, donor3_CNhs11998_11382-118B5_forward Regulation 
CD4TCellsDonor2_CNhs11955_ctss_rev Cd4+TCellsD2- CD4+ T Cells, donor2_CNhs11955_11306-117C1_reverse Regulation 
CD4TCellsDonor2_CNhs11955_ctss_fwd Cd4+TCellsD2+ CD4+ T Cells, donor2_CNhs11955_11306-117C1_forward Regulation 
CD4TCellsDonor1_CNhs10853_ctss_rev Cd4+TCellsD1- CD4+ T Cells, donor1_CNhs10853_11225-116C1_reverse Regulation 
CD4TCellsDonor1_CNhs10853_ctss_fwd Cd4+TCellsD1+ CD4+ T Cells, donor1_CNhs10853_11225-116C1_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor3_CNhs13921_ctss_rev Cd4+cd25-cd45ra-ExpdD3- CD4+CD25-CD45RA- memory conventional T cells expanded, donor3_CNhs13921_11918-125H1_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor3_CNhs13921_ctss_fwd Cd4+cd25-cd45ra-ExpdD3+ CD4+CD25-CD45RA- memory conventional T cells expanded, donor3_CNhs13921_11918-125H1_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor2_CNhs13920_ctss_rev Cd4+cd25-cd45ra-ExpdD2- CD4+CD25-CD45RA- memory conventional T cells expanded, donor2_CNhs13920_11914-125G6_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor2_CNhs13920_ctss_fwd Cd4+cd25-cd45ra-ExpdD2+ CD4+CD25-CD45RA- memory conventional T cells expanded, donor2_CNhs13920_11914-125G6_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor1_CNhs13215_ctss_rev Cd4+cd25-cd45ra-ExpdD1- CD4+CD25-CD45RA- memory conventional T cells expanded, donor1_CNhs13215_11792-124C1_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor1_CNhs13215_ctss_fwd Cd4+cd25-cd45ra-ExpdD1+ CD4+CD25-CD45RA- memory conventional T cells expanded, donor1_CNhs13215_11792-124C1_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor3_CNhs13539_ctss_rev Cd4+cd25-cd45ra-D3- CD4+CD25-CD45RA- memory conventional T cells, donor3_CNhs13539_11909-125G1_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor3_CNhs13539_ctss_fwd Cd4+cd25-cd45ra-D3+ CD4+CD25-CD45RA- memory conventional T cells, donor3_CNhs13539_11909-125G1_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor3_CNhs13814_ctss_rev Cd4+cd25-cd45ra+ExpdD3- CD4+CD25-CD45RA+ naive conventional T cells expanded, donor3_CNhs13814_11917-125G9_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor3_CNhs13814_ctss_fwd Cd4+cd25-cd45ra+ExpdD3+ CD4+CD25-CD45RA+ naive conventional T cells expanded, donor3_CNhs13814_11917-125G9_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor2_CNhs13813_ctss_rev Cd4+cd25-cd45ra+ExpdD2- CD4+CD25-CD45RA+ naive conventional T cells expanded, donor2_CNhs13813_11913-125G5_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor2_CNhs13813_ctss_fwd Cd4+cd25-cd45ra+ExpdD2+ CD4+CD25-CD45RA+ naive conventional T cells expanded, donor2_CNhs13813_11913-125G5_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor1_CNhs13202_ctss_rev Cd4+cd25-cd45ra+ExpdD1- CD4+CD25-CD45RA+ naive conventional T cells expanded, donor1_CNhs13202_11791-124B9_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor1_CNhs13202_ctss_fwd Cd4+cd25-cd45ra+ExpdD1+ CD4+CD25-CD45RA+ naive conventional T cells expanded, donor1_CNhs13202_11791-124B9_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor3_CNhs13512_ctss_rev Cd4+cd25-cd45ra+D3- CD4+CD25-CD45RA+ naive conventional T cells, donor3_CNhs13512_11906-125F7_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor3_CNhs13512_ctss_fwd Cd4+cd25-cd45ra+D3+ CD4+CD25-CD45RA+ naive conventional T cells, donor3_CNhs13512_11906-125F7_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor2_CNhs13205_ctss_rev Cd4+cd25-cd45ra+D2- CD4+CD25-CD45RA+ naive conventional T cells, donor2_CNhs13205_11795-124C4_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor2_CNhs13205_ctss_fwd Cd4+cd25-cd45ra+D2+ CD4+CD25-CD45RA+ naive conventional T cells, donor2_CNhs13205_11795-124C4_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor1_CNhs13223_ctss_rev Cd4+cd25-cd45ra+D1- CD4+CD25-CD45RA+ naive conventional T cells, donor1_CNhs13223_11784-124B2_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor1_CNhs13223_ctss_fwd Cd4+cd25-cd45ra+D1+ CD4+CD25-CD45RA+ naive conventional T cells, donor1_CNhs13223_11784-124B2_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor3_CNhs13812_ctss_rev Cd4+cd25+cd45ra-ExpdD3- CD4+CD25+CD45RA- memory regulatory T cells expanded, donor3_CNhs13812_11920-125H3_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor3_CNhs13812_ctss_fwd Cd4+cd25+cd45ra-ExpdD3+ CD4+CD25+CD45RA- memory regulatory T cells expanded, donor3_CNhs13812_11920-125H3_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor2_CNhs13811_ctss_rev Cd4+cd25+cd45ra-ExpdD2- CD4+CD25+CD45RA- memory regulatory T cells expanded, donor2_CNhs13811_11916-125G8_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor2_CNhs13811_ctss_fwd Cd4+cd25+cd45ra-ExpdD2+ CD4+CD25+CD45RA- memory regulatory T cells expanded, donor2_CNhs13811_11916-125G8_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor1_CNhs13204_ctss_rev Cd4+cd25+cd45ra-ExpdD1- CD4+CD25+CD45RA- memory regulatory T cells expanded, donor1_CNhs13204_11794-124C3_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor1_CNhs13204_ctss_fwd Cd4+cd25+cd45ra-ExpdD1+ CD4+CD25+CD45RA- memory regulatory T cells expanded, donor1_CNhs13204_11794-124C3_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor3_CNhs13538_ctss_rev Cd4+cd25+cd45ra-D3- CD4+CD25+CD45RA- memory regulatory T cells, donor3_CNhs13538_11908-125F9_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor3_CNhs13538_ctss_fwd Cd4+cd25+cd45ra-D3+ CD4+CD25+CD45RA- memory regulatory T cells, donor3_CNhs13538_11908-125F9_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor2_CNhs13206_ctss_rev Cd4+cd25+cd45ra-D2- CD4+CD25+CD45RA- memory regulatory T cells, donor2_CNhs13206_11797-124C6_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor2_CNhs13206_ctss_fwd Cd4+cd25+cd45ra-D2+ CD4+CD25+CD45RA- memory regulatory T cells, donor2_CNhs13206_11797-124C6_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor1_CNhs13195_ctss_rev Cd4+cd25+cd45ra-D1- CD4+CD25+CD45RA- memory regulatory T cells, donor1_CNhs13195_11782-124A9_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor1_CNhs13195_ctss_fwd Cd4+cd25+cd45ra-D1+ CD4+CD25+CD45RA- memory regulatory T cells, donor1_CNhs13195_11782-124A9_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor3_CNhs13919_ctss_rev Cd4+cd25+cd45ra+ExpdD3- CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor3_CNhs13919_11919-125H2_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor3_CNhs13919_ctss_fwd Cd4+cd25+cd45ra+ExpdD3+ CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor3_CNhs13919_11919-125H2_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor2_CNhs13918_ctss_rev Cd4+cd25+cd45ra+ExpdD2- CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor2_CNhs13918_11915-125G7_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor2_CNhs13918_ctss_fwd Cd4+cd25+cd45ra+ExpdD2+ CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor2_CNhs13918_11915-125G7_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor1_CNhs13203_ctss_rev Cd4+cd25+cd45ra+ExpdD1- CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor1_CNhs13203_11793-124C2_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor1_CNhs13203_ctss_fwd Cd4+cd25+cd45ra+ExpdD1+ CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor1_CNhs13203_11793-124C2_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor3_CNhs13513_ctss_rev Cd4+cd25+cd45ra+D3- CD4+CD25+CD45RA+ naive regulatory T cells, donor3_CNhs13513_11907-125F8_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor3_CNhs13513_ctss_fwd Cd4+cd25+cd45ra+D3+ CD4+CD25+CD45RA+ naive regulatory T cells, donor3_CNhs13513_11907-125F8_forward Regulation 
CD34CellsDifferentiatedToErythrocyteLineageBiol_Rep2_CNhs13553_ctss_rev Cd34ErythrocyteBr2- CD34 cells differentiated to erythrocyte lineage, biol_ rep2_CNhs13553_11932-125I6_reverse Regulation 
CD34CellsDifferentiatedToErythrocyteLineageBiol_Rep2_CNhs13553_ctss_fwd Cd34ErythrocyteBr2+ CD34 cells differentiated to erythrocyte lineage, biol_ rep2_CNhs13553_11932-125I6_forward Regulation 
CD34CellsDifferentiatedToErythrocyteLineageBiol_Rep1_CNhs13552_ctss_rev Cd34ErythrocyteBr1- CD34 cells differentiated to erythrocyte lineage, biol_ rep1_CNhs13552_11931-125I5_reverse Regulation 
CD34CellsDifferentiatedToErythrocyteLineageBiol_Rep1_CNhs13552_ctss_fwd Cd34ErythrocyteBr1+ CD34 cells differentiated to erythrocyte lineage, biol_ rep1_CNhs13552_11931-125I5_forward Regulation 
CD34StemCellsAdultBoneMarrowDerivedDonor1TechRep1_CNhs12588_ctss_rev Cd34+StemCellsAdultBoneMarrowD1Tr1- CD34+ stem cells - adult bone marrow derived, donor1, tech_rep1_CNhs12588_12225-129F2_reverse Regulation 
CD34StemCellsAdultBoneMarrowDerivedDonor1TechRep1_CNhs12588_ctss_fwd Cd34+StemCellsAdultBoneMarrowD1Tr1+ CD34+ stem cells - adult bone marrow derived, donor1, tech_rep1_CNhs12588_12225-129F2_forward Regulation 
CD19BCellsDonor3_CNhs12354_ctss_rev Cd19+BCellsD3- CD19+ B Cells, donor3_CNhs12354_11705-123B4_reverse Regulation 
CD19BCellsDonor3_CNhs12354_ctss_fwd Cd19+BCellsD3+ CD19+ B Cells, donor3_CNhs12354_11705-123B4_forward Regulation 
CD19BCellsDonor2_CNhs12352_ctss_rev Cd19+BCellsD2- CD19+ B Cells, donor2_CNhs12352_11624-122B4_reverse Regulation 
CD19BCellsDonor2_CNhs12352_ctss_fwd Cd19+BCellsD2+ CD19+ B Cells, donor2_CNhs12352_11624-122B4_forward Regulation 
CD19BCellsDonor1_CNhs12343_ctss_rev Cd19+BCellsD1- CD19+ B Cells, donor1_CNhs12343_11544-120B5_reverse Regulation 
CD19BCellsDonor1_CNhs12343_ctss_fwd Cd19+BCellsD1+ CD19+ B Cells, donor1_CNhs12343_11544-120B5_forward Regulation 
CD14CD16MonocytesDonor3_CNhs13548_ctss_rev Cd14-cd16+MonocytesD3- CD14-CD16+ Monocytes, donor3_CNhs13548_11911-125G3_reverse Regulation 
CD14CD16MonocytesDonor3_CNhs13548_ctss_fwd Cd14-cd16+MonocytesD3+ CD14-CD16+ Monocytes, donor3_CNhs13548_11911-125G3_forward Regulation 
CD14CD16MonocytesDonor2_CNhs13207_ctss_rev Cd14-cd16+MonocytesD2- CD14-CD16+ Monocytes, donor2_CNhs13207_11800-124C9_reverse Regulation 
CD14CD16MonocytesDonor2_CNhs13207_ctss_fwd Cd14-cd16+MonocytesD2+ CD14-CD16+ Monocytes, donor2_CNhs13207_11800-124C9_forward Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor3_CNhs13544_ctss_rev Cd14+MoW/TrehaloseDimycolateD3- CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor3_CNhs13544_11882-125D1_reverse Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor3_CNhs13544_ctss_fwd Cd14+MoW/TrehaloseDimycolateD3+ CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor3_CNhs13544_11882-125D1_forward Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor2_CNhs13483_ctss_rev Cd14+MoW/TrehaloseDimycolateD2- CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor2_CNhs13483_11872-125B9_reverse Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor2_CNhs13483_ctss_fwd Cd14+MoW/TrehaloseDimycolateD2+ CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor2_CNhs13483_11872-125B9_forward Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor1_CNhs13467_ctss_rev Cd14+MoW/TrehaloseDimycolateD1- CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor1_CNhs13467_11862-125A8_reverse Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor1_CNhs13467_ctss_fwd Cd14+MoW/TrehaloseDimycolateD1+ CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor1_CNhs13467_11862-125A8_forward Regulation 
CD14MonocytesTreatedWithSalmonellaDonor3_CNhs13493_ctss_rev Cd14+MoW/SalmonellaD3- CD14+ monocytes - treated with Salmonella, donor3_CNhs13493_11886-125D5_reverse Regulation 
CD14MonocytesTreatedWithSalmonellaDonor3_CNhs13493_ctss_fwd Cd14+MoW/SalmonellaD3+ CD14+ monocytes - treated with Salmonella, donor3_CNhs13493_11886-125D5_forward Regulation 
CD14MonocytesTreatedWithSalmonellaDonor2_CNhs13485_ctss_rev Cd14+MoW/SalmonellaD2- CD14+ monocytes - treated with Salmonella, donor2_CNhs13485_11876-125C4_reverse Regulation 
CD14MonocytesTreatedWithSalmonellaDonor2_CNhs13485_ctss_fwd Cd14+MoW/SalmonellaD2+ CD14+ monocytes - treated with Salmonella, donor2_CNhs13485_11876-125C4_forward Regulation 
CD14MonocytesTreatedWithSalmonellaDonor1_CNhs13471_ctss_rev Cd14+MoW/SalmonellaD1- CD14+ monocytes - treated with Salmonella, donor1_CNhs13471_11866-125B3_reverse Regulation 
CD14MonocytesTreatedWithSalmonellaDonor1_CNhs13471_ctss_fwd Cd14+MoW/SalmonellaD1+ CD14+ monocytes - treated with Salmonella, donor1_CNhs13471_11866-125B3_forward Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor3_CNhs13545_ctss_rev Cd14+MoW/LipopolysaccharideD3- CD14+ monocytes - treated with lipopolysaccharide, donor3_CNhs13545_11885-125D4_reverse Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor3_CNhs13545_ctss_fwd Cd14+MoW/LipopolysaccharideD3+ CD14+ monocytes - treated with lipopolysaccharide, donor3_CNhs13545_11885-125D4_forward Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor2_CNhs13533_ctss_rev Cd14+MoW/LipopolysaccharideD2- CD14+ monocytes - treated with lipopolysaccharide, donor2_CNhs13533_11875-125C3_reverse Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor2_CNhs13533_ctss_fwd Cd14+MoW/LipopolysaccharideD2+ CD14+ monocytes - treated with lipopolysaccharide, donor2_CNhs13533_11875-125C3_forward Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor1_CNhs13470_ctss_rev Cd14+MoW/LipopolysaccharideD1- CD14+ monocytes - treated with lipopolysaccharide, donor1_CNhs13470_11865-125B2_reverse Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor1_CNhs13470_ctss_fwd Cd14+MoW/LipopolysaccharideD1+ CD14+ monocytes - treated with lipopolysaccharide, donor1_CNhs13470_11865-125B2_forward Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor3_CNhs13490_ctss_rev Cd14+MoW/Ifn+N-hexaneD3- CD14+ monocytes - treated with IFN + N-hexane, donor3_CNhs13490_11881-125C9_reverse Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor3_CNhs13490_ctss_fwd Cd14+MoW/Ifn+N-hexaneD3+ CD14+ monocytes - treated with IFN + N-hexane, donor3_CNhs13490_11881-125C9_forward Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor2_CNhs13476_ctss_rev Cd14+MoW/Ifn+N-hexaneD2- CD14+ monocytes - treated with IFN + N-hexane, donor2_CNhs13476_11871-125B8_reverse Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor2_CNhs13476_ctss_fwd Cd14+MoW/Ifn+N-hexaneD2+ CD14+ monocytes - treated with IFN + N-hexane, donor2_CNhs13476_11871-125B8_forward Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor1_CNhs13466_ctss_rev Cd14+MoW/Ifn+N-hexaneD1- CD14+ monocytes - treated with IFN + N-hexane, donor1_CNhs13466_11861-125A7_reverse Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor1_CNhs13466_ctss_fwd Cd14+MoW/Ifn+N-hexaneD1+ CD14+ monocytes - treated with IFN + N-hexane, donor1_CNhs13466_11861-125A7_forward Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor3_CNhs13492_ctss_rev Cd14+MoW/GroupAStreptococciD3- CD14+ monocytes - treated with Group A streptococci, donor3_CNhs13492_11884-125D3_reverse Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor3_CNhs13492_ctss_fwd Cd14+MoW/GroupAStreptococciD3+ CD14+ monocytes - treated with Group A streptococci, donor3_CNhs13492_11884-125D3_forward Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor2_CNhs13532_ctss_rev Cd14+MoW/GroupAStreptococciD2- CD14+ monocytes - treated with Group A streptococci, donor2_CNhs13532_11874-125C2_reverse Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor2_CNhs13532_ctss_fwd Cd14+MoW/GroupAStreptococciD2+ CD14+ monocytes - treated with Group A streptococci, donor2_CNhs13532_11874-125C2_forward Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor1_CNhs13469_ctss_rev Cd14+MoW/GroupAStreptococciD1- CD14+ monocytes - treated with Group A streptococci, donor1_CNhs13469_11864-125B1_reverse Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor1_CNhs13469_ctss_fwd Cd14+MoW/GroupAStreptococciD1+ CD14+ monocytes - treated with Group A streptococci, donor1_CNhs13469_11864-125B1_forward Regulation 
CD14MonocytesTreatedWithCryptococcusDonor3_CNhs13546_ctss_rev Cd14+MoW/CryptococcusD3- CD14+ monocytes - treated with Cryptococcus, donor3_CNhs13546_11887-125D6_reverse Regulation 
CD14MonocytesTreatedWithCryptococcusDonor3_CNhs13546_ctss_fwd Cd14+MoW/CryptococcusD3+ CD14+ monocytes - treated with Cryptococcus, donor3_CNhs13546_11887-125D6_forward Regulation 
CD14MonocytesTreatedWithCryptococcusDonor2_CNhs13487_ctss_rev Cd14+MoW/CryptococcusD2- CD14+ monocytes - treated with Cryptococcus, donor2_CNhs13487_11877-125C5_reverse Regulation 
CD14MonocytesTreatedWithCryptococcusDonor2_CNhs13487_ctss_fwd Cd14+MoW/CryptococcusD2+ CD14+ monocytes - treated with Cryptococcus, donor2_CNhs13487_11877-125C5_forward Regulation 
CD14MonocytesTreatedWithCryptococcusDonor1_CNhs13472_ctss_rev Cd14+MoW/CryptococcusD1- CD14+ monocytes - treated with Cryptococcus, donor1_CNhs13472_11867-125B4_reverse Regulation 
CD14MonocytesTreatedWithCryptococcusDonor1_CNhs13472_ctss_fwd Cd14+MoW/CryptococcusD1+ CD14+ monocytes - treated with Cryptococcus, donor1_CNhs13472_11867-125B4_forward Regulation 
CD14MonocytesTreatedWithCandidaDonor3_CNhs13494_ctss_rev Cd14+MoW/CandidaD3- CD14+ monocytes - treated with Candida, donor3_CNhs13494_11888-125D7_reverse Regulation 
CD14MonocytesTreatedWithCandidaDonor3_CNhs13494_ctss_fwd Cd14+MoW/CandidaD3+ CD14+ monocytes - treated with Candida, donor3_CNhs13494_11888-125D7_forward Regulation 
CD14MonocytesTreatedWithCandidaDonor2_CNhs13488_ctss_rev Cd14+MoW/CandidaD2- CD14+ monocytes - treated with Candida, donor2_CNhs13488_11878-125C6_reverse Regulation 
CD14MonocytesTreatedWithCandidaDonor2_CNhs13488_ctss_fwd Cd14+MoW/CandidaD2+ CD14+ monocytes - treated with Candida, donor2_CNhs13488_11878-125C6_forward Regulation 
CD14MonocytesTreatedWithCandidaDonor1_CNhs13473_ctss_rev Cd14+MoW/CandidaD1- CD14+ monocytes - treated with Candida, donor1_CNhs13473_11868-125B5_reverse Regulation 
CD14MonocytesTreatedWithCandidaDonor1_CNhs13473_ctss_fwd Cd14+MoW/CandidaD1+ CD14+ monocytes - treated with Candida, donor1_CNhs13473_11868-125B5_forward Regulation 
CD14MonocytesTreatedWithBCGDonor3_CNhs13543_ctss_rev Cd14+MoW/BcgD3- CD14+ monocytes - treated with BCG, donor3_CNhs13543_11880-125C8_reverse Regulation 
CD14MonocytesTreatedWithBCGDonor3_CNhs13543_ctss_fwd Cd14+MoW/BcgD3+ CD14+ monocytes - treated with BCG, donor3_CNhs13543_11880-125C8_forward Regulation 
CD14MonocytesTreatedWithBCGDonor2_CNhs13475_ctss_rev Cd14+MoW/BcgD2- CD14+ monocytes - treated with BCG, donor2_CNhs13475_11870-125B7_reverse Regulation 
CD14MonocytesTreatedWithBCGDonor2_CNhs13475_ctss_fwd Cd14+MoW/BcgD2+ CD14+ monocytes - treated with BCG, donor2_CNhs13475_11870-125B7_forward Regulation 
CD14MonocytesTreatedWithBCGDonor1_CNhs13465_ctss_rev Cd14+MoW/BcgD1- CD14+ monocytes - treated with BCG, donor1_CNhs13465_11860-125A6_reverse Regulation 
CD14MonocytesTreatedWithBCGDonor1_CNhs13465_ctss_fwd Cd14+MoW/BcgD1+ CD14+ monocytes - treated with BCG, donor1_CNhs13465_11860-125A6_forward Regulation 
CD14MonocytesTreatedWithBglucanDonor3_CNhs13495_ctss_rev Cd14+MoW/B-glucanD3- CD14+ monocytes - treated with B-glucan, donor3_CNhs13495_11889-125D8_reverse Regulation 
CD14MonocytesTreatedWithBglucanDonor3_CNhs13495_ctss_fwd Cd14+MoW/B-glucanD3+ CD14+ monocytes - treated with B-glucan, donor3_CNhs13495_11889-125D8_forward Regulation 
CD14MonocytesTreatedWithBglucanDonor2_CNhs13489_ctss_rev Cd14+MoW/B-glucanD2- CD14+ monocytes - treated with B-glucan, donor2_CNhs13489_11879-125C7_reverse Regulation 
CD14MonocytesTreatedWithBglucanDonor2_CNhs13489_ctss_fwd Cd14+MoW/B-glucanD2+ CD14+ monocytes - treated with B-glucan, donor2_CNhs13489_11879-125C7_forward Regulation 
CD14MonocytesTreatedWithBglucanDonor1_CNhs13474_ctss_rev Cd14+MoW/B-glucanD1- CD14+ monocytes - treated with B-glucan, donor1_CNhs13474_11869-125B6_reverse Regulation 
CD14MonocytesTreatedWithBglucanDonor1_CNhs13474_ctss_fwd Cd14+MoW/B-glucanD1+ CD14+ monocytes - treated with B-glucan, donor1_CNhs13474_11869-125B6_forward Regulation 
CD14MonocytesMockTreatedDonor3_CNhs13491_ctss_rev Cd14+MoMockTreatedD3- CD14+ monocytes - mock treated, donor3_CNhs13491_11883-125D2_reverse Regulation 
CD14MonocytesMockTreatedDonor3_CNhs13491_ctss_fwd Cd14+MoMockTreatedD3+ CD14+ monocytes - mock treated, donor3_CNhs13491_11883-125D2_forward Regulation 
CD14MonocytesMockTreatedDonor2_CNhs13484_ctss_rev Cd14+MoMockTreatedD2- CD14+ monocytes - mock treated, donor2_CNhs13484_11873-125C1_reverse Regulation 
CD14MonocytesMockTreatedDonor2_CNhs13484_ctss_fwd Cd14+MoMockTreatedD2+ CD14+ monocytes - mock treated, donor2_CNhs13484_11873-125C1_forward Regulation 
CD14MonocytesMockTreatedDonor1_CNhs13468_ctss_rev Cd14+MoMockTreatedD1- CD14+ monocytes - mock treated, donor1_CNhs13468_11863-125A9_reverse Regulation 
CD14MonocytesMockTreatedDonor1_CNhs13468_ctss_fwd Cd14+MoMockTreatedD1+ CD14+ monocytes - mock treated, donor1_CNhs13468_11863-125A9_forward Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor3_CNhs11904_ctss_rev Cd14+MoEndothelialProgenitorCellsD3- CD14+ monocyte derived endothelial progenitor cells, donor3_CNhs11904_11386-118B9_reverse Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor3_CNhs11904_ctss_fwd Cd14+MoEndothelialProgenitorCellsD3+ CD14+ monocyte derived endothelial progenitor cells, donor3_CNhs11904_11386-118B9_forward Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor2_CNhs11897_ctss_rev Cd14+MoEndothelialProgenitorCellsD2- CD14+ monocyte derived endothelial progenitor cells, donor2_CNhs11897_11310-117C5_reverse Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor2_CNhs11897_ctss_fwd Cd14+MoEndothelialProgenitorCellsD2+ CD14+ monocyte derived endothelial progenitor cells, donor2_CNhs11897_11310-117C5_forward Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor1_CNhs10858_ctss_rev Cd14+MoEndothelialProgenitorCellsD1- CD14+ monocyte derived endothelial progenitor cells, donor1_CNhs10858_11229-116C5_reverse Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor1_CNhs10858_ctss_fwd Cd14+MoEndothelialProgenitorCellsD1+ CD14+ monocyte derived endothelial progenitor cells, donor1_CNhs10858_11229-116C5_forward Regulation 
CD14MonocytesDonor3_CNhs11997_ctss_rev Cd14+MoD3- CD14+ Monocytes, donor3_CNhs11997_11381-118B4_reverse Regulation 
CD14MonocytesDonor3_CNhs11997_ctss_fwd Cd14+MoD3+ CD14+ Monocytes, donor3_CNhs11997_11381-118B4_forward Regulation 
CD14MonocytesDonor2_CNhs11954_ctss_rev Cd14+MoD2- CD14+ Monocytes, donor2_CNhs11954_11305-117B9_reverse Regulation 
CD14MonocytesDonor2_CNhs11954_ctss_fwd Cd14+MoD2+ CD14+ Monocytes, donor2_CNhs11954_11305-117B9_forward Regulation 
CD14MonocytesDonor1_CNhs10852_ctss_rev Cd14+MoD1- CD14+ Monocytes, donor1_CNhs10852_11224-116B9_reverse Regulation 
CD14MonocytesDonor1_CNhs10852_ctss_fwd Cd14+MoD1+ CD14+ Monocytes, donor1_CNhs10852_11224-116B9_forward Regulation 
CD14CD16MonocytesDonor3_CNhs13540_ctss_rev Cd14+cd16-MonocytesD3- CD14+CD16- Monocytes, donor3_CNhs13540_11910-125G2_reverse Regulation 
CD14CD16MonocytesDonor3_CNhs13540_ctss_fwd Cd14+cd16-MonocytesD3+ CD14+CD16- Monocytes, donor3_CNhs13540_11910-125G2_forward Regulation 
CD14CD16MonocytesDonor2_CNhs13216_ctss_rev Cd14+cd16-MonocytesD2- CD14+CD16- Monocytes, donor2_CNhs13216_11799-124C8_reverse Regulation 
CD14CD16MonocytesDonor2_CNhs13216_ctss_fwd Cd14+cd16-MonocytesD2+ CD14+CD16- Monocytes, donor2_CNhs13216_11799-124C8_forward Regulation 
CD14CD16MonocytesDonor1_CNhs13224_ctss_rev Cd14+cd16-MonocytesD1- CD14+CD16- Monocytes, donor1_CNhs13224_11788-124B6_reverse Regulation 
CD14CD16MonocytesDonor1_CNhs13224_ctss_fwd Cd14+cd16-MonocytesD1+ CD14+CD16- Monocytes, donor1_CNhs13224_11788-124B6_forward Regulation 
CD14CD16MonocytesDonor3_CNhs13549_ctss_rev Cd14+cd16+MonocytesD3- CD14+CD16+ Monocytes, donor3_CNhs13549_11912-125G4_reverse Regulation 
CD14CD16MonocytesDonor3_CNhs13549_ctss_fwd Cd14+cd16+MonocytesD3+ CD14+CD16+ Monocytes, donor3_CNhs13549_11912-125G4_forward Regulation 
CD14CD16MonocytesDonor2_CNhs13208_ctss_rev Cd14+cd16+MonocytesD2- CD14+CD16+ Monocytes, donor2_CNhs13208_11801-124D1_reverse Regulation 
CD14CD16MonocytesDonor2_CNhs13208_ctss_fwd Cd14+cd16+MonocytesD2+ CD14+CD16+ Monocytes, donor2_CNhs13208_11801-124D1_forward Regulation 
CD14CD16MonocytesDonor1_CNhs13541_ctss_rev Cd14+cd16+MonocytesD1- CD14+CD16+ Monocytes, donor1_CNhs13541_11789-124B7_reverse Regulation 
CD14CD16MonocytesDonor1_CNhs13541_ctss_fwd Cd14+cd16+MonocytesD1+ CD14+CD16+ Monocytes, donor1_CNhs13541_11789-124B7_forward Regulation 
MultipotentCordBloodUnrestrictedSomaticStemCellsDonor2_CNhs12105_ctss_rev CbStemCellsD2- Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor2_CNhs12105_11629-122B9_reverse Regulation 
MultipotentCordBloodUnrestrictedSomaticStemCellsDonor2_CNhs12105_ctss_fwd CbStemCellsD2+ Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor2_CNhs12105_11629-122B9_forward Regulation 
MultipotentCordBloodUnrestrictedSomaticStemCellsDonor1_CNhs11350_ctss_rev CbStemCellsD1- Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor1_CNhs11350_11549-120C1_reverse Regulation 
MultipotentCordBloodUnrestrictedSomaticStemCellsDonor1_CNhs11350_ctss_fwd CbStemCellsD1+ Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor1_CNhs11350_11549-120C1_forward Regulation 
CardiacMyocyteDonor3_CNhs12571_ctss_rev CardiacMyocyteD3- Cardiac Myocyte, donor3_CNhs12571_11686-122I3_reverse Regulation 
CardiacMyocyteDonor3_CNhs12571_ctss_fwd CardiacMyocyteD3+ Cardiac Myocyte, donor3_CNhs12571_11686-122I3_forward Regulation 
CardiacMyocyteDonor2_CNhs12350_ctss_rev CardiacMyocyteD2- Cardiac Myocyte, donor2_CNhs12350_11605-120I3_reverse Regulation 
CardiacMyocyteDonor2_CNhs12350_ctss_fwd CardiacMyocyteD2+ Cardiac Myocyte, donor2_CNhs12350_11605-120I3_forward Regulation 
CardiacMyocyteDonor1_CNhs12341_ctss_rev CardiacMyocyteD1- Cardiac Myocyte, donor1_CNhs12341_11525-119I4_reverse Regulation 
CardiacMyocyteDonor1_CNhs12341_ctss_fwd CardiacMyocyteD1+ Cardiac Myocyte, donor1_CNhs12341_11525-119I4_forward Regulation 
BronchialEpithelialCellDonor7_CNhs12642_ctss_rev BronchialEpithelialCellD7- Bronchial Epithelial Cell, donor7_CNhs12642_11769-123I5_reverse Regulation 
BronchialEpithelialCellDonor7_CNhs12642_ctss_fwd BronchialEpithelialCellD7+ Bronchial Epithelial Cell, donor7_CNhs12642_11769-123I5_forward Regulation 
BronchialEpithelialCellDonor6_CNhs12062_ctss_rev BronchialEpithelialCellD6- Bronchial Epithelial Cell, donor6_CNhs12062_11461-119B3_reverse Regulation 
BronchialEpithelialCellDonor6_CNhs12062_ctss_fwd BronchialEpithelialCellD6+ Bronchial Epithelial Cell, donor6_CNhs12062_11461-119B3_forward Regulation 
BronchialEpithelialCellDonor5_CNhs12058_ctss_rev BronchialEpithelialCellD5- Bronchial Epithelial Cell, donor5_CNhs12058_11457-119A8_reverse Regulation 
BronchialEpithelialCellDonor5_CNhs12058_ctss_fwd BronchialEpithelialCellD5+ Bronchial Epithelial Cell, donor5_CNhs12058_11457-119A8_forward Regulation 
BronchialEpithelialCellDonor4_CNhs12054_ctss_rev BronchialEpithelialCellD4- Bronchial Epithelial Cell, donor4_CNhs12054_11453-119A4_reverse Regulation 
BronchialEpithelialCellDonor4_CNhs12054_ctss_fwd BronchialEpithelialCellD4+ Bronchial Epithelial Cell, donor4_CNhs12054_11453-119A4_forward Regulation 
BronchialEpithelialCellDonor3_CNhs12623_ctss_rev BronchialEpithelialCellD3- Bronchial Epithelial Cell, donor3_CNhs12623_11672-122G7_reverse Regulation 
BronchialEpithelialCellDonor3_CNhs12623_ctss_fwd BronchialEpithelialCellD3+ Bronchial Epithelial Cell, donor3_CNhs12623_11672-122G7_forward Regulation 
BronchialEpithelialCellDonor2_CNhs12085_ctss_rev BronchialEpithelialCellD2- Bronchial Epithelial Cell, donor2_CNhs12085_11591-120G7_reverse Regulation 
BronchialEpithelialCellDonor2_CNhs12085_ctss_fwd BronchialEpithelialCellD2+ Bronchial Epithelial Cell, donor2_CNhs12085_11591-120G7_forward Regulation 
BronchialEpithelialCellDonor1_CNhs11327_ctss_rev BronchialEpithelialCellD1- Bronchial Epithelial Cell, donor1_CNhs11327_11511-119G8_reverse Regulation 
BronchialEpithelialCellDonor1_CNhs11327_ctss_fwd BronchialEpithelialCellD1+ Bronchial Epithelial Cell, donor1_CNhs11327_11511-119G8_forward Regulation 
BasophilsDonor3_CNhs12575_ctss_rev BasophilsD3- Basophils, donor3_CNhs12575_12243-129H2_reverse Regulation 
BasophilsDonor3_CNhs12575_ctss_fwd BasophilsD3+ Basophils, donor3_CNhs12575_12243-129H2_forward Regulation 
AstrocyteCerebralCortexDonor3_CNhs12005_ctss_rev AstrocyteCerebralCortexD3- Astrocyte - cerebral cortex, donor3_CNhs12005_11392-118C6_reverse Regulation 
AstrocyteCerebralCortexDonor3_CNhs12005_ctss_fwd AstrocyteCerebralCortexD3+ Astrocyte - cerebral cortex, donor3_CNhs12005_11392-118C6_forward Regulation 
AstrocyteCerebralCortexDonor2_CNhs11960_ctss_rev AstrocyteCerebralCortexD2- Astrocyte - cerebral cortex, donor2_CNhs11960_11316-117D2_reverse Regulation 
AstrocyteCerebralCortexDonor2_CNhs11960_ctss_fwd AstrocyteCerebralCortexD2+ Astrocyte - cerebral cortex, donor2_CNhs11960_11316-117D2_forward Regulation 
AstrocyteCerebralCortexDonor1_CNhs10864_ctss_rev AstrocyteCerebralCortexD1- Astrocyte - cerebral cortex, donor1_CNhs10864_11235-116D2_reverse Regulation 
AstrocyteCerebralCortexDonor1_CNhs10864_ctss_fwd AstrocyteCerebralCortexD1+ Astrocyte - cerebral cortex, donor1_CNhs10864_11235-116D2_forward Regulation 
AstrocyteCerebellumDonor3_CNhs12117_ctss_rev AstrocyteCerebellumD3- Astrocyte - cerebellum, donor3_CNhs12117_11661-122F5_reverse Regulation 
AstrocyteCerebellumDonor3_CNhs12117_ctss_fwd AstrocyteCerebellumD3+ Astrocyte - cerebellum, donor3_CNhs12117_11661-122F5_forward Regulation 
AstrocyteCerebellumDonor2_CNhs12081_ctss_rev AstrocyteCerebellumD2- Astrocyte - cerebellum, donor2_CNhs12081_11580-120F5_reverse Regulation 
AstrocyteCerebellumDonor2_CNhs12081_ctss_fwd AstrocyteCerebellumD2+ Astrocyte - cerebellum, donor2_CNhs12081_11580-120F5_forward Regulation 
AstrocyteCerebellumDonor1_CNhs11321_ctss_rev AstrocyteCerebellumD1- Astrocyte - cerebellum, donor1_CNhs11321_11500-119F6_reverse Regulation 
AstrocyteCerebellumDonor1_CNhs11321_ctss_fwd AstrocyteCerebellumD1+ Astrocyte - cerebellum, donor1_CNhs11321_11500-119F6_forward Regulation 
AnulusPulposusCellDonor2_CNhs12064_ctss_rev AnulusPulposusCellD2- Anulus Pulposus Cell, donor2_CNhs12064_11463-119B5_reverse Regulation 
AnulusPulposusCellDonor2_CNhs12064_ctss_fwd AnulusPulposusCellD2+ Anulus Pulposus Cell, donor2_CNhs12064_11463-119B5_forward Regulation 
AnulusPulposusCellDonor1_CNhs10876_ctss_rev AnulusPulposusCellD1- Anulus Pulposus Cell, donor1_CNhs10876_11248-116E6_reverse Regulation 
AnulusPulposusCellDonor1_CNhs10876_ctss_fwd AnulusPulposusCellD1+ Anulus Pulposus Cell, donor1_CNhs10876_11248-116E6_forward Regulation 
AmnioticMembraneCellsDonor3_CNhs12379_ctss_rev AmnioticMembraneCellsD3- amniotic membrane cells, donor3_CNhs12379_12237-129G5_reverse Regulation 
AmnioticMembraneCellsDonor3_CNhs12379_ctss_fwd AmnioticMembraneCellsD3+ amniotic membrane cells, donor3_CNhs12379_12237-129G5_forward Regulation 
AmnioticMembraneCellsDonor2_CNhs12503_ctss_rev AmnioticMembraneCellsD2- amniotic membrane cells, donor2_CNhs12503_12236-129G4_reverse Regulation 
AmnioticMembraneCellsDonor2_CNhs12503_ctss_fwd AmnioticMembraneCellsD2+ amniotic membrane cells, donor2_CNhs12503_12236-129G4_forward Regulation 
AmnioticMembraneCellsDonor1_CNhs12502_ctss_rev AmnioticMembraneCellsD1- amniotic membrane cells, donor1_CNhs12502_12235-129G3_reverse Regulation 
AmnioticMembraneCellsDonor1_CNhs12502_ctss_fwd AmnioticMembraneCellsD1+ amniotic membrane cells, donor1_CNhs12502_12235-129G3_forward Regulation 
AmnioticEpithelialCellsDonor3_CNhs12125_ctss_rev AmnioticEpithelialCellsD3- Amniotic Epithelial Cells, donor3_CNhs12125_11694-123A2_reverse Regulation 
AmnioticEpithelialCellsDonor3_CNhs12125_ctss_fwd AmnioticEpithelialCellsD3+ Amniotic Epithelial Cells, donor3_CNhs12125_11694-123A2_forward Regulation 
AmnioticEpithelialCellsDonor2_CNhs12098_ctss_rev AmnioticEpithelialCellsD2- Amniotic Epithelial Cells, donor2_CNhs12098_11613-122A2_reverse Regulation 
AmnioticEpithelialCellsDonor2_CNhs12098_ctss_fwd AmnioticEpithelialCellsD2+ Amniotic Epithelial Cells, donor2_CNhs12098_11613-122A2_forward Regulation 
AmnioticEpithelialCellsDonor1_CNhs11341_ctss_rev AmnioticEpithelialCellsD1- Amniotic Epithelial Cells, donor1_CNhs11341_11533-120A3_reverse Regulation 
AmnioticEpithelialCellsDonor1_CNhs11341_ctss_fwd AmnioticEpithelialCellsD1+ Amniotic Epithelial Cells, donor1_CNhs11341_11533-120A3_forward Regulation 
AlveolarEpithelialCellsDonor3_CNhs12119_ctss_rev AlveolarEpithelialCellsD3- Alveolar Epithelial Cells, donor3_CNhs12119_11671-122G6_reverse Regulation 
AlveolarEpithelialCellsDonor3_CNhs12119_ctss_fwd AlveolarEpithelialCellsD3+ Alveolar Epithelial Cells, donor3_CNhs12119_11671-122G6_forward Regulation 
AlveolarEpithelialCellsDonor2_CNhs12084_ctss_rev AlveolarEpithelialCellsD2- Alveolar Epithelial Cells, donor2_CNhs12084_11590-120G6_reverse Regulation 
AlveolarEpithelialCellsDonor2_CNhs12084_ctss_fwd AlveolarEpithelialCellsD2+ Alveolar Epithelial Cells, donor2_CNhs12084_11590-120G6_forward Regulation 
AlveolarEpithelialCellsDonor1_CNhs11325_ctss_rev AlveolarEpithelialCellsD1- Alveolar Epithelial Cells, donor1_CNhs11325_11510-119G7_reverse Regulation 
AlveolarEpithelialCellsDonor1_CNhs11325_ctss_fwd AlveolarEpithelialCellsD1+ Alveolar Epithelial Cells, donor1_CNhs11325_11510-119G7_forward Regulation 
AdipocyteSubcutaneousDonor3_CNhs12017_ctss_rev AdipocyteSubcutaneousD3- Adipocyte - subcutaneous, donor3_CNhs12017_11408-118E4_reverse Regulation 
AdipocyteSubcutaneousDonor3_CNhs12017_ctss_fwd AdipocyteSubcutaneousD3+ Adipocyte - subcutaneous, donor3_CNhs12017_11408-118E4_forward Regulation 
AdipocyteSubcutaneousDonor2_CNhs11371_ctss_rev AdipocyteSubcutaneousD2- Adipocyte - subcutaneous, donor2_CNhs11371_11336-117F4_reverse Regulation 
AdipocyteSubcutaneousDonor2_CNhs11371_ctss_fwd AdipocyteSubcutaneousD2+ Adipocyte - subcutaneous, donor2_CNhs11371_11336-117F4_forward Regulation 
AdipocyteSubcutaneousDonor1_CNhs12494_ctss_rev AdipocyteSubcutaneousD1- Adipocyte - subcutaneous, donor1_CNhs12494_11259-116F8_reverse Regulation 
AdipocyteSubcutaneousDonor1_CNhs12494_ctss_fwd AdipocyteSubcutaneousD1+ Adipocyte - subcutaneous, donor1_CNhs12494_11259-116F8_forward Regulation 
AdipocytePerirenalDonor1_CNhs12069_ctss_rev AdipocytePerirenalD1- Adipocyte - perirenal, donor1_CNhs12069_11476-119C9_reverse Regulation 
AdipocytePerirenalDonor1_CNhs12069_ctss_fwd AdipocytePerirenalD1+ Adipocyte - perirenal, donor1_CNhs12069_11476-119C9_forward Regulation 
AdipocyteOmentalDonor3_CNhs12068_ctss_rev AdipocyteOmentalD3- Adipocyte - omental, donor3_CNhs12068_11475-119C8_reverse Regulation 
AdipocyteOmentalDonor3_CNhs12068_ctss_fwd AdipocyteOmentalD3+ Adipocyte - omental, donor3_CNhs12068_11475-119C8_forward Regulation 
AdipocyteOmentalDonor2_CNhs12067_ctss_rev AdipocyteOmentalD2- Adipocyte - omental, donor2_CNhs12067_11474-119C7_reverse Regulation 
AdipocyteOmentalDonor2_CNhs12067_ctss_fwd AdipocyteOmentalD2+ Adipocyte - omental, donor2_CNhs12067_11474-119C7_forward Regulation 
AdipocyteOmentalDonor1_CNhs11054_ctss_rev AdipocyteOmentalD1- Adipocyte - omental, donor1_CNhs11054_11473-119C6_reverse Regulation 
AdipocyteOmentalDonor1_CNhs11054_ctss_fwd AdipocyteOmentalD1+ Adipocyte - omental, donor1_CNhs11054_11473-119C6_forward Regulation 
AdipocyteBreastDonor2_CNhs11969_ctss_rev AdipocyteBreastD2- Adipocyte - breast, donor2_CNhs11969_11327-117E4_reverse Regulation 
AdipocyteBreastDonor2_CNhs11969_ctss_fwd AdipocyteBreastD2+ Adipocyte - breast, donor2_CNhs11969_11327-117E4_forward Regulation 
AdipocyteBreastDonor1_CNhs11051_ctss_rev AdipocyteBreastD1- Adipocyte - breast, donor1_CNhs11051_11376-118A8_reverse Regulation 
AdipocyteBreastDonor1_CNhs11051_ctss_fwd AdipocyteBreastD1+ Adipocyte - breast, donor1_CNhs11051_11376-118A8_forward Regulation 
PromyelocytesmyelocytesPMCDonor3_CNhs12529_ctss_rev Promyelocytes/myelocytesPmcD3- promyelocytes/myelocytes PMC, donor3_CNhs12529_12140-128E7_reverse Regulation 
PromyelocytesmyelocytesPMCDonor3_CNhs12529_ctss_fwd Promyelocytes/myelocytesPmcD3+ promyelocytes/myelocytes PMC, donor3_CNhs12529_12140-128E7_forward Regulation 
PromyelocytesmyelocytesPMCDonor2_CNhs12525_ctss_rev Promyelocytes/myelocytesPmcD2- promyelocytes/myelocytes PMC, donor2_CNhs12525_12136-128E3_reverse Regulation 
PromyelocytesmyelocytesPMCDonor2_CNhs12525_ctss_fwd Promyelocytes/myelocytesPmcD2+ promyelocytes/myelocytes PMC, donor2_CNhs12525_12136-128E3_forward Regulation 
PromyelocytesmyelocytesPMCDonor1_CNhs12520_ctss_rev Promyelocytes/myelocytesPmcD1- promyelocytes/myelocytes PMC, donor1_CNhs12520_12132-128D8_reverse Regulation 
PromyelocytesmyelocytesPMCDonor1_CNhs12520_ctss_fwd Promyelocytes/myelocytesPmcD1+ promyelocytes/myelocytes PMC, donor1_CNhs12520_12132-128D8_forward Regulation 
NeutrophilPMNDonor3_CNhs12530_ctss_rev NeutrophilPmnD3- neutrophil PMN, donor3_CNhs12530_12141-128E8_reverse Regulation 
NeutrophilPMNDonor3_CNhs12530_ctss_fwd NeutrophilPmnD3+ neutrophil PMN, donor3_CNhs12530_12141-128E8_forward Regulation 
NeutrophilPMNDonor2_CNhs12526_ctss_rev NeutrophilPmnD2- neutrophil PMN, donor2_CNhs12526_12137-128E4_reverse Regulation 
NeutrophilPMNDonor2_CNhs12526_ctss_fwd NeutrophilPmnD2+ neutrophil PMN, donor2_CNhs12526_12137-128E4_forward Regulation 
NeutrophilPMNDonor1_CNhs12522_ctss_rev NeutrophilPmnD1- neutrophil PMN, donor1_CNhs12522_12133-128D9_reverse Regulation 
NeutrophilPMNDonor1_CNhs12522_ctss_fwd NeutrophilPmnD1+ neutrophil PMN, donor1_CNhs12522_12133-128D9_forward Regulation 
NasalEpithelialCellsDonor1TechRep2_CNhs12554_ctss_rev NasalEpithelialCellsD1Tr2- nasal epithelial cells, donor1, tech_rep2_CNhs12554_12226-129F3_reverse Regulation 
NasalEpithelialCellsDonor1TechRep2_CNhs12554_ctss_fwd NasalEpithelialCellsD1Tr2+ nasal epithelial cells, donor1, tech_rep2_CNhs12554_12226-129F3_forward Regulation 
MesothelialCellsDonor2_CNhs12197_ctss_rev MesothelialCellsD2- Mesothelial Cells, donor2_CNhs12197_12156-128G5_reverse Regulation 
MesothelialCellsDonor2_CNhs12197_ctss_fwd MesothelialCellsD2+ Mesothelial Cells, donor2_CNhs12197_12156-128G5_forward Regulation 
MatureAdipocyteDonor4_CNhs12562_ctss_rev MatureAdipocyteD4- mature adipocyte, donor4_CNhs12562_12234-129G2_reverse Regulation 
MatureAdipocyteDonor4_CNhs12562_ctss_fwd MatureAdipocyteD4+ mature adipocyte, donor4_CNhs12562_12234-129G2_forward Regulation 
MatureAdipocyteDonor3_CNhs12560_ctss_rev MatureAdipocyteD3- mature adipocyte, donor3_CNhs12560_12233-129G1_reverse Regulation 
MatureAdipocyteDonor3_CNhs12560_ctss_fwd MatureAdipocyteD3+ mature adipocyte, donor3_CNhs12560_12233-129G1_forward Regulation 
MatureAdipocyteDonor2_CNhs12559_ctss_rev MatureAdipocyteD2- mature adipocyte, donor2_CNhs12559_12232-129F9_reverse Regulation 
MatureAdipocyteDonor2_CNhs12559_ctss_fwd MatureAdipocyteD2+ mature adipocyte, donor2_CNhs12559_12232-129F9_forward Regulation 
MatureAdipocyteDonor1_CNhs12558_ctss_rev MatureAdipocyteD1- mature adipocyte, donor1_CNhs12558_12231-129F8_reverse Regulation 
MatureAdipocyteDonor1_CNhs12558_ctss_fwd MatureAdipocyteD1+ mature adipocyte, donor1_CNhs12558_12231-129F8_forward Regulation 
MallassezderivedCellsDonor1MZH3_CNhs12538_ctss_rev MallassezCellsD1- Mallassez-derived cells, donor1 (MZH3)_CNhs12538_12142-128E9_reverse Regulation 
MallassezderivedCellsDonor1MZH3_CNhs12538_ctss_fwd MallassezCellsD1+ Mallassez-derived cells, donor1 (MZH3)_CNhs12538_12142-128E9_forward Regulation 
GranulocyteMacrophageProgenitorDonor3_CNhs12528_ctss_rev GranulocyteMacrophageProgenitorD3- granulocyte macrophage progenitor, donor3_CNhs12528_12139-128E6_reverse Regulation 
GranulocyteMacrophageProgenitorDonor3_CNhs12528_ctss_fwd GranulocyteMacrophageProgenitorD3+ granulocyte macrophage progenitor, donor3_CNhs12528_12139-128E6_forward Regulation 
GranulocyteMacrophageProgenitorDonor2_CNhs12524_ctss_rev GranulocyteMacrophageProgenitorD2- granulocyte macrophage progenitor, donor2_CNhs12524_12135-128E2_reverse Regulation 
GranulocyteMacrophageProgenitorDonor2_CNhs12524_ctss_fwd GranulocyteMacrophageProgenitorD2+ granulocyte macrophage progenitor, donor2_CNhs12524_12135-128E2_forward Regulation 
GranulocyteMacrophageProgenitorDonor1_CNhs12519_ctss_rev GranulocyteMacrophageProgenitorD1- granulocyte macrophage progenitor, donor1_CNhs12519_12131-128D7_reverse Regulation 
GranulocyteMacrophageProgenitorDonor1_CNhs12519_ctss_fwd GranulocyteMacrophageProgenitorD1+ granulocyte macrophage progenitor, donor1_CNhs12519_12131-128D7_forward Regulation 
EosinophilsDonor3_CNhs12549_ctss_rev EosinophilsD3- Eosinophils, donor3_CNhs12549_12246-129H5_reverse Regulation 
EosinophilsDonor3_CNhs12549_ctss_fwd EosinophilsD3+ Eosinophils, donor3_CNhs12549_12246-129H5_forward Regulation 
EosinophilsDonor2_CNhs12548_ctss_rev EosinophilsD2- Eosinophils, donor2_CNhs12548_12245-129H4_reverse Regulation 
EosinophilsDonor2_CNhs12548_ctss_fwd EosinophilsD2+ Eosinophils, donor2_CNhs12548_12245-129H4_forward Regulation 
EosinophilsDonor1_CNhs12547_ctss_rev EosinophilsD1- Eosinophils, donor1_CNhs12547_12244-129H3_reverse Regulation 
EosinophilsDonor1_CNhs12547_ctss_fwd EosinophilsD1+ Eosinophils, donor1_CNhs12547_12244-129H3_forward Regulation 
DendriticCellsPlasmacytoidDonor3_CNhs12200_ctss_rev DendriticCellsPlasmacytoidD3- Dendritic Cells - plasmacytoid, donor3_CNhs12200_11385-118B8_reverse Regulation 
DendriticCellsPlasmacytoidDonor3_CNhs12200_ctss_fwd DendriticCellsPlasmacytoidD3+ Dendritic Cells - plasmacytoid, donor3_CNhs12200_11385-118B8_forward Regulation 
DendriticCellsPlasmacytoidDonor2_CNhs12196_ctss_rev DendriticCellsPlasmacytoidD2- Dendritic Cells - plasmacytoid, donor2_CNhs12196_11309-117C4_reverse Regulation 
DendriticCellsPlasmacytoidDonor2_CNhs12196_ctss_fwd DendriticCellsPlasmacytoidD2+ Dendritic Cells - plasmacytoid, donor2_CNhs12196_11309-117C4_forward Regulation 
DendriticCellsMonocyteImmatureDerivedDonor2_CNhs12195_ctss_rev DendriticCellsMonocyteImmatureD2- Dendritic Cells - monocyte immature derived, donor2_CNhs12195_11308-117C3_reverse Regulation 
DendriticCellsMonocyteImmatureDerivedDonor2_CNhs12195_ctss_fwd DendriticCellsMonocyteImmatureD2+ Dendritic Cells - monocyte immature derived, donor2_CNhs12195_11308-117C3_forward Regulation 
CommonMyeloidProgenitorCMPDonor2_CNhs12523_ctss_rev CommonMyeloidProgenitorCmpD2- common myeloid progenitor CMP, donor2_CNhs12523_12134-128E1_reverse Regulation 
CommonMyeloidProgenitorCMPDonor2_CNhs12523_ctss_fwd CommonMyeloidProgenitorCmpD2+ common myeloid progenitor CMP, donor2_CNhs12523_12134-128E1_forward Regulation 
CommonMyeloidProgenitorCMPDonor1_CNhs12518_ctss_rev CommonMyeloidProgenitorCmpD1- common myeloid progenitor CMP, donor1_CNhs12518_12130-128D6_reverse Regulation 
CommonMyeloidProgenitorCMPDonor1_CNhs12518_ctss_fwd CommonMyeloidProgenitorCmpD1+ common myeloid progenitor CMP, donor1_CNhs12518_12130-128D6_forward Regulation 
CD8TCellsPluriselectDonor090612Donation3_CNhs12187_ctss_rev Cd8+TCellsPluriD090612Dn3- CD8+ T Cells (pluriselect), donor090612, donation3_CNhs12187_12211-129D6_reverse Regulation 
CD8TCellsPluriselectDonor090612Donation3_CNhs12187_ctss_fwd Cd8+TCellsPluriD090612Dn3+ CD8+ T Cells (pluriselect), donor090612, donation3_CNhs12187_12211-129D6_forward Regulation 
CD8TCellsPluriselectDonor090612Donation2_CNhs12184_ctss_rev Cd8+TCellsPluriD090612Dn2- CD8+ T Cells (pluriselect), donor090612, donation2_CNhs12184_12206-129D1_reverse Regulation 
CD8TCellsPluriselectDonor090612Donation2_CNhs12184_ctss_fwd Cd8+TCellsPluriD090612Dn2+ CD8+ T Cells (pluriselect), donor090612, donation2_CNhs12184_12206-129D1_forward Regulation 
CD8TCellsPluriselectDonor090612Donation1_CNhs12182_ctss_rev Cd8+TCellsPluriD090612Dn1- CD8+ T Cells (pluriselect), donor090612, donation1_CNhs12182_12201-129C5_reverse Regulation 
CD8TCellsPluriselectDonor090612Donation1_CNhs12182_ctss_fwd Cd8+TCellsPluriD090612Dn1+ CD8+ T Cells (pluriselect), donor090612, donation1_CNhs12182_12201-129C5_forward Regulation 
CD8TCellsPluriselectDonor090325Donation2_CNhs12199_ctss_rev Cd8+TCellsPluriD090325Dn2- CD8+ T Cells (pluriselect), donor090325, donation2_CNhs12199_12171-128I2_reverse Regulation 
CD8TCellsPluriselectDonor090325Donation2_CNhs12199_ctss_fwd Cd8+TCellsPluriD090325Dn2+ CD8+ T Cells (pluriselect), donor090325, donation2_CNhs12199_12171-128I2_forward Regulation 
CD8TCellsPluriselectDonor090325Donation1_CNhs12201_ctss_rev Cd8+TCellsPluriD090325Dn1- CD8+ T Cells (pluriselect), donor090325, donation1_CNhs12201_12148-128F6_reverse Regulation 
CD8TCellsPluriselectDonor090325Donation1_CNhs12201_ctss_fwd Cd8+TCellsPluriD090325Dn1+ CD8+ T Cells (pluriselect), donor090325, donation1_CNhs12201_12148-128F6_forward Regulation 
CD8TCellsPluriselectDonor090309Donation3_CNhs12180_ctss_rev Cd8+TCellsPluriD090309Dn3- CD8+ T Cells (pluriselect), donor090309, donation3_CNhs12180_12196-129B9_reverse Regulation 
CD8TCellsPluriselectDonor090309Donation3_CNhs12180_ctss_fwd Cd8+TCellsPluriD090309Dn3+ CD8+ T Cells (pluriselect), donor090309, donation3_CNhs12180_12196-129B9_forward Regulation 
CD8TCellsPluriselectDonor090309Donation2_CNhs12178_ctss_rev Cd8+TCellsPluriD090309Dn2- CD8+ T Cells (pluriselect), donor090309, donation2_CNhs12178_12191-129B4_reverse Regulation 
CD8TCellsPluriselectDonor090309Donation2_CNhs12178_ctss_fwd Cd8+TCellsPluriD090309Dn2+ CD8+ T Cells (pluriselect), donor090309, donation2_CNhs12178_12191-129B4_forward Regulation 
CD8TCellsPluriselectDonor090309Donation1_CNhs12176_ctss_rev Cd8+TCellsPluriD090309Dn1- CD8+ T Cells (pluriselect), donor090309, donation1_CNhs12176_12186-129A8_reverse Regulation 
CD8TCellsPluriselectDonor090309Donation1_CNhs12176_ctss_fwd Cd8+TCellsPluriD090309Dn1+ CD8+ T Cells (pluriselect), donor090309, donation1_CNhs12176_12186-129A8_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor2_CNhs13237_ctss_rev Cd4+cd25-cd45ra-D2- CD4+CD25-CD45RA- memory conventional T cells, donor2_CNhs13237_11798-124C7_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor2_CNhs13237_ctss_fwd Cd4+cd25-cd45ra-D2+ CD4+CD25-CD45RA- memory conventional T cells, donor2_CNhs13237_11798-124C7_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor1_CNhs13239_ctss_rev Cd4+cd25-cd45ra-D1- CD4+CD25-CD45RA- memory conventional T cells, donor1_CNhs13239_11786-124B4_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor1_CNhs13239_ctss_fwd Cd4+cd25-cd45ra-D1+ CD4+CD25-CD45RA- memory conventional T cells, donor1_CNhs13239_11786-124B4_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor2_CNhs13235_ctss_rev Cd4+cd25+cd45ra+D2- CD4+CD25+CD45RA+ naive regulatory T cells, donor2_CNhs13235_11796-124C5_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor2_CNhs13235_ctss_fwd Cd4+cd25+cd45ra+D2+ CD4+CD25+CD45RA+ naive regulatory T cells, donor2_CNhs13235_11796-124C5_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor1_CNhs13238_ctss_rev Cd4+cd25+cd45ra+D1- CD4+CD25+CD45RA+ naive regulatory T cells, donor1_CNhs13238_11780-124A7_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor1_CNhs13238_ctss_fwd Cd4+cd25+cd45ra+D1+ CD4+CD25+CD45RA+ naive regulatory T cells, donor1_CNhs13238_11780-124A7_forward Regulation 
CD34StemCellsAdultBoneMarrowDerivedDonor1TechRep2_CNhs12553_ctss_rev Cd34+StemCellsAdultBoneMarrowD1Tr2- CD34+ stem cells - adult bone marrow derived, donor1, tech_rep2_CNhs12553_12225-129F2_reverse Regulation 
CD34StemCellsAdultBoneMarrowDerivedDonor1TechRep2_CNhs12553_ctss_fwd Cd34+StemCellsAdultBoneMarrowD1Tr2+ CD34+ stem cells - adult bone marrow derived, donor1, tech_rep2_CNhs12553_12225-129F2_forward Regulation 
CD34ProgenitorsDonor2_CNhs12205_ctss_rev Cd34+ProgenitorsD2- CD34+ Progenitors, donor2_CNhs12205_11625-122B5_reverse Regulation 
CD34ProgenitorsDonor2_CNhs12205_ctss_fwd Cd34+ProgenitorsD2+ CD34+ Progenitors, donor2_CNhs12205_11625-122B5_forward Regulation 
CD34ProgenitorsDonor1_CNhs13227_ctss_rev Cd34+ProgenitorsD1- CD34+ Progenitors, donor1_CNhs13227_11545-120B6_reverse Regulation 
CD34ProgenitorsDonor1_CNhs13227_ctss_fwd Cd34+ProgenitorsD1+ CD34+ Progenitors, donor1_CNhs13227_11545-120B6_forward Regulation 
CD19BCellsPluriselectDonor090612Donation3_CNhs12188_ctss_rev Cd19+BCellsPluriD090612Dn3- CD19+ B Cells (pluriselect), donor090612, donation3_CNhs12188_12214-129D9_reverse Regulation 
CD19BCellsPluriselectDonor090612Donation3_CNhs12188_ctss_fwd Cd19+BCellsPluriD090612Dn3+ CD19+ B Cells (pluriselect), donor090612, donation3_CNhs12188_12214-129D9_forward Regulation 
CD19BCellsPluriselectDonor090612Donation2_CNhs12185_ctss_rev Cd19+BCellsPluriD090612Dn2- CD19+ B Cells (pluriselect), donor090612, donation2_CNhs12185_12209-129D4_reverse Regulation 
CD19BCellsPluriselectDonor090612Donation2_CNhs12185_ctss_fwd Cd19+BCellsPluriD090612Dn2+ CD19+ B Cells (pluriselect), donor090612, donation2_CNhs12185_12209-129D4_forward Regulation 
CD19BCellsPluriselectDonor090612Donation1_CNhs12183_ctss_rev Cd19+BCellsPluriD090612Dn1- CD19+ B Cells (pluriselect), donor090612, donation1_CNhs12183_12204-129C8_reverse Regulation 
CD19BCellsPluriselectDonor090612Donation1_CNhs12183_ctss_fwd Cd19+BCellsPluriD090612Dn1+ CD19+ B Cells (pluriselect), donor090612, donation1_CNhs12183_12204-129C8_forward Regulation 
CD19BCellsPluriselectDonor090325Donation2_CNhs12175_ctss_rev Cd19+BCellsPluriD090325Dn2- CD19+ B Cells (pluriselect), donor090325, donation2_CNhs12175_12174-128I5_reverse Regulation 
CD19BCellsPluriselectDonor090325Donation2_CNhs12175_ctss_fwd Cd19+BCellsPluriD090325Dn2+ CD19+ B Cells (pluriselect), donor090325, donation2_CNhs12175_12174-128I5_forward Regulation 
CD19BCellsPluriselectDonor090325Donation1_CNhs12531_ctss_rev Cd19+BCellsPluriD090325Dn1- CD19+ B Cells (pluriselect), donor090325, donation1_CNhs12531_12151-128F9_reverse Regulation 
CD19BCellsPluriselectDonor090325Donation1_CNhs12531_ctss_fwd Cd19+BCellsPluriD090325Dn1+ CD19+ B Cells (pluriselect), donor090325, donation1_CNhs12531_12151-128F9_forward Regulation 
CD19BCellsPluriselectDonor090309Donation3_CNhs12181_ctss_rev Cd19+BCellsPluriD090309Dn3- CD19+ B Cells (pluriselect), donor090309, donation3_CNhs12181_12199-129C3_reverse Regulation 
CD19BCellsPluriselectDonor090309Donation3_CNhs12181_ctss_fwd Cd19+BCellsPluriD090309Dn3+ CD19+ B Cells (pluriselect), donor090309, donation3_CNhs12181_12199-129C3_forward Regulation 
CD19BCellsPluriselectDonor090309Donation2_CNhs12179_ctss_rev Cd19+BCellsPluriD090309Dn2- CD19+ B Cells (pluriselect), donor090309, donation2_CNhs12179_12194-129B7_reverse Regulation 
CD19BCellsPluriselectDonor090309Donation2_CNhs12179_ctss_fwd Cd19+BCellsPluriD090309Dn2+ CD19+ B Cells (pluriselect), donor090309, donation2_CNhs12179_12194-129B7_forward Regulation 
CD19BCellsPluriselectDonor090309Donation1_CNhs12177_ctss_rev Cd19+BCellsPluriD090309Dn1- CD19+ B Cells (pluriselect), donor090309, donation1_CNhs12177_12189-129B2_reverse Regulation 
CD19BCellsPluriselectDonor090309Donation1_CNhs12177_ctss_fwd Cd19+BCellsPluriD090309Dn1+ CD19+ B Cells (pluriselect), donor090309, donation1_CNhs12177_12189-129B2_forward Regulation 
CD14CD16MonocytesDonor1_CNhs13229_ctss_rev Cd14-cd16+MonocytesD1- CD14-CD16+ Monocytes, donor1_CNhs13229_11790-124B8_reverse Regulation 
CD14CD16MonocytesDonor1_CNhs13229_ctss_fwd Cd14-cd16+MonocytesD1+ CD14-CD16+ Monocytes, donor1_CNhs13229_11790-124B8_forward Regulation 
CD133StemCellsCordBloodDerivedPool1_CNhs12545_ctss_rev Cd133+StemCellsCordBloodPl1- CD133+ stem cells - cord blood derived, pool1_CNhs12545_12223-129E9_reverse Regulation 
CD133StemCellsCordBloodDerivedPool1_CNhs12545_ctss_fwd Cd133+StemCellsCordBloodPl1+ CD133+ stem cells - cord blood derived, pool1_CNhs12545_12223-129E9_forward Regulation 
CD133StemCellsAdultBoneMarrowDerivedPool1_CNhs12552_ctss_rev Cd133+StemCellsAdultBoneMarrowPl1- CD133+ stem cells - adult bone marrow derived, pool1_CNhs12552_12224-129F1_reverse Regulation 
CD133StemCellsAdultBoneMarrowDerivedPool1_CNhs12552_ctss_fwd Cd133+StemCellsAdultBoneMarrowPl1+ CD133+ stem cells - adult bone marrow derived, pool1_CNhs12552_12224-129F1_forward Regulation 
BasophilsDonor2_CNhs12563_ctss_rev BasophilsD2- Basophils, donor2_CNhs12563_12242-129H1_reverse Regulation 
BasophilsDonor2_CNhs12563_ctss_fwd BasophilsD2+ Basophils, donor2_CNhs12563_12242-129H1_forward Regulation 
BasophilsDonor1_CNhs12546_ctss_rev BasophilsD1- Basophils, donor1_CNhs12546_12241-129G9_reverse Regulation 
BasophilsDonor1_CNhs12546_ctss_fwd BasophilsD1+ Basophils, donor1_CNhs12546_12241-129G9_forward Regulation 
SmoothMuscleCellsAorticDonor0NuclearFraction_CNhs12402_ctss_rev SmcAorticCytofracD0- Smooth Muscle Cells - Aortic, donor0 (nuclear fraction)_CNhs12402_14314-155D3_reverse Regulation 
SmoothMuscleCellsAorticDonor0CytoplasmicFraction_CNhs12401_ctss_rev SmcAorticCytofracD0- Smooth Muscle Cells - Aortic, donor0 (cytoplasmic fraction)_CNhs12401_14313-155D2_reverse Regulation 
SmoothMuscleCellsAorticDonor0NuclearFraction_CNhs12402_ctss_fwd SmcAorticCytofracD0+ Smooth Muscle Cells - Aortic, donor0 (nuclear fraction)_CNhs12402_14314-155D3_forward Regulation 
SmoothMuscleCellsAorticDonor0CytoplasmicFraction_CNhs12401_ctss_fwd SmcAorticCytofracD0+ Smooth Muscle Cells - Aortic, donor0 (cytoplasmic fraction)_CNhs12401_14313-155D2_forward Regulation 
SmallAirwayEpithelialCellsDonor3NuclearFraction_CNhs12583_ctss_rev SmallAirwayEpithelialCellsD3- Small Airway Epithelial Cells, donor3 (nuclear fraction)_CNhs12583_14317-155D6_reverse Regulation 
SmallAirwayEpithelialCellsDonor3CytoplasmicFraction_CNhs14563_ctss_rev SmallAirwayEpithelialCellsD3- Small Airway Epithelial Cells donor3 (cytoplasmic fraction)_CNhs14563_14316-155D5_reverse Regulation 
SmallAirwayEpithelialCellsDonor3NuclearFraction_CNhs12583_ctss_fwd SmallAirwayEpithelialCellsD3+ Small Airway Epithelial Cells, donor3 (nuclear fraction)_CNhs12583_14317-155D6_forward Regulation 
SmallAirwayEpithelialCellsDonor3CytoplasmicFraction_CNhs14563_ctss_fwd SmallAirwayEpithelialCellsD3+ Small Airway Epithelial Cells donor3 (cytoplasmic fraction)_CNhs14563_14316-155D5_forward Regulation 
SmallAirwayEpithelialCellsDonor2NuclearFraction_CNhs14565_ctss_rev SmallAirwayEpithelialCellsD2- Small Airway Epithelial Cells donor2 (nuclear fraction)_CNhs14565_14335-155F6_reverse Regulation 
SmallAirwayEpithelialCellsDonor2CytoplasmicFraction_CNhs14564_ctss_rev SmallAirwayEpithelialCellsD2- Small Airway Epithelial Cells donor2 (cytoplasmic fraction)_CNhs14564_14334-155F5_reverse Regulation 
SmallAirwayEpithelialCellsDonor2NuclearFraction_CNhs14565_ctss_fwd SmallAirwayEpithelialCellsD2+ Small Airway Epithelial Cells donor2 (nuclear fraction)_CNhs14565_14335-155F6_forward Regulation 
SmallAirwayEpithelialCellsDonor2CytoplasmicFraction_CNhs14564_ctss_fwd SmallAirwayEpithelialCellsD2+ Small Airway Epithelial Cells donor2 (cytoplasmic fraction)_CNhs14564_14334-155F5_forward Regulation 
PreadipocyteBreastDonor2NuclearFraction_CNhs12584_ctss_rev PreadipocyteBreastD2- Preadipocyte - breast, donor2 (nuclear fraction)_CNhs12584_14320-155D9_reverse Regulation 
PreadipocyteBreastDonor2CytoplasmicFraction_CNhs14562_ctss_rev PreadipocyteBreastD2- Preadipocyte - breast donor2 (cytoplasmic fraction)_CNhs14562_14319-155D8_reverse Regulation 
PreadipocyteBreastDonor2NuclearFraction_CNhs12584_ctss_fwd PreadipocyteBreastD2+ Preadipocyte - breast, donor2 (nuclear fraction)_CNhs12584_14320-155D9_forward Regulation 
PreadipocyteBreastDonor2CytoplasmicFraction_CNhs14562_ctss_fwd PreadipocyteBreastD2+ Preadipocyte - breast donor2 (cytoplasmic fraction)_CNhs14562_14319-155D8_forward Regulation 
FibroblastSkinNormalDonor2CytoplasmicFraction_CNhs14561_ctss_rev FibrosSkinD2- Fibroblast - skin, normal donor2 (cytoplasmic fraction)_CNhs14561_14301-155B8_reverse Regulation 
FibroblastSkinNormalDonor2CytoplasmicFraction_CNhs14561_ctss_fwd FibrosSkinD2+ Fibroblast - skin, normal donor2 (cytoplasmic fraction)_CNhs14561_14301-155B8_forward Regulation 
FibroblastSkinNormalDonor1CytoplasmicFraction_CNhs14560_ctss_rev FibrosSkinD1- Fibroblast - skin, normal donor1 (cytoplasmic fraction)_CNhs14560_14322-155E2_reverse Regulation 
FibroblastSkinNormalDonor1CytoplasmicFraction_CNhs14560_ctss_fwd FibrosSkinD1+ Fibroblast - skin, normal donor1 (cytoplasmic fraction)_CNhs14560_14322-155E2_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor3NuclearFraction_CNhs12398_ctss_rev FibroSkinSpinalMuscularAtrophyNucfracD3- Fibroblast - skin spinal muscular atrophy, donor3 (nuclear fraction)_CNhs12398_14305-155C3_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor3NuclearFraction_CNhs12398_ctss_fwd FibroSkinSpinalMuscularAtrophyNucfracD3+ Fibroblast - skin spinal muscular atrophy, donor3 (nuclear fraction)_CNhs12398_14305-155C3_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor1NuclearFraction_CNhs12404_ctss_rev FibroSkinSpinalMuscularAtrophyNucfracD1- Fibroblast - skin spinal muscular atrophy, donor1 (nuclear fraction)_CNhs12404_14326-155E6_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor1NuclearFraction_CNhs12404_ctss_fwd FibroSkinSpinalMuscularAtrophyNucfracD1+ Fibroblast - skin spinal muscular atrophy, donor1 (nuclear fraction)_CNhs12404_14326-155E6_forward Regulation 
FibroblastSkinNormalDonor2NuclearFraction_CNhs12582_ctss_rev FibroSkinNormalNucfracD2- Fibroblast - skin normal, donor2 (nuclear fraction)_CNhs12582_14302-155B9_reverse Regulation 
FibroblastSkinNormalDonor2NuclearFraction_CNhs12582_ctss_fwd FibroSkinNormalNucfracD2+ Fibroblast - skin normal, donor2 (nuclear fraction)_CNhs12582_14302-155B9_forward Regulation 
FibroblastSkinNormalDonor1NuclearFraction_CNhs12403_ctss_rev FibroSkinNormalNucfracD1- Fibroblast - skin normal, donor1 (nuclear fraction)_CNhs12403_14323-155E3_reverse Regulation 
FibroblastSkinNormalDonor1NuclearFraction_CNhs12403_ctss_fwd FibroSkinNormalNucfracD1+ Fibroblast - skin normal, donor1 (nuclear fraction)_CNhs12403_14323-155E3_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor3NuclearFraction_CNhs12399_ctss_rev FibroSkinDystrophiaMyotonicaNucfracD3- Fibroblast - skin dystrophia myotonica, donor3 (nuclear fraction)_CNhs12399_14308-155C6_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor3NuclearFraction_CNhs12399_ctss_fwd FibroSkinDystrophiaMyotonicaNucfracD3+ Fibroblast - skin dystrophia myotonica, donor3 (nuclear fraction)_CNhs12399_14308-155C6_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor1NuclearFraction_CNhs12405_ctss_rev FibroSkinDystrophiaMyotonicaNucfracD1- Fibroblast - skin dystrophia myotonica, donor1 (nuclear fraction)_CNhs12405_14329-155E9_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor1NuclearFraction_CNhs12405_ctss_fwd FibroSkinDystrophiaMyotonicaNucfracD1+ Fibroblast - skin dystrophia myotonica, donor1 (nuclear fraction)_CNhs12405_14329-155E9_forward Regulation 
FibroblastAorticAdventitialDonor3CytoplasmicFraction_CNhs14559_ctss_rev FibroAorticAdventitialD3- Fibroblast - Aortic Adventitial donor3 (cytoplasmic fraction)_CNhs14559_14310-155C8_reverse Regulation 
FibroblastAorticAdventitialDonor3NuclearFraction_CNhs12400_ctss_rev FibroAorticAdventitialD3- Fibroblast - Aortic Adventitial, donor3 (nuclear fraction)_CNhs12400_14311-155C9_reverse Regulation 
FibroblastAorticAdventitialDonor3CytoplasmicFraction_CNhs14559_ctss_fwd FibroAorticAdventitialD3+ Fibroblast - Aortic Adventitial donor3 (cytoplasmic fraction)_CNhs14559_14310-155C8_forward Regulation 
FibroblastAorticAdventitialDonor3NuclearFraction_CNhs12400_ctss_fwd FibroAorticAdventitialD3+ Fibroblast - Aortic Adventitial, donor3 (nuclear fraction)_CNhs12400_14311-155C9_forward Regulation 
FibroblastAorticAdventitialDonor2NuclearFraction_CNhs12581_ctss_rev FibroAorticAdventitialD2- Fibroblast - Aortic Adventitial, donor2 (nuclear fraction)_CNhs12581_14332-155F3_reverse Regulation 
FibroblastAorticAdventitialDonor2CytoplasmicFraction_CNhs14558_ctss_rev FibroAorticAdventitialD2- Fibroblast - Aortic Adventitial donor2 (cytoplasmic fraction)_CNhs14558_14331-155F2_reverse Regulation 
FibroblastAorticAdventitialDonor2NuclearFraction_CNhs12581_ctss_fwd FibroAorticAdventitialD2+ Fibroblast - Aortic Adventitial, donor2 (nuclear fraction)_CNhs12581_14332-155F3_forward Regulation 
FibroblastAorticAdventitialDonor2CytoplasmicFraction_CNhs14558_ctss_fwd FibroAorticAdventitialD2+ Fibroblast - Aortic Adventitial donor2 (cytoplasmic fraction)_CNhs14558_14331-155F2_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1CytoplasmicFraction_CNhs14556_ctss_rev Cl:THP-1cyto- acute myeloid leukemia (FAB M5) cell line:THP-1 (cytoplasmic fraction)_CNhs14556_14298-155B5_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1CytoplasmicFraction_CNhs14556_ctss_fwd Cl:THP-1cyto+ acute myeloid leukemia (FAB M5) cell line:THP-1 (cytoplasmic fraction)_CNhs14556_14298-155B5_forward Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep3_CNhs13499_ctss_rev Hep2W/StreptococciJrs4Br3- Hep-2 cells treated with Streptococci strain JRS4, biol_rep3_CNhs13499_11896-125E6_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep3_CNhs13499_ctss_fwd Hep2W/StreptococciJrs4Br3+ Hep-2 cells treated with Streptococci strain JRS4, biol_rep3_CNhs13499_11896-125E6_forward Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep2_CNhs13498_ctss_rev Hep2W/StreptococciJrs4Br2- Hep-2 cells treated with Streptococci strain JRS4, biol_rep2_CNhs13498_11895-125E5_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep2_CNhs13498_ctss_fwd Hep2W/StreptococciJrs4Br2+ Hep-2 cells treated with Streptococci strain JRS4, biol_rep2_CNhs13498_11895-125E5_forward Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep1_CNhs13478_ctss_rev Hep2W/StreptococciJrs4Br1- Hep-2 cells treated with Streptococci strain JRS4, biol_rep1_CNhs13478_11894-125E4_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep1_CNhs13478_ctss_fwd Hep2W/StreptococciJrs4Br1+ Hep-2 cells treated with Streptococci strain JRS4, biol_rep1_CNhs13478_11894-125E4_forward Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep3_CNhs13497_ctss_rev Hep2W/Streptococci5448Br3- Hep-2 cells treated with Streptococci strain 5448, biol_rep3_CNhs13497_11892-125E2_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep3_CNhs13497_ctss_fwd Hep2W/Streptococci5448Br3+ Hep-2 cells treated with Streptococci strain 5448, biol_rep3_CNhs13497_11892-125E2_forward Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep2_CNhs13496_ctss_rev Hep2W/Streptococci5448Br2- Hep-2 cells treated with Streptococci strain 5448, biol_rep2_CNhs13496_11891-125E1_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep2_CNhs13496_ctss_fwd Hep2W/Streptococci5448Br2+ Hep-2 cells treated with Streptococci strain 5448, biol_rep2_CNhs13496_11891-125E1_forward Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep1_CNhs13477_ctss_rev Hep2W/Streptococci5448Br1- Hep-2 cells treated with Streptococci strain 5448, biol_rep1_CNhs13477_11890-125D9_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep1_CNhs13477_ctss_fwd Hep2W/Streptococci5448Br1+ Hep-2 cells treated with Streptococci strain 5448, biol_rep1_CNhs13477_11890-125D9_forward Regulation 
Hep2CellsMockTreatedBiolRep3_CNhs13501_ctss_rev Hep2MockTreatedBr3- Hep-2 cells mock treated, biol_rep3_CNhs13501_11900-125F1_reverse Regulation 
Hep2CellsMockTreatedBiolRep3_CNhs13501_ctss_fwd Hep2MockTreatedBr3+ Hep-2 cells mock treated, biol_rep3_CNhs13501_11900-125F1_forward Regulation 
Hep2CellsMockTreatedBiolRep2_CNhs13500_ctss_rev Hep2MockTreatedBr2- Hep-2 cells mock treated, biol_rep2_CNhs13500_11899-125E9_reverse Regulation 
Hep2CellsMockTreatedBiolRep2_CNhs13500_ctss_fwd Hep2MockTreatedBr2+ Hep-2 cells mock treated, biol_rep2_CNhs13500_11899-125E9_forward Regulation 
Hep2CellsMockTreatedBiolRep1_CNhs13479_ctss_rev Hep2MockTreatedBr1- Hep-2 cells mock treated, biol_rep1_CNhs13479_11898-125E8_reverse Regulation 
Hep2CellsMockTreatedBiolRep1_CNhs13479_ctss_fwd Hep2MockTreatedBr1+ Hep-2 cells mock treated, biol_rep1_CNhs13479_11898-125E8_forward Regulation 
RetinoblastomaCellLineY79_CNhs11267_ctss_rev Cl:Y79- retinoblastoma cell line:Y79_CNhs11267_10475-106I7_reverse Regulation 
RetinoblastomaCellLineY79_CNhs11267_ctss_fwd Cl:Y79+ retinoblastoma cell line:Y79_CNhs11267_10475-106I7_forward Regulation 
XerodermaPigentosumBCellLineXPL17_CNhs11813_ctss_rev Cl:XPL17- xeroderma pigentosum b cell line:XPL 17_CNhs11813_10563-108A5_reverse Regulation 
XerodermaPigentosumBCellLineXPL17_CNhs11813_ctss_fwd Cl:XPL17+ xeroderma pigentosum b cell line:XPL 17_CNhs11813_10563-108A5_forward Regulation 
HereditarySpherocyticAnemiaCellLineWIL2NS_CNhs11891_ctss_rev Cl:WIL2-NS- hereditary spherocytic anemia cell line:WIL2-NS_CNhs11891_10808-111A7_reverse Regulation 
HereditarySpherocyticAnemiaCellLineWIL2NS_CNhs11891_ctss_fwd Cl:WIL2-NS+ hereditary spherocytic anemia cell line:WIL2-NS_CNhs11891_10808-111A7_forward Regulation 
SmallCellLungCarcinomaCellLineWAhT_CNhs11812_ctss_rev Cl:WA-hT- small cell lung carcinoma cell line:WA-hT_CNhs11812_10562-108A4_reverse Regulation 
SmallCellLungCarcinomaCellLineWAhT_CNhs11812_ctss_fwd Cl:WA-hT+ small cell lung carcinoma cell line:WA-hT_CNhs11812_10562-108A4_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineU937DE4_CNhs13058_ctss_rev Cl:U-937DE-4- acute myeloid leukemia (FAB M5) cell line:U-937 DE-4_CNhs13058_10834-111D6_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineU937DE4_CNhs13058_ctss_fwd Cl:U-937DE-4+ acute myeloid leukemia (FAB M5) cell line:U-937 DE-4_CNhs13058_10834-111D6_forward Regulation 
ThymicCarcinomaCellLineTy82_CNhs14139_ctss_rev Cl:Ty-82- thymic carcinoma cell line:Ty-82_CNhs14139_10803-111A2_reverse Regulation 
ThymicCarcinomaCellLineTy82_CNhs14139_ctss_fwd Cl:Ty-82+ thymic carcinoma cell line:Ty-82_CNhs14139_10803-111A2_forward Regulation 
RenalCellCarcinomaCellLineTUHR10TKB_CNhs11257_ctss_rev Cl:TUHR10TKB- renal cell carcinoma cell line:TUHR10TKB_CNhs11257_10471-106I3_reverse Regulation 
RenalCellCarcinomaCellLineTUHR10TKB_CNhs11257_ctss_fwd Cl:TUHR10TKB+ renal cell carcinoma cell line:TUHR10TKB_CNhs11257_10471-106I3_forward Regulation 
RectalCancerCellLineTT1TKB_CNhs11255_ctss_rev Cl:TT1TKB- rectal cancer cell line:TT1TKB_CNhs11255_10469-106I1_reverse Regulation 
RectalCancerCellLineTT1TKB_CNhs11255_ctss_fwd Cl:TT1TKB+ rectal cancer cell line:TT1TKB_CNhs11255_10469-106I1_forward Regulation 
AstrocytomaCellLineTM31_CNhs10742_ctss_rev Cl:TM-31- astrocytoma cell line:TM-31_CNhs10742_10425-106D2_reverse Regulation 
AstrocytomaCellLineTM31_CNhs10742_ctss_fwd Cl:TM-31+ astrocytoma cell line:TM-31_CNhs10742_10425-106D2_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Thawed_CNhs10724_ctss_rev Cl:THP-1thawed- acute myeloid leukemia (FAB M5) cell line:THP-1 (thawed)_CNhs10724_10405-106A9_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Thawed_CNhs10724_ctss_fwd Cl:THP-1thawed+ acute myeloid leukemia (FAB M5) cell line:THP-1 (thawed)_CNhs10724_10405-106A9_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Revived_CNhs10723_ctss_rev Cl:THP-1revived- acute myeloid leukemia (FAB M5) cell line:THP-1 (revived)_CNhs10723_10400-106A4_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Revived_CNhs10723_ctss_fwd Cl:THP-1revived+ acute myeloid leukemia (FAB M5) cell line:THP-1 (revived)_CNhs10723_10400-106A4_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Fresh_CNhs10722_ctss_rev Cl:THP-1fresh- acute myeloid leukemia (FAB M5) cell line:THP-1 (fresh)_CNhs10722_10399-106A3_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Fresh_CNhs10722_ctss_fwd Cl:THP-1fresh+ acute myeloid leukemia (FAB M5) cell line:THP-1 (fresh)_CNhs10722_10399-106A3_forward Regulation 
GallBladderCarcinomaCellLineTGBC2TKB_CNhs10733_ctss_rev Cl:TGBC2TKB- gall bladder carcinoma cell line:TGBC2TKB_CNhs10733_10415-106C1_reverse Regulation 
GallBladderCarcinomaCellLineTGBC2TKB_CNhs10733_ctss_fwd Cl:TGBC2TKB+ gall bladder carcinoma cell line:TGBC2TKB_CNhs10733_10415-106C1_forward Regulation 
PapillotubularAdenocarcinomaCellLineTGBC18TKB_CNhs10734_ctss_rev Cl:TGBC18TKB- papillotubular adenocarcinoma cell line:TGBC18TKB_CNhs10734_10417-106C3_reverse Regulation 
PapillotubularAdenocarcinomaCellLineTGBC18TKB_CNhs10734_ctss_fwd Cl:TGBC18TKB+ papillotubular adenocarcinoma cell line:TGBC18TKB_CNhs10734_10417-106C3_forward Regulation 
GallBladderCarcinomaCellLineTGBC14TKB_CNhs11256_ctss_rev Cl:TGBC14TKB- gall bladder carcinoma cell line:TGBC14TKB_CNhs11256_10470-106I2_reverse Regulation 
GallBladderCarcinomaCellLineTGBC14TKB_CNhs11256_ctss_fwd Cl:TGBC14TKB+ gall bladder carcinoma cell line:TGBC14TKB_CNhs11256_10470-106I2_forward Regulation 
BileDuctCarcinomaCellLineTFK1_CNhs11265_ctss_rev Cl:TFK-1- bile duct carcinoma cell line:TFK-1_CNhs11265_10496-107C1_reverse Regulation 
BileDuctCarcinomaCellLineTFK1_CNhs11265_ctss_fwd Cl:TFK-1+ bile duct carcinoma cell line:TFK-1_CNhs11265_10496-107C1_forward Regulation 
ClearCellCarcinomaCellLineTEN_CNhs11930_ctss_rev Cl:TEN- clear cell carcinoma cell line:TEN_CNhs11930_10636-108I6_reverse Regulation 
ClearCellCarcinomaCellLineTEN_CNhs11930_ctss_fwd Cl:TEN+ clear cell carcinoma cell line:TEN_CNhs11930_10636-108I6_forward Regulation 
BasalCellCarcinomaCellLineTE354_T_CNhs11932_ctss_rev Cl:TE354_T- basal cell carcinoma cell line:TE 354_T_CNhs11932_10702-109G9_reverse Regulation 
BasalCellCarcinomaCellLineTE354_T_CNhs11932_ctss_fwd Cl:TE354_T+ basal cell carcinoma cell line:TE 354_T_CNhs11932_10702-109G9_forward Regulation 
ThyroidCarcinomaCellLineTCO1_CNhs11872_ctss_rev Cl:TCO-1- thyroid carcinoma cell line:TCO-1_CNhs11872_10783-110G9_reverse Regulation 
ThyroidCarcinomaCellLineTCO1_CNhs11872_ctss_fwd Cl:TCO-1+ thyroid carcinoma cell line:TCO-1_CNhs11872_10783-110G9_forward Regulation 
ArgyrophilSmallCellCarcinomaCellLineTCYIK_CNhs11725_ctss_rev Cl:TC-YIK- argyrophil small cell carcinoma cell line:TC-YIK_CNhs11725_10589-108D4_reverse Regulation 
ArgyrophilSmallCellCarcinomaCellLineTCYIK_CNhs11725_ctss_fwd Cl:TC-YIK+ argyrophil small cell carcinoma cell line:TC-YIK_CNhs11725_10589-108D4_forward Regulation 
NeuroectodermalTumorCellLineTASK1_CNhs11866_ctss_rev Cl:TASK1- neuroectodermal tumor cell line:TASK1_CNhs11866_10774-110F9_reverse Regulation 
NeuroectodermalTumorCellLineTASK1_CNhs11866_ctss_fwd Cl:TASK1+ neuroectodermal tumor cell line:TASK1_CNhs11866_10774-110F9_forward Regulation 
GlioblastomaCellLineT98G_CNhs11272_ctss_rev Cl:T98G- glioblastoma cell line:T98G_CNhs11272_10485-107A8_reverse Regulation 
GlioblastomaCellLineT98G_CNhs11272_ctss_fwd Cl:T98G+ glioblastoma cell line:T98G_CNhs11272_10485-107A8_forward Regulation 
SquamousCellCarcinomaCellLineT3M5_CNhs11739_ctss_rev Cl:T3M-5- squamous cell carcinoma cell line:T3M-5_CNhs11739_10616-108G4_reverse Regulation 
SquamousCellCarcinomaCellLineT3M5_CNhs11739_ctss_fwd Cl:T3M-5+ squamous cell carcinoma cell line:T3M-5_CNhs11739_10616-108G4_forward Regulation 
ChoriocarcinomaCellLineT3M3_CNhs11820_ctss_rev Cl:T3M-3- choriocarcinoma cell line:T3M-3_CNhs11820_10618-108G6_reverse Regulation 
ChoriocarcinomaCellLineT3M3_CNhs11820_ctss_fwd Cl:T3M-3+ choriocarcinoma cell line:T3M-3_CNhs11820_10618-108G6_forward Regulation 
LiposarcomaCellLineSW872_CNhs11851_ctss_rev Cl:SW872- liposarcoma cell line:SW 872_CNhs11851_10726-110A6_reverse Regulation 
LiposarcomaCellLineSW872_CNhs11851_ctss_fwd Cl:SW872+ liposarcoma cell line:SW 872_CNhs11851_10726-110A6_forward Regulation 
AlveolarCellCarcinomaCellLineSW1573_CNhs11838_ctss_rev Cl:SW1573- alveolar cell carcinoma cell line:SW 1573_CNhs11838_10708-109H6_reverse Regulation 
AlveolarCellCarcinomaCellLineSW1573_CNhs11838_ctss_fwd Cl:SW1573+ alveolar cell carcinoma cell line:SW 1573_CNhs11838_10708-109H6_forward Regulation 
ChondrosarcomaCellLineSW1353_CNhs11833_ctss_rev Cl:SW1353- chondrosarcoma cell line:SW 1353_CNhs11833_10700-109G7_reverse Regulation 
ChondrosarcomaCellLineSW1353_CNhs11833_ctss_fwd Cl:SW1353+ chondrosarcoma cell line:SW 1353_CNhs11833_10700-109G7_forward Regulation 
AdrenalCortexAdenocarcinomaCellLineSW13_CNhs11893_ctss_rev Cl:SW-13- adrenal cortex adenocarcinoma cell line:SW-13_CNhs11893_10810-111A9_reverse Regulation 
AdrenalCortexAdenocarcinomaCellLineSW13_CNhs11893_ctss_fwd Cl:SW-13+ adrenal cortex adenocarcinoma cell line:SW-13_CNhs11893_10810-111A9_forward Regulation 
TubularAdenocarcinomaCellLineSUIT2_CNhs11883_ctss_rev Cl:SUIT-2- tubular adenocarcinoma cell line:SUIT-2_CNhs11883_10797-110I5_reverse Regulation 
TubularAdenocarcinomaCellLineSUIT2_CNhs11883_ctss_fwd Cl:SUIT-2+ tubular adenocarcinoma cell line:SUIT-2_CNhs11883_10797-110I5_forward Regulation 
BoneMarrowStromalCellLineStromaNKtert_CNhs11931_ctss_rev Cl:StromaNKtert- bone marrow stromal cell line:StromaNKtert_CNhs11931_10686-109F2_reverse Regulation 
BoneMarrowStromalCellLineStromaNKtert_CNhs11931_ctss_fwd Cl:StromaNKtert+ bone marrow stromal cell line:StromaNKtert_CNhs11931_10686-109F2_forward Regulation 
LensEpithelialCellLineSRA0104_CNhs11750_ctss_rev Cl:SRA01/04- lens epithelial cell line:SRA 01/04_CNhs11750_10647-109A8_reverse Regulation 
LensEpithelialCellLineSRA0104_CNhs11750_ctss_fwd Cl:SRA01/04+ lens epithelial cell line:SRA 01/04_CNhs11750_10647-109A8_forward Regulation 
PleomorphicHepatocellularCarcinomaCellLineSNU387_CNhs11933_ctss_rev Cl:SNU-387- pleomorphic hepatocellular carcinoma cell line:SNU-387_CNhs11933_10706-109H4_reverse Regulation 
PleomorphicHepatocellularCarcinomaCellLineSNU387_CNhs11933_ctss_fwd Cl:SNU-387+ pleomorphic hepatocellular carcinoma cell line:SNU-387_CNhs11933_10706-109H4_forward Regulation 
SplenicLymphomaWithVillousLymphocytesCellLineSLVL_CNhs10741_ctss_rev Cl:SLVL- splenic lymphoma with villous lymphocytes cell line:SLVL_CNhs10741_10424-106D1_reverse Regulation 
SplenicLymphomaWithVillousLymphocytesCellLineSLVL_CNhs10741_ctss_fwd Cl:SLVL+ splenic lymphoma with villous lymphocytes cell line:SLVL_CNhs10741_10424-106D1_forward Regulation 
ChronicLymphocyticLeukemiaTCLLCellLineSKW3_CNhs11714_ctss_rev Cl:SKW-3- chronic lymphocytic leukemia (T-CLL) cell line:SKW-3_CNhs11714_10416-106C2_reverse Regulation 
ChronicLymphocyticLeukemiaTCLLCellLineSKW3_CNhs11714_ctss_fwd Cl:SKW-3+ chronic lymphocytic leukemia (T-CLL) cell line:SKW-3_CNhs11714_10416-106C2_forward Regulation 
MyelodysplasticSyndromeCellLineSKM1_CNhs11934_ctss_rev Cl:SKM-1- myelodysplastic syndrome cell line:SKM-1_CNhs11934_10772-110F7_reverse Regulation 
MyelodysplasticSyndromeCellLineSKM1_CNhs11934_ctss_fwd Cl:SKM-1+ myelodysplastic syndrome cell line:SKM-1_CNhs11934_10772-110F7_forward Regulation 
LargeCellNonkeratinizingSquamousCarcinomaCellLineSKGIISF_CNhs11825_ctss_rev Cl:SKG-II-SF- large cell non-keratinizing squamous carcinoma cell line:SKG-II-SF_CNhs11825_10692-109F8_reverse Regulation 
LargeCellNonkeratinizingSquamousCarcinomaCellLineSKGIISF_CNhs11825_ctss_fwd Cl:SKG-II-SF+ large cell non-keratinizing squamous carcinoma cell line:SKG-II-SF_CNhs11825_10692-109F8_forward Regulation 
CarcinoidCellLineSKPNDW_CNhs11846_ctss_rev Cl:SK-PN-DW- carcinoid cell line:SK-PN-DW_CNhs11846_10719-109I8_reverse Regulation 
CarcinoidCellLineSKPNDW_CNhs11846_ctss_fwd Cl:SK-PN-DW+ carcinoid cell line:SK-PN-DW_CNhs11846_10719-109I8_forward Regulation 
SerousAdenocarcinomaCellLineSKOV3RAfterCocultureWithSOC5702GBiolRep1_CNhs13508_ctss_rev Cl:SK-OV-3-RwithSOC-57-02-GBr1- serous adenocarcinoma cell line:SK-OV-3-R after co-culture with SOC-57-02-G, biol_rep1_CNhs13508_11843-124H7_reverse Regulation 
SerousAdenocarcinomaCellLineSKOV3RAfterCocultureWithSOC5702GBiolRep1_CNhs13508_ctss_fwd Cl:SK-OV-3-RwithSOC-57-02-GBr1+ serous adenocarcinoma cell line:SK-OV-3-R after co-culture with SOC-57-02-G, biol_rep1_CNhs13508_11843-124H7_forward Regulation 
SerousAdenocarcinomaCellLineSKOV3RBiolRep1_CNhs13099_ctss_rev Cl:SK-OV-3-RBr1- serous adenocarcinoma cell line:SK-OV-3-R, biol_rep1_CNhs13099_11841-124H5_reverse Regulation 
SerousAdenocarcinomaCellLineSKOV3RBiolRep1_CNhs13099_ctss_fwd Cl:SK-OV-3-RBr1+ serous adenocarcinoma cell line:SK-OV-3-R, biol_rep1_CNhs13099_11841-124H5_forward Regulation 
NeuroepitheliomaCellLineSKNMC_CNhs11853_ctss_rev Cl:SK-N-MC- neuroepithelioma cell line:SK-N-MC_CNhs11853_10728-110A8_reverse Regulation 
NeuroepitheliomaCellLineSKNMC_CNhs11853_ctss_fwd Cl:SK-N-MC+ neuroepithelioma cell line:SK-N-MC_CNhs11853_10728-110A8_forward Regulation 
ChoriocarcinomaCellLineSCH_CNhs11875_ctss_rev Cl:SCH- choriocarcinoma cell line:SCH_CNhs11875_10785-110H2_reverse Regulation 
ChoriocarcinomaCellLineSCH_CNhs11875_ctss_fwd Cl:SCH+ choriocarcinoma cell line:SCH_CNhs11875_10785-110H2_forward Regulation 
OralSquamousCellCarcinomaCellLineSAS_CNhs11810_ctss_rev Cl:SAS- oral squamous cell carcinoma cell line:SAS_CNhs11810_10544-107H4_reverse Regulation 
OralSquamousCellCarcinomaCellLineSAS_CNhs11810_ctss_fwd Cl:SAS+ oral squamous cell carcinoma cell line:SAS_CNhs11810_10544-107H4_forward Regulation 
AnaplasticSquamousCellCarcinomaCellLineRPMI2650_CNhs11889_ctss_rev Cl:RPMI2650- anaplastic squamous cell carcinoma cell line:RPMI 2650_CNhs11889_10805-111A4_reverse Regulation 
AnaplasticSquamousCellCarcinomaCellLineRPMI2650_CNhs11889_ctss_fwd Cl:RPMI2650+ anaplastic squamous cell carcinoma cell line:RPMI 2650_CNhs11889_10805-111A4_forward Regulation 
BCellLineRPMI1788_CNhs10744_ctss_rev Cl:RPMI1788- b cell line:RPMI1788_CNhs10744_10427-106D4_reverse Regulation 
BCellLineRPMI1788_CNhs10744_ctss_fwd Cl:RPMI1788+ b cell line:RPMI1788_CNhs10744_10427-106D4_forward Regulation 
RhabdomyosarcomaCellLineRMSYM_CNhs11269_ctss_rev Cl:RMS-YM- rhabdomyosarcoma cell line:RMS-YM_CNhs11269_10477-106I9_reverse Regulation 
RhabdomyosarcomaCellLineRMSYM_CNhs11269_ctss_fwd Cl:RMS-YM+ rhabdomyosarcoma cell line:RMS-YM_CNhs11269_10477-106I9_forward Regulation 
SquamousCellLungCarcinomaCellLineRERFLCAI_CNhs14240_ctss_rev Cl:RERF-LC-AI- squamous cell lung carcinoma cell line:RERF-LC-AI_CNhs14240_10501-107C6_reverse Regulation 
SquamousCellLungCarcinomaCellLineRERFLCAI_CNhs14240_ctss_fwd Cl:RERF-LC-AI+ squamous cell lung carcinoma cell line:RERF-LC-AI_CNhs14240_10501-107C6_forward Regulation 
BurkittsLymphomaCellLineRAJI_CNhs11268_ctss_rev Cl:RAJI- Burkitt's lymphoma cell line:RAJI_CNhs11268_10476-106I8_reverse Regulation 
BurkittsLymphomaCellLineRAJI_CNhs11268_ctss_fwd Cl:RAJI+ Burkitt's lymphoma cell line:RAJI_CNhs11268_10476-106I8_forward Regulation 
SomatostatinomaCellLineQGP1_CNhs11869_ctss_rev Cl:QGP-1- somatostatinoma cell line:QGP-1_CNhs11869_10781-110G7_reverse Regulation 
SomatostatinomaCellLineQGP1_CNhs11869_ctss_fwd Cl:QGP-1+ somatostatinoma cell line:QGP-1_CNhs11869_10781-110G7_forward Regulation 
MyelomaCellLinePCM6_CNhs11258_ctss_rev Cl:PCM6- myeloma cell line:PCM6_CNhs11258_10474-106I6_reverse Regulation 
MyelomaCellLinePCM6_CNhs11258_ctss_fwd Cl:PCM6+ myeloma cell line:PCM6_CNhs11258_10474-106I6_forward Regulation 
ProstateCancerCellLinePC3_CNhs11243_ctss_rev Cl:PC-3- prostate cancer cell line:PC-3_CNhs11243_10439-106E7_reverse Regulation 
ProstateCancerCellLinePC3_CNhs11243_ctss_fwd Cl:PC-3+ prostate cancer cell line:PC-3_CNhs11243_10439-106E7_forward Regulation 
LungAdenocarcinomaCellLinePC14_CNhs10726_ctss_rev Cl:PC-14- lung adenocarcinoma cell line:PC-14_CNhs10726_10408-106B3_reverse Regulation 
LungAdenocarcinomaCellLinePC14_CNhs10726_ctss_fwd Cl:PC-14+ lung adenocarcinoma cell line:PC-14_CNhs10726_10408-106B3_forward Regulation 
TeratocarcinomaCellLinePA1_CNhs11890_ctss_rev Cl:PA-1- teratocarcinoma cell line:PA-1_CNhs11890_10807-111A6_reverse Regulation 
TeratocarcinomaCellLinePA1_CNhs11890_ctss_fwd Cl:PA-1+ teratocarcinoma cell line:PA-1_CNhs11890_10807-111A6_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineP31FUJ_CNhs13051_ctss_rev Cl:P31/FUJ- acute myeloid leukemia (FAB M5) cell line:P31/FUJ_CNhs13051_10770-110F5_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineP31FUJ_CNhs13051_ctss_fwd Cl:P31/FUJ+ acute myeloid leukemia (FAB M5) cell line:P31/FUJ_CNhs13051_10770-110F5_forward Regulation 
NonTNonBAcuteLymphoblasticLeukemiaALLCellLineP30OHK_CNhs10747_ctss_rev Cl:P30/OHK- non T non B acute lymphoblastic leukemia (ALL) cell line:P30/OHK_CNhs10747_10430-106D7_reverse Regulation 
NonTNonBAcuteLymphoblasticLeukemiaALLCellLineP30OHK_CNhs10747_ctss_fwd Cl:P30/OHK+ non T non B acute lymphoblastic leukemia (ALL) cell line:P30/OHK_CNhs10747_10430-106D7_forward Regulation 
RenalCellCarcinomaCellLineOSRC2_CNhs10729_ctss_rev Cl:OS-RC-2- renal cell carcinoma cell line:OS-RC-2_CNhs10729_10411-106B6_reverse Regulation 
RenalCellCarcinomaCellLineOSRC2_CNhs10729_ctss_fwd Cl:OS-RC-2+ renal cell carcinoma cell line:OS-RC-2_CNhs10729_10411-106B6_forward Regulation 
MedulloblastomaCellLineONS76_CNhs11861_ctss_rev Cl:ONS-76- medulloblastoma cell line:ONS-76_CNhs11861_10759-110E3_reverse Regulation 
MedulloblastomaCellLineONS76_CNhs11861_ctss_fwd Cl:ONS-76+ medulloblastoma cell line:ONS-76_CNhs11861_10759-110E3_forward Regulation 
MesotheliomaCellLineONE58_CNhs13075_ctss_rev Cl:ONE58- mesothelioma cell line:ONE58_CNhs13075_10858-111G3_reverse Regulation 
MesotheliomaCellLineONE58_CNhs13075_ctss_fwd Cl:ONE58+ mesothelioma cell line:ONE58_CNhs13075_10858-111G3_forward Regulation 
EndometrialStromalSarcomaCellLineOMC9_CNhs11249_ctss_rev Cl:OMC-9- endometrial stromal sarcoma cell line:OMC-9_CNhs11249_10448-106F7_reverse Regulation 
EndometrialStromalSarcomaCellLineOMC9_CNhs11249_ctss_fwd Cl:OMC-9+ endometrial stromal sarcoma cell line:OMC-9_CNhs11249_10448-106F7_forward Regulation 
EndometrialCarcinomaCellLineOMC2_CNhs11266_ctss_rev Cl:OMC-2- endometrial carcinoma cell line:OMC-2_CNhs11266_10497-107C2_reverse Regulation 
EndometrialCarcinomaCellLineOMC2_CNhs11266_ctss_fwd Cl:OMC-2+ endometrial carcinoma cell line:OMC-2_CNhs11266_10497-107C2_forward Regulation 
SignetRingCarcinomaCellLineNUGC4_CNhs11270_ctss_rev Cl:NUGC-4- signet ring carcinoma cell line:NUGC-4_CNhs11270_10483-107A6_reverse Regulation 
SignetRingCarcinomaCellLineNUGC4_CNhs11270_ctss_fwd Cl:NUGC-4+ signet ring carcinoma cell line:NUGC-4_CNhs11270_10483-107A6_forward Regulation 
PancreaticCarcinomaCellLineNORP1_CNhs11832_ctss_rev Cl:NOR-P1- pancreatic carcinoma cell line:NOR-P1_CNhs11832_10698-109G5_reverse Regulation 
PancreaticCarcinomaCellLineNORP1_CNhs11832_ctss_fwd Cl:NOR-P1+ pancreatic carcinoma cell line:NOR-P1_CNhs11832_10698-109G5_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineNOMO1_CNhs13050_ctss_rev Cl:NOMO-1- acute myeloid leukemia (FAB M5) cell line:NOMO-1_CNhs13050_10764-110E8_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineNOMO1_CNhs13050_ctss_fwd Cl:NOMO-1+ acute myeloid leukemia (FAB M5) cell line:NOMO-1_CNhs13050_10764-110E8_forward Regulation 
MesotheliomaCellLineNo36_CNhs13074_ctss_rev Cl:No36- mesothelioma cell line:No36_CNhs13074_10857-111G2_reverse Regulation 
MesotheliomaCellLineNo36_CNhs13074_ctss_fwd Cl:No36+ mesothelioma cell line:No36_CNhs13074_10857-111G2_forward Regulation 
MyxofibrosarcomaCellLineNMFH1_CNhs11821_ctss_rev Cl:NMFH-1- myxofibrosarcoma cell line:NMFH-1_CNhs11821_10684-109E9_reverse Regulation 
MyxofibrosarcomaCellLineNMFH1_CNhs11821_ctss_fwd Cl:NMFH-1+ myxofibrosarcoma cell line:NMFH-1_CNhs11821_10684-109E9_forward Regulation 
AcuteMyeloidLeukemiaFABM2CellLineNKM1_CNhs11864_ctss_rev Cl:NKM-1- acute myeloid leukemia (FAB M2) cell line:NKM-1_CNhs11864_10765-110E9_reverse Regulation 
AcuteMyeloidLeukemiaFABM2CellLineNKM1_CNhs11864_ctss_fwd Cl:NKM-1+ acute myeloid leukemia (FAB M2) cell line:NKM-1_CNhs11864_10765-110E9_forward Regulation 
NeuroblastomaCellLineNH12_CNhs11811_ctss_rev Cl:NH-12- neuroblastoma cell line:NH-12_CNhs11811_10555-107I6_reverse Regulation 
NeuroblastomaCellLineNH12_CNhs11811_ctss_fwd Cl:NH-12+ neuroblastoma cell line:NH-12_CNhs11811_10555-107I6_forward Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC8_CNhs11726_ctss_rev Cl:NEC8- testicular germ cell embryonal carcinoma cell line:NEC8_CNhs11726_10590-108D5_reverse Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC8_CNhs11726_ctss_fwd Cl:NEC8+ testicular germ cell embryonal carcinoma cell line:NEC8_CNhs11726_10590-108D5_forward Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC15_CNhs12362_ctss_rev Cl:NEC15- testicular germ cell embryonal carcinoma cell line:NEC15_CNhs12362_10593-108D8_reverse Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC15_CNhs12362_ctss_fwd Cl:NEC15+ testicular germ cell embryonal carcinoma cell line:NEC15_CNhs12362_10593-108D8_forward Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC14_CNhs12351_ctss_rev Cl:NEC14- testicular germ cell embryonal carcinoma cell line:NEC14_CNhs12351_10591-108D6_reverse Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC14_CNhs12351_ctss_fwd Cl:NEC14+ testicular germ cell embryonal carcinoma cell line:NEC14_CNhs12351_10591-108D6_forward Regulation 
TeratocarcinomaCellLineNCRG1_CNhs11884_ctss_rev Cl:NCR-G1- teratocarcinoma cell line:NCR-G1_CNhs11884_10798-110I6_reverse Regulation 
TeratocarcinomaCellLineNCRG1_CNhs11884_ctss_fwd Cl:NCR-G1+ teratocarcinoma cell line:NCR-G1_CNhs11884_10798-110I6_forward Regulation 
SmallCellLungCarcinomaCellLineNCIH82_CNhs12809_ctss_rev Cl:NCI-H82- small cell lung carcinoma cell line:NCI-H82_CNhs12809_10842-111E5_reverse Regulation 
SmallCellLungCarcinomaCellLineNCIH82_CNhs12809_ctss_fwd Cl:NCI-H82+ small cell lung carcinoma cell line:NCI-H82_CNhs12809_10842-111E5_forward Regulation 
CarcinoidCellLineNCIH727_CNhs14244_ctss_rev Cl:NCI-H727- carcinoid cell line:NCI-H727_CNhs14244_10735-110B6_reverse Regulation 
CarcinoidCellLineNCIH727_CNhs14244_ctss_fwd Cl:NCI-H727+ carcinoid cell line:NCI-H727_CNhs14244_10735-110B6_forward Regulation 
BronchioalveolarCarcinomaCellLineNCIH650_CNhs14138_ctss_rev Cl:NCI-H650- bronchioalveolar carcinoma cell line:NCI-H650_CNhs14138_10715-109I4_reverse Regulation 
BronchioalveolarCarcinomaCellLineNCIH650_CNhs14138_ctss_fwd Cl:NCI-H650+ bronchioalveolar carcinoma cell line:NCI-H650_CNhs14138_10715-109I4_forward Regulation 
LargeCellLungCarcinomaCellLineNCIH460_CNhs12806_ctss_rev Cl:NCI-H460- large cell lung carcinoma cell line:NCI-H460_CNhs12806_10839-111E2_reverse Regulation 
LargeCellLungCarcinomaCellLineNCIH460_CNhs12806_ctss_fwd Cl:NCI-H460+ large cell lung carcinoma cell line:NCI-H460_CNhs12806_10839-111E2_forward Regulation 
LungAdenocarcinomaPapillaryCellLineNCIH441_CNhs14245_ctss_rev Cl:NCI-H441- lung adenocarcinoma, papillary cell line:NCI-H441_CNhs14245_10742-110C4_reverse Regulation 
LungAdenocarcinomaPapillaryCellLineNCIH441_CNhs14245_ctss_fwd Cl:NCI-H441+ lung adenocarcinoma, papillary cell line:NCI-H441_CNhs14245_10742-110C4_forward Regulation 
BronchioalveolarCarcinomaCellLineNCIH358_CNhs11840_ctss_rev Cl:NCI-H358- bronchioalveolar carcinoma cell line:NCI-H358_CNhs11840_10709-109H7_reverse Regulation 
BronchioalveolarCarcinomaCellLineNCIH358_CNhs11840_ctss_fwd Cl:NCI-H358+ bronchioalveolar carcinoma cell line:NCI-H358_CNhs11840_10709-109H7_forward Regulation 
MesotheliomaCellLineNCIH28_CNhs13061_ctss_rev Cl:NCI-H28- mesothelioma cell line:NCI-H28_CNhs13061_10845-111E8_reverse Regulation 
MesotheliomaCellLineNCIH28_CNhs13061_ctss_fwd Cl:NCI-H28+ mesothelioma cell line:NCI-H28_CNhs13061_10845-111E8_forward Regulation 
MesotheliomaCellLineNCIH2452_CNhs13064_ctss_rev Cl:NCI-H2452- mesothelioma cell line:NCI-H2452_CNhs13064_10848-111F2_reverse Regulation 
MesotheliomaCellLineNCIH2452_CNhs13064_ctss_fwd Cl:NCI-H2452+ mesothelioma cell line:NCI-H2452_CNhs13064_10848-111F2_forward Regulation 
MesotheliomaCellLineNCIH226_CNhs13062_ctss_rev Cl:NCI-H226- mesothelioma cell line:NCI-H226_CNhs13062_10846-111E9_reverse Regulation 
MesotheliomaCellLineNCIH226_CNhs13062_ctss_fwd Cl:NCI-H226+ mesothelioma cell line:NCI-H226_CNhs13062_10846-111E9_forward Regulation 
MesotheliomaCellLineNCIH2052_CNhs13063_ctss_rev Cl:NCI-H2052- mesothelioma cell line:NCI-H2052_CNhs13063_10847-111F1_reverse Regulation 
MesotheliomaCellLineNCIH2052_CNhs13063_ctss_fwd Cl:NCI-H2052+ mesothelioma cell line:NCI-H2052_CNhs13063_10847-111F1_forward Regulation 
CarcinoidCellLineNCIH1770_CNhs11834_ctss_rev Cl:NCI-H1770- carcinoid cell line:NCI-H1770_CNhs11834_10703-109H1_reverse Regulation 
CarcinoidCellLineNCIH1770_CNhs11834_ctss_fwd Cl:NCI-H1770+ carcinoid cell line:NCI-H1770_CNhs11834_10703-109H1_forward Regulation 
TeratocarcinomaCellLineNCCITA3_CNhs11878_ctss_rev Cl:NCC-IT-A3- teratocarcinoma cell line:NCC-IT-A3_CNhs11878_10790-110H7_reverse Regulation 
TeratocarcinomaCellLineNCCITA3_CNhs11878_ctss_fwd Cl:NCC-IT-A3+ teratocarcinoma cell line:NCC-IT-A3_CNhs11878_10790-110H7_forward Regulation 
NeuroblastomaCellLineNBsusSR_CNhs11818_ctss_rev Cl:NBsusSR- neuroblastoma cell line:NBsusSR_CNhs11818_10607-108F4_reverse Regulation 
NeuroblastomaCellLineNBsusSR_CNhs11818_ctss_fwd Cl:NBsusSR+ neuroblastoma cell line:NBsusSR_CNhs11818_10607-108F4_forward Regulation 
NeuroblastomaCellLineNB1_CNhs11284_ctss_rev Cl:NB-1- neuroblastoma cell line:NB-1_CNhs11284_10539-107G8_reverse Regulation 
NeuroblastomaCellLineNB1_CNhs11284_ctss_fwd Cl:NB-1+ neuroblastoma cell line:NB-1_CNhs11284_10539-107G8_forward Regulation 
AcuteLymphoblasticLeukemiaBALLCellLineNALM6_CNhs11282_ctss_rev Cl:NALM-6- acute lymphoblastic leukemia (B-ALL) cell line:NALM-6_CNhs11282_10534-107G3_reverse Regulation 
AcuteLymphoblasticLeukemiaBALLCellLineNALM6_CNhs11282_ctss_fwd Cl:NALM-6+ acute lymphoblastic leukemia (B-ALL) cell line:NALM-6_CNhs11282_10534-107G3_forward Regulation 
BiphenotypicBMyelomonocyticLeukemiaCellLineMV411_CNhs11845_ctss_rev Cl:MV-4-11- biphenotypic B myelomonocytic leukemia cell line:MV-4-11_CNhs11845_10718-109I7_reverse Regulation 
BiphenotypicBMyelomonocyticLeukemiaCellLineMV411_CNhs11845_ctss_fwd Cl:MV-4-11+ biphenotypic B myelomonocytic leukemia cell line:MV-4-11_CNhs11845_10718-109I7_forward Regulation 
MerkelCellCarcinomaCellLineMS1_CNhs12839_ctss_rev Cl:MS-1- merkel cell carcinoma cell line:MS-1_CNhs12839_10844-111E7_reverse Regulation 
MerkelCellCarcinomaCellLineMS1_CNhs12839_ctss_fwd Cl:MS-1+ merkel cell carcinoma cell line:MS-1_CNhs12839_10844-111E7_forward Regulation 
HairyCellLeukemiaCellLineMo_CNhs11843_ctss_rev Cl:Mo- hairy cell leukemia cell line:Mo_CNhs11843_10712-109I1_reverse Regulation 
HairyCellLeukemiaCellLineMo_CNhs11843_ctss_fwd Cl:Mo+ hairy cell leukemia cell line:Mo_CNhs11843_10712-109I1_forward Regulation 
LymphomaMalignantHairyBcellCellLineMLMA_CNhs11935_ctss_rev Cl:MLMA- lymphoma, malignant, hairy B-cell cell line:MLMA_CNhs11935_10775-110G1_reverse Regulation 
LymphomaMalignantHairyBcellCellLineMLMA_CNhs11935_ctss_fwd Cl:MLMA+ lymphoma, malignant, hairy B-cell cell line:MLMA_CNhs11935_10775-110G1_forward Regulation 
AcuteMyeloidLeukemiaFABM7CellLineMKPL1_CNhs11888_ctss_rev Cl:MKPL-1- acute myeloid leukemia (FAB M7) cell line:MKPL-1_CNhs11888_10802-111A1_reverse Regulation 
AcuteMyeloidLeukemiaFABM7CellLineMKPL1_CNhs11888_ctss_fwd Cl:MKPL-1+ acute myeloid leukemia (FAB M7) cell line:MKPL-1_CNhs11888_10802-111A1_forward Regulation 
GastricAdenocarcinomaCellLineMKN45_CNhs11819_ctss_rev Cl:MKN45- gastric adenocarcinoma cell line:MKN45_CNhs11819_10612-108F9_reverse Regulation 
GastricAdenocarcinomaCellLineMKN45_CNhs11819_ctss_fwd Cl:MKN45+ gastric adenocarcinoma cell line:MKN45_CNhs11819_10612-108F9_forward Regulation 
GastricAdenocarcinomaCellLineMKN1_CNhs11737_ctss_rev Cl:MKN1- gastric adenocarcinoma cell line:MKN1_CNhs11737_10614-108G2_reverse Regulation 
GastricAdenocarcinomaCellLineMKN1_CNhs11737_ctss_fwd Cl:MKN1+ gastric adenocarcinoma cell line:MKN1_CNhs11737_10614-108G2_forward Regulation 
MerkelCellCarcinomaCellLineMKL1_CNhs12838_ctss_rev Cl:MKL-1- merkel cell carcinoma cell line:MKL-1_CNhs12838_10843-111E6_reverse Regulation 
MerkelCellCarcinomaCellLineMKL1_CNhs12838_ctss_fwd Cl:MKL-1+ merkel cell carcinoma cell line:MKL-1_CNhs12838_10843-111E6_forward Regulation 
DuctalCellCarcinomaCellLineMIAPaca2_CNhs11259_ctss_rev Cl:MIAPaca2- ductal cell carcinoma cell line:MIA Paca2_CNhs11259_10488-107B2_reverse Regulation 
DuctalCellCarcinomaCellLineMIAPaca2_CNhs11259_ctss_fwd Cl:MIAPaca2+ ductal cell carcinoma cell line:MIA Paca2_CNhs11259_10488-107B2_forward Regulation 
MyxofibrosarcomaCellLineMFHino_CNhs11729_ctss_rev Cl:MFH-ino- myxofibrosarcoma cell line:MFH-ino_CNhs11729_10600-108E6_reverse Regulation 
MyxofibrosarcomaCellLineMFHino_CNhs11729_ctss_fwd Cl:MFH-ino+ myxofibrosarcoma cell line:MFH-ino_CNhs11729_10600-108E6_forward Regulation 
MesotheliomaCellLineMero95_CNhs13073_ctss_rev Cl:Mero-95- mesothelioma cell line:Mero-95_CNhs13073_10856-111G1_reverse Regulation 
MesotheliomaCellLineMero95_CNhs13073_ctss_fwd Cl:Mero-95+ mesothelioma cell line:Mero-95_CNhs13073_10856-111G1_forward Regulation 
MesotheliomaCellLineMero84_CNhs13072_ctss_rev Cl:Mero-84- mesothelioma cell line:Mero-84_CNhs13072_10855-111F9_reverse Regulation 
MesotheliomaCellLineMero84_CNhs13072_ctss_fwd Cl:Mero-84+ mesothelioma cell line:Mero-84_CNhs13072_10855-111F9_forward Regulation 
MesotheliomaCellLineMero83_CNhs13070_ctss_rev Cl:Mero-83- mesothelioma cell line:Mero-83_CNhs13070_10854-111F8_reverse Regulation 
MesotheliomaCellLineMero83_CNhs13070_ctss_fwd Cl:Mero-83+ mesothelioma cell line:Mero-83_CNhs13070_10854-111F8_forward Regulation 
MesotheliomaCellLineMero82_CNhs13069_ctss_rev Cl:Mero-82- mesothelioma cell line:Mero-82_CNhs13069_10853-111F7_reverse Regulation 
MesotheliomaCellLineMero82_CNhs13069_ctss_fwd Cl:Mero-82+ mesothelioma cell line:Mero-82_CNhs13069_10853-111F7_forward Regulation 
MesotheliomaCellLineMero48a_CNhs13068_ctss_rev Cl:Mero-48a- mesothelioma cell line:Mero-48a_CNhs13068_10852-111F6_reverse Regulation 
MesotheliomaCellLineMero48a_CNhs13068_ctss_fwd Cl:Mero-48a+ mesothelioma cell line:Mero-48a_CNhs13068_10852-111F6_forward Regulation 
MesotheliomaCellLineMero41_CNhs13067_ctss_rev Cl:Mero-41- mesothelioma cell line:Mero-41_CNhs13067_10851-111F5_reverse Regulation 
MesotheliomaCellLineMero41_CNhs13067_ctss_fwd Cl:Mero-41+ mesothelioma cell line:Mero-41_CNhs13067_10851-111F5_forward Regulation 
MesotheliomaCellLineMero25_CNhs13066_ctss_rev Cl:Mero-25- mesothelioma cell line:Mero-25_CNhs13066_10850-111F4_reverse Regulation 
MesotheliomaCellLineMero25_CNhs13066_ctss_fwd Cl:Mero-25+ mesothelioma cell line:Mero-25_CNhs13066_10850-111F4_forward Regulation 
MesotheliomaCellLineMero14TechRep1_CNhs13065_ctss_rev Cl:Mero-14Tr1- mesothelioma cell line:Mero-14, tech_rep1_CNhs13065_10849-111F3_reverse Regulation 
MesotheliomaCellLineMero14TechRep1_CNhs13065_ctss_fwd Cl:Mero-14Tr1+ mesothelioma cell line:Mero-14, tech_rep1_CNhs13065_10849-111F3_forward Regulation 
ChronicMyelogenousLeukemiaCMLCellLineMEGA2_CNhs11865_ctss_rev Cl:MEG-A2- chronic myelogenous leukemia (CML) cell line:MEG-A2_CNhs11865_10766-110F1_reverse Regulation 
ChronicMyelogenousLeukemiaCMLCellLineMEGA2_CNhs11865_ctss_fwd Cl:MEG-A2+ chronic myelogenous leukemia (CML) cell line:MEG-A2_CNhs11865_10766-110F1_forward Regulation 
LeukemiaChronicMegakaryoblasticCellLineMEG01_CNhs11859_ctss_rev Cl:MEG-01- leukemia, chronic megakaryoblastic cell line:MEG-01_CNhs11859_10752-110D5_reverse Regulation 
LeukemiaChronicMegakaryoblasticCellLineMEG01_CNhs11859_ctss_fwd Cl:MEG-01+ leukemia, chronic megakaryoblastic cell line:MEG-01_CNhs11859_10752-110D5_forward Regulation 
CervicalCancerCellLineME180_CNhs11289_ctss_rev Cl:ME-180- cervical cancer cell line:ME-180_CNhs11289_10553-107I4_reverse Regulation 
CervicalCancerCellLineME180_CNhs11289_ctss_fwd Cl:ME-180+ cervical cancer cell line:ME-180_CNhs11289_10553-107I4_forward Regulation 
BreastCarcinomaCellLineMDAMB453_CNhs10736_ctss_rev Cl:MDA-MB-453- breast carcinoma cell line:MDA-MB-453_CNhs10736_10419-106C5_reverse Regulation 
BreastCarcinomaCellLineMDAMB453_CNhs10736_ctss_fwd Cl:MDA-MB-453+ breast carcinoma cell line:MDA-MB-453_CNhs10736_10419-106C5_forward Regulation 
BreastCarcinomaCellLineMCF7_CNhs11943_ctss_rev Cl:MCF7- breast carcinoma cell line:MCF7_CNhs11943_10482-107A5_reverse Regulation 
BreastCarcinomaCellLineMCF7_CNhs11943_ctss_fwd Cl:MCF7+ breast carcinoma cell line:MCF7_CNhs11943_10482-107A5_forward Regulation 
MucinousCystadenocarcinomaCellLineMCAS_CNhs11873_ctss_rev Cl:MCAS- mucinous cystadenocarcinoma cell line:MCAS_CNhs11873_10784-110H1_reverse Regulation 
MucinousCystadenocarcinomaCellLineMCAS_CNhs11873_ctss_fwd Cl:MCAS+ mucinous cystadenocarcinoma cell line:MCAS_CNhs11873_10784-110H1_forward Regulation 
AcuteMyeloidLeukemiaFABM7CellLineMMOK_CNhs13049_ctss_rev Cl:M-MOK- acute myeloid leukemia (FAB M7) cell line:M-MOK_CNhs13049_10699-109G6_reverse Regulation 
AcuteMyeloidLeukemiaFABM7CellLineMMOK_CNhs13049_ctss_fwd Cl:M-MOK+ acute myeloid leukemia (FAB M7) cell line:M-MOK_CNhs13049_10699-109G6_forward Regulation 
GiantCellCarcinomaCellLineLu99B_CNhs10751_ctss_rev Cl:Lu99B- giant cell carcinoma cell line:Lu99B_CNhs10751_10433-106E1_reverse Regulation 
GiantCellCarcinomaCellLineLu99B_CNhs10751_ctss_fwd Cl:Lu99B+ giant cell carcinoma cell line:Lu99B_CNhs10751_10433-106E1_forward Regulation 
GiantCellCarcinomaCellLineLU65_CNhs11274_ctss_rev Cl:LU65- giant cell carcinoma cell line:LU65_CNhs11274_10487-107B1_reverse Regulation 
GiantCellCarcinomaCellLineLU65_CNhs11274_ctss_fwd Cl:LU65+ giant cell carcinoma cell line:LU65_CNhs11274_10487-107B1_forward Regulation 
SmallCellLungCarcinomaCellLineLK2_CNhs11285_ctss_rev Cl:LK-2- small cell lung carcinoma cell line:LK-2_CNhs11285_10541-107H1_reverse Regulation 
SmallCellLungCarcinomaCellLineLK2_CNhs11285_ctss_fwd Cl:LK-2+ small cell lung carcinoma cell line:LK-2_CNhs11285_10541-107H1_forward Regulation 
HepaticMesenchymalTumorCellLineLI90_CNhs11868_ctss_rev Cl:LI90- hepatic mesenchymal tumor cell line:LI90_CNhs11868_10778-110G4_reverse Regulation 
HepaticMesenchymalTumorCellLineLI90_CNhs11868_ctss_fwd Cl:LI90+ hepatic mesenchymal tumor cell line:LI90_CNhs11868_10778-110G4_forward Regulation 
HepatomaCellLineLi7_CNhs11271_ctss_rev Cl:Li-7- hepatoma cell line:Li-7_CNhs11271_10484-107A7_reverse Regulation 
HepatomaCellLineLi7_CNhs11271_ctss_fwd Cl:Li-7+ hepatoma cell line:Li-7_CNhs11271_10484-107A7_forward Regulation 
SquamousCellLungCarcinomaCellLineLC1F_CNhs14238_ctss_rev Cl:LC-1F- squamous cell lung carcinoma cell line:LC-1F_CNhs14238_10457-106G7_reverse Regulation 
SquamousCellLungCarcinomaCellLineLC1F_CNhs14238_ctss_fwd Cl:LC-1F+ squamous cell lung carcinoma cell line:LC-1F_CNhs14238_10457-106G7_forward Regulation 
RhabdomyosarcomaCellLineKYM1_CNhs11877_ctss_rev Cl:KYM-1- rhabdomyosarcoma cell line:KYM-1_CNhs11877_10787-110H4_reverse Regulation 
RhabdomyosarcomaCellLineKYM1_CNhs11877_ctss_fwd Cl:KYM-1+ rhabdomyosarcoma cell line:KYM-1_CNhs11877_10787-110H4_forward Regulation 
ChronicMyelogenousLeukemiaCellLineKU812_CNhs10727_ctss_rev Cl:KU812- chronic myelogenous leukemia cell line:KU812_CNhs10727_10409-106B4_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineKU812_CNhs10727_ctss_fwd Cl:KU812+ chronic myelogenous leukemia cell line:KU812_CNhs10727_10409-106B4_forward Regulation 
PeripheralNeuroectodermalTumorCellLineKUSN_CNhs11830_ctss_rev Cl:KU-SN- peripheral neuroectodermal tumor cell line:KU-SN_CNhs11830_10697-109G4_reverse Regulation 
PeripheralNeuroectodermalTumorCellLineKUSN_CNhs11830_ctss_fwd Cl:KU-SN+ peripheral neuroectodermal tumor cell line:KU-SN_CNhs11830_10697-109G4_forward Regulation 
BronchialSquamousCellCarcinomaCellLineKNS62_CNhs11862_ctss_rev Cl:KNS-62- bronchial squamous cell carcinoma cell line:KNS-62_CNhs11862_10760-110E4_reverse Regulation 
BronchialSquamousCellCarcinomaCellLineKNS62_CNhs11862_ctss_fwd Cl:KNS-62+ bronchial squamous cell carcinoma cell line:KNS-62_CNhs11862_10760-110E4_forward Regulation 
LiposarcomaCellLineKMLS1_CNhs11870_ctss_rev Cl:KMLS-1- liposarcoma cell line:KMLS-1_CNhs11870_10782-110G8_reverse Regulation 
LiposarcomaCellLineKMLS1_CNhs11870_ctss_fwd Cl:KMLS-1+ liposarcoma cell line:KMLS-1_CNhs11870_10782-110G8_forward Regulation 
DuctalCellCarcinomaCellLineKLM1_CNhs11100_ctss_rev Cl:KLM-1- ductal cell carcinoma cell line:KLM-1_CNhs11100_10438-106E6_reverse Regulation 
DuctalCellCarcinomaCellLineKLM1_CNhs11100_ctss_fwd Cl:KLM-1+ ductal cell carcinoma cell line:KLM-1_CNhs11100_10438-106E6_forward Regulation 
AnaplasticLargeCellLymphomaCellLineKiJK_CNhs11881_ctss_rev Cl:Ki-JK- anaplastic large cell lymphoma cell line:Ki-JK_CNhs11881_10795-110I3_reverse Regulation 
AnaplasticLargeCellLymphomaCellLineKiJK_CNhs11881_ctss_fwd Cl:Ki-JK+ anaplastic large cell lymphoma cell line:Ki-JK_CNhs11881_10795-110I3_forward Regulation 
NKTCellLeukemiaCellLineKHYG1_CNhs11867_ctss_rev Cl:KHYG-1- NK T cell leukemia cell line:KHYG-1_CNhs11867_10777-110G3_reverse Regulation 
NKTCellLeukemiaCellLineKHYG1_CNhs11867_ctss_fwd Cl:KHYG-1+ NK T cell leukemia cell line:KHYG-1_CNhs11867_10777-110G3_forward Regulation 
ThyroidCarcinomaCellLineKHM5M_CNhs14140_ctss_rev Cl:KHM-5M- thyroid carcinoma cell line:KHM-5M_CNhs14140_10776-110G2_reverse Regulation 
ThyroidCarcinomaCellLineKHM5M_CNhs14140_ctss_fwd Cl:KHM-5M+ thyroid carcinoma cell line:KHM-5M_CNhs14140_10776-110G2_forward Regulation 
GranulosaCellTumorCellLineKGN_CNhs11740_ctss_rev Cl:KGN- granulosa cell tumor cell line:KGN_CNhs11740_10624-108H3_reverse Regulation 
GranulosaCellTumorCellLineKGN_CNhs11740_ctss_fwd Cl:KGN+ granulosa cell tumor cell line:KGN_CNhs11740_10624-108H3_forward Regulation 
AcuteMyeloidLeukemiaFABM0CellLineKG1_CNhs13053_ctss_rev Cl:KG-1- acute myeloid leukemia (FAB M0) cell line:KG-1_CNhs13053_10827-111C8_reverse Regulation 
AcuteMyeloidLeukemiaFABM0CellLineKG1_CNhs13053_ctss_fwd Cl:KG-1+ acute myeloid leukemia (FAB M0) cell line:KG-1_CNhs13053_10827-111C8_forward Regulation 
ChronicMyeloblasticLeukemiaCMLCellLineKCL22_CNhs11886_ctss_rev Cl:KCL-22- chronic myeloblastic leukemia (CML) cell line:KCL-22_CNhs11886_10801-110I9_reverse Regulation 
ChronicMyeloblasticLeukemiaCMLCellLineKCL22_CNhs11886_ctss_fwd Cl:KCL-22+ chronic myeloblastic leukemia (CML) cell line:KCL-22_CNhs11886_10801-110I9_forward Regulation 
SignetRingCarcinomaCellLineKatoIII_CNhs10753_ctss_rev Cl:KatoIII- signet ring carcinoma cell line:Kato III_CNhs10753_10436-106E4_reverse Regulation 
SignetRingCarcinomaCellLineKatoIII_CNhs10753_ctss_fwd Cl:KatoIII+ signet ring carcinoma cell line:Kato III_CNhs10753_10436-106E4_forward Regulation 
AcuteMyeloidLeukemiaFABM2CellLineKasumi6_CNhs13052_ctss_rev Cl:Kasumi-6- acute myeloid leukemia (FAB M2) cell line:Kasumi-6_CNhs13052_10792-110H9_reverse Regulation 
AcuteMyeloidLeukemiaFABM2CellLineKasumi6_CNhs13052_ctss_fwd Cl:Kasumi-6+ acute myeloid leukemia (FAB M2) cell line:Kasumi-6_CNhs13052_10792-110H9_forward Regulation 
AcuteMyeloidLeukemiaFABM2CellLineKasumi1_CNhs13502_ctss_rev Cl:Kasumi-1- acute myeloid leukemia (FAB M2) cell line:Kasumi-1_CNhs13502_10788-110H5_reverse Regulation 
AcuteMyeloidLeukemiaFABM2CellLineKasumi1_CNhs13502_ctss_fwd Cl:Kasumi-1+ acute myeloid leukemia (FAB M2) cell line:Kasumi-1_CNhs13502_10788-110H5_forward Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep3_CNhs12336_ctss_rev Cl:K562Br3- chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep3_CNhs12336_10826-111C7_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep3_CNhs12336_ctss_fwd Cl:K562Br3+ chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep3_CNhs12336_10826-111C7_forward Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep2_CNhs12335_ctss_rev Cl:K562Br2- chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep2_CNhs12335_10825-111C6_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep2_CNhs12335_ctss_fwd Cl:K562Br2+ chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep2_CNhs12335_10825-111C6_forward Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep1_CNhs12334_ctss_rev Cl:K562Br1- chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep1_CNhs12334_10824-111C5_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep1_CNhs12334_ctss_fwd Cl:K562Br1+ chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep1_CNhs12334_10824-111C5_forward Regulation 
ChronicMyelogenousLeukemiaCellLineK562_CNhs11250_ctss_rev Cl:K562- chronic myelogenous leukemia cell line:K562_CNhs11250_10454-106G4_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineK562_CNhs11250_ctss_fwd Cl:K562+ chronic myelogenous leukemia cell line:K562_CNhs11250_10454-106G4_forward Regulation 
AcuteLymphoblasticLeukemiaTALLCellLineJurkat_CNhs11253_ctss_rev Cl:Jurkat- acute lymphoblastic leukemia (T-ALL) cell line:Jurkat_CNhs11253_10464-106H5_reverse Regulation 
AcuteLymphoblasticLeukemiaTALLCellLineJurkat_CNhs11253_ctss_fwd Cl:Jurkat+ acute lymphoblastic leukemia (T-ALL) cell line:Jurkat_CNhs11253_10464-106H5_forward Regulation 
TransitionalcellCarcinomaCellLineJMSU1_CNhs11261_ctss_rev Cl:JMSU1- transitional-cell carcinoma cell line:JMSU1_CNhs11261_10492-107B6_reverse Regulation 
TransitionalcellCarcinomaCellLineJMSU1_CNhs11261_ctss_fwd Cl:JMSU1+ transitional-cell carcinoma cell line:JMSU1_CNhs11261_10492-107B6_forward Regulation 
SquamousCellCarcinomaCellLineJHUSnk1_CNhs11749_ctss_rev Cl:JHUS-nk1- squamous cell carcinoma cell line:JHUS-nk1_CNhs11749_10646-109A7_reverse Regulation 
SquamousCellCarcinomaCellLineJHUSnk1_CNhs11749_ctss_fwd Cl:JHUS-nk1+ squamous cell carcinoma cell line:JHUS-nk1_CNhs11749_10646-109A7_forward Regulation 
EndometrioidAdenocarcinomaCellLineJHUEM1_CNhs11748_ctss_rev Cl:JHUEM-1- endometrioid adenocarcinoma cell line:JHUEM-1_CNhs11748_10643-109A4_reverse Regulation 
EndometrioidAdenocarcinomaCellLineJHUEM1_CNhs11748_ctss_fwd Cl:JHUEM-1+ endometrioid adenocarcinoma cell line:JHUEM-1_CNhs11748_10643-109A4_forward Regulation 
CarcinosarcomaCellLineJHUCS1_CNhs11747_ctss_rev Cl:JHUCS-1- carcinosarcoma cell line:JHUCS-1_CNhs11747_10642-109A3_reverse Regulation 
CarcinosarcomaCellLineJHUCS1_CNhs11747_ctss_fwd Cl:JHUCS-1+ carcinosarcoma cell line:JHUCS-1_CNhs11747_10642-109A3_forward Regulation 
SerousAdenocarcinomaCellLineJHOS2_CNhs11746_ctss_rev Cl:JHOS-2- serous adenocarcinoma cell line:JHOS-2_CNhs11746_10639-108I9_reverse Regulation 
SerousAdenocarcinomaCellLineJHOS2_CNhs11746_ctss_fwd Cl:JHOS-2+ serous adenocarcinoma cell line:JHOS-2_CNhs11746_10639-108I9_forward Regulation 
MucinousAdenocarcinomaCellLineJHOM1_CNhs11752_ctss_rev Cl:JHOM-1- mucinous adenocarcinoma cell line:JHOM-1_CNhs11752_10648-109A9_reverse Regulation 
MucinousAdenocarcinomaCellLineJHOM1_CNhs11752_ctss_fwd Cl:JHOM-1+ mucinous adenocarcinoma cell line:JHOM-1_CNhs11752_10648-109A9_forward Regulation 
ClearCellCarcinomaCellLineJHOC5_CNhs11745_ctss_rev Cl:JHOC-5- clear cell carcinoma cell line:JHOC-5_CNhs11745_10638-108I8_reverse Regulation 
ClearCellCarcinomaCellLineJHOC5_CNhs11745_ctss_fwd Cl:JHOC-5+ clear cell carcinoma cell line:JHOC-5_CNhs11745_10638-108I8_forward Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineITOII_CNhs11876_ctss_rev Cl:ITO-II- testicular germ cell embryonal carcinoma cell line:ITO-II_CNhs11876_10786-110H3_reverse Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineITOII_CNhs11876_ctss_fwd Cl:ITO-II+ testicular germ cell embryonal carcinoma cell line:ITO-II_CNhs11876_10786-110H3_forward Regulation 
AdenocarcinomaCellLineIM95m_CNhs11882_ctss_rev Cl:IM95m- adenocarcinoma cell line:IM95m_CNhs11882_10796-110I4_reverse Regulation 
AdenocarcinomaCellLineIM95m_CNhs11882_ctss_fwd Cl:IM95m+ adenocarcinoma cell line:IM95m_CNhs11882_10796-110I4_forward Regulation 
LargeCellLungCarcinomaCellLineIALM_CNhs11277_ctss_rev Cl:IA-LM- large cell lung carcinoma cell line:IA-LM_CNhs11277_10509-107D5_reverse Regulation 
LargeCellLungCarcinomaCellLineIALM_CNhs11277_ctss_fwd Cl:IA-LM+ large cell lung carcinoma cell line:IA-LM_CNhs11277_10509-107D5_forward Regulation 
AcuteMyeloidLeukemiaFABM1CellLineHYT1_CNhs13054_ctss_rev Cl:HYT-1- acute myeloid leukemia (FAB M1) cell line:HYT-1_CNhs13054_10828-111C9_reverse Regulation 
AcuteMyeloidLeukemiaFABM1CellLineHYT1_CNhs13054_ctss_fwd Cl:HYT-1+ acute myeloid leukemia (FAB M1) cell line:HYT-1_CNhs13054_10828-111C9_forward Regulation 
MycosisFungoidesTCellLymphomaCellLineHuT102TIB162_CNhs11858_ctss_rev Cl:HuT102TIB-162- mycosis fungoides, T cell lymphoma cell line:HuT 102 TIB-162_CNhs11858_10744-110C6_reverse Regulation 
MycosisFungoidesTCellLymphomaCellLineHuT102TIB162_CNhs11858_ctss_fwd Cl:HuT102TIB-162+ mycosis fungoides, T cell lymphoma cell line:HuT 102 TIB-162_CNhs11858_10744-110C6_forward Regulation 
HepatoblastomaCellLineHuH6_CNhs11742_ctss_rev Cl:HuH-6- hepatoblastoma cell line:HuH-6_CNhs11742_10633-108I3_reverse Regulation 
HepatoblastomaCellLineHuH6_CNhs11742_ctss_fwd Cl:HuH-6+ hepatoblastoma cell line:HuH-6_CNhs11742_10633-108I3_forward Regulation 
CholangiocellularCarcinomaCellLineHuH28_CNhs11283_ctss_rev Cl:HuH-28- cholangiocellular carcinoma cell line:HuH-28_CNhs11283_10536-107G5_reverse Regulation 
CholangiocellularCarcinomaCellLineHuH28_CNhs11283_ctss_fwd Cl:HuH-28+ cholangiocellular carcinoma cell line:HuH-28_CNhs11283_10536-107G5_forward Regulation 
BileDuctCarcinomaCellLineHuCCT1_CNhs10750_ctss_rev Cl:HuCCT1- bile duct carcinoma cell line:HuCCT1_CNhs10750_10432-106D9_reverse Regulation 
BileDuctCarcinomaCellLineHuCCT1_CNhs10750_ctss_fwd Cl:HuCCT1+ bile duct carcinoma cell line:HuCCT1_CNhs10750_10432-106D9_forward Regulation 
MesenchymalStemCellLineHu5E18_CNhs11718_ctss_rev Cl:Hu5/E18- mesenchymal stem cell line:Hu5/E18_CNhs11718_10568-108B1_reverse Regulation 
MesenchymalStemCellLineHu5E18_CNhs11718_ctss_fwd Cl:Hu5/E18+ mesenchymal stem cell line:Hu5/E18_CNhs11718_10568-108B1_forward Regulation 
SacrococcigealTeratomaCellLineHTST_CNhs11829_ctss_rev Cl:HTST- sacrococcigeal teratoma cell line:HTST_CNhs11829_10695-109G2_reverse Regulation 
SacrococcigealTeratomaCellLineHTST_CNhs11829_ctss_fwd Cl:HTST+ sacrococcigeal teratoma cell line:HTST_CNhs11829_10695-109G2_forward Regulation 
SerousCystadenocarcinomaCellLineHTOA_CNhs11827_ctss_rev Cl:HTOA- serous cystadenocarcinoma cell line:HTOA_CNhs11827_10693-109F9_reverse Regulation 
SerousCystadenocarcinomaCellLineHTOA_CNhs11827_ctss_fwd Cl:HTOA+ serous cystadenocarcinoma cell line:HTOA_CNhs11827_10693-109F9_forward Regulation 
MixedMullerianTumorCellLineHTMMT_CNhs11944_ctss_rev Cl:HTMMT- mixed mullerian tumor cell line:HTMMT_CNhs11944_10689-109F5_reverse Regulation 
MixedMullerianTumorCellLineHTMMT_CNhs11944_ctss_fwd Cl:HTMMT+ mixed mullerian tumor cell line:HTMMT_CNhs11944_10689-109F5_forward Regulation 
FibrosarcomaCellLineHT1080_CNhs11860_ctss_rev Cl:HT-1080- fibrosarcoma cell line:HT-1080_CNhs11860_10758-110E2_reverse Regulation 
FibrosarcomaCellLineHT1080_CNhs11860_ctss_fwd Cl:HT-1080+ fibrosarcoma cell line:HT-1080_CNhs11860_10758-110E2_forward Regulation 
MaxillarySinusTumorCellLineHSQ89_CNhs10732_ctss_rev Cl:HSQ-89- maxillary sinus tumor cell line:HSQ-89_CNhs10732_10414-106B9_reverse Regulation 
MaxillarySinusTumorCellLineHSQ89_CNhs10732_ctss_fwd Cl:HSQ-89+ maxillary sinus tumor cell line:HSQ-89_CNhs10732_10414-106B9_forward Regulation 
KrukenbergTumorCellLineHSKTC_CNhs11822_ctss_rev Cl:HSKTC- Krukenberg tumor cell line:HSKTC_CNhs11822_10687-109F3_reverse Regulation 
KrukenbergTumorCellLineHSKTC_CNhs11822_ctss_fwd Cl:HSKTC+ Krukenberg tumor cell line:HSKTC_CNhs11822_10687-109F3_forward Regulation 
OralSquamousCellCarcinomaCellLineHSC3_CNhs11717_ctss_rev Cl:HSC-3- oral squamous cell carcinoma cell line:HSC-3_CNhs11717_10545-107H5_reverse Regulation 
OralSquamousCellCarcinomaCellLineHSC3_CNhs11717_ctss_fwd Cl:HSC-3+ oral squamous cell carcinoma cell line:HSC-3_CNhs11717_10545-107H5_forward Regulation 
PagetoidSarcomaCellLineHs925_T_CNhs11856_ctss_rev Cl:Hs925_T- pagetoid sarcoma cell line:Hs 925_T_CNhs11856_10732-110B3_reverse Regulation 
PagetoidSarcomaCellLineHs925_T_CNhs11856_ctss_fwd Cl:Hs925_T+ pagetoid sarcoma cell line:Hs 925_T_CNhs11856_10732-110B3_forward Regulation 
EwingsSarcomaCellLineHs863_T_CNhs11836_ctss_rev Cl:Hs863_T- Ewing's sarcoma cell line:Hs 863_T_CNhs11836_10705-109H3_reverse Regulation 
EwingsSarcomaCellLineHs863_T_CNhs11836_ctss_fwd Cl:Hs863_T+ Ewing's sarcoma cell line:Hs 863_T_CNhs11836_10705-109H3_forward Regulation 
TransitionalCellCarcinomaCellLineHs769_T_CNhs11837_ctss_rev Cl:Hs769_T- transitional cell carcinoma cell line:Hs 769_T_CNhs11837_10707-109H5_reverse Regulation 
TransitionalCellCarcinomaCellLineHs769_T_CNhs11837_ctss_fwd Cl:Hs769_T+ transitional cell carcinoma cell line:Hs 769_T_CNhs11837_10707-109H5_forward Regulation 
OsteoclastomaCellLineHs706_T_CNhs11835_ctss_rev Cl:Hs706_T- osteoclastoma cell line:Hs 706_T_CNhs11835_10704-109H2_reverse Regulation 
OsteoclastomaCellLineHs706_T_CNhs11835_ctss_fwd Cl:Hs706_T+ osteoclastoma cell line:Hs 706_T_CNhs11835_10704-109H2_forward Regulation 
NeurofibromaCellLineHs53_T_CNhs11854_ctss_rev Cl:Hs53_T- neurofibroma cell line:Hs 53_T_CNhs11854_10729-110A9_reverse Regulation 
NeurofibromaCellLineHs53_T_CNhs11854_ctss_fwd Cl:Hs53_T+ neurofibroma cell line:Hs 53_T_CNhs11854_10729-110A9_forward Regulation 
SpindleCellSarcomaCellLineHs132_T_CNhs11857_ctss_rev Cl:Hs132_T- spindle cell sarcoma cell line:Hs 132_T_CNhs11857_10737-110B8_reverse Regulation 
SpindleCellSarcomaCellLineHs132_T_CNhs11857_ctss_fwd Cl:Hs132_T+ spindle cell sarcoma cell line:Hs 132_T_CNhs11857_10737-110B8_forward Regulation 
SynovialSarcomaCellLineHSSYII_CNhs11244_ctss_rev Cl:HS-SY-II- synovial sarcoma cell line:HS-SY-II_CNhs11244_10441-106E9_reverse Regulation 
SynovialSarcomaCellLineHSSYII_CNhs11244_ctss_fwd Cl:HS-SY-II+ synovial sarcoma cell line:HS-SY-II_CNhs11244_10441-106E9_forward Regulation 
SchwannomaCellLineHSPSSTechRep2_CNhs11245_ctss_rev Cl:HS-PSSTr2- schwannoma cell line:HS-PSS, tech_rep2_CNhs11245_10442-106F1_reverse Regulation 
SchwannomaCellLineHSPSSTechRep2_CNhs11245_ctss_fwd Cl:HS-PSSTr2+ schwannoma cell line:HS-PSS, tech_rep2_CNhs11245_10442-106F1_forward Regulation 
SchwannomaCellLineHSPSS_CNhs11183_ctss_rev Cl:HS-PSS- schwannoma cell line:HS-PSS_CNhs11183_10442-106F1_reverse Regulation 
SchwannomaCellLineHSPSS_CNhs11183_ctss_fwd Cl:HS-PSS+ schwannoma cell line:HS-PSS_CNhs11183_10442-106F1_forward Regulation 
OsteosarcomaCellLineHSOs1_CNhs11290_ctss_rev Cl:HS-Os-1- osteosarcoma cell line:HS-Os-1_CNhs11290_10558-107I9_reverse Regulation 
OsteosarcomaCellLineHSOs1_CNhs11290_ctss_fwd Cl:HS-Os-1+ osteosarcoma cell line:HS-Os-1_CNhs11290_10558-107I9_forward Regulation 
EpithelioidSarcomaCellLineHSES2R_CNhs14239_ctss_rev Cl:HS-ES-2R- epithelioid sarcoma cell line:HS-ES-2R_CNhs14239_10495-107B9_reverse Regulation 
EpithelioidSarcomaCellLineHSES2R_CNhs14239_ctss_fwd Cl:HS-ES-2R+ epithelioid sarcoma cell line:HS-ES-2R_CNhs14239_10495-107B9_forward Regulation 
EpithelioidSarcomaCellLineHSES1_CNhs11247_ctss_rev Cl:HS-ES-1- epithelioid sarcoma cell line:HS-ES-1_CNhs11247_10443-106F2_reverse Regulation 
EpithelioidSarcomaCellLineHSES1_CNhs11247_ctss_fwd Cl:HS-ES-1+ epithelioid sarcoma cell line:HS-ES-1_CNhs11247_10443-106F2_forward Regulation 
AcuteLymphoblasticLeukemiaTALLCellLineHPBALL_CNhs10746_ctss_rev Cl:HPB-ALL- acute lymphoblastic leukemia (T-ALL) cell line:HPB-ALL_CNhs10746_10429-106D6_reverse Regulation 
AcuteLymphoblasticLeukemiaTALLCellLineHPBALL_CNhs10746_ctss_fwd Cl:HPB-ALL+ acute lymphoblastic leukemia (T-ALL) cell line:HPB-ALL_CNhs10746_10429-106D6_forward Regulation 
GlassyCellCarcinomaCellLineHOKUG_CNhs11824_ctss_rev Cl:HOKUG- glassy cell carcinoma cell line:HOKUG_CNhs11824_10688-109F4_reverse Regulation 
GlassyCellCarcinomaCellLineHOKUG_CNhs11824_ctss_fwd Cl:HOKUG+ glassy cell carcinoma cell line:HOKUG_CNhs11824_10688-109F4_forward Regulation 
OralSquamousCellCarcinomaCellLineHO1u1_CNhs11287_ctss_rev Cl:HO-1-u-1- oral squamous cell carcinoma cell line:HO-1-u-1_CNhs11287_10550-107I1_reverse Regulation 
OralSquamousCellCarcinomaCellLineHO1u1_CNhs11287_ctss_fwd Cl:HO-1-u-1+ oral squamous cell carcinoma cell line:HO-1-u-1_CNhs11287_10550-107I1_forward Regulation 
AcuteMyeloidLeukemiaFABM4CellLineHNT34_CNhs13504_ctss_rev Cl:HNT-34- acute myeloid leukemia (FAB M4) cell line:HNT-34_CNhs13504_10831-111D3_reverse Regulation 
AcuteMyeloidLeukemiaFABM4CellLineHNT34_CNhs13504_ctss_fwd Cl:HNT-34+ acute myeloid leukemia (FAB M4) cell line:HNT-34_CNhs13504_10831-111D3_forward Regulation 
AcuteMyeloidLeukemiaFABM3CellLineHL60_CNhs13055_ctss_rev Cl:HL60- acute myeloid leukemia (FAB M3) cell line:HL60_CNhs13055_10829-111D1_reverse Regulation 
AcuteMyeloidLeukemiaFABM3CellLineHL60_CNhs13055_ctss_fwd Cl:HL60+ acute myeloid leukemia (FAB M3) cell line:HL60_CNhs13055_10829-111D1_forward Regulation 
MeningiomaCellLineHKBMM_CNhs11945_ctss_rev Cl:HKBMM- meningioma cell line:HKBMM_CNhs11945_10691-109F7_reverse Regulation 
MeningiomaCellLineHKBMM_CNhs11945_ctss_fwd Cl:HKBMM+ meningioma cell line:HKBMM_CNhs11945_10691-109F7_forward Regulation 
KeratoacanthomaCellLineHKA1_CNhs11880_ctss_rev Cl:HKA-1- keratoacanthoma cell line:HKA-1_CNhs11880_10791-110H8_reverse Regulation 
KeratoacanthomaCellLineHKA1_CNhs11880_ctss_fwd Cl:HKA-1+ keratoacanthoma cell line:HKA-1_CNhs11880_10791-110H8_forward Regulation 
TridermalTeratomaCellLineHGRT_CNhs11828_ctss_rev Cl:HGRT- tridermal teratoma cell line:HGRT_CNhs11828_10694-109G1_reverse Regulation 
TridermalTeratomaCellLineHGRT_CNhs11828_ctss_fwd Cl:HGRT+ tridermal teratoma cell line:HGRT_CNhs11828_10694-109G1_forward Regulation 
WilmsTumorCellLineHFWT_CNhs11728_ctss_rev Cl:HFWT- Wilms' tumor cell line:HFWT_CNhs11728_10597-108E3_reverse Regulation 
WilmsTumorCellLineHFWT_CNhs11728_ctss_fwd Cl:HFWT+ Wilms' tumor cell line:HFWT_CNhs11728_10597-108E3_forward Regulation 
NormalEmbryonicPalatalMesenchymalCellLineHEPM_CNhs11894_ctss_rev Cl:HEPM- normal embryonic palatal mesenchymal cell line:HEPM_CNhs11894_10813-111B3_reverse Regulation 
NormalEmbryonicPalatalMesenchymalCellLineHEPM_CNhs11894_ctss_fwd Cl:HEPM+ normal embryonic palatal mesenchymal cell line:HEPM_CNhs11894_10813-111B3_forward Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep3_CNhs12330_ctss_rev Cl:HepG2Br3- hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep3_CNhs12330_10820-111C1_reverse Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep3_CNhs12330_ctss_fwd Cl:HepG2Br3+ hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep3_CNhs12330_10820-111C1_forward Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep2_CNhs12329_ctss_rev Cl:HepG2Br2- hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep2_CNhs12329_10819-111B9_reverse Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep2_CNhs12329_ctss_fwd Cl:HepG2Br2+ hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep2_CNhs12329_10819-111B9_forward Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep1_CNhs12328_ctss_rev Cl:HepG2Br1- hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep1_CNhs12328_10818-111B8_reverse Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep1_CNhs12328_ctss_fwd Cl:HepG2Br1+ hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep1_CNhs12328_10818-111B8_forward Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep3_CNhs12327_ctss_rev Cl:HelaS3Br3- epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep3_CNhs12327_10817-111B7_reverse Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep3_CNhs12327_ctss_fwd Cl:HelaS3Br3+ epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep3_CNhs12327_10817-111B7_forward Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep2_CNhs12326_ctss_rev Cl:HelaS3Br2- epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep2_CNhs12326_10816-111B6_reverse Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep2_CNhs12326_ctss_fwd Cl:HelaS3Br2+ epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep2_CNhs12326_10816-111B6_forward Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep1_CNhs12325_ctss_rev Cl:HelaS3Br1- epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep1_CNhs12325_10815-111B5_reverse Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep1_CNhs12325_ctss_fwd Cl:HelaS3Br1+ epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep1_CNhs12325_10815-111B5_forward Regulation 
EmbryonicKidneyCellLineHEK293SLAMUntreated_CNhs11046_ctss_rev Cl:HEK293/SLAMuntreated- embryonic kidney cell line: HEK293/SLAM untreated_CNhs11046_10450-106F9_reverse Regulation 
EmbryonicKidneyCellLineHEK293SLAMUntreated_CNhs11046_ctss_fwd Cl:HEK293/SLAMuntreated+ embryonic kidney cell line: HEK293/SLAM untreated_CNhs11046_10450-106F9_forward Regulation 
EmbryonicKidneyCellLineHEK293SLAMInfection24hr_CNhs11047_ctss_rev Cl:HEK293/SLAMinfection,24hr- embryonic kidney cell line: HEK293/SLAM infection, 24hr_CNhs11047_10451-106G1_reverse Regulation 
EmbryonicKidneyCellLineHEK293SLAMInfection24hr_CNhs11047_ctss_fwd Cl:HEK293/SLAMinfection,24hr+ embryonic kidney cell line: HEK293/SLAM infection, 24hr_CNhs11047_10451-106G1_forward Regulation 
HodgkinsLymphomaCellLineHDMar2_CNhs11715_ctss_rev Cl:HD-Mar2- Hodgkin's lymphoma cell line:HD-Mar2_CNhs11715_10435-106E3_reverse Regulation 
HodgkinsLymphomaCellLineHDMar2_CNhs11715_ctss_fwd Cl:HD-Mar2+ Hodgkin's lymphoma cell line:HD-Mar2_CNhs11715_10435-106E3_forward Regulation 
SmallCellCervicalCancerCellLineHCSC1_CNhs11885_ctss_rev Cl:HCSC-1- small cell cervical cancer cell line:HCSC-1_CNhs11885_10800-110I8_reverse Regulation 
SmallCellCervicalCancerCellLineHCSC1_CNhs11885_ctss_fwd Cl:HCSC-1+ small cell cervical cancer cell line:HCSC-1_CNhs11885_10800-110I8_forward Regulation 
AcantholyticSquamousCarcinomaCellLineHCC1806_CNhs11844_ctss_rev Cl:HCC1806- acantholytic squamous carcinoma cell line:HCC1806_CNhs11844_10717-109I6_reverse Regulation 
AcantholyticSquamousCarcinomaCellLineHCC1806_CNhs11844_ctss_fwd Cl:HCC1806+ acantholytic squamous carcinoma cell line:HCC1806_CNhs11844_10717-109I6_forward Regulation 
ExtraskeletalMyxoidChondrosarcomaCellLineHEMCSS_CNhs10728_ctss_rev Cl:H-EMC-SS- extraskeletal myxoid chondrosarcoma cell line:H-EMC-SS_CNhs10728_10410-106B5_reverse Regulation 
ExtraskeletalMyxoidChondrosarcomaCellLineHEMCSS_CNhs10728_ctss_fwd Cl:H-EMC-SS+ extraskeletal myxoid chondrosarcoma cell line:H-EMC-SS_CNhs10728_10410-106B5_forward Regulation 
GastricCancerCellLineGSS_CNhs14241_ctss_rev Cl:GSS- gastric cancer cell line:GSS_CNhs14241_10560-108A2_reverse Regulation 
GastricCancerCellLineGSS_CNhs14241_ctss_fwd Cl:GSS+ gastric cancer cell line:GSS_CNhs14241_10560-108A2_forward Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep3_CNhs12333_ctss_rev Cl:GM12878Br3- B lymphoblastoid cell line: GM12878 ENCODE, biol_rep3_CNhs12333_10823-111C4_reverse Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep3_CNhs12333_ctss_fwd Cl:GM12878Br3+ B lymphoblastoid cell line: GM12878 ENCODE, biol_rep3_CNhs12333_10823-111C4_forward Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep2_CNhs12332_ctss_rev Cl:GM12878Br2- B lymphoblastoid cell line: GM12878 ENCODE, biol_rep2_CNhs12332_10822-111C3_reverse Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep2_CNhs12332_ctss_fwd Cl:GM12878Br2+ B lymphoblastoid cell line: GM12878 ENCODE, biol_rep2_CNhs12332_10822-111C3_forward Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep1_CNhs12331_ctss_rev Cl:GM12878Br1- B lymphoblastoid cell line: GM12878 ENCODE, biol_rep1_CNhs12331_10821-111C2_reverse Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep1_CNhs12331_ctss_fwd Cl:GM12878Br1+ B lymphoblastoid cell line: GM12878 ENCODE, biol_rep1_CNhs12331_10821-111C2_forward Regulation 
GliomaCellLineGI1_CNhs10731_ctss_rev Cl:GI-1- glioma cell line:GI-1_CNhs10731_10413-106B8_reverse Regulation 
GliomaCellLineGI1_CNhs10731_ctss_fwd Cl:GI-1+ glioma cell line:GI-1_CNhs10731_10413-106B8_forward Regulation 
FibrousHistiocytomaCellLineGCTTIB223_CNhs11842_ctss_rev Cl:GCTTIB-223- fibrous histiocytoma cell line:GCT TIB-223_CNhs11842_10711-109H9_reverse Regulation 
FibrousHistiocytomaCellLineGCTTIB223_CNhs11842_ctss_fwd Cl:GCTTIB-223+ fibrous histiocytoma cell line:GCT TIB-223_CNhs11842_10711-109H9_forward Regulation 
LeiomyoblastomaCellLineG402_CNhs11848_ctss_rev Cl:G-402- leiomyoblastoma cell line:G-402_CNhs11848_10721-110A1_reverse Regulation 
LeiomyoblastomaCellLineG402_CNhs11848_ctss_fwd Cl:G-402+ leiomyoblastoma cell line:G-402_CNhs11848_10721-110A1_forward Regulation 
WilmsTumorCellLineG401_CNhs11892_ctss_rev Cl:G-401- Wilms' tumor cell line:G-401_CNhs11892_10809-111A8_reverse Regulation 
WilmsTumorCellLineG401_CNhs11892_ctss_fwd Cl:G-401+ Wilms' tumor cell line:G-401_CNhs11892_10809-111A8_forward Regulation 
MelanomaCellLineG361_CNhs11254_ctss_rev Cl:G-361- melanoma cell line:G-361_CNhs11254_10465-106H6_reverse Regulation 
MelanomaCellLineG361_CNhs11254_ctss_fwd Cl:G-361+ melanoma cell line:G-361_CNhs11254_10465-106H6_forward Regulation 
NeuroectodermalTumorCellLineFURPNT2_CNhs11753_ctss_rev Cl:FU-RPNT-2- neuroectodermal tumor cell line:FU-RPNT-2_CNhs11753_10663-109C6_reverse Regulation 
NeuroectodermalTumorCellLineFURPNT2_CNhs11753_ctss_fwd Cl:FU-RPNT-2+ neuroectodermal tumor cell line:FU-RPNT-2_CNhs11753_10663-109C6_forward Regulation 
NeuroectodermalTumorCellLineFURPNT1_CNhs11744_ctss_rev Cl:FU-RPNT-1- neuroectodermal tumor cell line:FU-RPNT-1_CNhs11744_10637-108I7_reverse Regulation 
NeuroectodermalTumorCellLineFURPNT1_CNhs11744_ctss_fwd Cl:FU-RPNT-1+ neuroectodermal tumor cell line:FU-RPNT-1_CNhs11744_10637-108I7_forward Regulation 
AcuteMyeloidLeukemiaFABM4CellLineFKH1_CNhs13503_ctss_rev Cl:FKH-1- acute myeloid leukemia (FAB M4) cell line:FKH-1_CNhs13503_10830-111D2_reverse Regulation 
AcuteMyeloidLeukemiaFABM4CellLineFKH1_CNhs13503_ctss_fwd Cl:FKH-1+ acute myeloid leukemia (FAB M4) cell line:FKH-1_CNhs13503_10830-111D2_forward Regulation 
NormalIntestinalEpithelialCellLineFHs74Int_CNhs11950_ctss_rev Cl:FHs74Int- normal intestinal epithelial cell line:FHs 74 Int_CNhs11950_10812-111B2_reverse Regulation 
NormalIntestinalEpithelialCellLineFHs74Int_CNhs11950_ctss_fwd Cl:FHs74Int+ normal intestinal epithelial cell line:FHs 74 Int_CNhs11950_10812-111B2_forward Regulation 
AcuteMyeloidLeukemiaFABM6CellLineF36P_CNhs13505_ctss_rev Cl:F-36P- acute myeloid leukemia (FAB M6) cell line:F-36P_CNhs13505_10837-111D9_reverse Regulation 
AcuteMyeloidLeukemiaFABM6CellLineF36P_CNhs13505_ctss_fwd Cl:F-36P+ acute myeloid leukemia (FAB M6) cell line:F-36P_CNhs13505_10837-111D9_forward Regulation 
AcuteMyeloidLeukemiaFABM6CellLineF36E_CNhs13060_ctss_rev Cl:F-36E- acute myeloid leukemia (FAB M6) cell line:F-36E_CNhs13060_10836-111D8_reverse Regulation 
AcuteMyeloidLeukemiaFABM6CellLineF36E_CNhs13060_ctss_fwd Cl:F-36E+ acute myeloid leukemia (FAB M6) cell line:F-36E_CNhs13060_10836-111D8_forward Regulation 
AcuteMyeloidLeukemiaFABM4eoCellLineEoL3_CNhs13057_ctss_rev Cl:EoL-3- acute myeloid leukemia (FAB M4eo) cell line:EoL-3_CNhs13057_10833-111D5_reverse Regulation 
AcuteMyeloidLeukemiaFABM4eoCellLineEoL3_CNhs13057_ctss_fwd Cl:EoL-3+ acute myeloid leukemia (FAB M4eo) cell line:EoL-3_CNhs13057_10833-111D5_forward Regulation 
AcuteMyeloidLeukemiaFABM4eoCellLineEoL1_CNhs13056_ctss_rev Cl:EoL-1- acute myeloid leukemia (FAB M4eo) cell line:EoL-1_CNhs13056_10832-111D4_reverse Regulation 
AcuteMyeloidLeukemiaFABM4eoCellLineEoL1_CNhs13056_ctss_fwd Cl:EoL-1+ acute myeloid leukemia (FAB M4eo) cell line:EoL-1_CNhs13056_10832-111D4_forward Regulation 
AcuteMyeloidLeukemiaFABM6CellLineEEB_CNhs13059_ctss_rev Cl:EEB- acute myeloid leukemia (FAB M6) cell line:EEB_CNhs13059_10835-111D7_reverse Regulation 
AcuteMyeloidLeukemiaFABM6CellLineEEB_CNhs13059_ctss_fwd Cl:EEB+ acute myeloid leukemia (FAB M6) cell line:EEB_CNhs13059_10835-111D7_forward Regulation 
SmallcellGastrointestinalCarcinomaCellLineECC4_CNhs11734_ctss_rev Cl:ECC4- small-cell gastrointestinal carcinoma cell line:ECC4_CNhs11734_10609-108F6_reverse Regulation 
SmallcellGastrointestinalCarcinomaCellLineECC4_CNhs11734_ctss_fwd Cl:ECC4+ small-cell gastrointestinal carcinoma cell line:ECC4_CNhs11734_10609-108F6_forward Regulation 
GastrointestinalCarcinomaCellLineECC12_CNhs11738_ctss_rev Cl:ECC12- gastrointestinal carcinoma cell line:ECC12_CNhs11738_10615-108G3_reverse Regulation 
GastrointestinalCarcinomaCellLineECC12_CNhs11738_ctss_fwd Cl:ECC12+ gastrointestinal carcinoma cell line:ECC12_CNhs11738_10615-108G3_forward Regulation 
SmallCellGastrointestinalCarcinomaCellLineECC10_CNhs11736_ctss_rev Cl:ECC10- small cell gastrointestinal carcinoma cell line:ECC10_CNhs11736_10610-108F7_reverse Regulation 
SmallCellGastrointestinalCarcinomaCellLineECC10_CNhs11736_ctss_fwd Cl:ECC10+ small cell gastrointestinal carcinoma cell line:ECC10_CNhs11736_10610-108F7_forward Regulation 
SquamousCellCarcinomaCellLineECGI10_CNhs11252_ctss_rev Cl:EC-GI-10- squamous cell carcinoma cell line:EC-GI-10_CNhs11252_10463-106H4_reverse Regulation 
SquamousCellCarcinomaCellLineECGI10_CNhs11252_ctss_fwd Cl:EC-GI-10+ squamous cell carcinoma cell line:EC-GI-10_CNhs11252_10463-106H4_forward Regulation 
SquamousCellLungCarcinomaCellLineEBC1_CNhs11273_ctss_rev Cl:EBC-1- squamous cell lung carcinoma cell line:EBC-1_CNhs11273_10486-107A9_reverse Regulation 
SquamousCellLungCarcinomaCellLineEBC1_CNhs11273_ctss_fwd Cl:EBC-1+ squamous cell lung carcinoma cell line:EBC-1_CNhs11273_10486-107A9_forward Regulation 
ProstateCancerCellLineDU145_CNhs11260_ctss_rev Cl:DU145- prostate cancer cell line:DU145_CNhs11260_10490-107B4_reverse Regulation 
ProstateCancerCellLineDU145_CNhs11260_ctss_fwd Cl:DU145+ prostate cancer cell line:DU145_CNhs11260_10490-107B4_forward Regulation 
LymphangiectasiaCellLineDS1_CNhs11852_ctss_rev Cl:DS-1- lymphangiectasia cell line:DS-1_CNhs11852_10727-110A7_reverse Regulation 
LymphangiectasiaCellLineDS1_CNhs11852_ctss_fwd Cl:DS-1+ lymphangiectasia cell line:DS-1_CNhs11852_10727-110A7_forward Regulation 
SmallCellLungCarcinomaCellLineDMS144_CNhs12808_ctss_rev Cl:DMS144- small cell lung carcinoma cell line:DMS 144_CNhs12808_10841-111E4_reverse Regulation 
SmallCellLungCarcinomaCellLineDMS144_CNhs12808_ctss_fwd Cl:DMS144+ small cell lung carcinoma cell line:DMS 144_CNhs12808_10841-111E4_forward Regulation 
MalignantTrichilemmalCystCellLineDJM1_CNhs10730_ctss_rev Cl:DJM-1- malignant trichilemmal cyst cell line:DJM-1_CNhs10730_10412-106B7_reverse Regulation 
MalignantTrichilemmalCystCellLineDJM1_CNhs10730_ctss_fwd Cl:DJM-1+ malignant trichilemmal cyst cell line:DJM-1_CNhs10730_10412-106B7_forward Regulation 
PharyngealCarcinomaCellLineDetroit562_CNhs11849_ctss_rev Cl:Detroit562- pharyngeal carcinoma cell line:Detroit 562_CNhs11849_10723-110A3_reverse Regulation 
PharyngealCarcinomaCellLineDetroit562_CNhs11849_ctss_fwd Cl:Detroit562+ pharyngeal carcinoma cell line:Detroit 562_CNhs11849_10723-110A3_forward Regulation 
BurkittsLymphomaCellLineDAUDI_CNhs10739_ctss_rev Cl:DAUDI- Burkitt's lymphoma cell line:DAUDI_CNhs10739_10422-106C8_reverse Regulation 
BurkittsLymphomaCellLineDAUDI_CNhs10739_ctss_fwd Cl:DAUDI+ Burkitt's lymphoma cell line:DAUDI_CNhs10739_10422-106C8_forward Regulation 
CervicalCancerCellLineD98AH2_CNhs11288_ctss_rev Cl:D98-AH2- cervical cancer cell line:D98-AH2_CNhs11288_10552-107I3_reverse Regulation 
CervicalCancerCellLineD98AH2_CNhs11288_ctss_fwd Cl:D98-AH2+ cervical cancer cell line:D98-AH2_CNhs11288_10552-107I3_forward Regulation 
MedulloblastomaCellLineD283Med_CNhs12805_ctss_rev Cl:D283Med- medulloblastoma cell line:D283 Med_CNhs12805_10838-111E1_reverse Regulation 
MedulloblastomaCellLineD283Med_CNhs12805_ctss_fwd Cl:D283Med+ medulloblastoma cell line:D283 Med_CNhs12805_10838-111E1_forward Regulation 
DiffuseLargeBcellLymphomaCellLineCTB1_CNhs11741_ctss_rev Cl:CTB-1- diffuse large B-cell lymphoma cell line:CTB-1_CNhs11741_10631-108I1_reverse Regulation 
DiffuseLargeBcellLymphomaCellLineCTB1_CNhs11741_ctss_fwd Cl:CTB-1+ diffuse large B-cell lymphoma cell line:CTB-1_CNhs11741_10631-108I1_forward Regulation 
MelanomaCellLineCOLO679_CNhs11281_ctss_rev Cl:COLO679- melanoma cell line:COLO 679_CNhs11281_10514-107E1_reverse Regulation 
MelanomaCellLineCOLO679_CNhs11281_ctss_fwd Cl:COLO679+ melanoma cell line:COLO 679_CNhs11281_10514-107E1_forward Regulation 
ColonCarcinomaCellLineCOLO320_CNhs10737_ctss_rev Cl:COLO-320- colon carcinoma cell line:COLO-320_CNhs10737_10420-106C6_reverse Regulation 
ColonCarcinomaCellLineCOLO320_CNhs10737_ctss_fwd Cl:COLO-320+ colon carcinoma cell line:COLO-320_CNhs10737_10420-106C6_forward Regulation 
CordBloodDerivedCellLineCOBLaUntreated_CNhs11045_ctss_rev Cl:COBL-auntreated- cord blood derived cell line:COBL-a untreated_CNhs11045_10449-106F8_reverse Regulation 
CordBloodDerivedCellLineCOBLaUntreated_CNhs11045_ctss_fwd Cl:COBL-auntreated+ cord blood derived cell line:COBL-a untreated_CNhs11045_10449-106F8_forward Regulation 
CordBloodDerivedCellLineCOBLa24hInfection_CNhs11050_ctss_rev Cl:COBL-a24hinfection- cord blood derived cell line:COBL-a 24h infection_CNhs11050_10453-106G3_reverse Regulation 
CordBloodDerivedCellLineCOBLa24hInfection_CNhs11050_ctss_fwd Cl:COBL-a24hinfection+ cord blood derived cell line:COBL-a 24h infection_CNhs11050_10453-106G3_forward Regulation 
CordBloodDerivedCellLineCOBLa24hInfectionC_CNhs11049_ctss_rev Cl:COBL-a24hinfection(-C)- cord blood derived cell line:COBL-a 24h infection(-C)_CNhs11049_10452-106G2_reverse Regulation 
CordBloodDerivedCellLineCOBLa24hInfectionC_CNhs11049_ctss_fwd Cl:COBL-a24hinfection(-C)+ cord blood derived cell line:COBL-a 24h infection(-C)_CNhs11049_10452-106G2_forward Regulation 
NeuroblastomaCellLineCHP134_CNhs11276_ctss_rev Cl:CHP-134- neuroblastoma cell line:CHP-134_CNhs11276_10508-107D4_reverse Regulation 
NeuroblastomaCellLineCHP134_CNhs11276_ctss_fwd Cl:CHP-134+ neuroblastoma cell line:CHP-134_CNhs11276_10508-107D4_forward Regulation 
BronchogenicCarcinomaCellLineChaGoK1_CNhs11841_ctss_rev Cl:ChaGo-K-1- bronchogenic carcinoma cell line:ChaGo-K-1_CNhs11841_10710-109H8_reverse Regulation 
BronchogenicCarcinomaCellLineChaGoK1_CNhs11841_ctss_fwd Cl:ChaGo-K-1+ bronchogenic carcinoma cell line:ChaGo-K-1_CNhs11841_10710-109H8_forward Regulation 
EpidermoidCarcinomaCellLineCaSki_CNhs10748_ctss_rev Cl:CaSki- epidermoid carcinoma cell line:Ca Ski_CNhs10748_10431-106D8_reverse Regulation 
EpidermoidCarcinomaCellLineCaSki_CNhs10748_ctss_fwd Cl:CaSki+ epidermoid carcinoma cell line:Ca Ski_CNhs10748_10431-106D8_forward Regulation 
ColonCarcinomaCellLineCACO2_CNhs11280_ctss_rev Cl:CACO-2- colon carcinoma cell line:CACO-2_CNhs11280_10513-107D9_reverse Regulation 
ColonCarcinomaCellLineCACO2_CNhs11280_ctss_fwd Cl:CACO-2+ colon carcinoma cell line:CACO-2_CNhs11280_10513-107D9_forward Regulation 
OralSquamousCellCarcinomaCellLineCa922_CNhs10752_ctss_rev Cl:Ca9-22- oral squamous cell carcinoma cell line:Ca9-22_CNhs10752_10434-106E2_reverse Regulation 
OralSquamousCellCarcinomaCellLineCa922_CNhs10752_ctss_fwd Cl:Ca9-22+ oral squamous cell carcinoma cell line:Ca9-22_CNhs10752_10434-106E2_forward Regulation 
ChoriocarcinomaCellLineBeWo_CNhs10740_ctss_rev Cl:BeWo- choriocarcinoma cell line:BeWo_CNhs10740_10423-106C9_reverse Regulation 
ChoriocarcinomaCellLineBeWo_CNhs10740_ctss_fwd Cl:BeWo+ choriocarcinoma cell line:BeWo_CNhs10740_10423-106C9_forward Regulation 
AcuteLymphoblasticLeukemiaBALLCellLineBALL1_CNhs11251_ctss_rev Cl:BALL-1- acute lymphoblastic leukemia (B-ALL) cell line:BALL-1_CNhs11251_10455-106G5_reverse Regulation 
AcuteLymphoblasticLeukemiaBALLCellLineBALL1_CNhs11251_ctss_fwd Cl:BALL-1+ acute lymphoblastic leukemia (B-ALL) cell line:BALL-1_CNhs11251_10455-106G5_forward Regulation 
GastricCancerCellLineAZ521_CNhs11286_ctss_rev Cl:AZ521- gastric cancer cell line:AZ521_CNhs11286_10549-107H9_reverse Regulation 
GastricCancerCellLineAZ521_CNhs11286_ctss_fwd Cl:AZ521+ gastric cancer cell line:AZ521_CNhs11286_10549-107H9_forward Regulation 
AdultTcellLeukemiaCellLineATN1_CNhs10738_ctss_rev Cl:ATN-1- adult T-cell leukemia cell line:ATN-1_CNhs10738_10421-106C7_reverse Regulation 
AdultTcellLeukemiaCellLineATN1_CNhs10738_ctss_fwd Cl:ATN-1+ adult T-cell leukemia cell line:ATN-1_CNhs10738_10421-106C7_forward Regulation 
PlasmaCellLeukemiaCellLineARH77_CNhs12807_ctss_rev Cl:ARH-77- plasma cell leukemia cell line:ARH-77_CNhs12807_10840-111E3_reverse Regulation 
PlasmaCellLeukemiaCellLineARH77_CNhs12807_ctss_fwd Cl:ARH-77+ plasma cell leukemia cell line:ARH-77_CNhs12807_10840-111E3_forward Regulation 
MesotheliomaCellLineACCMESO4_CNhs11264_ctss_rev Cl:ACC-MESO-4- mesothelioma cell line:ACC-MESO-4_CNhs11264_10494-107B8_reverse Regulation 
MesotheliomaCellLineACCMESO4_CNhs11264_ctss_fwd Cl:ACC-MESO-4+ mesothelioma cell line:ACC-MESO-4_CNhs11264_10494-107B8_forward Regulation 
MesotheliomaCellLineACCMESO1_CNhs11263_ctss_rev Cl:ACC-MESO-1- mesothelioma cell line:ACC-MESO-1_CNhs11263_10493-107B7_reverse Regulation 
MesotheliomaCellLineACCMESO1_CNhs11263_ctss_fwd Cl:ACC-MESO-1+ mesothelioma cell line:ACC-MESO-1_CNhs11263_10493-107B7_forward Regulation 
LungAdenocarcinomaCellLineA549_CNhs11275_ctss_rev Cl:A549- lung adenocarcinoma cell line:A549_CNhs11275_10499-107C4_reverse Regulation 
LungAdenocarcinomaCellLineA549_CNhs11275_ctss_fwd Cl:A549+ lung adenocarcinoma cell line:A549_CNhs11275_10499-107C4_forward Regulation 
EpidermoidCarcinomaCellLineA431_CNhs10743_ctss_rev Cl:A431- epidermoid carcinoma cell line:A431_CNhs10743_10426-106D3_reverse Regulation 
EpidermoidCarcinomaCellLineA431_CNhs10743_ctss_fwd Cl:A431+ epidermoid carcinoma cell line:A431_CNhs10743_10426-106D3_forward Regulation 
GlioblastomaCellLineA172TechRep2_CNhs11248_ctss_rev Cl:A172Tr2- glioblastoma cell line:A172, tech_rep2_CNhs11248_10444-106F3_reverse Regulation 
GlioblastomaCellLineA172TechRep2_CNhs11248_ctss_fwd Cl:A172Tr2+ glioblastoma cell line:A172, tech_rep2_CNhs11248_10444-106F3_forward Regulation 
GlioblastomaCellLineA172_CNhs11185_ctss_rev Cl:A172- glioblastoma cell line:A172_CNhs11185_10444-106F3_reverse Regulation 
GlioblastomaCellLineA172_CNhs11185_ctss_fwd Cl:A172+ glioblastoma cell line:A172_CNhs11185_10444-106F3_forward Regulation 
PapillaryAdenocarcinomaCellLine8505C_CNhs11716_ctss_rev Cl:8505C- papillary adenocarcinoma cell line:8505C_CNhs11716_10437-106E5_reverse Regulation 
PapillaryAdenocarcinomaCellLine8505C_CNhs11716_ctss_fwd Cl:8505C+ papillary adenocarcinoma cell line:8505C_CNhs11716_10437-106E5_forward Regulation 
AnaplasticCarcinomaCellLine8305C_CNhs10745_ctss_rev Cl:8305C- anaplastic carcinoma cell line:8305C_CNhs10745_10428-106D5_reverse Regulation 
AnaplasticCarcinomaCellLine8305C_CNhs10745_ctss_fwd Cl:8305C+ anaplastic carcinoma cell line:8305C_CNhs10745_10428-106D5_forward Regulation 
TransitionalcellCarcinomaCellLine5637_CNhs10735_ctss_rev Cl:5637- transitional-cell carcinoma cell line:5637_CNhs10735_10418-106C4_reverse Regulation 
TransitionalcellCarcinomaCellLine5637_CNhs10735_ctss_fwd Cl:5637+ transitional-cell carcinoma cell line:5637_CNhs10735_10418-106C4_forward Regulation 
EmbryonicPancreasCellLine2C6_CNhs11814_ctss_rev Cl:2C6- embryonic pancreas cell line:2C6_CNhs11814_10603-108E9_reverse Regulation 
EmbryonicPancreasCellLine2C6_CNhs11814_ctss_fwd Cl:2C6+ embryonic pancreas cell line:2C6_CNhs11814_10603-108E9_forward Regulation 
EmbryonicPancreasCellLine1C3IKEI_CNhs11733_ctss_rev Cl:1C3IKEI- embryonic pancreas cell line:1C3IKEI_CNhs11733_10606-108F3_reverse Regulation 
EmbryonicPancreasCellLine1C3IKEI_CNhs11733_ctss_fwd Cl:1C3IKEI+ embryonic pancreas cell line:1C3IKEI_CNhs11733_10606-108F3_forward Regulation 
EmbryonicPancreasCellLine1C3D3_CNhs11732_ctss_rev Cl:1C3D3- embryonic pancreas cell line:1C3D3_CNhs11732_10605-108F2_reverse Regulation 
EmbryonicPancreasCellLine1C3D3_CNhs11732_ctss_fwd Cl:1C3D3+ embryonic pancreas cell line:1C3D3_CNhs11732_10605-108F2_forward Regulation 
EmbryonicPancreasCellLine1B2C6_CNhs11731_ctss_rev Cl:1B2C6- embryonic pancreas cell line:1B2C6_CNhs11731_10604-108F1_reverse Regulation 
EmbryonicPancreasCellLine1B2C6_CNhs11731_ctss_fwd Cl:1B2C6+ embryonic pancreas cell line:1B2C6_CNhs11731_10604-108F1_forward Regulation 
LeiomyomaCellLine15425_CNhs11724_ctss_rev Cl:15425- leiomyoma cell line:15425_CNhs11724_10571-108B4_reverse Regulation 
LeiomyomaCellLine15425_CNhs11724_ctss_fwd Cl:15425+ leiomyoma cell line:15425_CNhs11724_10571-108B4_forward Regulation 
LeiomyomaCellLine15242A_CNhs11723_ctss_rev Cl:15242A- leiomyoma cell line:15242A_CNhs11723_10570-108B3_reverse Regulation 
LeiomyomaCellLine15242A_CNhs11723_ctss_fwd Cl:15242A+ leiomyoma cell line:15242A_CNhs11723_10570-108B3_forward Regulation 
OsteosarcomaCellLine143BTKneoR_CNhs11279_ctss_rev Cl:143B/TK^(-)neo^(R)- osteosarcoma cell line:143B/TK^(-)neo^(R)_CNhs11279_10510-107D6_reverse Regulation 
OsteosarcomaCellLine143BTKneoR_CNhs11279_ctss_fwd Cl:143B/TK^(-)neo^(R)+ osteosarcoma cell line:143B/TK^(-)neo^(R)_CNhs11279_10510-107D6_forward Regulation 
LeiomyomaCellLine10964C_CNhs11722_ctss_rev Cl:10964C- leiomyoma cell line:10964C_CNhs11722_10569-108B2_reverse Regulation 
LeiomyomaCellLine10964C_CNhs11722_ctss_fwd Cl:10964C+ leiomyoma cell line:10964C_CNhs11722_10569-108B2_forward Regulation 
NonsmallCellLungCancerCellLineNCIH1385_CNhs12193_ctss_rev Cl:NCI-H1385- non-small cell lung cancer cell line:NCI-H1385_CNhs12193_10730-110B1_reverse Regulation 
NonsmallCellLungCancerCellLineNCIH1385_CNhs12193_ctss_fwd Cl:NCI-H1385+ non-small cell lung cancer cell line:NCI-H1385_CNhs12193_10730-110B1_forward Regulation 
MesotheliomaCellLineMero14TechRep2_CNhs14376_ctss_rev Cl:Mero-14Tr2- mesothelioma cell line:Mero-14, tech_rep2_CNhs14376_10849-111F3_reverse Regulation 
MesotheliomaCellLineMero14TechRep2_CNhs14376_ctss_fwd Cl:Mero-14Tr2+ mesothelioma cell line:Mero-14, tech_rep2_CNhs14376_10849-111F3_forward Regulation 
AcuteMyeloidLeukemiaFABM0CellLineKasumi3_CNhs13241_ctss_rev Cl:Kasumi-3- acute myeloid leukemia (FAB M0) cell line:Kasumi-3_CNhs13241_10789-110H6_reverse Regulation 
AcuteMyeloidLeukemiaFABM0CellLineKasumi3_CNhs13241_ctss_fwd Cl:Kasumi-3+ acute myeloid leukemia (FAB M0) cell line:Kasumi-3_CNhs13241_10789-110H6_forward Regulation 
LeiomyosarcomaCellLineHs5_T_CNhs12192_ctss_rev Cl:Hs5_T- leiomyosarcoma cell line:Hs 5_T_CNhs12192_10722-110A2_reverse Regulation 
LeiomyosarcomaCellLineHs5_T_CNhs12192_ctss_fwd Cl:Hs5_T+ leiomyosarcoma cell line:Hs 5_T_CNhs12192_10722-110A2_forward Regulation 
MesodermalTumorCellLineHIRSBM_CNhs12191_ctss_rev Cl:HIRS-BM- mesodermal tumor cell line:HIRS-BM_CNhs12191_10696-109G3_reverse Regulation 
MesodermalTumorCellLineHIRSBM_CNhs12191_ctss_fwd Cl:HIRS-BM+ mesodermal tumor cell line:HIRS-BM_CNhs12191_10696-109G3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep3A3T17_CNhs12892_ctss_rev Saos-2W/AscorbicAcidBgp_Day28Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep3 (A3 T17)_CNhs12892_12875-137F4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep3A3T17_CNhs12892_ctss_fwd Saos-2W/AscorbicAcidBgp_Day28Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep3 (A3 T17)_CNhs12892_12875-137F4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep2A2T17_CNhs12876_ctss_rev Saos-2W/AscorbicAcidBgp_Day28Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep2 (A2 T17)_CNhs12876_12777-136D5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep2A2T17_CNhs12876_ctss_fwd Saos-2W/AscorbicAcidBgp_Day28Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep2 (A2 T17)_CNhs12876_12777-136D5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep1A1T17_CNhs11919_ctss_rev Saos-2W/AscorbicAcidBgp_Day28Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep1 (A1 T17)_CNhs11919_12679-135B6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep1A1T17_CNhs11919_ctss_fwd Saos-2W/AscorbicAcidBgp_Day28Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep1 (A1 T17)_CNhs11919_12679-135B6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep3A3T16_CNhs12891_ctss_rev Saos-2W/AscorbicAcidBgp_Day21Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep3 (A3 T16)_CNhs12891_12874-137F3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep3A3T16_CNhs12891_ctss_fwd Saos-2W/AscorbicAcidBgp_Day21Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep3 (A3 T16)_CNhs12891_12874-137F3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep2A2T16_CNhs12875_ctss_rev Saos-2W/AscorbicAcidBgp_Day21Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep2 (A2 T16)_CNhs12875_12776-136D4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep2A2T16_CNhs12875_ctss_fwd Saos-2W/AscorbicAcidBgp_Day21Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep2 (A2 T16)_CNhs12875_12776-136D4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep1A1T16_CNhs12397_ctss_rev Saos-2W/AscorbicAcidBgp_Day21Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep1 (A1 T16)_CNhs12397_12678-135B5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep1A1T16_CNhs12397_ctss_fwd Saos-2W/AscorbicAcidBgp_Day21Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep1 (A1 T16)_CNhs12397_12678-135B5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep3A3T15_CNhs12890_ctss_rev Saos-2W/AscorbicAcidBgp_Day14Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep3 (A3 T15)_CNhs12890_12873-137F2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep3A3T15_CNhs12890_ctss_fwd Saos-2W/AscorbicAcidBgp_Day14Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep3 (A3 T15)_CNhs12890_12873-137F2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep2A2T15_CNhs12953_ctss_rev Saos-2W/AscorbicAcidBgp_Day14Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep2 (A2 T15)_CNhs12953_12775-136D3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep2A2T15_CNhs12953_ctss_fwd Saos-2W/AscorbicAcidBgp_Day14Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep2 (A2 T15)_CNhs12953_12775-136D3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep1A1T15_CNhs12396_ctss_rev Saos-2W/AscorbicAcidBgp_Day14Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep1 (A1 T15)_CNhs12396_12677-135B4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep1A1T15_CNhs12396_ctss_fwd Saos-2W/AscorbicAcidBgp_Day14Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep1 (A1 T15)_CNhs12396_12677-135B4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep3A3T14_CNhs12888_ctss_rev Saos-2W/AscorbicAcidBgp_Day07Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep3 (A3 T14)_CNhs12888_12872-137F1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep3A3T14_CNhs12888_ctss_fwd Saos-2W/AscorbicAcidBgp_Day07Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep3 (A3 T14)_CNhs12888_12872-137F1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep2A2T14_CNhs12874_ctss_rev Saos-2W/AscorbicAcidBgp_Day07Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep2 (A2 T14)_CNhs12874_12774-136D2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep2A2T14_CNhs12874_ctss_fwd Saos-2W/AscorbicAcidBgp_Day07Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep2 (A2 T14)_CNhs12874_12774-136D2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep1A1T14_CNhs12395_ctss_rev Saos-2W/AscorbicAcidBgp_Day07Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep1 (A1 T14)_CNhs12395_12676-135B3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep1A1T14_CNhs12395_ctss_fwd Saos-2W/AscorbicAcidBgp_Day07Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep1 (A1 T14)_CNhs12395_12676-135B3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep3A3T13_CNhs12887_ctss_rev Saos-2W/AscorbicAcidBgp_Day04Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep3 (A3 T13)_CNhs12887_12871-137E9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep3A3T13_CNhs12887_ctss_fwd Saos-2W/AscorbicAcidBgp_Day04Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep3 (A3 T13)_CNhs12887_12871-137E9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep2A2T13_CNhs12873_ctss_rev Saos-2W/AscorbicAcidBgp_Day04Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep2 (A2 T13)_CNhs12873_12773-136D1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep2A2T13_CNhs12873_ctss_fwd Saos-2W/AscorbicAcidBgp_Day04Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep2 (A2 T13)_CNhs12873_12773-136D1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep1A1T13_CNhs12394_ctss_rev Saos-2W/AscorbicAcidBgp_Day04Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep1 (A1 T13)_CNhs12394_12675-135B2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep1A1T13_CNhs12394_ctss_fwd Saos-2W/AscorbicAcidBgp_Day04Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep1 (A1 T13)_CNhs12394_12675-135B2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep3A3T12_CNhs12886_ctss_rev Saos-2W/AscorbicAcidBgp_24hrBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep3 (A3 T12)_CNhs12886_12870-137E8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep3A3T12_CNhs12886_ctss_fwd Saos-2W/AscorbicAcidBgp_24hrBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep3 (A3 T12)_CNhs12886_12870-137E8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep2A2T12_CNhs12872_ctss_rev Saos-2W/AscorbicAcidBgp_24hrBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep2 (A2 T12)_CNhs12872_12772-136C9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep2A2T12_CNhs12872_ctss_fwd Saos-2W/AscorbicAcidBgp_24hrBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep2 (A2 T12)_CNhs12872_12772-136C9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep1A1T12_CNhs12393_ctss_rev Saos-2W/AscorbicAcidBgp_24hrBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep1 (A1 T12)_CNhs12393_12674-135B1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep1A1T12_CNhs12393_ctss_fwd Saos-2W/AscorbicAcidBgp_24hrBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep1 (A1 T12)_CNhs12393_12674-135B1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep3A3T11_CNhs12885_ctss_rev Saos-2W/AscorbicAcidBgp_08hrBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep3 (A3 T11)_CNhs12885_12869-137E7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep3A3T11_CNhs12885_ctss_fwd Saos-2W/AscorbicAcidBgp_08hrBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep3 (A3 T11)_CNhs12885_12869-137E7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep2A2T11_CNhs12871_ctss_rev Saos-2W/AscorbicAcidBgp_08hrBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep2 (A2 T11)_CNhs12871_12771-136C8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep2A2T11_CNhs12871_ctss_fwd Saos-2W/AscorbicAcidBgp_08hrBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep2 (A2 T11)_CNhs12871_12771-136C8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep1A1T11_CNhs12392_ctss_rev Saos-2W/AscorbicAcidBgp_08hrBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep1 (A1 T11)_CNhs12392_12673-135A9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep1A1T11_CNhs12392_ctss_fwd Saos-2W/AscorbicAcidBgp_08hrBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep1 (A1 T11)_CNhs12392_12673-135A9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep3A3T10_CNhs12884_ctss_rev Saos-2W/AscorbicAcidBgp_04hrBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep3 (A3 T10)_CNhs12884_12868-137E6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep3A3T10_CNhs12884_ctss_fwd Saos-2W/AscorbicAcidBgp_04hrBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep3 (A3 T10)_CNhs12884_12868-137E6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep2A2T10_CNhs12870_ctss_rev Saos-2W/AscorbicAcidBgp_04hrBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep2 (A2 T10)_CNhs12870_12770-136C7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep2A2T10_CNhs12870_ctss_fwd Saos-2W/AscorbicAcidBgp_04hrBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep2 (A2 T10)_CNhs12870_12770-136C7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep1A1T10_CNhs12391_ctss_rev Saos-2W/AscorbicAcidBgp_04hrBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep1 (A1 T10)_CNhs12391_12672-135A8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep1A1T10_CNhs12391_ctss_fwd Saos-2W/AscorbicAcidBgp_04hrBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep1 (A1 T10)_CNhs12391_12672-135A8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep3A3T9_CNhs12883_ctss_rev Saos-2W/AscorbicAcidBgp_03hrBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep3 (A3 T9)_CNhs12883_12867-137E5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep3A3T9_CNhs12883_ctss_fwd Saos-2W/AscorbicAcidBgp_03hrBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep3 (A3 T9)_CNhs12883_12867-137E5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep2A2T9_CNhs12869_ctss_rev Saos-2W/AscorbicAcidBgp_03hrBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep2 (A2 T9)_CNhs12869_12769-136C6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep2A2T9_CNhs12869_ctss_fwd Saos-2W/AscorbicAcidBgp_03hrBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep2 (A2 T9)_CNhs12869_12769-136C6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep1A1T9_CNhs12390_ctss_rev Saos-2W/AscorbicAcidBgp_03hrBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep1 (A1 T9)_CNhs12390_12671-135A7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep1A1T9_CNhs12390_ctss_fwd Saos-2W/AscorbicAcidBgp_03hrBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep1 (A1 T9)_CNhs12390_12671-135A7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep3A3T8_CNhs12882_ctss_rev Saos-2W/AscorbicAcidBgp_02hr30minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep3 (A3 T8)_CNhs12882_12866-137E4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep3A3T8_CNhs12882_ctss_fwd Saos-2W/AscorbicAcidBgp_02hr30minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep3 (A3 T8)_CNhs12882_12866-137E4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep2A2T8_CNhs12868_ctss_rev Saos-2W/AscorbicAcidBgp_02hr30minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep2 (A2 T8)_CNhs12868_12768-136C5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep2A2T8_CNhs12868_ctss_fwd Saos-2W/AscorbicAcidBgp_02hr30minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep2 (A2 T8)_CNhs12868_12768-136C5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep1A1T8_CNhs12389_ctss_rev Saos-2W/AscorbicAcidBgp_02hr30minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep1 (A1 T8)_CNhs12389_12670-135A6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep1A1T8_CNhs12389_ctss_fwd Saos-2W/AscorbicAcidBgp_02hr30minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep1 (A1 T8)_CNhs12389_12670-135A6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep3A3T7_CNhs12881_ctss_rev Saos-2W/AscorbicAcidBgp_02hr00minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep3 (A3 T7)_CNhs12881_12865-137E3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep3A3T7_CNhs12881_ctss_fwd Saos-2W/AscorbicAcidBgp_02hr00minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep3 (A3 T7)_CNhs12881_12865-137E3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep2A2T7_CNhs12867_ctss_rev Saos-2W/AscorbicAcidBgp_02hr00minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep2 (A2 T7)_CNhs12867_12767-136C4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep2A2T7_CNhs12867_ctss_fwd Saos-2W/AscorbicAcidBgp_02hr00minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep2 (A2 T7)_CNhs12867_12767-136C4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep1A1T7_CNhs12388_ctss_rev Saos-2W/AscorbicAcidBgp_02hr00minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep1 (A1 T7)_CNhs12388_12669-135A5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep1A1T7_CNhs12388_ctss_fwd Saos-2W/AscorbicAcidBgp_02hr00minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep1 (A1 T7)_CNhs12388_12669-135A5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep3A3T6_CNhs12880_ctss_rev Saos-2W/AscorbicAcidBgp_01hr40minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep3 (A3 T6)_CNhs12880_12864-137E2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep3A3T6_CNhs12880_ctss_fwd Saos-2W/AscorbicAcidBgp_01hr40minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep3 (A3 T6)_CNhs12880_12864-137E2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep2A2T6_CNhs12866_ctss_rev Saos-2W/AscorbicAcidBgp_01hr40minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep2 (A2 T6)_CNhs12866_12766-136C3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep2A2T6_CNhs12866_ctss_fwd Saos-2W/AscorbicAcidBgp_01hr40minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep2 (A2 T6)_CNhs12866_12766-136C3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep1A1T6_CNhs12387_ctss_rev Saos-2W/AscorbicAcidBgp_01hr40minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep1 (A1 T6)_CNhs12387_12668-135A4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep1A1T6_CNhs12387_ctss_fwd Saos-2W/AscorbicAcidBgp_01hr40minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep1 (A1 T6)_CNhs12387_12668-135A4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep3A3T5_CNhs12879_ctss_rev Saos-2W/AscorbicAcidBgp_01hr20minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep3 (A3 T5)_CNhs12879_12863-137E1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep3A3T5_CNhs12879_ctss_fwd Saos-2W/AscorbicAcidBgp_01hr20minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep3 (A3 T5)_CNhs12879_12863-137E1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep2A2T5_CNhs12864_ctss_rev Saos-2W/AscorbicAcidBgp_01hr20minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep2 (A2 T5)_CNhs12864_12765-136C2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep2A2T5_CNhs12864_ctss_fwd Saos-2W/AscorbicAcidBgp_01hr20minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep2 (A2 T5)_CNhs12864_12765-136C2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep1A1T5_CNhs12386_ctss_rev Saos-2W/AscorbicAcidBgp_01hr20minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep1 (A1 T5)_CNhs12386_12667-135A3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep1A1T5_CNhs12386_ctss_fwd Saos-2W/AscorbicAcidBgp_01hr20minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep1 (A1 T5)_CNhs12386_12667-135A3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep3A3T4_CNhs12955_ctss_rev Saos-2W/AscorbicAcidBgp_01hr00minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep3 (A3 T4)_CNhs12955_12862-137D9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep3A3T4_CNhs12955_ctss_fwd Saos-2W/AscorbicAcidBgp_01hr00minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep3 (A3 T4)_CNhs12955_12862-137D9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep2A2T4_CNhs12863_ctss_rev Saos-2W/AscorbicAcidBgp_01hr00minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep2 (A2 T4)_CNhs12863_12764-136C1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep2A2T4_CNhs12863_ctss_fwd Saos-2W/AscorbicAcidBgp_01hr00minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep2 (A2 T4)_CNhs12863_12764-136C1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep1A1T4_CNhs12384_ctss_rev Saos-2W/AscorbicAcidBgp_01hr00minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep1 (A1 T4)_CNhs12384_12666-135A2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep1A1T4_CNhs12384_ctss_fwd Saos-2W/AscorbicAcidBgp_01hr00minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep1 (A1 T4)_CNhs12384_12666-135A2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep3A3T3_CNhs12878_ctss_rev Saos-2W/AscorbicAcidBgp_00hr45minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep3 (A3 T3)_CNhs12878_12861-137D8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep3A3T3_CNhs12878_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr45minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep3 (A3 T3)_CNhs12878_12861-137D8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep2A2T3_CNhs12862_ctss_rev Saos-2W/AscorbicAcidBgp_00hr45minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep2 (A2 T3)_CNhs12862_12763-136B9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep2A2T3_CNhs12862_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr45minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep2 (A2 T3)_CNhs12862_12763-136B9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep1A1T3_CNhs12383_ctss_rev Saos-2W/AscorbicAcidBgp_00hr45minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep1 (A1 T3)_CNhs12383_12665-135A1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep1A1T3_CNhs12383_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr45minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep1 (A1 T3)_CNhs12383_12665-135A1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep3A3T2_CNhs12954_ctss_rev Saos-2W/AscorbicAcidBgp_00hr30minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep3 (A3 T2)_CNhs12954_12860-137D7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep3A3T2_CNhs12954_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr30minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep3 (A3 T2)_CNhs12954_12860-137D7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep2A2T2_CNhs12861_ctss_rev Saos-2W/AscorbicAcidBgp_00hr30minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep2 (A2 T2)_CNhs12861_12762-136B8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep2A2T2_CNhs12861_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr30minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep2 (A2 T2)_CNhs12861_12762-136B8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep1A1T2_CNhs12382_ctss_rev Saos-2W/AscorbicAcidBgp_00hr30minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep1 (A1 T2)_CNhs12382_12664-134I9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep1A1T2_CNhs12382_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr30minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep1 (A1 T2)_CNhs12382_12664-134I9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep3A3T1_CNhs12877_ctss_rev Saos-2W/AscorbicAcidBgp_00hr15minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep3 (A3 T1)_CNhs12877_12859-137D6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep3A3T1_CNhs12877_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr15minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep3 (A3 T1)_CNhs12877_12859-137D6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep2A2T1_CNhs12860_ctss_rev Saos-2W/AscorbicAcidBgp_00hr15minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep2 (A2 T1)_CNhs12860_12761-136B7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep2A2T1_CNhs12860_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr15minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep2 (A2 T1)_CNhs12860_12761-136B7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep1A1T1_CNhs12381_ctss_rev Saos-2W/AscorbicAcidBgp_00hr15minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep1 (A1 T1)_CNhs12381_12663-134I8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep1A1T1_CNhs12381_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr15minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep1 (A1 T1)_CNhs12381_12663-134I8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep3A3T0_CNhs12952_ctss_rev Saos-2W/AscorbicAcidBgp_00hr00minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep3 (A3 T0)_CNhs12952_12858-137D5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep3A3T0_CNhs12952_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr00minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep3 (A3 T0)_CNhs12952_12858-137D5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep2A2T0_CNhs12859_ctss_rev Saos-2W/AscorbicAcidBgp_00hr00minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep2 (A2 T0)_CNhs12859_12760-136B6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep2A2T0_CNhs12859_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr00minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep2 (A2 T0)_CNhs12859_12760-136B6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep1A1T0_CNhs11918_ctss_rev Saos-2W/AscorbicAcidBgp_00hr00minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep1 (A1 T0)_CNhs11918_12662-134I7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep1A1T0_CNhs11918_ctss_fwd Saos-2W/AscorbicAcidBgp_00hr00minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep1 (A1 T0)_CNhs11918_12662-134I7_forward Regulation 
COBLaRinderpestInfection48hrBiolRep3_CNhs14434_ctss_rev Tc:COBL-aRinderpest_48hrBr3- COBL-a rinderpest infection, 48hr, biol_rep3_CNhs14434_13567-146B3_reverse Regulation 
COBLaRinderpestInfection48hrBiolRep3_CNhs14434_ctss_fwd Tc:COBL-aRinderpest_48hrBr3+ COBL-a rinderpest infection, 48hr, biol_rep3_CNhs14434_13567-146B3_forward Regulation 
COBLaRinderpestInfection48hrBiolRep2_CNhs14432_ctss_rev Tc:COBL-aRinderpest_48hrBr2- COBL-a rinderpest infection, 48hr, biol_rep2_CNhs14432_13566-146B2_reverse Regulation 
COBLaRinderpestInfection48hrBiolRep2_CNhs14432_ctss_fwd Tc:COBL-aRinderpest_48hrBr2+ COBL-a rinderpest infection, 48hr, biol_rep2_CNhs14432_13566-146B2_forward Regulation 
COBLaRinderpestInfection48hrBiolRep1_CNhs14431_ctss_rev Tc:COBL-aRinderpest_48hrBr1- COBL-a rinderpest infection, 48hr, biol_rep1_CNhs14431_13565-146B1_reverse Regulation 
COBLaRinderpestInfection48hrBiolRep1_CNhs14431_ctss_fwd Tc:COBL-aRinderpest_48hrBr1+ COBL-a rinderpest infection, 48hr, biol_rep1_CNhs14431_13565-146B1_forward Regulation 
COBLaRinderpestInfection24hrBiolRep3_CNhs14430_ctss_rev Tc:COBL-aRinderpest_24hrBr3- COBL-a rinderpest infection, 24hr, biol_rep3_CNhs14430_13564-146A9_reverse Regulation 
COBLaRinderpestInfection24hrBiolRep3_CNhs14430_ctss_fwd Tc:COBL-aRinderpest_24hrBr3+ COBL-a rinderpest infection, 24hr, biol_rep3_CNhs14430_13564-146A9_forward Regulation 
COBLaRinderpestInfection24hrBiolRep2_CNhs14429_ctss_rev Tc:COBL-aRinderpest_24hrBr2- COBL-a rinderpest infection, 24hr, biol_rep2_CNhs14429_13563-146A8_reverse Regulation 
COBLaRinderpestInfection24hrBiolRep2_CNhs14429_ctss_fwd Tc:COBL-aRinderpest_24hrBr2+ COBL-a rinderpest infection, 24hr, biol_rep2_CNhs14429_13563-146A8_forward Regulation 
COBLaRinderpestInfection24hrBiolRep1_CNhs14428_ctss_rev Tc:COBL-aRinderpest_24hrBr1- COBL-a rinderpest infection, 24hr, biol_rep1_CNhs14428_13562-146A7_reverse Regulation 
COBLaRinderpestInfection24hrBiolRep1_CNhs14428_ctss_fwd Tc:COBL-aRinderpest_24hrBr1+ COBL-a rinderpest infection, 24hr, biol_rep1_CNhs14428_13562-146A7_forward Regulation 
COBLaRinderpestInfection12hrBiolRep3_CNhs14427_ctss_rev Tc:COBL-aRinderpest_12hrBr3- COBL-a rinderpest infection, 12hr, biol_rep3_CNhs14427_13561-146A6_reverse Regulation 
COBLaRinderpestInfection12hrBiolRep3_CNhs14427_ctss_fwd Tc:COBL-aRinderpest_12hrBr3+ COBL-a rinderpest infection, 12hr, biol_rep3_CNhs14427_13561-146A6_forward Regulation 
COBLaRinderpestInfection12hrBiolRep2_CNhs14426_ctss_rev Tc:COBL-aRinderpest_12hrBr2- COBL-a rinderpest infection, 12hr, biol_rep2_CNhs14426_13560-146A5_reverse Regulation 
COBLaRinderpestInfection12hrBiolRep2_CNhs14426_ctss_fwd Tc:COBL-aRinderpest_12hrBr2+ COBL-a rinderpest infection, 12hr, biol_rep2_CNhs14426_13560-146A5_forward Regulation 
COBLaRinderpestInfection12hrBiolRep1_CNhs14425_ctss_rev Tc:COBL-aRinderpest_12hrBr1- COBL-a rinderpest infection, 12hr, biol_rep1_CNhs14425_13559-146A4_reverse Regulation 
COBLaRinderpestInfection12hrBiolRep1_CNhs14425_ctss_fwd Tc:COBL-aRinderpest_12hrBr1+ COBL-a rinderpest infection, 12hr, biol_rep1_CNhs14425_13559-146A4_forward Regulation 
COBLaRinderpestInfection06hrBiolRep3_CNhs14424_ctss_rev Tc:COBL-aRinderpest_06hrBr3- COBL-a rinderpest infection, 06hr, biol_rep3_CNhs14424_13558-146A3_reverse Regulation 
COBLaRinderpestInfection06hrBiolRep3_CNhs14424_ctss_fwd Tc:COBL-aRinderpest_06hrBr3+ COBL-a rinderpest infection, 06hr, biol_rep3_CNhs14424_13558-146A3_forward Regulation 
COBLaRinderpestInfection06hrBiolRep2_CNhs14423_ctss_rev Tc:COBL-aRinderpest_06hrBr2- COBL-a rinderpest infection, 06hr, biol_rep2_CNhs14423_13557-146A2_reverse Regulation 
COBLaRinderpestInfection06hrBiolRep2_CNhs14423_ctss_fwd Tc:COBL-aRinderpest_06hrBr2+ COBL-a rinderpest infection, 06hr, biol_rep2_CNhs14423_13557-146A2_forward Regulation 
COBLaRinderpestInfection06hrBiolRep1_CNhs14422_ctss_rev Tc:COBL-aRinderpest_06hrBr1- COBL-a rinderpest infection, 06hr, biol_rep1_CNhs14422_13556-146A1_reverse Regulation 
COBLaRinderpestInfection06hrBiolRep1_CNhs14422_ctss_fwd Tc:COBL-aRinderpest_06hrBr1+ COBL-a rinderpest infection, 06hr, biol_rep1_CNhs14422_13556-146A1_forward Regulation 
COBLaRinderpestInfection00hrBiolRep3_CNhs14421_ctss_rev Tc:COBL-aRinderpest_00hrBr3- COBL-a rinderpest infection, 00hr, biol_rep3_CNhs14421_13555-145I9_reverse Regulation 
COBLaRinderpestInfection00hrBiolRep3_CNhs14421_ctss_fwd Tc:COBL-aRinderpest_00hrBr3+ COBL-a rinderpest infection, 00hr, biol_rep3_CNhs14421_13555-145I9_forward Regulation 
COBLaRinderpestInfection00hrBiolRep2_CNhs14420_ctss_rev Tc:COBL-aRinderpest_00hrBr2- COBL-a rinderpest infection, 00hr, biol_rep2_CNhs14420_13554-145I8_reverse Regulation 
COBLaRinderpestInfection00hrBiolRep2_CNhs14420_ctss_fwd Tc:COBL-aRinderpest_00hrBr2+ COBL-a rinderpest infection, 00hr, biol_rep2_CNhs14420_13554-145I8_forward Regulation 
COBLaRinderpestInfection00hrBiolRep1_CNhs14419_ctss_rev Tc:COBL-aRinderpest_00hrBr1- COBL-a rinderpest infection, 00hr, biol_rep1_CNhs14419_13553-145I7_reverse Regulation 
COBLaRinderpestInfection00hrBiolRep1_CNhs14419_ctss_fwd Tc:COBL-aRinderpest_00hrBr1+ COBL-a rinderpest infection, 00hr, biol_rep1_CNhs14419_13553-145I7_forward Regulation 
COBLaRinderpestCInfection48hrBiolRep3_CNhs14446_ctss_rev Tc:COBL-aRinderpest(-C)_48hrBr3- COBL-a rinderpest(-C) infection, 48hr, biol_rep3_CNhs14446_13579-146C6_reverse Regulation 
COBLaRinderpestCInfection48hrBiolRep3_CNhs14446_ctss_fwd Tc:COBL-aRinderpest(-C)_48hrBr3+ COBL-a rinderpest(-C) infection, 48hr, biol_rep3_CNhs14446_13579-146C6_forward Regulation 
COBLaRinderpestCInfection48hrBiolRep2_CNhs14445_ctss_rev Tc:COBL-aRinderpest(-C)_48hrBr2- COBL-a rinderpest(-C) infection, 48hr, biol_rep2_CNhs14445_13578-146C5_reverse Regulation 
COBLaRinderpestCInfection48hrBiolRep2_CNhs14445_ctss_fwd Tc:COBL-aRinderpest(-C)_48hrBr2+ COBL-a rinderpest(-C) infection, 48hr, biol_rep2_CNhs14445_13578-146C5_forward Regulation 
COBLaRinderpestCInfection48hrBiolRep1_CNhs14444_ctss_rev Tc:COBL-aRinderpest(-C)_48hrBr1- COBL-a rinderpest(-C) infection, 48hr, biol_rep1_CNhs14444_13577-146C4_reverse Regulation 
COBLaRinderpestCInfection48hrBiolRep1_CNhs14444_ctss_fwd Tc:COBL-aRinderpest(-C)_48hrBr1+ COBL-a rinderpest(-C) infection, 48hr, biol_rep1_CNhs14444_13577-146C4_forward Regulation 
COBLaRinderpestCInfection24hrBiolRep3_CNhs14443_ctss_rev Tc:COBL-aRinderpest(-C)_24hrBr3- COBL-a rinderpest(-C) infection, 24hr, biol_rep3_CNhs14443_13576-146C3_reverse Regulation 
COBLaRinderpestCInfection24hrBiolRep3_CNhs14443_ctss_fwd Tc:COBL-aRinderpest(-C)_24hrBr3+ COBL-a rinderpest(-C) infection, 24hr, biol_rep3_CNhs14443_13576-146C3_forward Regulation 
COBLaRinderpestCInfection24hrBiolRep2_CNhs14442_ctss_rev Tc:COBL-aRinderpest(-C)_24hrBr2- COBL-a rinderpest(-C) infection, 24hr, biol_rep2_CNhs14442_13575-146C2_reverse Regulation 
COBLaRinderpestCInfection24hrBiolRep2_CNhs14442_ctss_fwd Tc:COBL-aRinderpest(-C)_24hrBr2+ COBL-a rinderpest(-C) infection, 24hr, biol_rep2_CNhs14442_13575-146C2_forward Regulation 
COBLaRinderpestCInfection24hrBiolRep1_CNhs14441_ctss_rev Tc:COBL-aRinderpest(-C)_24hrBr1- COBL-a rinderpest(-C) infection, 24hr, biol_rep1_CNhs14441_13574-146C1_reverse Regulation 
COBLaRinderpestCInfection24hrBiolRep1_CNhs14441_ctss_fwd Tc:COBL-aRinderpest(-C)_24hrBr1+ COBL-a rinderpest(-C) infection, 24hr, biol_rep1_CNhs14441_13574-146C1_forward Regulation 
COBLaRinderpestCInfection12hrBiolRep3_CNhs14440_ctss_rev Tc:COBL-aRinderpest(-C)_12hrBr3- COBL-a rinderpest(-C) infection, 12hr, biol_rep3_CNhs14440_13573-146B9_reverse Regulation 
COBLaRinderpestCInfection12hrBiolRep3_CNhs14440_ctss_fwd Tc:COBL-aRinderpest(-C)_12hrBr3+ COBL-a rinderpest(-C) infection, 12hr, biol_rep3_CNhs14440_13573-146B9_forward Regulation 
COBLaRinderpestCInfection12hrBiolRep2_CNhs14439_ctss_rev Tc:COBL-aRinderpest(-C)_12hrBr2- COBL-a rinderpest(-C) infection, 12hr, biol_rep2_CNhs14439_13572-146B8_reverse Regulation 
COBLaRinderpestCInfection12hrBiolRep2_CNhs14439_ctss_fwd Tc:COBL-aRinderpest(-C)_12hrBr2+ COBL-a rinderpest(-C) infection, 12hr, biol_rep2_CNhs14439_13572-146B8_forward Regulation 
COBLaRinderpestCInfection12hrBiolRep1_CNhs14438_ctss_rev Tc:COBL-aRinderpest(-C)_12hrBr1- COBL-a rinderpest(-C) infection, 12hr, biol_rep1_CNhs14438_13571-146B7_reverse Regulation 
COBLaRinderpestCInfection12hrBiolRep1_CNhs14438_ctss_fwd Tc:COBL-aRinderpest(-C)_12hrBr1+ COBL-a rinderpest(-C) infection, 12hr, biol_rep1_CNhs14438_13571-146B7_forward Regulation 
COBLaRinderpestCInfection06hrBiolRep3_CNhs14437_ctss_rev Tc:COBL-aRinderpest(-C)_06hrBr3- COBL-a rinderpest(-C) infection, 06hr, biol_rep3_CNhs14437_13570-146B6_reverse Regulation 
COBLaRinderpestCInfection06hrBiolRep3_CNhs14437_ctss_fwd Tc:COBL-aRinderpest(-C)_06hrBr3+ COBL-a rinderpest(-C) infection, 06hr, biol_rep3_CNhs14437_13570-146B6_forward Regulation 
COBLaRinderpestCInfection06hrBiolRep2_CNhs14436_ctss_rev Tc:COBL-aRinderpest(-C)_06hrBr2- COBL-a rinderpest(-C) infection, 06hr, biol_rep2_CNhs14436_13569-146B5_reverse Regulation 
COBLaRinderpestCInfection06hrBiolRep2_CNhs14436_ctss_fwd Tc:COBL-aRinderpest(-C)_06hrBr2+ COBL-a rinderpest(-C) infection, 06hr, biol_rep2_CNhs14436_13569-146B5_forward Regulation 
COBLaRinderpestCInfection06hrBiolRep1_CNhs14435_ctss_rev Tc:COBL-aRinderpest(-C)_06hrBr1- COBL-a rinderpest(-C) infection, 06hr, biol_rep1_CNhs14435_13568-146B4_reverse Regulation 
COBLaRinderpestCInfection06hrBiolRep1_CNhs14435_ctss_fwd Tc:COBL-aRinderpest(-C)_06hrBr1+ COBL-a rinderpest(-C) infection, 06hr, biol_rep1_CNhs14435_13568-146B4_forward Regulation 
293SLAMRinderpestInfection24hrBiolRep3_CNhs14418_ctss_rev Tc:293SlamRinderpest_24hrBr3- 293SLAM rinderpest infection, 24hr, biol_rep3_CNhs14418_13552-145I6_reverse Regulation 
293SLAMRinderpestInfection24hrBiolRep3_CNhs14418_ctss_fwd Tc:293SlamRinderpest_24hrBr3+ 293SLAM rinderpest infection, 24hr, biol_rep3_CNhs14418_13552-145I6_forward Regulation 
293SLAMRinderpestInfection24hrBiolRep2_CNhs14417_ctss_rev Tc:293SlamRinderpest_24hrBr2- 293SLAM rinderpest infection, 24hr, biol_rep2_CNhs14417_13551-145I5_reverse Regulation 
293SLAMRinderpestInfection24hrBiolRep2_CNhs14417_ctss_fwd Tc:293SlamRinderpest_24hrBr2+ 293SLAM rinderpest infection, 24hr, biol_rep2_CNhs14417_13551-145I5_forward Regulation 
293SLAMRinderpestInfection24hrBiolRep1_CNhs14416_ctss_rev Tc:293SlamRinderpest_24hrBr1- 293SLAM rinderpest infection, 24hr, biol_rep1_CNhs14416_13550-145I4_reverse Regulation 
293SLAMRinderpestInfection24hrBiolRep1_CNhs14416_ctss_fwd Tc:293SlamRinderpest_24hrBr1+ 293SLAM rinderpest infection, 24hr, biol_rep1_CNhs14416_13550-145I4_forward Regulation 
293SLAMRinderpestInfection12hrBiolRep3_CNhs14415_ctss_rev Tc:293SlamRinderpest_12hrBr3- 293SLAM rinderpest infection, 12hr, biol_rep3_CNhs14415_13549-145I3_reverse Regulation 
293SLAMRinderpestInfection12hrBiolRep3_CNhs14415_ctss_fwd Tc:293SlamRinderpest_12hrBr3+ 293SLAM rinderpest infection, 12hr, biol_rep3_CNhs14415_13549-145I3_forward Regulation 
293SLAMRinderpestInfection12hrBiolRep2_CNhs14414_ctss_rev Tc:293SlamRinderpest_12hrBr2- 293SLAM rinderpest infection, 12hr, biol_rep2_CNhs14414_13548-145I2_reverse Regulation 
293SLAMRinderpestInfection12hrBiolRep2_CNhs14414_ctss_fwd Tc:293SlamRinderpest_12hrBr2+ 293SLAM rinderpest infection, 12hr, biol_rep2_CNhs14414_13548-145I2_forward Regulation 
293SLAMRinderpestInfection12hrBiolRep1_CNhs14413_ctss_rev Tc:293SlamRinderpest_12hrBr1- 293SLAM rinderpest infection, 12hr, biol_rep1_CNhs14413_13547-145I1_reverse Regulation 
293SLAMRinderpestInfection12hrBiolRep1_CNhs14413_ctss_fwd Tc:293SlamRinderpest_12hrBr1+ 293SLAM rinderpest infection, 12hr, biol_rep1_CNhs14413_13547-145I1_forward Regulation 
293SLAMRinderpestInfection06hrBiolRep3_CNhs14412_ctss_rev Tc:293SlamRinderpest_06hrBr3- 293SLAM rinderpest infection, 06hr, biol_rep3_CNhs14412_13546-145H9_reverse Regulation 
293SLAMRinderpestInfection06hrBiolRep3_CNhs14412_ctss_fwd Tc:293SlamRinderpest_06hrBr3+ 293SLAM rinderpest infection, 06hr, biol_rep3_CNhs14412_13546-145H9_forward Regulation 
293SLAMRinderpestInfection06hrBiolRep2_CNhs14411_ctss_rev Tc:293SlamRinderpest_06hrBr2- 293SLAM rinderpest infection, 06hr, biol_rep2_CNhs14411_13545-145H8_reverse Regulation 
293SLAMRinderpestInfection06hrBiolRep2_CNhs14411_ctss_fwd Tc:293SlamRinderpest_06hrBr2+ 293SLAM rinderpest infection, 06hr, biol_rep2_CNhs14411_13545-145H8_forward Regulation 
293SLAMRinderpestInfection06hrBiolRep1_CNhs14410_ctss_rev Tc:293SlamRinderpest_06hrBr1- 293SLAM rinderpest infection, 06hr, biol_rep1_CNhs14410_13544-145H7_reverse Regulation 
293SLAMRinderpestInfection06hrBiolRep1_CNhs14410_ctss_fwd Tc:293SlamRinderpest_06hrBr1+ 293SLAM rinderpest infection, 06hr, biol_rep1_CNhs14410_13544-145H7_forward Regulation 
293SLAMRinderpestInfection00hrBiolRep3_CNhs14408_ctss_rev Tc:293SlamRinderpest_00hrBr3- 293SLAM rinderpest infection, 00hr, biol_rep3_CNhs14408_13543-145H6_reverse Regulation 
293SLAMRinderpestInfection00hrBiolRep3_CNhs14408_ctss_fwd Tc:293SlamRinderpest_00hrBr3+ 293SLAM rinderpest infection, 00hr, biol_rep3_CNhs14408_13543-145H6_forward Regulation 
293SLAMRinderpestInfection00hrBiolRep2_CNhs14407_ctss_rev Tc:293SlamRinderpest_00hrBr2- 293SLAM rinderpest infection, 00hr, biol_rep2_CNhs14407_13542-145H5_reverse Regulation 
293SLAMRinderpestInfection00hrBiolRep2_CNhs14407_ctss_fwd Tc:293SlamRinderpest_00hrBr2+ 293SLAM rinderpest infection, 00hr, biol_rep2_CNhs14407_13542-145H5_forward Regulation 
293SLAMRinderpestInfection00hrBiolRep1_CNhs14406_ctss_rev Tc:293SlamRinderpest_00hrBr1- 293SLAM rinderpest infection, 00hr, biol_rep1_CNhs14406_13541-145H4_reverse Regulation 
293SLAMRinderpestInfection00hrBiolRep1_CNhs14406_ctss_fwd Tc:293SlamRinderpest_00hrBr1+ 293SLAM rinderpest infection, 00hr, biol_rep1_CNhs14406_13541-145H4_forward Regulation 
AdipocyteDifferentiationDay12Donor4_CNhs13419_ctss_rev Tc:AdipoDiff_Day12D4- Adipocyte differentiation, day12, donor4_CNhs13419_13030-139E6_reverse Regulation 
AdipocyteDifferentiationDay12Donor4_CNhs13419_ctss_fwd Tc:AdipoDiff_Day12D4+ Adipocyte differentiation, day12, donor4_CNhs13419_13030-139E6_forward Regulation 
AdipocyteDifferentiationDay12Donor3_CNhs13416_ctss_rev Tc:AdipoDiff_Day12D3- Adipocyte differentiation, day12, donor3_CNhs13416_13027-139E3_reverse Regulation 
AdipocyteDifferentiationDay12Donor3_CNhs13416_ctss_fwd Tc:AdipoDiff_Day12D3+ Adipocyte differentiation, day12, donor3_CNhs13416_13027-139E3_forward Regulation 
AdipocyteDifferentiationDay12Donor2_CNhs13412_ctss_rev Tc:AdipoDiff_Day12D2- Adipocyte differentiation, day12, donor2_CNhs13412_13024-139D9_reverse Regulation 
AdipocyteDifferentiationDay12Donor2_CNhs13412_ctss_fwd Tc:AdipoDiff_Day12D2+ Adipocyte differentiation, day12, donor2_CNhs13412_13024-139D9_forward Regulation 
AdipocyteDifferentiationDay12Donor1_CNhs13336_ctss_rev Tc:AdipoDiff_Day12D1- Adipocyte differentiation, day12, donor1_CNhs13336_13021-139D6_reverse Regulation 
AdipocyteDifferentiationDay12Donor1_CNhs13336_ctss_fwd Tc:AdipoDiff_Day12D1+ Adipocyte differentiation, day12, donor1_CNhs13336_13021-139D6_forward Regulation 
AdipocyteDifferentiationDay08Donor4_CNhs13418_ctss_rev Tc:AdipoDiff_Day08D4- Adipocyte differentiation, day08, donor4_CNhs13418_13029-139E5_reverse Regulation 
AdipocyteDifferentiationDay08Donor4_CNhs13418_ctss_fwd Tc:AdipoDiff_Day08D4+ Adipocyte differentiation, day08, donor4_CNhs13418_13029-139E5_forward Regulation 
AdipocyteDifferentiationDay08Donor3_CNhs13415_ctss_rev Tc:AdipoDiff_Day08D3- Adipocyte differentiation, day08, donor3_CNhs13415_13026-139E2_reverse Regulation 
AdipocyteDifferentiationDay08Donor3_CNhs13415_ctss_fwd Tc:AdipoDiff_Day08D3+ Adipocyte differentiation, day08, donor3_CNhs13415_13026-139E2_forward Regulation 
AdipocyteDifferentiationDay08Donor2_CNhs13411_ctss_rev Tc:AdipoDiff_Day08D2- Adipocyte differentiation, day08, donor2_CNhs13411_13023-139D8_reverse Regulation 
AdipocyteDifferentiationDay08Donor2_CNhs13411_ctss_fwd Tc:AdipoDiff_Day08D2+ Adipocyte differentiation, day08, donor2_CNhs13411_13023-139D8_forward Regulation 
AdipocyteDifferentiationDay08Donor1_CNhs12517_ctss_rev Tc:AdipoDiff_Day08D1- Adipocyte differentiation, day08, donor1_CNhs12517_13020-139D5_reverse Regulation 
AdipocyteDifferentiationDay08Donor1_CNhs12517_ctss_fwd Tc:AdipoDiff_Day08D1+ Adipocyte differentiation, day08, donor1_CNhs12517_13020-139D5_forward Regulation 
AdipocyteDifferentiationDay04Donor4_CNhs13417_ctss_rev Tc:AdipoDiff_Day04D4- Adipocyte differentiation, day04, donor4_CNhs13417_13028-139E4_reverse Regulation 
AdipocyteDifferentiationDay04Donor4_CNhs13417_ctss_fwd Tc:AdipoDiff_Day04D4+ Adipocyte differentiation, day04, donor4_CNhs13417_13028-139E4_forward Regulation 
AdipocyteDifferentiationDay04Donor3_CNhs13413_ctss_rev Tc:AdipoDiff_Day04D3- Adipocyte differentiation, day04, donor3_CNhs13413_13025-139E1_reverse Regulation 
AdipocyteDifferentiationDay04Donor3_CNhs13413_ctss_fwd Tc:AdipoDiff_Day04D3+ Adipocyte differentiation, day04, donor3_CNhs13413_13025-139E1_forward Regulation 
AdipocyteDifferentiationDay04Donor2_CNhs13410_ctss_rev Tc:AdipoDiff_Day04D2- Adipocyte differentiation, day04, donor2_CNhs13410_13022-139D7_reverse Regulation 
AdipocyteDifferentiationDay04Donor2_CNhs13410_ctss_fwd Tc:AdipoDiff_Day04D2+ Adipocyte differentiation, day04, donor2_CNhs13410_13022-139D7_forward Regulation 
AdipocyteDifferentiationDay04Donor1_CNhs12516_ctss_rev Tc:AdipoDiff_Day04D1- Adipocyte differentiation, day04, donor1_CNhs12516_13019-139D4_reverse Regulation 
AdipocyteDifferentiationDay04Donor1_CNhs12516_ctss_fwd Tc:AdipoDiff_Day04D1+ Adipocyte differentiation, day04, donor1_CNhs12516_13019-139D4_forward Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor3_CNhs14613_ctss_rev MyoblastToMyotubes_Day12D3- Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor3_CNhs14613_13522-145F3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor3_CNhs14585_ctss_rev MyoblastToMyotubes_Day12D3- Myoblast differentiation to myotubes, day12, control donor3_CNhs14585_13495-145C3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor3_CNhs14613_ctss_fwd MyoblastToMyotubes_Day12D3+ Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor3_CNhs14613_13522-145F3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor3_CNhs14585_ctss_fwd MyoblastToMyotubes_Day12D3+ Myoblast differentiation to myotubes, day12, control donor3_CNhs14585_13495-145C3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor2_CNhs14604_ctss_rev MyoblastToMyotubes_Day12D2- Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor2_CNhs14604_13513-145E3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor2_CNhs14576_ctss_rev MyoblastToMyotubes_Day12D2- Myoblast differentiation to myotubes, day12, control donor2_CNhs14576_13486-145B3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor2_CNhs14604_ctss_fwd MyoblastToMyotubes_Day12D2+ Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor2_CNhs14604_13513-145E3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor2_CNhs14576_ctss_fwd MyoblastToMyotubes_Day12D2+ Myoblast differentiation to myotubes, day12, control donor2_CNhs14576_13486-145B3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor1_CNhs14566_ctss_rev MyoblastToMyotubes_Day12D1- Myoblast differentiation to myotubes, day12, control donor1_CNhs14566_13477-145A3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor1_CNhs14595_ctss_rev MyoblastToMyotubes_Day12D1- Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor1_CNhs14595_13504-145D3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor1_CNhs14566_ctss_fwd MyoblastToMyotubes_Day12D1+ Myoblast differentiation to myotubes, day12, control donor1_CNhs14566_13477-145A3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor1_CNhs14595_ctss_fwd MyoblastToMyotubes_Day12D1+ Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor1_CNhs14595_13504-145D3_forward Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor3_CNhs14612_ctss_rev MyoblastToMyotubes_Day10D3- Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor3_CNhs14612_13521-145F2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor3_CNhs14612_ctss_fwd MyoblastToMyotubes_Day10D3+ Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor3_CNhs14612_13521-145F2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor2_CNhs14575_ctss_rev MyoblastToMyotubes_Day10D2- Myoblast differentiation to myotubes, day10, control donor2_CNhs14575_13485-145B2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor2_CNhs14603_ctss_rev MyoblastToMyotubes_Day10D2- Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor2_CNhs14603_13512-145E2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor2_CNhs14575_ctss_fwd MyoblastToMyotubes_Day10D2+ Myoblast differentiation to myotubes, day10, control donor2_CNhs14575_13485-145B2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor2_CNhs14603_ctss_fwd MyoblastToMyotubes_Day10D2+ Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor2_CNhs14603_13512-145E2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor1_CNhs14594_ctss_rev MyoblastToMyotubes_Day10D1- Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor1_CNhs14594_13503-145D2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor1_CNhs13854_ctss_rev MyoblastToMyotubes_Day10D1- Myoblast differentiation to myotubes, day10, control donor1_CNhs13854_13476-145A2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor1_CNhs13854_ctss_fwd MyoblastToMyotubes_Day10D1+ Myoblast differentiation to myotubes, day10, control donor1_CNhs13854_13476-145A2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor1_CNhs14594_ctss_fwd MyoblastToMyotubes_Day10D1+ Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor1_CNhs14594_13503-145D2_forward Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor3_CNhs14611_ctss_rev MyoblastToMyotubes_Day08D3- Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor3_CNhs14611_13520-145F1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor3_CNhs14583_ctss_rev MyoblastToMyotubes_Day08D3- Myoblast differentiation to myotubes, day08, control donor3_CNhs14583_13493-145C1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor3_CNhs14611_ctss_fwd MyoblastToMyotubes_Day08D3+ Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor3_CNhs14611_13520-145F1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor3_CNhs14583_ctss_fwd MyoblastToMyotubes_Day08D3+ Myoblast differentiation to myotubes, day08, control donor3_CNhs14583_13493-145C1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor2_CNhs14602_ctss_rev MyoblastToMyotubes_Day08D2- Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor2_CNhs14602_13511-145E1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor2_CNhs14574_ctss_rev MyoblastToMyotubes_Day08D2- Myoblast differentiation to myotubes, day08, control donor2_CNhs14574_13484-145B1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor2_CNhs14602_ctss_fwd MyoblastToMyotubes_Day08D2+ Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor2_CNhs14602_13511-145E1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor2_CNhs14574_ctss_fwd MyoblastToMyotubes_Day08D2+ Myoblast differentiation to myotubes, day08, control donor2_CNhs14574_13484-145B1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor1_CNhs13853_ctss_rev MyoblastToMyotubes_Day08D1- Myoblast differentiation to myotubes, day08, control donor1_CNhs13853_13475-145A1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor1_CNhs14592_ctss_rev MyoblastToMyotubes_Day08D1- Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor1_CNhs14592_13502-145D1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor1_CNhs13853_ctss_fwd MyoblastToMyotubes_Day08D1+ Myoblast differentiation to myotubes, day08, control donor1_CNhs13853_13475-145A1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor1_CNhs14592_ctss_fwd MyoblastToMyotubes_Day08D1+ Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor1_CNhs14592_13502-145D1_forward Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor3_CNhs14610_ctss_rev MyoblastToMyotubes_Day06D3- Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor3_CNhs14610_13519-145E9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor3_CNhs14582_ctss_rev MyoblastToMyotubes_Day06D3- Myoblast differentiation to myotubes, day06, control donor3_CNhs14582_13492-145B9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor3_CNhs14610_ctss_fwd MyoblastToMyotubes_Day06D3+ Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor3_CNhs14610_13519-145E9_forward Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor3_CNhs14582_ctss_fwd MyoblastToMyotubes_Day06D3+ Myoblast differentiation to myotubes, day06, control donor3_CNhs14582_13492-145B9_forward Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor2_CNhs14573_ctss_rev MyoblastToMyotubes_Day06D2- Myoblast differentiation to myotubes, day06, control donor2_CNhs14573_13483-145A9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor2_CNhs14573_ctss_fwd MyoblastToMyotubes_Day06D2+ Myoblast differentiation to myotubes, day06, control donor2_CNhs14573_13483-145A9_forward Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor1_CNhs14591_ctss_rev MyoblastToMyotubes_Day06D1- Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor1_CNhs14591_13501-145C9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor1_CNhs13852_ctss_rev MyoblastToMyotubes_Day06D1- Myoblast differentiation to myotubes, day06, control donor1_CNhs13852_13474-144I9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor1_CNhs14591_ctss_fwd MyoblastToMyotubes_Day06D1+ Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor1_CNhs14591_13501-145C9_forward Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor1_CNhs13852_ctss_fwd MyoblastToMyotubes_Day06D1+ Myoblast differentiation to myotubes, day06, control donor1_CNhs13852_13474-144I9_forward Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor3_CNhs14581_ctss_rev MyoblastToMyotubes_Day04D3- Myoblast differentiation to myotubes, day04, control donor3_CNhs14581_13491-145B8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor3_CNhs14609_ctss_rev MyoblastToMyotubes_Day04D3- Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor3_CNhs14609_13518-145E8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor3_CNhs14581_ctss_fwd MyoblastToMyotubes_Day04D3+ Myoblast differentiation to myotubes, day04, control donor3_CNhs14581_13491-145B8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor3_CNhs14609_ctss_fwd MyoblastToMyotubes_Day04D3+ Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor3_CNhs14609_13518-145E8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor2_CNhs14572_ctss_rev MyoblastToMyotubes_Day04D2- Myoblast differentiation to myotubes, day04, control donor2_CNhs14572_13482-145A8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor2_CNhs14600_ctss_rev MyoblastToMyotubes_Day04D2- Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor2_CNhs14600_13509-145D8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor2_CNhs14572_ctss_fwd MyoblastToMyotubes_Day04D2+ Myoblast differentiation to myotubes, day04, control donor2_CNhs14572_13482-145A8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor2_CNhs14600_ctss_fwd MyoblastToMyotubes_Day04D2+ Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor2_CNhs14600_13509-145D8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor1_CNhs13851_ctss_rev MyoblastToMyotubes_Day04D1- Myoblast differentiation to myotubes, day04, control donor1_CNhs13851_13473-144I8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor1_CNhs14590_ctss_rev MyoblastToMyotubes_Day04D1- Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor1_CNhs14590_13500-145C8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor1_CNhs13851_ctss_fwd MyoblastToMyotubes_Day04D1+ Myoblast differentiation to myotubes, day04, control donor1_CNhs13851_13473-144I8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor1_CNhs14590_ctss_fwd MyoblastToMyotubes_Day04D1+ Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor1_CNhs14590_13500-145C8_forward Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor3_CNhs14580_ctss_rev MyoblastToMyotubes_Day03D3- Myoblast differentiation to myotubes, day03, control donor3_CNhs14580_13490-145B7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor3_CNhs14580_ctss_fwd MyoblastToMyotubes_Day03D3+ Myoblast differentiation to myotubes, day03, control donor3_CNhs14580_13490-145B7_forward Regulation 
MyoblastDifferentiationToMyotubesDay03DuchenneMuscularDystrophyDonor2_CNhs14599_ctss_rev MyoblastToMyotubes_Day03D2- Myoblast differentiation to myotubes, day03, Duchenne Muscular Dystrophy donor2_CNhs14599_13508-145D7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor2_CNhs14571_ctss_rev MyoblastToMyotubes_Day03D2- Myoblast differentiation to myotubes, day03, control donor2_CNhs14571_13481-145A7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03DuchenneMuscularDystrophyDonor2_CNhs14599_ctss_fwd MyoblastToMyotubes_Day03D2+ Myoblast differentiation to myotubes, day03, Duchenne Muscular Dystrophy donor2_CNhs14599_13508-145D7_forward Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor2_CNhs14571_ctss_fwd MyoblastToMyotubes_Day03D2+ Myoblast differentiation to myotubes, day03, control donor2_CNhs14571_13481-145A7_forward Regulation 
MyoblastDifferentiationToMyotubesDay03DuchenneMuscularDystrophyDonor1_CNhs14589_ctss_rev MyoblastToMyotubes_Day03D1- Myoblast differentiation to myotubes, day03, Duchenne Muscular Dystrophy donor1_CNhs14589_13499-145C7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor1_CNhs13850_ctss_rev MyoblastToMyotubes_Day03D1- Myoblast differentiation to myotubes, day03, control donor1_CNhs13850_13472-144I7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03DuchenneMuscularDystrophyDonor1_CNhs14589_ctss_fwd MyoblastToMyotubes_Day03D1+ Myoblast differentiation to myotubes, day03, Duchenne Muscular Dystrophy donor1_CNhs14589_13499-145C7_forward Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor1_CNhs13850_ctss_fwd MyoblastToMyotubes_Day03D1+ Myoblast differentiation to myotubes, day03, control donor1_CNhs13850_13472-144I7_forward Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor3_CNhs14607_ctss_rev MyoblastToMyotubes_Day02D3- Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor3_CNhs14607_13516-145E6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor3_CNhs14579_ctss_rev MyoblastToMyotubes_Day02D3- Myoblast differentiation to myotubes, day02, control donor3_CNhs14579_13489-145B6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor3_CNhs14607_ctss_fwd MyoblastToMyotubes_Day02D3+ Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor3_CNhs14607_13516-145E6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor3_CNhs14579_ctss_fwd MyoblastToMyotubes_Day02D3+ Myoblast differentiation to myotubes, day02, control donor3_CNhs14579_13489-145B6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor2_CNhs14570_ctss_rev MyoblastToMyotubes_Day02D2- Myoblast differentiation to myotubes, day02, control donor2_CNhs14570_13480-145A6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor2_CNhs14598_ctss_rev MyoblastToMyotubes_Day02D2- Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor2_CNhs14598_13507-145D6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor2_CNhs14570_ctss_fwd MyoblastToMyotubes_Day02D2+ Myoblast differentiation to myotubes, day02, control donor2_CNhs14570_13480-145A6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor2_CNhs14598_ctss_fwd MyoblastToMyotubes_Day02D2+ Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor2_CNhs14598_13507-145D6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor1_CNhs13849_ctss_rev MyoblastToMyotubes_Day02D1- Myoblast differentiation to myotubes, day02, control donor1_CNhs13849_13471-144I6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor1_CNhs14588_ctss_rev MyoblastToMyotubes_Day02D1- Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor1_CNhs14588_13498-145C6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor1_CNhs13849_ctss_fwd MyoblastToMyotubes_Day02D1+ Myoblast differentiation to myotubes, day02, control donor1_CNhs13849_13471-144I6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor1_CNhs14588_ctss_fwd MyoblastToMyotubes_Day02D1+ Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor1_CNhs14588_13498-145C6_forward Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor3_CNhs14606_ctss_rev MyoblastToMyotubes_Day01D3- Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor3_CNhs14606_13515-145E5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor3_CNhs14578_ctss_rev MyoblastToMyotubes_Day01D3- Myoblast differentiation to myotubes, day01, control donor3_CNhs14578_13488-145B5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor3_CNhs14578_ctss_fwd MyoblastToMyotubes_Day01D3+ Myoblast differentiation to myotubes, day01, control donor3_CNhs14578_13488-145B5_forward Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor3_CNhs14606_ctss_fwd MyoblastToMyotubes_Day01D3+ Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor3_CNhs14606_13515-145E5_forward Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor2_CNhs14597_ctss_rev MyoblastToMyotubes_Day01D2- Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor2_CNhs14597_13506-145D5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor2_CNhs14597_ctss_fwd MyoblastToMyotubes_Day01D2+ Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor2_CNhs14597_13506-145D5_forward Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor1_CNhs13848_ctss_rev MyoblastToMyotubes_Day01D1- Myoblast differentiation to myotubes, day01, control donor1_CNhs13848_13470-144I5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor1_CNhs14587_ctss_rev MyoblastToMyotubes_Day01D1- Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor1_CNhs14587_13497-145C5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor1_CNhs13848_ctss_fwd MyoblastToMyotubes_Day01D1+ Myoblast differentiation to myotubes, day01, control donor1_CNhs13848_13470-144I5_forward Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor1_CNhs14587_ctss_fwd MyoblastToMyotubes_Day01D1+ Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor1_CNhs14587_13497-145C5_forward Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor3_CNhs14577_ctss_rev MyoblastToMyotubes_Day00D3- Myoblast differentiation to myotubes, day00, control donor3_CNhs14577_13487-145B4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor3_CNhs14605_ctss_rev MyoblastToMyotubes_Day00D3- Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor3_CNhs14605_13514-145E4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor3_CNhs14577_ctss_fwd MyoblastToMyotubes_Day00D3+ Myoblast differentiation to myotubes, day00, control donor3_CNhs14577_13487-145B4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor3_CNhs14605_ctss_fwd MyoblastToMyotubes_Day00D3+ Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor3_CNhs14605_13514-145E4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor2_CNhs14567_ctss_rev MyoblastToMyotubes_Day00D2- Myoblast differentiation to myotubes, day00, control donor2_CNhs14567_13478-145A4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor2_CNhs14596_ctss_rev MyoblastToMyotubes_Day00D2- Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor2_CNhs14596_13505-145D4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor2_CNhs14596_ctss_fwd MyoblastToMyotubes_Day00D2+ Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor2_CNhs14596_13505-145D4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor2_CNhs14567_ctss_fwd MyoblastToMyotubes_Day00D2+ Myoblast differentiation to myotubes, day00, control donor2_CNhs14567_13478-145A4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor1_CNhs14586_ctss_rev MyoblastToMyotubes_Day00D1- Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor1_CNhs14586_13496-145C4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor1_CNhs13847_ctss_rev MyoblastToMyotubes_Day00D1- Myoblast differentiation to myotubes, day00, control donor1_CNhs13847_13469-144I4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor1_CNhs14586_ctss_fwd MyoblastToMyotubes_Day00D1+ Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor1_CNhs14586_13496-145C4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor1_CNhs13847_ctss_fwd MyoblastToMyotubes_Day00D1+ Myoblast differentiation to myotubes, day00, control donor1_CNhs13847_13469-144I4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS48hrDonor2T26Subject2_CNhs13405_ctss_rev Tc:MdmToLps_48hrD2- Monocyte-derived macrophages response to LPS, 48hr, donor2 (t26 Subject2)_CNhs13405_12821-136I4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS48hrDonor2T26Subject2_CNhs13405_ctss_fwd Tc:MdmToLps_48hrD2+ Monocyte-derived macrophages response to LPS, 48hr, donor2 (t26 Subject2)_CNhs13405_12821-136I4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS48hrDonor1T26Subject1_CNhs11942_ctss_rev Tc:MdmToLps_48hrD1- Monocyte-derived macrophages response to LPS, 48hr, donor1 (t26 Subject1)_CNhs11942_12723-135G5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS48hrDonor1T26Subject1_CNhs11942_ctss_fwd Tc:MdmToLps_48hrD1+ Monocyte-derived macrophages response to LPS, 48hr, donor1 (t26 Subject1)_CNhs11942_12723-135G5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor3T25Subject3_CNhs13335_ctss_rev Tc:MdmToLps_36hrD3- Monocyte-derived macrophages response to LPS, 36hr, donor3 (t25 Subject3)_CNhs13335_12918-138B2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor3T25Subject3_CNhs13335_ctss_fwd Tc:MdmToLps_36hrD3+ Monocyte-derived macrophages response to LPS, 36hr, donor3 (t25 Subject3)_CNhs13335_12918-138B2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor2T25Subject2_CNhs13404_ctss_rev Tc:MdmToLps_36hrD2- Monocyte-derived macrophages response to LPS, 36hr, donor2 (t25 Subject2)_CNhs13404_12820-136I3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor2T25Subject2_CNhs13404_ctss_fwd Tc:MdmToLps_36hrD2+ Monocyte-derived macrophages response to LPS, 36hr, donor2 (t25 Subject2)_CNhs13404_12820-136I3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor1T25Subject1_CNhs12933_ctss_rev Tc:MdmToLps_36hrD1- Monocyte-derived macrophages response to LPS, 36hr, donor1 (t25 Subject1)_CNhs12933_12722-135G4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor1T25Subject1_CNhs12933_ctss_fwd Tc:MdmToLps_36hrD1+ Monocyte-derived macrophages response to LPS, 36hr, donor1 (t25 Subject1)_CNhs12933_12722-135G4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor3T24Subject3_CNhs13334_ctss_rev Tc:MdmToLps_24hrD3- Monocyte-derived macrophages response to LPS, 24hr, donor3 (t24 Subject3)_CNhs13334_12917-138B1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor3T24Subject3_CNhs13334_ctss_fwd Tc:MdmToLps_24hrD3+ Monocyte-derived macrophages response to LPS, 24hr, donor3 (t24 Subject3)_CNhs13334_12917-138B1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor2T24Subject2_CNhs13403_ctss_rev Tc:MdmToLps_24hrD2- Monocyte-derived macrophages response to LPS, 24hr, donor2 (t24 Subject2)_CNhs13403_12819-136I2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor2T24Subject2_CNhs13403_ctss_fwd Tc:MdmToLps_24hrD2+ Monocyte-derived macrophages response to LPS, 24hr, donor2 (t24 Subject2)_CNhs13403_12819-136I2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor1T24Subject1_CNhs12932_ctss_rev Tc:MdmToLps_24hrD1- Monocyte-derived macrophages response to LPS, 24hr, donor1 (t24 Subject1)_CNhs12932_12721-135G3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor1T24Subject1_CNhs12932_ctss_fwd Tc:MdmToLps_24hrD1+ Monocyte-derived macrophages response to LPS, 24hr, donor1 (t24 Subject1)_CNhs12932_12721-135G3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor3T23Subject3_CNhs13333_ctss_rev Tc:MdmToLps_22hrD3- Monocyte-derived macrophages response to LPS, 22hr, donor3 (t23 Subject3)_CNhs13333_12916-138A9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor3T23Subject3_CNhs13333_ctss_fwd Tc:MdmToLps_22hrD3+ Monocyte-derived macrophages response to LPS, 22hr, donor3 (t23 Subject3)_CNhs13333_12916-138A9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor2T23Subject2_CNhs13402_ctss_rev Tc:MdmToLps_22hrD2- Monocyte-derived macrophages response to LPS, 22hr, donor2 (t23 Subject2)_CNhs13402_12818-136I1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor2T23Subject2_CNhs13402_ctss_fwd Tc:MdmToLps_22hrD2+ Monocyte-derived macrophages response to LPS, 22hr, donor2 (t23 Subject2)_CNhs13402_12818-136I1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor1T23Subject1_CNhs12815_ctss_rev Tc:MdmToLps_22hrD1- Monocyte-derived macrophages response to LPS, 22hr, donor1 (t23 Subject1)_CNhs12815_12720-135G2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor1T23Subject1_CNhs12815_ctss_fwd Tc:MdmToLps_22hrD1+ Monocyte-derived macrophages response to LPS, 22hr, donor1 (t23 Subject1)_CNhs12815_12720-135G2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor3T22Subject3_CNhs13332_ctss_rev Tc:MdmToLps_20hrD3- Monocyte-derived macrophages response to LPS, 20hr, donor3 (t22 Subject3)_CNhs13332_12915-138A8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor3T22Subject3_CNhs13332_ctss_fwd Tc:MdmToLps_20hrD3+ Monocyte-derived macrophages response to LPS, 20hr, donor3 (t22 Subject3)_CNhs13332_12915-138A8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor2T22Subject2_CNhs13401_ctss_rev Tc:MdmToLps_20hrD2- Monocyte-derived macrophages response to LPS, 20hr, donor2 (t22 Subject2)_CNhs13401_12817-136H9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor2T22Subject2_CNhs13401_ctss_fwd Tc:MdmToLps_20hrD2+ Monocyte-derived macrophages response to LPS, 20hr, donor2 (t22 Subject2)_CNhs13401_12817-136H9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor1T22Subject1_CNhs12931_ctss_rev Tc:MdmToLps_20hrD1- Monocyte-derived macrophages response to LPS, 20hr, donor1 (t22 Subject1)_CNhs12931_12719-135G1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor1T22Subject1_CNhs12931_ctss_fwd Tc:MdmToLps_20hrD1+ Monocyte-derived macrophages response to LPS, 20hr, donor1 (t22 Subject1)_CNhs12931_12719-135G1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor3T21Subject3_CNhs13331_ctss_rev Tc:MdmToLps_18hrD3- Monocyte-derived macrophages response to LPS, 18hr, donor3 (t21 Subject3)_CNhs13331_12914-138A7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor3T21Subject3_CNhs13331_ctss_fwd Tc:MdmToLps_18hrD3+ Monocyte-derived macrophages response to LPS, 18hr, donor3 (t21 Subject3)_CNhs13331_12914-138A7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor2T21Subject2_CNhs13400_ctss_rev Tc:MdmToLps_18hrD2- Monocyte-derived macrophages response to LPS, 18hr, donor2 (t21 Subject2)_CNhs13400_12816-136H8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor2T21Subject2_CNhs13400_ctss_fwd Tc:MdmToLps_18hrD2+ Monocyte-derived macrophages response to LPS, 18hr, donor2 (t21 Subject2)_CNhs13400_12816-136H8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor1T21Subject1_CNhs12814_ctss_rev Tc:MdmToLps_18hrD1- Monocyte-derived macrophages response to LPS, 18hr, donor1 (t21 Subject1)_CNhs12814_12718-135F9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor1T21Subject1_CNhs12814_ctss_fwd Tc:MdmToLps_18hrD1+ Monocyte-derived macrophages response to LPS, 18hr, donor1 (t21 Subject1)_CNhs12814_12718-135F9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor3T20Subject3_CNhs13330_ctss_rev Tc:MdmToLps_16hrD3- Monocyte-derived macrophages response to LPS, 16hr, donor3 (t20 Subject3)_CNhs13330_12913-138A6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor3T20Subject3_CNhs13330_ctss_fwd Tc:MdmToLps_16hrD3+ Monocyte-derived macrophages response to LPS, 16hr, donor3 (t20 Subject3)_CNhs13330_12913-138A6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor2T20Subject2_CNhs13399_ctss_rev Tc:MdmToLps_16hrD2- Monocyte-derived macrophages response to LPS, 16hr, donor2 (t20 Subject2)_CNhs13399_12815-136H7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor2T20Subject2_CNhs13399_ctss_fwd Tc:MdmToLps_16hrD2+ Monocyte-derived macrophages response to LPS, 16hr, donor2 (t20 Subject2)_CNhs13399_12815-136H7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor3T19Subject3_CNhs13329_ctss_rev Tc:MdmToLps_14hrD3- Monocyte-derived macrophages response to LPS, 14hr, donor3 (t19 Subject3)_CNhs13329_12912-138A5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor3T19Subject3_CNhs13329_ctss_fwd Tc:MdmToLps_14hrD3+ Monocyte-derived macrophages response to LPS, 14hr, donor3 (t19 Subject3)_CNhs13329_12912-138A5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor2T19Subject2_CNhs13398_ctss_rev Tc:MdmToLps_14hrD2- Monocyte-derived macrophages response to LPS, 14hr, donor2 (t19 Subject2)_CNhs13398_12814-136H6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor2T19Subject2_CNhs13398_ctss_fwd Tc:MdmToLps_14hrD2+ Monocyte-derived macrophages response to LPS, 14hr, donor2 (t19 Subject2)_CNhs13398_12814-136H6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor1T19Subject1_CNhs12929_ctss_rev Tc:MdmToLps_14hrD1- Monocyte-derived macrophages response to LPS, 14hr, donor1 (t19 Subject1)_CNhs12929_12716-135F7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor1T19Subject1_CNhs12929_ctss_fwd Tc:MdmToLps_14hrD1+ Monocyte-derived macrophages response to LPS, 14hr, donor1 (t19 Subject1)_CNhs12929_12716-135F7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor3T18Subject3_CNhs13328_ctss_rev Tc:MdmToLps_12hrD3- Monocyte-derived macrophages response to LPS, 12hr, donor3 (t18 Subject3)_CNhs13328_12911-138A4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor3T18Subject3_CNhs13328_ctss_fwd Tc:MdmToLps_12hrD3+ Monocyte-derived macrophages response to LPS, 12hr, donor3 (t18 Subject3)_CNhs13328_12911-138A4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor2T18Subject2_CNhs13397_ctss_rev Tc:MdmToLps_12hrD2- Monocyte-derived macrophages response to LPS, 12hr, donor2 (t18 Subject2)_CNhs13397_12813-136H5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor2T18Subject2_CNhs13397_ctss_fwd Tc:MdmToLps_12hrD2+ Monocyte-derived macrophages response to LPS, 12hr, donor2 (t18 Subject2)_CNhs13397_12813-136H5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor1T18Subject1_CNhs12813_ctss_rev Tc:MdmToLps_12hrD1- Monocyte-derived macrophages response to LPS, 12hr, donor1 (t18 Subject1)_CNhs12813_12715-135F6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor1T18Subject1_CNhs12813_ctss_fwd Tc:MdmToLps_12hrD1+ Monocyte-derived macrophages response to LPS, 12hr, donor1 (t18 Subject1)_CNhs12813_12715-135F6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor3T17Subject3_CNhs13327_ctss_rev Tc:MdmToLps_10hrD3- Monocyte-derived macrophages response to LPS, 10hr, donor3 (t17 Subject3)_CNhs13327_12910-138A3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor3T17Subject3_CNhs13327_ctss_fwd Tc:MdmToLps_10hrD3+ Monocyte-derived macrophages response to LPS, 10hr, donor3 (t17 Subject3)_CNhs13327_12910-138A3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor2T17Subject2_CNhs13396_ctss_rev Tc:MdmToLps_10hrD2- Monocyte-derived macrophages response to LPS, 10hr, donor2 (t17 Subject2)_CNhs13396_12812-136H4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor2T17Subject2_CNhs13396_ctss_fwd Tc:MdmToLps_10hrD2+ Monocyte-derived macrophages response to LPS, 10hr, donor2 (t17 Subject2)_CNhs13396_12812-136H4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor3T16Subject3_CNhs13326_ctss_rev Tc:MdmToLps_08hrD3- Monocyte-derived macrophages response to LPS, 08hr, donor3 (t16 Subject3)_CNhs13326_12909-138A2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor3T16Subject3_CNhs13326_ctss_fwd Tc:MdmToLps_08hrD3+ Monocyte-derived macrophages response to LPS, 08hr, donor3 (t16 Subject3)_CNhs13326_12909-138A2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor2T16Subject2_CNhs13395_ctss_rev Tc:MdmToLps_08hrD2- Monocyte-derived macrophages response to LPS, 08hr, donor2 (t16 Subject2)_CNhs13395_12811-136H3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor2T16Subject2_CNhs13395_ctss_fwd Tc:MdmToLps_08hrD2+ Monocyte-derived macrophages response to LPS, 08hr, donor2 (t16 Subject2)_CNhs13395_12811-136H3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor1T16Subject1_CNhs12927_ctss_rev Tc:MdmToLps_08hrD1- Monocyte-derived macrophages response to LPS, 08hr, donor1 (t16 Subject1)_CNhs12927_12713-135F4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor1T16Subject1_CNhs12927_ctss_fwd Tc:MdmToLps_08hrD1+ Monocyte-derived macrophages response to LPS, 08hr, donor1 (t16 Subject1)_CNhs12927_12713-135F4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor3T13Subject3_CNhs13186_ctss_rev Tc:MdmToLps_05hrD3- Monocyte-derived macrophages response to LPS, 05hr, donor3 (t13 Subject3)_CNhs13186_12906-137I8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor3T13Subject3_CNhs13186_ctss_fwd Tc:MdmToLps_05hrD3+ Monocyte-derived macrophages response to LPS, 05hr, donor3 (t13 Subject3)_CNhs13186_12906-137I8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor2T13Subject2_CNhs13392_ctss_rev Tc:MdmToLps_05hrD2- Monocyte-derived macrophages response to LPS, 05hr, donor2 (t13 Subject2)_CNhs13392_12808-136G9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor2T13Subject2_CNhs13392_ctss_fwd Tc:MdmToLps_05hrD2+ Monocyte-derived macrophages response to LPS, 05hr, donor2 (t13 Subject2)_CNhs13392_12808-136G9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor1T13Subject1_CNhs13155_ctss_rev Tc:MdmToLps_05hrD1- Monocyte-derived macrophages response to LPS, 05hr, donor1 (t13 Subject1)_CNhs13155_12710-135F1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor1T13Subject1_CNhs13155_ctss_fwd Tc:MdmToLps_05hrD1+ Monocyte-derived macrophages response to LPS, 05hr, donor1 (t13 Subject1)_CNhs13155_12710-135F1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor3T12Subject3_CNhs13185_ctss_rev Tc:MdmToLps_04hrD3- Monocyte-derived macrophages response to LPS, 04hr, donor3 (t12 Subject3)_CNhs13185_12905-137I7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor3T12Subject3_CNhs13185_ctss_fwd Tc:MdmToLps_04hrD3+ Monocyte-derived macrophages response to LPS, 04hr, donor3 (t12 Subject3)_CNhs13185_12905-137I7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor2T12Subject2_CNhs13391_ctss_rev Tc:MdmToLps_04hrD2- Monocyte-derived macrophages response to LPS, 04hr, donor2 (t12 Subject2)_CNhs13391_12807-136G8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor2T12Subject2_CNhs13391_ctss_fwd Tc:MdmToLps_04hrD2+ Monocyte-derived macrophages response to LPS, 04hr, donor2 (t12 Subject2)_CNhs13391_12807-136G8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor3T11Subject3_CNhs13184_ctss_rev Tc:MdmToLps_03hr30minD3- Monocyte-derived macrophages response to LPS, 03hr30min, donor3 (t11 Subject3)_CNhs13184_12904-137I6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor3T11Subject3_CNhs13184_ctss_fwd Tc:MdmToLps_03hr30minD3+ Monocyte-derived macrophages response to LPS, 03hr30min, donor3 (t11 Subject3)_CNhs13184_12904-137I6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor2T11Subject2_CNhs13389_ctss_rev Tc:MdmToLps_03hr30minD2- Monocyte-derived macrophages response to LPS, 03hr30min, donor2 (t11 Subject2)_CNhs13389_12806-136G7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor2T11Subject2_CNhs13389_ctss_fwd Tc:MdmToLps_03hr30minD2+ Monocyte-derived macrophages response to LPS, 03hr30min, donor2 (t11 Subject2)_CNhs13389_12806-136G7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor3T10Subject3_CNhs13183_ctss_rev Tc:MdmToLps_03hr00minD3- Monocyte-derived macrophages response to LPS, 03hr00min, donor3 (t10 Subject3)_CNhs13183_12903-137I5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor3T10Subject3_CNhs13183_ctss_fwd Tc:MdmToLps_03hr00minD3+ Monocyte-derived macrophages response to LPS, 03hr00min, donor3 (t10 Subject3)_CNhs13183_12903-137I5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor2T10Subject2_CNhs13388_ctss_rev Tc:MdmToLps_03hr00minD2- Monocyte-derived macrophages response to LPS, 03hr00min, donor2 (t10 Subject2)_CNhs13388_12805-136G6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor2T10Subject2_CNhs13388_ctss_fwd Tc:MdmToLps_03hr00minD2+ Monocyte-derived macrophages response to LPS, 03hr00min, donor2 (t10 Subject2)_CNhs13388_12805-136G6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor1T10Subject1_CNhs12924_ctss_rev Tc:MdmToLps_03hr00minD1- Monocyte-derived macrophages response to LPS, 03hr00min, donor1 (t10 Subject1)_CNhs12924_12707-135E7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor1T10Subject1_CNhs12924_ctss_fwd Tc:MdmToLps_03hr00minD1+ Monocyte-derived macrophages response to LPS, 03hr00min, donor1 (t10 Subject1)_CNhs12924_12707-135E7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor3T9Subject3_CNhs13182_ctss_rev Tc:MdmToLps_02hr30minD3- Monocyte-derived macrophages response to LPS, 02hr30min, donor3 (t9 Subject3)_CNhs13182_12902-137I4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor3T9Subject3_CNhs13182_ctss_fwd Tc:MdmToLps_02hr30minD3+ Monocyte-derived macrophages response to LPS, 02hr30min, donor3 (t9 Subject3)_CNhs13182_12902-137I4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor2T9Subject2_CNhs13387_ctss_rev Tc:MdmToLps_02hr30minD2- Monocyte-derived macrophages response to LPS, 02hr30min, donor2 (t9 Subject2)_CNhs13387_12804-136G5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor2T9Subject2_CNhs13387_ctss_fwd Tc:MdmToLps_02hr30minD2+ Monocyte-derived macrophages response to LPS, 02hr30min, donor2 (t9 Subject2)_CNhs13387_12804-136G5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor1T9Subject1_CNhs13152_ctss_rev Tc:MdmToLps_02hr30minD1- Monocyte-derived macrophages response to LPS, 02hr30min, donor1 (t9 Subject1)_CNhs13152_12706-135E6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor1T9Subject1_CNhs13152_ctss_fwd Tc:MdmToLps_02hr30minD1+ Monocyte-derived macrophages response to LPS, 02hr30min, donor1 (t9 Subject1)_CNhs13152_12706-135E6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor3T8Subject3_CNhs13181_ctss_rev Tc:MdmToLps_02hr00minD3- Monocyte-derived macrophages response to LPS, 02hr00min, donor3 (t8 Subject3)_CNhs13181_12901-137I3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor3T8Subject3_CNhs13181_ctss_fwd Tc:MdmToLps_02hr00minD3+ Monocyte-derived macrophages response to LPS, 02hr00min, donor3 (t8 Subject3)_CNhs13181_12901-137I3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor2T8Subject2_CNhs13386_ctss_rev Tc:MdmToLps_02hr00minD2- Monocyte-derived macrophages response to LPS, 02hr00min, donor2 (t8 Subject2)_CNhs13386_12803-136G4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor2T8Subject2_CNhs13386_ctss_fwd Tc:MdmToLps_02hr00minD2+ Monocyte-derived macrophages response to LPS, 02hr00min, donor2 (t8 Subject2)_CNhs13386_12803-136G4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor3T6Subject3_CNhs13179_ctss_rev Tc:MdmToLps_01hr20minD3- Monocyte-derived macrophages response to LPS, 01hr20min, donor3 (t6 Subject3)_CNhs13179_12899-137I1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor3T6Subject3_CNhs13179_ctss_fwd Tc:MdmToLps_01hr20minD3+ Monocyte-derived macrophages response to LPS, 01hr20min, donor3 (t6 Subject3)_CNhs13179_12899-137I1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor2T6Subject2_CNhs13384_ctss_rev Tc:MdmToLps_01hr20minD2- Monocyte-derived macrophages response to LPS, 01hr20min, donor2 (t6 Subject2)_CNhs13384_12801-136G2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor2T6Subject2_CNhs13384_ctss_fwd Tc:MdmToLps_01hr20minD2+ Monocyte-derived macrophages response to LPS, 01hr20min, donor2 (t6 Subject2)_CNhs13384_12801-136G2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor3T5Subject3_CNhs13178_ctss_rev Tc:MdmToLps_01hr00minD3- Monocyte-derived macrophages response to LPS, 01hr00min, donor3 (t5 Subject3)_CNhs13178_12898-137H9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor3T5Subject3_CNhs13178_ctss_fwd Tc:MdmToLps_01hr00minD3+ Monocyte-derived macrophages response to LPS, 01hr00min, donor3 (t5 Subject3)_CNhs13178_12898-137H9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor2T5Subject2_CNhs13383_ctss_rev Tc:MdmToLps_01hr00minD2- Monocyte-derived macrophages response to LPS, 01hr00min, donor2 (t5 Subject2)_CNhs13383_12800-136G1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor2T5Subject2_CNhs13383_ctss_fwd Tc:MdmToLps_01hr00minD2+ Monocyte-derived macrophages response to LPS, 01hr00min, donor2 (t5 Subject2)_CNhs13383_12800-136G1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor3T4Subject3_CNhs13177_ctss_rev Tc:MdmToLps_00hr45minD3- Monocyte-derived macrophages response to LPS, 00hr45min, donor3 (t4 Subject3)_CNhs13177_12897-137H8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor3T4Subject3_CNhs13177_ctss_fwd Tc:MdmToLps_00hr45minD3+ Monocyte-derived macrophages response to LPS, 00hr45min, donor3 (t4 Subject3)_CNhs13177_12897-137H8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor2T4Subject2_CNhs13382_ctss_rev Tc:MdmToLps_00hr45minD2- Monocyte-derived macrophages response to LPS, 00hr45min, donor2 (t4 Subject2)_CNhs13382_12799-136F9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor2T4Subject2_CNhs13382_ctss_fwd Tc:MdmToLps_00hr45minD2+ Monocyte-derived macrophages response to LPS, 00hr45min, donor2 (t4 Subject2)_CNhs13382_12799-136F9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor3T3Subject3_CNhs13176_ctss_rev Tc:MdmToLps_00hr30minD3- Monocyte-derived macrophages response to LPS, 00hr30min, donor3 (t3 Subject3)_CNhs13176_12896-137H7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor3T3Subject3_CNhs13176_ctss_fwd Tc:MdmToLps_00hr30minD3+ Monocyte-derived macrophages response to LPS, 00hr30min, donor3 (t3 Subject3)_CNhs13176_12896-137H7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor2T3Subject2_CNhs13381_ctss_rev Tc:MdmToLps_00hr30minD2- Monocyte-derived macrophages response to LPS, 00hr30min, donor2 (t3 Subject2)_CNhs13381_12798-136F8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor2T3Subject2_CNhs13381_ctss_fwd Tc:MdmToLps_00hr30minD2+ Monocyte-derived macrophages response to LPS, 00hr30min, donor2 (t3 Subject2)_CNhs13381_12798-136F8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor3T2Subject3_CNhs13175_ctss_rev Tc:MdmToLps_00hr15minD3- Monocyte-derived macrophages response to LPS, 00hr15min, donor3 (t2 Subject3)_CNhs13175_12895-137H6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor3T2Subject3_CNhs13175_ctss_fwd Tc:MdmToLps_00hr15minD3+ Monocyte-derived macrophages response to LPS, 00hr15min, donor3 (t2 Subject3)_CNhs13175_12895-137H6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor2T2Subject2_CNhs13380_ctss_rev Tc:MdmToLps_00hr15minD2- Monocyte-derived macrophages response to LPS, 00hr15min, donor2 (t2 Subject2)_CNhs13380_12797-136F7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor2T2Subject2_CNhs13380_ctss_fwd Tc:MdmToLps_00hr15minD2+ Monocyte-derived macrophages response to LPS, 00hr15min, donor2 (t2 Subject2)_CNhs13380_12797-136F7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor3T1Subject3_CNhs13174_ctss_rev Tc:MdmToLps_00hr00minD3- Monocyte-derived macrophages response to LPS, 00hr00min, donor3 (t1 Subject3)_CNhs13174_12894-137H5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor3T1Subject3_CNhs13174_ctss_fwd Tc:MdmToLps_00hr00minD3+ Monocyte-derived macrophages response to LPS, 00hr00min, donor3 (t1 Subject3)_CNhs13174_12894-137H5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor2T1Subject2_CNhs13379_ctss_rev Tc:MdmToLps_00hr00minD2- Monocyte-derived macrophages response to LPS, 00hr00min, donor2 (t1 Subject2)_CNhs13379_12796-136F6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor2T1Subject2_CNhs13379_ctss_fwd Tc:MdmToLps_00hr00minD2+ Monocyte-derived macrophages response to LPS, 00hr00min, donor2 (t1 Subject2)_CNhs13379_12796-136F6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor1T1Subject1_CNhs11941_ctss_rev Tc:MdmToLps_00hr00minD1- Monocyte-derived macrophages response to LPS, 00hr00min, donor1 (t1 Subject1)_CNhs11941_12698-135D7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor1T1Subject1_CNhs11941_ctss_fwd Tc:MdmToLps_00hr00minD1+ Monocyte-derived macrophages response to LPS, 00hr00min, donor1 (t1 Subject1)_CNhs11941_12698-135D7_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor4227_121MI_24h_CNhs13644_ctss_rev Tc:MdmToMock_24hr00minD4- Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor4 (227_121:MI_24h)_CNhs13644_13315-143A3_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor4227_121MI_24h_CNhs13644_ctss_fwd Tc:MdmToMock_24hr00minD4+ Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor4 (227_121:MI_24h)_CNhs13644_13315-143A3_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor3536_119MI_24h_CNhs13652_ctss_rev Tc:MdmToMock_24hr00minD3- Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor3 (536_119:MI_24h)_CNhs13652_13327-143B6_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor3536_119MI_24h_CNhs13652_ctss_fwd Tc:MdmToMock_24hr00minD3+ Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor3 (536_119:MI_24h)_CNhs13652_13327-143B6_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor2150_120MI_24h_CNhs13648_ctss_rev Tc:MdmToMock_24hr00minD2- Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor2 (150_120:MI_24h)_CNhs13648_13321-143A9_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor2150_120MI_24h_CNhs13648_ctss_fwd Tc:MdmToMock_24hr00minD2+ Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor2 (150_120:MI_24h)_CNhs13648_13321-143A9_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor1868_121MI_24h_CNhs13693_ctss_rev Tc:MdmToMock_24hr00minD1- Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor1 (868_121:MI_24h)_CNhs13693_13309-142I6_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor1868_121MI_24h_CNhs13693_ctss_fwd Tc:MdmToMock_24hr00minD1+ Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor1 (868_121:MI_24h)_CNhs13693_13309-142I6_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor4227_121MI_0h_CNhs13638_ctss_rev Tc:MdmToMock_00hr00minD4- Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor4 (227_121:MI_0h)_CNhs13638_13310-142I7_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor4227_121MI_0h_CNhs13638_ctss_fwd Tc:MdmToMock_00hr00minD4+ Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor4 (227_121:MI_0h)_CNhs13638_13310-142I7_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor3536_119MI_0h_CNhs13649_ctss_rev Tc:MdmToMock_00hr00minD3- Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor3 (536_119:MI_0h)_CNhs13649_13322-143B1_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor3536_119MI_0h_CNhs13649_ctss_fwd Tc:MdmToMock_00hr00minD3+ Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor3 (536_119:MI_0h)_CNhs13649_13322-143B1_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor2150_120MI_0h_CNhs13645_ctss_rev Tc:MdmToMock_00hr00minD2- Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor2 (150_120:MI_0h)_CNhs13645_13316-143A4_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor2150_120MI_0h_CNhs13645_ctss_fwd Tc:MdmToMock_00hr00minD2+ Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor2 (150_120:MI_0h)_CNhs13645_13316-143A4_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor3536_119Ud_24h_CNhs13562_ctss_rev MonocyteMacrophageUdornInfluenza_24hr00minD3- Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor3 (536_119:Ud_24h)_CNhs13562_13326-143B5_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor3536_119Ud_24h_CNhs13562_ctss_fwd MonocyteMacrophageUdornInfluenza_24hr00minD3+ Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor3 (536_119:Ud_24h)_CNhs13562_13326-143B5_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor2150_120Ud_24h_CNhs13560_ctss_rev MonocyteMacrophageUdornInfluenza_24hr00minD2- Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor2 (150_120:Ud_24h)_CNhs13560_13320-143A8_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor2150_120Ud_24h_CNhs13560_ctss_fwd MonocyteMacrophageUdornInfluenza_24hr00minD2+ Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor2 (150_120:Ud_24h)_CNhs13560_13320-143A8_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor1868_121Ud_24h_CNhs13557_ctss_rev MonocyteMacrophageUdornInfluenza_24hr00minD1- Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor1 (868_121:Ud_24h)_CNhs13557_13308-142I5_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor1868_121Ud_24h_CNhs13557_ctss_fwd MonocyteMacrophageUdornInfluenza_24hr00minD1+ Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor1 (868_121:Ud_24h)_CNhs13557_13308-142I5_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor4227_121Ud_7h_CNhs13641_ctss_rev MonocyteMacrophageUdornInfluenza_07hr00minD4- Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor4 (227_121:Ud_7h)_CNhs13641_13313-143A1_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor4227_121Ud_7h_CNhs13641_ctss_fwd MonocyteMacrophageUdornInfluenza_07hr00minD4+ Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor4 (227_121:Ud_7h)_CNhs13641_13313-143A1_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor3536_119Ud_7h_CNhs13561_ctss_rev MonocyteMacrophageUdornInfluenza_07hr00minD3- Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor3 (536_119:Ud_7h)_CNhs13561_13325-143B4_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor3536_119Ud_7h_CNhs13561_ctss_fwd MonocyteMacrophageUdornInfluenza_07hr00minD3+ Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor3 (536_119:Ud_7h)_CNhs13561_13325-143B4_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor2150_120Ud_7h_CNhs13559_ctss_rev MonocyteMacrophageUdornInfluenza_07hr00minD2- Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor2 (150_120:Ud_7h)_CNhs13559_13319-143A7_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor2150_120Ud_7h_CNhs13559_ctss_fwd MonocyteMacrophageUdornInfluenza_07hr00minD2+ Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor2 (150_120:Ud_7h)_CNhs13559_13319-143A7_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor1868_121Ud_7h_CNhs13556_ctss_rev MonocyteMacrophageUdornInfluenza_07hr00minD1- Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor1 (868_121:Ud_7h)_CNhs13556_13307-142I4_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor1868_121Ud_7h_CNhs13556_ctss_fwd MonocyteMacrophageUdornInfluenza_07hr00minD1+ Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor1 (868_121:Ud_7h)_CNhs13556_13307-142I4_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor4227_121Ud_2h_CNhs13640_ctss_rev MonocyteMacrophageUdornInfluenza_02hr00minD4- Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor4 (227_121:Ud_2h)_CNhs13640_13312-142I9_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor4227_121Ud_2h_CNhs13640_ctss_fwd MonocyteMacrophageUdornInfluenza_02hr00minD4+ Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor4 (227_121:Ud_2h)_CNhs13640_13312-142I9_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor3536_119Ud_2h_CNhs13651_ctss_rev MonocyteMacrophageUdornInfluenza_02hr00minD3- Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor3 (536_119:Ud_2h)_CNhs13651_13324-143B3_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor3536_119Ud_2h_CNhs13651_ctss_fwd MonocyteMacrophageUdornInfluenza_02hr00minD3+ Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor3 (536_119:Ud_2h)_CNhs13651_13324-143B3_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor1868_121Ud_2h_CNhs13555_ctss_rev MonocyteMacrophageUdornInfluenza_02hr00minD1- Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor1 (868_121:Ud_2h)_CNhs13555_13306-142I3_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor1868_121Ud_2h_CNhs13555_ctss_fwd MonocyteMacrophageUdornInfluenza_02hr00minD1+ Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor1 (868_121:Ud_2h)_CNhs13555_13306-142I3_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor4227_121Ud_0h_CNhs13639_ctss_rev MonocyteMacrophageUdornInfluenza_00hr00minD4- Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor4 (227_121:Ud_0h)_CNhs13639_13311-142I8_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor4227_121Ud_0h_CNhs13639_ctss_fwd MonocyteMacrophageUdornInfluenza_00hr00minD4+ Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor4 (227_121:Ud_0h)_CNhs13639_13311-142I8_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor3536_119Ud_0h_CNhs13650_ctss_rev MonocyteMacrophageUdornInfluenza_00hr00minD3- Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor3 (536_119:Ud_0h)_CNhs13650_13323-143B2_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor3536_119Ud_0h_CNhs13650_ctss_fwd MonocyteMacrophageUdornInfluenza_00hr00minD3+ Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor3 (536_119:Ud_0h)_CNhs13650_13323-143B2_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor2150_120Ud_0h_CNhs13646_ctss_rev MonocyteMacrophageUdornInfluenza_00hr00minD2- Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor2 (150_120:Ud_0h)_CNhs13646_13317-143A5_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor2150_120Ud_0h_CNhs13646_ctss_fwd MonocyteMacrophageUdornInfluenza_00hr00minD2+ Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor2 (150_120:Ud_0h)_CNhs13646_13317-143A5_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor1868_121Ud_0h_CNhs13554_ctss_rev MonocyteMacrophageUdornInfluenza_00hr00minD1- Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor1 (868_121:Ud_0h)_CNhs13554_13305-142I2_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor1868_121Ud_0h_CNhs13554_ctss_fwd MonocyteMacrophageUdornInfluenza_00hr00minD1+ Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor1 (868_121:Ud_0h)_CNhs13554_13305-142I2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep3_CNhs13632_ctss_rev MscAdipogenicInduction_Day14Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep3_CNhs13632_13279-142F3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep3_CNhs13632_ctss_fwd MscAdipogenicInduction_Day14Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep3_CNhs13632_13279-142F3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep1_CNhs13338_ctss_rev MscAdipogenicInduction_Day14Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep1_CNhs13338_13277-142F1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep1_CNhs13338_ctss_fwd MscAdipogenicInduction_Day14Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep1_CNhs13338_13277-142F1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep3_CNhs13630_ctss_rev MscAdipogenicInduction_Day12Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep3_CNhs13630_13276-142E9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep3_CNhs13630_ctss_fwd MscAdipogenicInduction_Day12Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep3_CNhs13630_13276-142E9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep2_CNhs13629_ctss_rev MscAdipogenicInduction_Day12Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep2_CNhs13629_13275-142E8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep2_CNhs13629_ctss_fwd MscAdipogenicInduction_Day12Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep2_CNhs13629_13275-142E8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep1_CNhs13628_ctss_rev MscAdipogenicInduction_Day12Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep1_CNhs13628_13274-142E7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep1_CNhs13628_ctss_fwd MscAdipogenicInduction_Day12Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep1_CNhs13628_13274-142E7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep3_CNhs13627_ctss_rev MscAdipogenicInduction_Day08Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep3_CNhs13627_13273-142E6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep3_CNhs13627_ctss_fwd MscAdipogenicInduction_Day08Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep3_CNhs13627_13273-142E6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep2_CNhs13626_ctss_rev MscAdipogenicInduction_Day08Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep2_CNhs13626_13272-142E5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep2_CNhs13626_ctss_fwd MscAdipogenicInduction_Day08Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep2_CNhs13626_13272-142E5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep1_CNhs13625_ctss_rev MscAdipogenicInduction_Day08Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep1_CNhs13625_13271-142E4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep1_CNhs13625_ctss_fwd MscAdipogenicInduction_Day08Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep1_CNhs13625_13271-142E4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep3_CNhs13624_ctss_rev MscAdipogenicInduction_Day04Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep3_CNhs13624_13270-142E3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep3_CNhs13624_ctss_fwd MscAdipogenicInduction_Day04Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep3_CNhs13624_13270-142E3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep1_CNhs13622_ctss_rev MscAdipogenicInduction_Day04Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep1_CNhs13622_13268-142E1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep1_CNhs13622_ctss_fwd MscAdipogenicInduction_Day04Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep1_CNhs13622_13268-142E1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep3_CNhs13621_ctss_rev MscAdipogenicInduction_Day02Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep3_CNhs13621_13267-142D9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep3_CNhs13621_ctss_fwd MscAdipogenicInduction_Day02Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep3_CNhs13621_13267-142D9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep2_CNhs13620_ctss_rev MscAdipogenicInduction_Day02Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep2_CNhs13620_13266-142D8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep2_CNhs13620_ctss_fwd MscAdipogenicInduction_Day02Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep2_CNhs13620_13266-142D8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep1_CNhs13619_ctss_rev MscAdipogenicInduction_Day02Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep1_CNhs13619_13265-142D7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep1_CNhs13619_ctss_fwd MscAdipogenicInduction_Day02Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep1_CNhs13619_13265-142D7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep3_CNhs13617_ctss_rev MscAdipogenicInduction_Day01Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep3_CNhs13617_13264-142D6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep3_CNhs13617_ctss_fwd MscAdipogenicInduction_Day01Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep3_CNhs13617_13264-142D6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep2_CNhs13616_ctss_rev MscAdipogenicInduction_Day01Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep2_CNhs13616_13263-142D5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep2_CNhs13616_ctss_fwd MscAdipogenicInduction_Day01Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep2_CNhs13616_13263-142D5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep3_CNhs13611_ctss_rev MscAdipogenicInduction_03hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep3_CNhs13611_13258-142C9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep3_CNhs13611_ctss_fwd MscAdipogenicInduction_03hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep3_CNhs13611_13258-142C9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep1_CNhs13609_ctss_rev MscAdipogenicInduction_03hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep1_CNhs13609_13256-142C7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep1_CNhs13609_ctss_fwd MscAdipogenicInduction_03hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep1_CNhs13609_13256-142C7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep3_CNhs13608_ctss_rev MscAdipogenicInduction_02hr30minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep3_CNhs13608_13255-142C6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep3_CNhs13608_ctss_fwd MscAdipogenicInduction_02hr30minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep3_CNhs13608_13255-142C6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep1_CNhs13606_ctss_rev MscAdipogenicInduction_02hr30minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep1_CNhs13606_13253-142C4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep1_CNhs13606_ctss_fwd MscAdipogenicInduction_02hr30minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep1_CNhs13606_13253-142C4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep2_CNhs13604_ctss_rev MscAdipogenicInduction_02hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep2_CNhs13604_13251-142C2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep2_CNhs13604_ctss_fwd MscAdipogenicInduction_02hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep2_CNhs13604_13251-142C2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep1_CNhs13603_ctss_rev MscAdipogenicInduction_02hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep1_CNhs13603_13250-142C1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep1_CNhs13603_ctss_fwd MscAdipogenicInduction_02hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep1_CNhs13603_13250-142C1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep3_CNhs13602_ctss_rev MscAdipogenicInduction_01hr40minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep3_CNhs13602_13249-142B9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep3_CNhs13602_ctss_fwd MscAdipogenicInduction_01hr40minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep3_CNhs13602_13249-142B9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep2_CNhs13601_ctss_rev MscAdipogenicInduction_01hr40minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep2_CNhs13601_13248-142B8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep2_CNhs13601_ctss_fwd MscAdipogenicInduction_01hr40minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep2_CNhs13601_13248-142B8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep1_CNhs13600_ctss_rev MscAdipogenicInduction_01hr40minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep1_CNhs13600_13247-142B7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep1_CNhs13600_ctss_fwd MscAdipogenicInduction_01hr40minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep1_CNhs13600_13247-142B7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep3_CNhs13433_ctss_rev MscAdipogenicInduction_01hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep3_CNhs13433_13243-142B3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep3_CNhs13433_ctss_fwd MscAdipogenicInduction_01hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep3_CNhs13433_13243-142B3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep2_CNhs13432_ctss_rev MscAdipogenicInduction_01hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep2_CNhs13432_13242-142B2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep2_CNhs13432_ctss_fwd MscAdipogenicInduction_01hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep2_CNhs13432_13242-142B2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep1_CNhs13431_ctss_rev MscAdipogenicInduction_01hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep1_CNhs13431_13241-142B1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep1_CNhs13431_ctss_fwd MscAdipogenicInduction_01hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep1_CNhs13431_13241-142B1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep3_CNhs13430_ctss_rev MscAdipogenicInduction_00hr45minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep3_CNhs13430_13240-142A9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep3_CNhs13430_ctss_fwd MscAdipogenicInduction_00hr45minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep3_CNhs13430_13240-142A9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep2_CNhs13429_ctss_rev MscAdipogenicInduction_00hr45minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep2_CNhs13429_13239-142A8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep2_CNhs13429_ctss_fwd MscAdipogenicInduction_00hr45minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep2_CNhs13429_13239-142A8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep1_CNhs13428_ctss_rev MscAdipogenicInduction_00hr45minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep1_CNhs13428_13238-142A7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep1_CNhs13428_ctss_fwd MscAdipogenicInduction_00hr45minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep1_CNhs13428_13238-142A7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep2_CNhs13426_ctss_rev MscAdipogenicInduction_00hr30minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep2_CNhs13426_13236-142A5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep2_CNhs13426_ctss_fwd MscAdipogenicInduction_00hr30minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep2_CNhs13426_13236-142A5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep1_CNhs13425_ctss_rev MscAdipogenicInduction_00hr30minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep1_CNhs13425_13235-142A4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep1_CNhs13425_ctss_fwd MscAdipogenicInduction_00hr30minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep1_CNhs13425_13235-142A4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep3_CNhs13424_ctss_rev MscAdipogenicInduction_00hr15minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep3_CNhs13424_13234-142A3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep3_CNhs13424_ctss_fwd MscAdipogenicInduction_00hr15minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep3_CNhs13424_13234-142A3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep2_CNhs13423_ctss_rev MscAdipogenicInduction_00hr15minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep2_CNhs13423_13233-142A2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep2_CNhs13423_ctss_fwd MscAdipogenicInduction_00hr15minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep2_CNhs13423_13233-142A2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep1_CNhs13422_ctss_rev MscAdipogenicInduction_00hr15minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep1_CNhs13422_13232-142A1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep1_CNhs13422_ctss_fwd MscAdipogenicInduction_00hr15minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep1_CNhs13422_13232-142A1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep3_CNhs13421_ctss_rev MscAdipogenicInduction_00hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep3_CNhs13421_13231-141I9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep3_CNhs13421_ctss_fwd MscAdipogenicInduction_00hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep3_CNhs13421_13231-141I9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep2_CNhs13420_ctss_rev MscAdipogenicInduction_00hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep2_CNhs13420_13230-141I8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep2_CNhs13420_ctss_fwd MscAdipogenicInduction_00hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep2_CNhs13420_13230-141I8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep1_CNhs13337_ctss_rev MscAdipogenicInduction_00hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep1_CNhs13337_13229-141I7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep1_CNhs13337_ctss_fwd MscAdipogenicInduction_00hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep1_CNhs13337_13229-141I7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep3_CNhs12768_ctss_rev Tc:Mcf7ToHrg_08hrBr3- MCF7 breast cancer cell line response to HRG, 08hr, biol_rep3_CNhs12768_13194-141E8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep3_CNhs12768_ctss_fwd Tc:Mcf7ToHrg_08hrBr3+ MCF7 breast cancer cell line response to HRG, 08hr, biol_rep3_CNhs12768_13194-141E8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep2_CNhs12667_ctss_rev Tc:Mcf7ToHrg_08hrBr2- MCF7 breast cancer cell line response to HRG, 08hr, biol_rep2_CNhs12667_13128-140G5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep2_CNhs12667_ctss_fwd Tc:Mcf7ToHrg_08hrBr2+ MCF7 breast cancer cell line response to HRG, 08hr, biol_rep2_CNhs12667_13128-140G5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep1_CNhs12740_ctss_rev Tc:Mcf7ToHrg_08hrBr1- MCF7 breast cancer cell line response to HRG, 08hr, biol_rep1_CNhs12740_13062-139I2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep1_CNhs12740_ctss_fwd Tc:Mcf7ToHrg_08hrBr1+ MCF7 breast cancer cell line response to HRG, 08hr, biol_rep1_CNhs12740_13062-139I2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep3_CNhs12767_ctss_rev Tc:Mcf7ToHrg_07hrBr3- MCF7 breast cancer cell line response to HRG, 07hr, biol_rep3_CNhs12767_13193-141E7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep3_CNhs12767_ctss_fwd Tc:Mcf7ToHrg_07hrBr3+ MCF7 breast cancer cell line response to HRG, 07hr, biol_rep3_CNhs12767_13193-141E7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep2_CNhs12666_ctss_rev Tc:Mcf7ToHrg_07hrBr2- MCF7 breast cancer cell line response to HRG, 07hr, biol_rep2_CNhs12666_13127-140G4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep2_CNhs12666_ctss_fwd Tc:Mcf7ToHrg_07hrBr2+ MCF7 breast cancer cell line response to HRG, 07hr, biol_rep2_CNhs12666_13127-140G4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep1_CNhs12448_ctss_rev Tc:Mcf7ToHrg_07hrBr1- MCF7 breast cancer cell line response to HRG, 07hr, biol_rep1_CNhs12448_13061-139I1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep1_CNhs12448_ctss_fwd Tc:Mcf7ToHrg_07hrBr1+ MCF7 breast cancer cell line response to HRG, 07hr, biol_rep1_CNhs12448_13061-139I1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep3_CNhs12766_ctss_rev Tc:Mcf7ToHrg_06hrBr3- MCF7 breast cancer cell line response to HRG, 06hr, biol_rep3_CNhs12766_13192-141E6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep3_CNhs12766_ctss_fwd Tc:Mcf7ToHrg_06hrBr3+ MCF7 breast cancer cell line response to HRG, 06hr, biol_rep3_CNhs12766_13192-141E6_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep2_CNhs12665_ctss_rev Tc:Mcf7ToHrg_06hrBr2- MCF7 breast cancer cell line response to HRG, 06hr, biol_rep2_CNhs12665_13126-140G3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep2_CNhs12665_ctss_fwd Tc:Mcf7ToHrg_06hrBr2+ MCF7 breast cancer cell line response to HRG, 06hr, biol_rep2_CNhs12665_13126-140G3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep1_CNhs12447_ctss_rev Tc:Mcf7ToHrg_06hrBr1- MCF7 breast cancer cell line response to HRG, 06hr, biol_rep1_CNhs12447_13060-139H9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep1_CNhs12447_ctss_fwd Tc:Mcf7ToHrg_06hrBr1+ MCF7 breast cancer cell line response to HRG, 06hr, biol_rep1_CNhs12447_13060-139H9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep3_CNhs12765_ctss_rev Tc:Mcf7ToHrg_05hrBr3- MCF7 breast cancer cell line response to HRG, 05hr, biol_rep3_CNhs12765_13191-141E5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep3_CNhs12765_ctss_fwd Tc:Mcf7ToHrg_05hrBr3+ MCF7 breast cancer cell line response to HRG, 05hr, biol_rep3_CNhs12765_13191-141E5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep2_CNhs12664_ctss_rev Tc:Mcf7ToHrg_05hrBr2- MCF7 breast cancer cell line response to HRG, 05hr, biol_rep2_CNhs12664_13125-140G2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep2_CNhs12664_ctss_fwd Tc:Mcf7ToHrg_05hrBr2+ MCF7 breast cancer cell line response to HRG, 05hr, biol_rep2_CNhs12664_13125-140G2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep1_CNhs12446_ctss_rev Tc:Mcf7ToHrg_05hrBr1- MCF7 breast cancer cell line response to HRG, 05hr, biol_rep1_CNhs12446_13059-139H8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep1_CNhs12446_ctss_fwd Tc:Mcf7ToHrg_05hrBr1+ MCF7 breast cancer cell line response to HRG, 05hr, biol_rep1_CNhs12446_13059-139H8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep3_CNhs12764_ctss_rev Tc:Mcf7ToHrg_04hrBr3- MCF7 breast cancer cell line response to HRG, 04hr, biol_rep3_CNhs12764_13190-141E4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep3_CNhs12764_ctss_fwd Tc:Mcf7ToHrg_04hrBr3+ MCF7 breast cancer cell line response to HRG, 04hr, biol_rep3_CNhs12764_13190-141E4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep2_CNhs12663_ctss_rev Tc:Mcf7ToHrg_04hrBr2- MCF7 breast cancer cell line response to HRG, 04hr, biol_rep2_CNhs12663_13124-140G1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep2_CNhs12663_ctss_fwd Tc:Mcf7ToHrg_04hrBr2+ MCF7 breast cancer cell line response to HRG, 04hr, biol_rep2_CNhs12663_13124-140G1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep1_CNhs12445_ctss_rev Tc:Mcf7ToHrg_04hrBr1- MCF7 breast cancer cell line response to HRG, 04hr, biol_rep1_CNhs12445_13058-139H7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep1_CNhs12445_ctss_fwd Tc:Mcf7ToHrg_04hrBr1+ MCF7 breast cancer cell line response to HRG, 04hr, biol_rep1_CNhs12445_13058-139H7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep3_CNhs12763_ctss_rev Tc:Mcf7ToHrg_03hr30minBr3- MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep3_CNhs12763_13189-141E3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep3_CNhs12763_ctss_fwd Tc:Mcf7ToHrg_03hr30minBr3+ MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep3_CNhs12763_13189-141E3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep2_CNhs12662_ctss_rev Tc:Mcf7ToHrg_03hr30minBr2- MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep2_CNhs12662_13123-140F9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep2_CNhs12662_ctss_fwd Tc:Mcf7ToHrg_03hr30minBr2+ MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep2_CNhs12662_13123-140F9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep1_CNhs12444_ctss_rev Tc:Mcf7ToHrg_03hr30minBr1- MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep1_CNhs12444_13057-139H6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep1_CNhs12444_ctss_fwd Tc:Mcf7ToHrg_03hr30minBr1+ MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep1_CNhs12444_13057-139H6_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep3_CNhs12762_ctss_rev Tc:Mcf7ToHrg_03hr00minBr3- MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep3_CNhs12762_13188-141E2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep3_CNhs12762_ctss_fwd Tc:Mcf7ToHrg_03hr00minBr3+ MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep3_CNhs12762_13188-141E2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep2_CNhs12660_ctss_rev Tc:Mcf7ToHrg_03hr00minBr2- MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep2_CNhs12660_13122-140F8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep2_CNhs12660_ctss_fwd Tc:Mcf7ToHrg_03hr00minBr2+ MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep2_CNhs12660_13122-140F8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep1_CNhs12443_ctss_rev Tc:Mcf7ToHrg_03hr00minBr1- MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep1_CNhs12443_13056-139H5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep1_CNhs12443_ctss_fwd Tc:Mcf7ToHrg_03hr00minBr1+ MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep1_CNhs12443_13056-139H5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep3_CNhs12761_ctss_rev Tc:Mcf7ToHrg_02hr30minBr3- MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep3_CNhs12761_13187-141E1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep3_CNhs12761_ctss_fwd Tc:Mcf7ToHrg_02hr30minBr3+ MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep3_CNhs12761_13187-141E1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep2_CNhs12659_ctss_rev Tc:Mcf7ToHrg_02hr30minBr2- MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep2_CNhs12659_13121-140F7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep2_CNhs12659_ctss_fwd Tc:Mcf7ToHrg_02hr30minBr2+ MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep2_CNhs12659_13121-140F7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep1_CNhs12442_ctss_rev Tc:Mcf7ToHrg_02hr30minBr1- MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep1_CNhs12442_13055-139H4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep1_CNhs12442_ctss_fwd Tc:Mcf7ToHrg_02hr30minBr1+ MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep1_CNhs12442_13055-139H4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep3_CNhs12760_ctss_rev Tc:Mcf7ToHrg_02hr00minBr3- MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep3_CNhs12760_13186-141D9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep3_CNhs12760_ctss_fwd Tc:Mcf7ToHrg_02hr00minBr3+ MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep3_CNhs12760_13186-141D9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep2_CNhs12658_ctss_rev Tc:Mcf7ToHrg_02hr00minBr2- MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep2_CNhs12658_13120-140F6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep2_CNhs12658_ctss_fwd Tc:Mcf7ToHrg_02hr00minBr2+ MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep2_CNhs12658_13120-140F6_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep1_CNhs12441_ctss_rev Tc:Mcf7ToHrg_02hr00minBr1- MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep1_CNhs12441_13054-139H3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep1_CNhs12441_ctss_fwd Tc:Mcf7ToHrg_02hr00minBr1+ MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep1_CNhs12441_13054-139H3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep3_CNhs12759_ctss_rev Tc:Mcf7ToHrg_01hr40minBr3- MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep3_CNhs12759_13185-141D8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep3_CNhs12759_ctss_fwd Tc:Mcf7ToHrg_01hr40minBr3+ MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep3_CNhs12759_13185-141D8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep2_CNhs12657_ctss_rev Tc:Mcf7ToHrg_01hr40minBr2- MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep2_CNhs12657_13119-140F5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep2_CNhs12657_ctss_fwd Tc:Mcf7ToHrg_01hr40minBr2+ MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep2_CNhs12657_13119-140F5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep1_CNhs12440_ctss_rev Tc:Mcf7ToHrg_01hr40minBr1- MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep1_CNhs12440_13053-139H2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep1_CNhs12440_ctss_fwd Tc:Mcf7ToHrg_01hr40minBr1+ MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep1_CNhs12440_13053-139H2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep3_CNhs12758_ctss_rev Tc:Mcf7ToHrg_01hr20minBr3- MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep3_CNhs12758_13184-141D7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep3_CNhs12758_ctss_fwd Tc:Mcf7ToHrg_01hr20minBr3+ MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep3_CNhs12758_13184-141D7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep2_CNhs12656_ctss_rev Tc:Mcf7ToHrg_01hr20minBr2- MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep2_CNhs12656_13118-140F4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep2_CNhs12656_ctss_fwd Tc:Mcf7ToHrg_01hr20minBr2+ MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep2_CNhs12656_13118-140F4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep1_CNhs12439_ctss_rev Tc:Mcf7ToHrg_01hr20minBr1- MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep1_CNhs12439_13052-139H1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep1_CNhs12439_ctss_fwd Tc:Mcf7ToHrg_01hr20minBr1+ MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep1_CNhs12439_13052-139H1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep3_CNhs12757_ctss_rev Tc:Mcf7ToHrg_01hr00minBr3- MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep3_CNhs12757_13183-141D6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep3_CNhs12757_ctss_fwd Tc:Mcf7ToHrg_01hr00minBr3+ MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep3_CNhs12757_13183-141D6_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep2_CNhs12655_ctss_rev Tc:Mcf7ToHrg_01hr00minBr2- MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep2_CNhs12655_13117-140F3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep2_CNhs12655_ctss_fwd Tc:Mcf7ToHrg_01hr00minBr2+ MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep2_CNhs12655_13117-140F3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep1_CNhs12438_ctss_rev Tc:Mcf7ToHrg_01hr00minBr1- MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep1_CNhs12438_13051-139G9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep1_CNhs12438_ctss_fwd Tc:Mcf7ToHrg_01hr00minBr1+ MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep1_CNhs12438_13051-139G9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep3_CNhs12756_ctss_rev Tc:Mcf7ToHrg_00hr45minBr3- MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep3_CNhs12756_13182-141D5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep3_CNhs12756_ctss_fwd Tc:Mcf7ToHrg_00hr45minBr3+ MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep3_CNhs12756_13182-141D5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep2_CNhs12654_ctss_rev Tc:Mcf7ToHrg_00hr45minBr2- MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep2_CNhs12654_13116-140F2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep2_CNhs12654_ctss_fwd Tc:Mcf7ToHrg_00hr45minBr2+ MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep2_CNhs12654_13116-140F2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep1_CNhs12437_ctss_rev Tc:Mcf7ToHrg_00hr45minBr1- MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep1_CNhs12437_13050-139G8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep1_CNhs12437_ctss_fwd Tc:Mcf7ToHrg_00hr45minBr1+ MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep1_CNhs12437_13050-139G8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep3_CNhs12755_ctss_rev Tc:Mcf7ToHrg_00hr30minBr3- MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep3_CNhs12755_13181-141D4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep3_CNhs12755_ctss_fwd Tc:Mcf7ToHrg_00hr30minBr3+ MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep3_CNhs12755_13181-141D4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep2_CNhs12653_ctss_rev Tc:Mcf7ToHrg_00hr30minBr2- MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep2_CNhs12653_13115-140F1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep2_CNhs12653_ctss_fwd Tc:Mcf7ToHrg_00hr30minBr2+ MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep2_CNhs12653_13115-140F1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep1_CNhs12436_ctss_rev Tc:Mcf7ToHrg_00hr30minBr1- MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep1_CNhs12436_13049-139G7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep1_CNhs12436_ctss_fwd Tc:Mcf7ToHrg_00hr30minBr1+ MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep1_CNhs12436_13049-139G7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep3_CNhs12754_ctss_rev Tc:Mcf7ToHrg_00hr15minBr3- MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep3_CNhs12754_13180-141D3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep3_CNhs12754_ctss_fwd Tc:Mcf7ToHrg_00hr15minBr3+ MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep3_CNhs12754_13180-141D3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep2_CNhs12652_ctss_rev Tc:Mcf7ToHrg_00hr15minBr2- MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep2_CNhs12652_13114-140E9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep2_CNhs12652_ctss_fwd Tc:Mcf7ToHrg_00hr15minBr2+ MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep2_CNhs12652_13114-140E9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep1_CNhs12435_ctss_rev Tc:Mcf7ToHrg_00hr15minBr1- MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep1_CNhs12435_13048-139G6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep1_CNhs12435_ctss_fwd Tc:Mcf7ToHrg_00hr15minBr1+ MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep1_CNhs12435_13048-139G6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep3_CNhs12753_ctss_rev Mcf7ToEgf1_08hrBr3- MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep3_CNhs12753_13178-141D1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep3_CNhs12753_ctss_fwd Mcf7ToEgf1_08hrBr3+ MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep3_CNhs12753_13178-141D1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep2_CNhs12491_ctss_rev Mcf7ToEgf1_08hrBr2- MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep2_CNhs12491_13112-140E7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep2_CNhs12491_ctss_fwd Mcf7ToEgf1_08hrBr2+ MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep2_CNhs12491_13112-140E7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep3_CNhs12752_ctss_rev Mcf7ToEgf1_07hrBr3- MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep3_CNhs12752_13177-141C9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep3_CNhs12752_ctss_fwd Mcf7ToEgf1_07hrBr3+ MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep3_CNhs12752_13177-141C9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep2_CNhs12490_ctss_rev Mcf7ToEgf1_07hrBr2- MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep2_CNhs12490_13111-140E6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep2_CNhs12490_ctss_fwd Mcf7ToEgf1_07hrBr2+ MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep2_CNhs12490_13111-140E6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep1_CNhs12434_ctss_rev Mcf7ToEgf1_07hrBr1- MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep1_CNhs12434_13045-139G3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep1_CNhs12434_ctss_fwd Mcf7ToEgf1_07hrBr1+ MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep1_CNhs12434_13045-139G3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep3_CNhs12751_ctss_rev Mcf7ToEgf1_06hrBr3- MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep3_CNhs12751_13176-141C8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep3_CNhs12751_ctss_fwd Mcf7ToEgf1_06hrBr3+ MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep3_CNhs12751_13176-141C8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep2_CNhs12489_ctss_rev Mcf7ToEgf1_06hrBr2- MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep2_CNhs12489_13110-140E5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep2_CNhs12489_ctss_fwd Mcf7ToEgf1_06hrBr2+ MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep2_CNhs12489_13110-140E5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep1_CNhs12432_ctss_rev Mcf7ToEgf1_06hrBr1- MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep1_CNhs12432_13044-139G2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep1_CNhs12432_ctss_fwd Mcf7ToEgf1_06hrBr1+ MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep1_CNhs12432_13044-139G2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep3_CNhs12750_ctss_rev Mcf7ToEgf1_05hrBr3- MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep3_CNhs12750_13175-141C7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep3_CNhs12750_ctss_fwd Mcf7ToEgf1_05hrBr3+ MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep3_CNhs12750_13175-141C7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep2_CNhs12488_ctss_rev Mcf7ToEgf1_05hrBr2- MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep2_CNhs12488_13109-140E4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep2_CNhs12488_ctss_fwd Mcf7ToEgf1_05hrBr2+ MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep2_CNhs12488_13109-140E4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep1_CNhs12431_ctss_rev Mcf7ToEgf1_05hrBr1- MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep1_CNhs12431_13043-139G1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep1_CNhs12431_ctss_fwd Mcf7ToEgf1_05hrBr1+ MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep1_CNhs12431_13043-139G1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep3_CNhs12749_ctss_rev Mcf7ToEgf1_04hrBr3- MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep3_CNhs12749_13174-141C6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep3_CNhs12749_ctss_fwd Mcf7ToEgf1_04hrBr3+ MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep3_CNhs12749_13174-141C6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep2_CNhs12487_ctss_rev Mcf7ToEgf1_04hrBr2- MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep2_CNhs12487_13108-140E3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep2_CNhs12487_ctss_fwd Mcf7ToEgf1_04hrBr2+ MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep2_CNhs12487_13108-140E3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep1_CNhs12430_ctss_rev Mcf7ToEgf1_04hrBr1- MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep1_CNhs12430_13042-139F9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep1_CNhs12430_ctss_fwd Mcf7ToEgf1_04hrBr1+ MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep1_CNhs12430_13042-139F9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep3_CNhs12748_ctss_rev Mcf7ToEgf1_03hr30minBr3- MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep3_CNhs12748_13173-141C5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep3_CNhs12748_ctss_fwd Mcf7ToEgf1_03hr30minBr3+ MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep3_CNhs12748_13173-141C5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep2_CNhs12486_ctss_rev Mcf7ToEgf1_03hr30minBr2- MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep2_CNhs12486_13107-140E2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep2_CNhs12486_ctss_fwd Mcf7ToEgf1_03hr30minBr2+ MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep2_CNhs12486_13107-140E2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep1_CNhs12429_ctss_rev Mcf7ToEgf1_03hr30minBr1- MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep1_CNhs12429_13041-139F8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep1_CNhs12429_ctss_fwd Mcf7ToEgf1_03hr30minBr1+ MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep1_CNhs12429_13041-139F8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep3_CNhs12747_ctss_rev Mcf7ToEgf1_03hr00minBr3- MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep3_CNhs12747_13172-141C4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep3_CNhs12747_ctss_fwd Mcf7ToEgf1_03hr00minBr3+ MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep3_CNhs12747_13172-141C4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep2_CNhs12485_ctss_rev Mcf7ToEgf1_03hr00minBr2- MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep2_CNhs12485_13106-140E1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep2_CNhs12485_ctss_fwd Mcf7ToEgf1_03hr00minBr2+ MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep2_CNhs12485_13106-140E1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep1_CNhs12428_ctss_rev Mcf7ToEgf1_03hr00minBr1- MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep1_CNhs12428_13040-139F7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep1_CNhs12428_ctss_fwd Mcf7ToEgf1_03hr00minBr1+ MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep1_CNhs12428_13040-139F7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep3_CNhs12746_ctss_rev Mcf7ToEgf1_02hr30minBr3- MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep3_CNhs12746_13171-141C3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep3_CNhs12746_ctss_fwd Mcf7ToEgf1_02hr30minBr3+ MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep3_CNhs12746_13171-141C3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep2_CNhs12484_ctss_rev Mcf7ToEgf1_02hr30minBr2- MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep2_CNhs12484_13105-140D9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep2_CNhs12484_ctss_fwd Mcf7ToEgf1_02hr30minBr2+ MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep2_CNhs12484_13105-140D9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep1_CNhs12427_ctss_rev Mcf7ToEgf1_02hr30minBr1- MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep1_CNhs12427_13039-139F6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep1_CNhs12427_ctss_fwd Mcf7ToEgf1_02hr30minBr1+ MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep1_CNhs12427_13039-139F6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep3_CNhs12744_ctss_rev Mcf7ToEgf1_02hr00minBr3- MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep3_CNhs12744_13170-141C2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep3_CNhs12744_ctss_fwd Mcf7ToEgf1_02hr00minBr3+ MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep3_CNhs12744_13170-141C2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep2_CNhs12483_ctss_rev Mcf7ToEgf1_02hr00minBr2- MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep2_CNhs12483_13104-140D8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep2_CNhs12483_ctss_fwd Mcf7ToEgf1_02hr00minBr2+ MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep2_CNhs12483_13104-140D8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep1_CNhs12426_ctss_rev Mcf7ToEgf1_02hr00minBr1- MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep1_CNhs12426_13038-139F5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep1_CNhs12426_ctss_fwd Mcf7ToEgf1_02hr00minBr1+ MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep1_CNhs12426_13038-139F5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep3_CNhs12743_ctss_rev Mcf7ToEgf1_01hr40minBr3- MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep3_CNhs12743_13169-141C1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep3_CNhs12743_ctss_fwd Mcf7ToEgf1_01hr40minBr3+ MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep3_CNhs12743_13169-141C1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep2_CNhs12482_ctss_rev Mcf7ToEgf1_01hr40minBr2- MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep2_CNhs12482_13103-140D7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep2_CNhs12482_ctss_fwd Mcf7ToEgf1_01hr40minBr2+ MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep2_CNhs12482_13103-140D7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep1_CNhs12425_ctss_rev Mcf7ToEgf1_01hr40minBr1- MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep1_CNhs12425_13037-139F4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep1_CNhs12425_ctss_fwd Mcf7ToEgf1_01hr40minBr1+ MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep1_CNhs12425_13037-139F4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep3_CNhs12742_ctss_rev Mcf7ToEgf1_01hr20minBr3- MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep3_CNhs12742_13168-141B9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep3_CNhs12742_ctss_fwd Mcf7ToEgf1_01hr20minBr3+ MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep3_CNhs12742_13168-141B9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep2_CNhs12480_ctss_rev Mcf7ToEgf1_01hr20minBr2- MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep2_CNhs12480_13102-140D6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep2_CNhs12480_ctss_fwd Mcf7ToEgf1_01hr20minBr2+ MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep2_CNhs12480_13102-140D6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep1_CNhs12424_ctss_rev Mcf7ToEgf1_01hr20minBr1- MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep1_CNhs12424_13036-139F3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep1_CNhs12424_ctss_fwd Mcf7ToEgf1_01hr20minBr1+ MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep1_CNhs12424_13036-139F3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep3_CNhs12705_ctss_rev Mcf7ToEgf1_01hr00minBr3- MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep3_CNhs12705_13167-141B8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep3_CNhs12705_ctss_fwd Mcf7ToEgf1_01hr00minBr3+ MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep3_CNhs12705_13167-141B8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep2_CNhs12479_ctss_rev Mcf7ToEgf1_01hr00minBr2- MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep2_CNhs12479_13101-140D5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep2_CNhs12479_ctss_fwd Mcf7ToEgf1_01hr00minBr2+ MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep2_CNhs12479_13101-140D5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep1_CNhs12423_ctss_rev Mcf7ToEgf1_01hr00minBr1- MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep1_CNhs12423_13035-139F2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep1_CNhs12423_ctss_fwd Mcf7ToEgf1_01hr00minBr1+ MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep1_CNhs12423_13035-139F2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep3_CNhs12739_ctss_rev Mcf7ToEgf1_00hr45minBr3- MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep3_CNhs12739_13166-141B7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep3_CNhs12739_ctss_fwd Mcf7ToEgf1_00hr45minBr3+ MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep3_CNhs12739_13166-141B7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep2_CNhs12478_ctss_rev Mcf7ToEgf1_00hr45minBr2- MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep2_CNhs12478_13100-140D4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep2_CNhs12478_ctss_fwd Mcf7ToEgf1_00hr45minBr2+ MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep2_CNhs12478_13100-140D4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep1_CNhs12422_ctss_rev Mcf7ToEgf1_00hr45minBr1- MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep1_CNhs12422_13034-139F1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep1_CNhs12422_ctss_fwd Mcf7ToEgf1_00hr45minBr1+ MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep1_CNhs12422_13034-139F1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep3_CNhs12738_ctss_rev Mcf7ToEgf1_00hr30minBr3- MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep3_CNhs12738_13165-141B6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep3_CNhs12738_ctss_fwd Mcf7ToEgf1_00hr30minBr3+ MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep3_CNhs12738_13165-141B6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep2_CNhs12477_ctss_rev Mcf7ToEgf1_00hr30minBr2- MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep2_CNhs12477_13099-140D3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep2_CNhs12477_ctss_fwd Mcf7ToEgf1_00hr30minBr2+ MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep2_CNhs12477_13099-140D3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep1_CNhs12421_ctss_rev Mcf7ToEgf1_00hr30minBr1- MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep1_CNhs12421_13033-139E9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep1_CNhs12421_ctss_fwd Mcf7ToEgf1_00hr30minBr1+ MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep1_CNhs12421_13033-139E9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep3_CNhs12704_ctss_rev Mcf7ToEgf1_00hr15minBr3- MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep3_CNhs12704_13164-141B5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep3_CNhs12704_ctss_fwd Mcf7ToEgf1_00hr15minBr3+ MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep3_CNhs12704_13164-141B5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep2_CNhs12476_ctss_rev Mcf7ToEgf1_00hr15minBr2- MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep2_CNhs12476_13098-140D2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep2_CNhs12476_ctss_fwd Mcf7ToEgf1_00hr15minBr2+ MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep2_CNhs12476_13098-140D2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep1_CNhs12420_ctss_rev Mcf7ToEgf1_00hr15minBr1- MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep1_CNhs12420_13032-139E8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep1_CNhs12420_ctss_fwd Mcf7ToEgf1_00hr15minBr1+ MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep1_CNhs12420_13032-139E8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep3_CNhs12703_ctss_rev Mcf7ToEgf1_00hr00minBr3- MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep3_CNhs12703_13163-141B4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep3_CNhs12703_ctss_fwd Mcf7ToEgf1_00hr00minBr3+ MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep3_CNhs12703_13163-141B4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep2_CNhs12475_ctss_rev Mcf7ToEgf1_00hr00minBr2- MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep2_CNhs12475_13097-140D1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep2_CNhs12475_ctss_fwd Mcf7ToEgf1_00hr00minBr2+ MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep2_CNhs12475_13097-140D1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep1_CNhs12565_ctss_rev Mcf7ToEgf1_08hrBr1- MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep1_CNhs12565_13046-139G4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep1_CNhs12565_ctss_fwd Mcf7ToEgf1_08hrBr1+ MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep1_CNhs12565_13046-139G4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep3MMXXII16_CNhs13291_ctss_rev LymphaticEndothelialCellsToVegfc_08hrBr3- Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep3 (MM XXII - 16)_CNhs13291_12519-133B8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep3MMXXII16_CNhs13291_ctss_fwd LymphaticEndothelialCellsToVegfc_08hrBr3+ Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep3 (MM XXII - 16)_CNhs13291_12519-133B8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep2MMXIV16_CNhs13173_ctss_rev LymphaticEndothelialCellsToVegfc_08hrBr2- Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep2 (MM XIV - 16)_CNhs13173_12397-131G3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep2MMXIV16_CNhs13173_ctss_fwd LymphaticEndothelialCellsToVegfc_08hrBr2+ Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep2 (MM XIV - 16)_CNhs13173_12397-131G3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep1MMXIX16_CNhs11937_ctss_rev LymphaticEndothelialCellsToVegfc_08hrBr1- Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep1 (MM XIX - 16)_CNhs11937_12275-130B7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep1MMXIX16_CNhs11937_ctss_fwd LymphaticEndothelialCellsToVegfc_08hrBr1+ Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep1 (MM XIX - 16)_CNhs11937_12275-130B7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep3MMXXII15_CNhs13290_ctss_rev LymphaticEndothelialCellsToVegfc_07hrBr3- Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep3 (MM XXII - 15)_CNhs13290_12518-133B7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep3MMXXII15_CNhs13290_ctss_fwd LymphaticEndothelialCellsToVegfc_07hrBr3+ Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep3 (MM XXII - 15)_CNhs13290_12518-133B7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep2MMXIV15_CNhs13172_ctss_rev LymphaticEndothelialCellsToVegfc_07hrBr2- Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep2 (MM XIV - 15)_CNhs13172_12396-131G2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep2MMXIV15_CNhs13172_ctss_fwd LymphaticEndothelialCellsToVegfc_07hrBr2+ Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep2 (MM XIV - 15)_CNhs13172_12396-131G2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep1MMXIX15_CNhs13113_ctss_rev LymphaticEndothelialCellsToVegfc_07hrBr1- Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep1 (MM XIX - 15)_CNhs13113_12274-130B6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep1MMXIX15_CNhs13113_ctss_fwd LymphaticEndothelialCellsToVegfc_07hrBr1+ Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep1 (MM XIX - 15)_CNhs13113_12274-130B6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep3MMXXII14_CNhs13289_ctss_rev LymphaticEndothelialCellsToVegfc_06hrBr3- Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep3 (MM XXII - 14)_CNhs13289_12517-133B6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep3MMXXII14_CNhs13289_ctss_fwd LymphaticEndothelialCellsToVegfc_06hrBr3+ Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep3 (MM XXII - 14)_CNhs13289_12517-133B6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep2MMXIV14_CNhs13171_ctss_rev LymphaticEndothelialCellsToVegfc_06hrBr2- Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep2 (MM XIV - 14)_CNhs13171_12395-131G1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep2MMXIV14_CNhs13171_ctss_fwd LymphaticEndothelialCellsToVegfc_06hrBr2+ Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep2 (MM XIV - 14)_CNhs13171_12395-131G1_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep1MMXIX14_CNhs13112_ctss_rev LymphaticEndothelialCellsToVegfc_06hrBr1- Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep1 (MM XIX - 14)_CNhs13112_12273-130B5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep1MMXIX14_CNhs13112_ctss_fwd LymphaticEndothelialCellsToVegfc_06hrBr1+ Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep1 (MM XIX - 14)_CNhs13112_12273-130B5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep3MMXXII13_CNhs13288_ctss_rev LymphaticEndothelialCellsToVegfc_05hrBr3- Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep3 (MM XXII - 13)_CNhs13288_12516-133B5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep3MMXXII13_CNhs13288_ctss_fwd LymphaticEndothelialCellsToVegfc_05hrBr3+ Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep3 (MM XXII - 13)_CNhs13288_12516-133B5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep2MMXIV13_CNhs13170_ctss_rev LymphaticEndothelialCellsToVegfc_05hrBr2- Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep2 (MM XIV - 13)_CNhs13170_12394-131F9_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep2MMXIV13_CNhs13170_ctss_fwd LymphaticEndothelialCellsToVegfc_05hrBr2+ Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep2 (MM XIV - 13)_CNhs13170_12394-131F9_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep1MMXIX13_CNhs13111_ctss_rev LymphaticEndothelialCellsToVegfc_05hrBr1- Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep1 (MM XIX - 13)_CNhs13111_12272-130B4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep1MMXIX13_CNhs13111_ctss_fwd LymphaticEndothelialCellsToVegfc_05hrBr1+ Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep1 (MM XIX - 13)_CNhs13111_12272-130B4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep3MMXXII12_CNhs13287_ctss_rev LymphaticEndothelialCellsToVegfc_04hrBr3- Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep3 (MM XXII - 12)_CNhs13287_12515-133B4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep3MMXXII12_CNhs13287_ctss_fwd LymphaticEndothelialCellsToVegfc_04hrBr3+ Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep3 (MM XXII - 12)_CNhs13287_12515-133B4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep2MMXIV12_CNhs13169_ctss_rev LymphaticEndothelialCellsToVegfc_04hrBr2- Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep2 (MM XIV - 12)_CNhs13169_12393-131F8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep2MMXIV12_CNhs13169_ctss_fwd LymphaticEndothelialCellsToVegfc_04hrBr2+ Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep2 (MM XIV - 12)_CNhs13169_12393-131F8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep1MMXIX12_CNhs13110_ctss_rev LymphaticEndothelialCellsToVegfc_04hrBr1- Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep1 (MM XIX - 12)_CNhs13110_12271-130B3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep1MMXIX12_CNhs13110_ctss_fwd LymphaticEndothelialCellsToVegfc_04hrBr1+ Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep1 (MM XIX - 12)_CNhs13110_12271-130B3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep3MMXXII11_CNhs13286_ctss_rev LymphaticEndothelialCellsToVegfc_03hr30minBr3- Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep3 (MM XXII - 11)_CNhs13286_12514-133B3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep3MMXXII11_CNhs13286_ctss_fwd LymphaticEndothelialCellsToVegfc_03hr30minBr3+ Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep3 (MM XXII - 11)_CNhs13286_12514-133B3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep2MMXIV11_CNhs13168_ctss_rev LymphaticEndothelialCellsToVegfc_03hr30minBr2- Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep2 (MM XIV - 11)_CNhs13168_12392-131F7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep2MMXIV11_CNhs13168_ctss_fwd LymphaticEndothelialCellsToVegfc_03hr30minBr2+ Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep2 (MM XIV - 11)_CNhs13168_12392-131F7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep1MMXIX11_CNhs13109_ctss_rev LymphaticEndothelialCellsToVegfc_03hr30minBr1- Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep1 (MM XIX - 11)_CNhs13109_12270-130B2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep1MMXIX11_CNhs13109_ctss_fwd LymphaticEndothelialCellsToVegfc_03hr30minBr1+ Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep1 (MM XIX - 11)_CNhs13109_12270-130B2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep3MMXXII10_CNhs13285_ctss_rev LymphaticEndothelialCellsToVegfc_03hr00minBr3- Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep3 (MM XXII - 10)_CNhs13285_12513-133B2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep3MMXXII10_CNhs13285_ctss_fwd LymphaticEndothelialCellsToVegfc_03hr00minBr3+ Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep3 (MM XXII - 10)_CNhs13285_12513-133B2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep2MMXIV10_CNhs13166_ctss_rev LymphaticEndothelialCellsToVegfc_03hr00minBr2- Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep2 (MM XIV - 10)_CNhs13166_12391-131F6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep2MMXIV10_CNhs13166_ctss_fwd LymphaticEndothelialCellsToVegfc_03hr00minBr2+ Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep2 (MM XIV - 10)_CNhs13166_12391-131F6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep1MMXIX10_CNhs13108_ctss_rev LymphaticEndothelialCellsToVegfc_03hr00minBr1- Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep1 (MM XIX - 10)_CNhs13108_12269-130B1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep1MMXIX10_CNhs13108_ctss_fwd LymphaticEndothelialCellsToVegfc_03hr00minBr1+ Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep1 (MM XIX - 10)_CNhs13108_12269-130B1_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep3MMXXII9_CNhs13284_ctss_rev LymphaticEndothelialCellsToVegfc_02hr30minBr3- Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep3 (MM XXII - 9)_CNhs13284_12512-133B1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep3MMXXII9_CNhs13284_ctss_fwd LymphaticEndothelialCellsToVegfc_02hr30minBr3+ Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep3 (MM XXII - 9)_CNhs13284_12512-133B1_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep2MMXIV9_CNhs13165_ctss_rev LymphaticEndothelialCellsToVegfc_02hr30minBr2- Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep2 (MM XIV - 9)_CNhs13165_12390-131F5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep2MMXIV9_CNhs13165_ctss_fwd LymphaticEndothelialCellsToVegfc_02hr30minBr2+ Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep2 (MM XIV - 9)_CNhs13165_12390-131F5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep1MMXIX9_CNhs13107_ctss_rev LymphaticEndothelialCellsToVegfc_02hr30minBr1- Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep1 (MM XIX - 9)_CNhs13107_12268-130A9_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep1MMXIX9_CNhs13107_ctss_fwd LymphaticEndothelialCellsToVegfc_02hr30minBr1+ Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep1 (MM XIX - 9)_CNhs13107_12268-130A9_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep3MMXXII8_CNhs13283_ctss_rev LymphaticEndothelialCellsToVegfc_02hr00minBr3- Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep3 (MM XXII - 8)_CNhs13283_12511-133A9_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep3MMXXII8_CNhs13283_ctss_fwd LymphaticEndothelialCellsToVegfc_02hr00minBr3+ Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep3 (MM XXII - 8)_CNhs13283_12511-133A9_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep2MMXIV8_CNhs13164_ctss_rev LymphaticEndothelialCellsToVegfc_02hr00minBr2- Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep2 (MM XIV - 8)_CNhs13164_12389-131F4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep2MMXIV8_CNhs13164_ctss_fwd LymphaticEndothelialCellsToVegfc_02hr00minBr2+ Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep2 (MM XIV - 8)_CNhs13164_12389-131F4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep1MMXIX8_CNhs13106_ctss_rev LymphaticEndothelialCellsToVegfc_02hr00minBr1- Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep1 (MM XIX - 8)_CNhs13106_12267-130A8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep1MMXIX8_CNhs13106_ctss_fwd LymphaticEndothelialCellsToVegfc_02hr00minBr1+ Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep1 (MM XIX - 8)_CNhs13106_12267-130A8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep3MMXXII7_CNhs13282_ctss_rev LymphaticEndothelialCellsToVegfc_01hr40minBr3- Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep3 (MM XXII - 7)_CNhs13282_12510-133A8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep3MMXXII7_CNhs13282_ctss_fwd LymphaticEndothelialCellsToVegfc_01hr40minBr3+ Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep3 (MM XXII - 7)_CNhs13282_12510-133A8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep2MMXIV7_CNhs13163_ctss_rev LymphaticEndothelialCellsToVegfc_01hr40minBr2- Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep2 (MM XIV - 7)_CNhs13163_12388-131F3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep2MMXIV7_CNhs13163_ctss_fwd LymphaticEndothelialCellsToVegfc_01hr40minBr2+ Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep2 (MM XIV - 7)_CNhs13163_12388-131F3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep1MMXIX7_CNhs13105_ctss_rev LymphaticEndothelialCellsToVegfc_01hr40minBr1- Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep1 (MM XIX - 7)_CNhs13105_12266-130A7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep1MMXIX7_CNhs13105_ctss_fwd LymphaticEndothelialCellsToVegfc_01hr40minBr1+ Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep1 (MM XIX - 7)_CNhs13105_12266-130A7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep3MMXXII6_CNhs13281_ctss_rev LymphaticEndothelialCellsToVegfc_01hr20minBr3- Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep3 (MM XXII - 6)_CNhs13281_12509-133A7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep3MMXXII6_CNhs13281_ctss_fwd LymphaticEndothelialCellsToVegfc_01hr20minBr3+ Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep3 (MM XXII - 6)_CNhs13281_12509-133A7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep2MMXIV6_CNhs13162_ctss_rev LymphaticEndothelialCellsToVegfc_01hr20minBr2- Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep2 (MM XIV - 6)_CNhs13162_12387-131F2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep2MMXIV6_CNhs13162_ctss_fwd LymphaticEndothelialCellsToVegfc_01hr20minBr2+ Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep2 (MM XIV - 6)_CNhs13162_12387-131F2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep1MMXIX6_CNhs13104_ctss_rev LymphaticEndothelialCellsToVegfc_01hr20minBr1- Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep1 (MM XIX - 6)_CNhs13104_12265-130A6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep1MMXIX6_CNhs13104_ctss_fwd LymphaticEndothelialCellsToVegfc_01hr20minBr1+ Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep1 (MM XIX - 6)_CNhs13104_12265-130A6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep3MMXXII5_CNhs13280_ctss_rev LymphaticEndothelialCellsToVegfc_01hr00minBr3- Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep3 (MM XXII - 5)_CNhs13280_12508-133A6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep3MMXXII5_CNhs13280_ctss_fwd LymphaticEndothelialCellsToVegfc_01hr00minBr3+ Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep3 (MM XXII - 5)_CNhs13280_12508-133A6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep2MMXIV5_CNhs13161_ctss_rev LymphaticEndothelialCellsToVegfc_01hr00minBr2- Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep2 (MM XIV - 5)_CNhs13161_12386-131F1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep2MMXIV5_CNhs13161_ctss_fwd LymphaticEndothelialCellsToVegfc_01hr00minBr2+ Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep2 (MM XIV - 5)_CNhs13161_12386-131F1_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep1MMXIX5_CNhs13103_ctss_rev LymphaticEndothelialCellsToVegfc_01hr00minBr1- Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep1 (MM XIX - 5)_CNhs13103_12264-130A5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep1MMXIX5_CNhs13103_ctss_fwd LymphaticEndothelialCellsToVegfc_01hr00minBr1+ Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep1 (MM XIX - 5)_CNhs13103_12264-130A5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep3MMXXII4_CNhs13279_ctss_rev LymphaticEndothelialCellsToVegfc_00hr45minBr3- Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep3 (MM XXII - 4)_CNhs13279_12507-133A5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep3MMXXII4_CNhs13279_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr45minBr3+ Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep3 (MM XXII - 4)_CNhs13279_12507-133A5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep2MMXIV4_CNhs13160_ctss_rev LymphaticEndothelialCellsToVegfc_00hr45minBr2- Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep2 (MM XIV - 4)_CNhs13160_12385-131E9_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep2MMXIV4_CNhs13160_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr45minBr2+ Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep2 (MM XIV - 4)_CNhs13160_12385-131E9_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep1MMXIX4_CNhs13102_ctss_rev LymphaticEndothelialCellsToVegfc_00hr45minBr1- Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep1 (MM XIX - 4)_CNhs13102_12263-130A4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep1MMXIX4_CNhs13102_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr45minBr1+ Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep1 (MM XIX - 4)_CNhs13102_12263-130A4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep3MMXXII3_CNhs13278_ctss_rev LymphaticEndothelialCellsToVegfc_00hr30minBr3- Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep3 (MM XXII - 3)_CNhs13278_12506-133A4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep3MMXXII3_CNhs13278_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr30minBr3+ Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep3 (MM XXII - 3)_CNhs13278_12506-133A4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep2MMXIV3_CNhs13159_ctss_rev LymphaticEndothelialCellsToVegfc_00hr30minBr2- Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep2 (MM XIV - 3)_CNhs13159_12384-131E8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep2MMXIV3_CNhs13159_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr30minBr2+ Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep2 (MM XIV - 3)_CNhs13159_12384-131E8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep1MMXIX3_CNhs13101_ctss_rev LymphaticEndothelialCellsToVegfc_00hr30minBr1- Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep1 (MM XIX - 3)_CNhs13101_12262-130A3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep1MMXIX3_CNhs13101_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr30minBr1+ Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep1 (MM XIX - 3)_CNhs13101_12262-130A3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep3MMXXII2_CNhs13277_ctss_rev LymphaticEndothelialCellsToVegfc_00hr15minBr3- Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep3 (MM XXII - 2)_CNhs13277_12505-133A3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep3MMXXII2_CNhs13277_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr15minBr3+ Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep3 (MM XXII - 2)_CNhs13277_12505-133A3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep2MMXIV2_CNhs13158_ctss_rev LymphaticEndothelialCellsToVegfc_00hr15minBr2- Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep2 (MM XIV - 2)_CNhs13158_12383-131E7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep2MMXIV2_CNhs13158_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr15minBr2+ Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep2 (MM XIV - 2)_CNhs13158_12383-131E7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep1MMXIX2_CNhs13100_ctss_rev LymphaticEndothelialCellsToVegfc_00hr15minBr1- Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep1 (MM XIX - 2)_CNhs13100_12261-130A2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep1MMXIX2_CNhs13100_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr15minBr1+ Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep1 (MM XIX - 2)_CNhs13100_12261-130A2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep3MMXXII1_CNhs13276_ctss_rev LymphaticEndothelialCellsToVegfc_00hr00minBr3- Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep3 (MM XXII - 1 )_CNhs13276_12504-133A2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep3MMXXII1_CNhs13276_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr00minBr3+ Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep3 (MM XXII - 1 )_CNhs13276_12504-133A2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep2MMXIV1_CNhs13157_ctss_rev LymphaticEndothelialCellsToVegfc_00hr00minBr2- Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep2 (MM XIV - 1)_CNhs13157_12382-131E6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep2MMXIV1_CNhs13157_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr00minBr2+ Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep2 (MM XIV - 1)_CNhs13157_12382-131E6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep1MMXIX1_CNhs11936_ctss_rev LymphaticEndothelialCellsToVegfc_00hr00minBr1- Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep1 (MM XIX - 1)_CNhs11936_12260-130A1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep1MMXIX1_CNhs11936_ctss_fwd LymphaticEndothelialCellsToVegfc_00hr00minBr1+ Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep1 (MM XIX - 1)_CNhs11936_12260-130A1_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep3_CNhs14055_ctss_rev IpsToNeuronControlDnC11-CRL2429Day18R3- iPS differentiation to neuron, control donor C32-CRL1502, day18, rep3_CNhs14055_13444-144F6_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep3_CNhs14055_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day18R3+ iPS differentiation to neuron, control donor C32-CRL1502, day18, rep3_CNhs14055_13444-144F6_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep2_CNhs13842_ctss_rev IpsToNeuronControlDnC11-CRL2429Day18R2- iPS differentiation to neuron, control donor C32-CRL1502, day18, rep2_CNhs13842_13440-144F2_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep2_CNhs13842_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day18R2+ iPS differentiation to neuron, control donor C32-CRL1502, day18, rep2_CNhs13842_13440-144F2_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep1_CNhs13829_ctss_rev IpsToNeuronControlDnC11-CRL2429Day18R1- iPS differentiation to neuron, control donor C32-CRL1502, day18, rep1_CNhs13829_13436-144E7_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep1_CNhs13829_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day18R1+ iPS differentiation to neuron, control donor C32-CRL1502, day18, rep1_CNhs13829_13436-144E7_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep3_CNhs14054_ctss_rev IpsToNeuronControlDnC11-CRL2429Day12R3- iPS differentiation to neuron, control donor C32-CRL1502, day12, rep3_CNhs14054_13443-144F5_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep3_CNhs14054_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day12R3+ iPS differentiation to neuron, control donor C32-CRL1502, day12, rep3_CNhs14054_13443-144F5_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep2_CNhs13841_ctss_rev IpsToNeuronControlDnC11-CRL2429Day12R2- iPS differentiation to neuron, control donor C32-CRL1502, day12, rep2_CNhs13841_13439-144F1_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep2_CNhs13841_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day12R2+ iPS differentiation to neuron, control donor C32-CRL1502, day12, rep2_CNhs13841_13439-144F1_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep1_CNhs13828_ctss_rev IpsToNeuronControlDnC11-CRL2429Day12R1- iPS differentiation to neuron, control donor C32-CRL1502, day12, rep1_CNhs13828_13435-144E6_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep1_CNhs13828_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day12R1+ iPS differentiation to neuron, control donor C32-CRL1502, day12, rep1_CNhs13828_13435-144E6_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep3_CNhs14053_ctss_rev IpsToNeuronControlDnC11-CRL2429Day06R3- iPS differentiation to neuron, control donor C32-CRL1502, day06, rep3_CNhs14053_13442-144F4_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep3_CNhs14053_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day06R3+ iPS differentiation to neuron, control donor C32-CRL1502, day06, rep3_CNhs14053_13442-144F4_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep2_CNhs13840_ctss_rev IpsToNeuronControlDnC11-CRL2429Day06R2- iPS differentiation to neuron, control donor C32-CRL1502, day06, rep2_CNhs13840_13438-144E9_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep2_CNhs13840_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day06R2+ iPS differentiation to neuron, control donor C32-CRL1502, day06, rep2_CNhs13840_13438-144E9_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep1_CNhs13827_ctss_rev IpsToNeuronControlDnC11-CRL2429Day06R1- iPS differentiation to neuron, control donor C32-CRL1502, day06, rep1_CNhs13827_13434-144E5_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep1_CNhs13827_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day06R1+ iPS differentiation to neuron, control donor C32-CRL1502, day06, rep1_CNhs13827_13434-144E5_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep3_CNhs14052_ctss_rev IpsToNeuronControlDnC11-CRL2429Day00R3- iPS differentiation to neuron, control donor C32-CRL1502, day00, rep3_CNhs14052_13441-144F3_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep3_CNhs14052_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day00R3+ iPS differentiation to neuron, control donor C32-CRL1502, day00, rep3_CNhs14052_13441-144F3_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep2_CNhs13839_ctss_rev IpsToNeuronControlDnC11-CRL2429Day00R2- iPS differentiation to neuron, control donor C32-CRL1502, day00, rep2_CNhs13839_13437-144E8_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep2_CNhs13839_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day00R2+ iPS differentiation to neuron, control donor C32-CRL1502, day00, rep2_CNhs13839_13437-144E8_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep1_CNhs13826_ctss_rev IpsToNeuronControlDnC11-CRL2429Day00R1- iPS differentiation to neuron, control donor C32-CRL1502, day00, rep1_CNhs13826_13433-144E4_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep1_CNhs13826_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day00R1+ iPS differentiation to neuron, control donor C32-CRL1502, day00, rep1_CNhs13826_13433-144E4_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep3_CNhs13917_ctss_rev IpsToNeuronControlDnC11-CRL2429Day18R3- iPS differentiation to neuron, control donor C11-CRL2429, day18, rep3_CNhs13917_13432-144E3_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep3_CNhs13917_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day18R3+ iPS differentiation to neuron, control donor C11-CRL2429, day18, rep3_CNhs13917_13432-144E3_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep2_CNhs13825_ctss_rev IpsToNeuronControlDnC11-CRL2429Day18R2- iPS differentiation to neuron, control donor C11-CRL2429, day18, rep2_CNhs13825_13428-144D8_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep2_CNhs13825_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day18R2+ iPS differentiation to neuron, control donor C11-CRL2429, day18, rep2_CNhs13825_13428-144D8_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep1_CNhs13916_ctss_rev IpsToNeuronControlDnC11-CRL2429Day18R1- iPS differentiation to neuron, control donor C11-CRL2429, day18, rep1_CNhs13916_13424-144D4_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep1_CNhs13916_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day18R1+ iPS differentiation to neuron, control donor C11-CRL2429, day18, rep1_CNhs13916_13424-144D4_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep3_CNhs14051_ctss_rev IpsToNeuronControlDnC11-CRL2429Day12R3- iPS differentiation to neuron, control donor C11-CRL2429, day12, rep3_CNhs14051_13431-144E2_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep3_CNhs14051_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day12R3+ iPS differentiation to neuron, control donor C11-CRL2429, day12, rep3_CNhs14051_13431-144E2_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep2_CNhs13824_ctss_rev IpsToNeuronControlDnC11-CRL2429Day12R2- iPS differentiation to neuron, control donor C11-CRL2429, day12, rep2_CNhs13824_13427-144D7_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep2_CNhs13824_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day12R2+ iPS differentiation to neuron, control donor C11-CRL2429, day12, rep2_CNhs13824_13427-144D7_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep1_CNhs14047_ctss_rev IpsToNeuronControlDnC11-CRL2429Day12R1- iPS differentiation to neuron, control donor C11-CRL2429, day12, rep1_CNhs14047_13423-144D3_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep1_CNhs14047_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day12R1+ iPS differentiation to neuron, control donor C11-CRL2429, day12, rep1_CNhs14047_13423-144D3_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep3_CNhs14050_ctss_rev IpsToNeuronControlDnC11-CRL2429Day06R3- iPS differentiation to neuron, control donor C11-CRL2429, day06, rep3_CNhs14050_13430-144E1_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep3_CNhs14050_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day06R3+ iPS differentiation to neuron, control donor C11-CRL2429, day06, rep3_CNhs14050_13430-144E1_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep2_CNhs13823_ctss_rev IpsToNeuronControlDnC11-CRL2429Day06R2- iPS differentiation to neuron, control donor C11-CRL2429, day06, rep2_CNhs13823_13426-144D6_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep2_CNhs13823_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day06R2+ iPS differentiation to neuron, control donor C11-CRL2429, day06, rep2_CNhs13823_13426-144D6_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep1_CNhs14046_ctss_rev IpsToNeuronControlDnC11-CRL2429Day06R1- iPS differentiation to neuron, control donor C11-CRL2429, day06, rep1_CNhs14046_13422-144D2_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep1_CNhs14046_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day06R1+ iPS differentiation to neuron, control donor C11-CRL2429, day06, rep1_CNhs14046_13422-144D2_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep3_CNhs14049_ctss_rev IpsToNeuronControlDnC11-CRL2429Day00R3- iPS differentiation to neuron, control donor C11-CRL2429, day00, rep3_CNhs14049_13429-144D9_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep3_CNhs14049_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day00R3+ iPS differentiation to neuron, control donor C11-CRL2429, day00, rep3_CNhs14049_13429-144D9_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep2_CNhs13822_ctss_rev IpsToNeuronControlDnC11-CRL2429Day00R2- iPS differentiation to neuron, control donor C11-CRL2429, day00, rep2_CNhs13822_13425-144D5_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep2_CNhs13822_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day00R2+ iPS differentiation to neuron, control donor C11-CRL2429, day00, rep2_CNhs13822_13425-144D5_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep1_CNhs14045_ctss_rev IpsToNeuronControlDnC11-CRL2429Day00R1- iPS differentiation to neuron, control donor C11-CRL2429, day00, rep1_CNhs14045_13421-144D1_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep1_CNhs14045_ctss_fwd IpsToNeuronControlDnC11-CRL2429Day00R1+ iPS differentiation to neuron, control donor C11-CRL2429, day00, rep1_CNhs14045_13421-144D1_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep3_CNhs14066_ctss_rev Tc:iPStoNeuronDs_Day18R3- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep3_CNhs14066_13468-144I3_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep3_CNhs14066_ctss_fwd Tc:iPStoNeuronDs_Day18R3+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep3_CNhs14066_13468-144I3_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep2_CNhs13922_ctss_rev Tc:iPStoNeuronDs_Day18R2- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep2_CNhs13922_13464-144H8_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep2_CNhs13922_ctss_fwd Tc:iPStoNeuronDs_Day18R2+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep2_CNhs13922_13464-144H8_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep1_CNhs13838_ctss_rev Tc:iPStoNeuronDs_Day18R1- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep1_CNhs13838_13460-144H4_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep1_CNhs13838_ctss_fwd Tc:iPStoNeuronDs_Day18R1+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep1_CNhs13838_13460-144H4_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep3_CNhs14065_ctss_rev Tc:iPStoNeuronDs_Day12R3- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep3_CNhs14065_13467-144I2_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep3_CNhs14065_ctss_fwd Tc:iPStoNeuronDs_Day12R3+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep3_CNhs14065_13467-144I2_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep2_CNhs14062_ctss_rev Tc:iPStoNeuronDs_Day12R2- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep2_CNhs14062_13463-144H7_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep2_CNhs14062_ctss_fwd Tc:iPStoNeuronDs_Day12R2+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep2_CNhs14062_13463-144H7_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep1_CNhs13837_ctss_rev Tc:iPStoNeuronDs_Day12R1- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep1_CNhs13837_13459-144H3_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep1_CNhs13837_ctss_fwd Tc:iPStoNeuronDs_Day12R1+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep1_CNhs13837_13459-144H3_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep3_CNhs14064_ctss_rev Tc:iPStoNeuronDs_Day06R3- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep3_CNhs14064_13466-144I1_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep3_CNhs14064_ctss_fwd Tc:iPStoNeuronDs_Day06R3+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep3_CNhs14064_13466-144I1_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep2_CNhs14061_ctss_rev Tc:iPStoNeuronDs_Day06R2- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep2_CNhs14061_13462-144H6_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep2_CNhs14061_ctss_fwd Tc:iPStoNeuronDs_Day06R2+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep2_CNhs14061_13462-144H6_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep1_CNhs13836_ctss_rev Tc:iPStoNeuronDs_Day06R1- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep1_CNhs13836_13458-144H2_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep1_CNhs13836_ctss_fwd Tc:iPStoNeuronDs_Day06R1+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep1_CNhs13836_13458-144H2_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep3_CNhs14063_ctss_rev Tc:iPStoNeuronDs_Day00R3- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep3_CNhs14063_13465-144H9_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep3_CNhs14063_ctss_fwd Tc:iPStoNeuronDs_Day00R3+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep3_CNhs14063_13465-144H9_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep2_CNhs14060_ctss_rev Tc:iPStoNeuronDs_Day00R2- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep2_CNhs14060_13461-144H5_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep2_CNhs14060_ctss_fwd Tc:iPStoNeuronDs_Day00R2+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep2_CNhs14060_13461-144H5_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep1_CNhs13835_ctss_rev Tc:iPStoNeuronDs_Day00R1- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep1_CNhs13835_13457-144H1_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep1_CNhs13835_ctss_fwd Tc:iPStoNeuronDs_Day00R1+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep1_CNhs13835_13457-144H1_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep3_CNhs14059_ctss_rev Tc:iPStoNeuronDs_Day18R3- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep3_CNhs14059_13456-144G9_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep3_CNhs14059_ctss_fwd Tc:iPStoNeuronDs_Day18R3+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep3_CNhs14059_13456-144G9_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep2_CNhs13846_ctss_rev Tc:iPStoNeuronDs_Day18R2- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep2_CNhs13846_13452-144G5_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep2_CNhs13846_ctss_fwd Tc:iPStoNeuronDs_Day18R2+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep2_CNhs13846_13452-144G5_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep1_CNhs13833_ctss_rev Tc:iPStoNeuronDs_Day18R1- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep1_CNhs13833_13448-144G1_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep1_CNhs13833_ctss_fwd Tc:iPStoNeuronDs_Day18R1+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep1_CNhs13833_13448-144G1_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep3_CNhs14058_ctss_rev Tc:iPStoNeuronDs_Day12R3- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep3_CNhs14058_13455-144G8_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep3_CNhs14058_ctss_fwd Tc:iPStoNeuronDs_Day12R3+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep3_CNhs14058_13455-144G8_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep2_CNhs13845_ctss_rev Tc:iPStoNeuronDs_Day12R2- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep2_CNhs13845_13451-144G4_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep2_CNhs13845_ctss_fwd Tc:iPStoNeuronDs_Day12R2+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep2_CNhs13845_13451-144G4_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep1_CNhs13832_ctss_rev Tc:iPStoNeuronDs_Day12R1- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep1_CNhs13832_13447-144F9_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep1_CNhs13832_ctss_fwd Tc:iPStoNeuronDs_Day12R1+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep1_CNhs13832_13447-144F9_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep3_CNhs14057_ctss_rev Tc:iPStoNeuronDs_Day06R3- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep3_CNhs14057_13454-144G7_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep3_CNhs14057_ctss_fwd Tc:iPStoNeuronDs_Day06R3+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep3_CNhs14057_13454-144G7_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep2_CNhs13844_ctss_rev Tc:iPStoNeuronDs_Day06R2- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep2_CNhs13844_13450-144G3_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep2_CNhs13844_ctss_fwd Tc:iPStoNeuronDs_Day06R2+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep2_CNhs13844_13450-144G3_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep1_CNhs13831_ctss_rev Tc:iPStoNeuronDs_Day06R1- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep1_CNhs13831_13446-144F8_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep1_CNhs13831_ctss_fwd Tc:iPStoNeuronDs_Day06R1+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep1_CNhs13831_13446-144F8_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep3_CNhs14056_ctss_rev Tc:iPStoNeuronDs_Day00R3- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep3_CNhs14056_13453-144G6_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep3_CNhs14056_ctss_fwd Tc:iPStoNeuronDs_Day00R3+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep3_CNhs14056_13453-144G6_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep2_CNhs13843_ctss_rev Tc:iPStoNeuronDs_Day00R2- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep2_CNhs13843_13449-144G2_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep2_CNhs13843_ctss_fwd Tc:iPStoNeuronDs_Day00R2+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep2_CNhs13843_13449-144G2_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep1_CNhs13830_ctss_rev Tc:iPStoNeuronDs_Day00R1- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep1_CNhs13830_13445-144F7_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep1_CNhs13830_ctss_fwd Tc:iPStoNeuronDs_Day00R1+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep1_CNhs13830_13445-144F7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep3_CNhs14543_ctss_rev Tc:ARPE-19Emt_60hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep3_CNhs14543_13687-147F6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep3_CNhs14543_ctss_fwd Tc:ARPE-19Emt_60hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep3_CNhs14543_13687-147F6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep2_CNhs14542_ctss_rev Tc:ARPE-19Emt_60hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep2_CNhs14542_13686-147F5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep2_CNhs14542_ctss_fwd Tc:ARPE-19Emt_60hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep2_CNhs14542_13686-147F5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep1_CNhs14541_ctss_rev Tc:ARPE-19Emt_60hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep1_CNhs14541_13685-147F4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep1_CNhs14541_ctss_fwd Tc:ARPE-19Emt_60hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep1_CNhs14541_13685-147F4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep3_CNhs14540_ctss_rev Tc:ARPE-19Emt_42hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep3_CNhs14540_13684-147F3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep3_CNhs14540_ctss_fwd Tc:ARPE-19Emt_42hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep3_CNhs14540_13684-147F3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep2_CNhs14539_ctss_rev Tc:ARPE-19Emt_42hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep2_CNhs14539_13683-147F2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep2_CNhs14539_ctss_fwd Tc:ARPE-19Emt_42hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep2_CNhs14539_13683-147F2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep1_CNhs14538_ctss_rev Tc:ARPE-19Emt_42hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep1_CNhs14538_13682-147F1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep1_CNhs14538_ctss_fwd Tc:ARPE-19Emt_42hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep1_CNhs14538_13682-147F1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep3_CNhs14537_ctss_rev Tc:ARPE-19Emt_24hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep3_CNhs14537_13681-147E9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep3_CNhs14537_ctss_fwd Tc:ARPE-19Emt_24hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep3_CNhs14537_13681-147E9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep1_CNhs14535_ctss_rev Tc:ARPE-19Emt_24hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep1_CNhs14535_13679-147E7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep1_CNhs14535_ctss_fwd Tc:ARPE-19Emt_24hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep1_CNhs14535_13679-147E7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep3_CNhs14534_ctss_rev Tc:ARPE-19Emt_16hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep3_CNhs14534_13678-147E6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep3_CNhs14534_ctss_fwd Tc:ARPE-19Emt_16hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep3_CNhs14534_13678-147E6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep2_CNhs14533_ctss_rev Tc:ARPE-19Emt_16hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep2_CNhs14533_13677-147E5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep2_CNhs14533_ctss_fwd Tc:ARPE-19Emt_16hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep2_CNhs14533_13677-147E5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep1_CNhs14532_ctss_rev Tc:ARPE-19Emt_16hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep1_CNhs14532_13676-147E4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep1_CNhs14532_ctss_fwd Tc:ARPE-19Emt_16hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep1_CNhs14532_13676-147E4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha12hr00minBiolRep3_CNhs14531_ctss_rev Tc:ARPE-19Emt_12hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 12hr00min, biol_rep3_CNhs14531_13675-147E3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha12hr00minBiolRep3_CNhs14531_ctss_fwd Tc:ARPE-19Emt_12hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 12hr00min, biol_rep3_CNhs14531_13675-147E3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha12hr00minBiolRep2_CNhs14530_ctss_rev Tc:ARPE-19Emt_12hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 12hr00min, biol_rep2_CNhs14530_13674-147E2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha12hr00minBiolRep2_CNhs14530_ctss_fwd Tc:ARPE-19Emt_12hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 12hr00min, biol_rep2_CNhs14530_13674-147E2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep3_CNhs14528_ctss_rev Tc:ARPE-19Emt_08hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep3_CNhs14528_13672-147D9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep3_CNhs14528_ctss_fwd Tc:ARPE-19Emt_08hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep3_CNhs14528_13672-147D9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep2_CNhs14527_ctss_rev Tc:ARPE-19Emt_08hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep2_CNhs14527_13671-147D8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep2_CNhs14527_ctss_fwd Tc:ARPE-19Emt_08hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep2_CNhs14527_13671-147D8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep1_CNhs14526_ctss_rev Tc:ARPE-19Emt_08hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep1_CNhs14526_13670-147D7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep1_CNhs14526_ctss_fwd Tc:ARPE-19Emt_08hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep1_CNhs14526_13670-147D7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep3_CNhs14525_ctss_rev Tc:ARPE-19Emt_07hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep3_CNhs14525_13669-147D6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep3_CNhs14525_ctss_fwd Tc:ARPE-19Emt_07hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep3_CNhs14525_13669-147D6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep2_CNhs14524_ctss_rev Tc:ARPE-19Emt_07hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep2_CNhs14524_13668-147D5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep2_CNhs14524_ctss_fwd Tc:ARPE-19Emt_07hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep2_CNhs14524_13668-147D5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep1_CNhs14523_ctss_rev Tc:ARPE-19Emt_07hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep1_CNhs14523_13667-147D4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep1_CNhs14523_ctss_fwd Tc:ARPE-19Emt_07hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep1_CNhs14523_13667-147D4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep3_CNhs14522_ctss_rev Tc:ARPE-19Emt_06hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep3_CNhs14522_13666-147D3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep3_CNhs14522_ctss_fwd Tc:ARPE-19Emt_06hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep3_CNhs14522_13666-147D3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep1_CNhs14519_ctss_rev Tc:ARPE-19Emt_06hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep1_CNhs14519_13664-147D1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep1_CNhs14519_ctss_fwd Tc:ARPE-19Emt_06hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep1_CNhs14519_13664-147D1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep3_CNhs14518_ctss_rev Tc:ARPE-19Emt_05hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep3_CNhs14518_13663-147C9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep3_CNhs14518_ctss_fwd Tc:ARPE-19Emt_05hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep3_CNhs14518_13663-147C9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep2_CNhs14501_ctss_rev Tc:ARPE-19Emt_05hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep2_CNhs14501_13662-147C8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep2_CNhs14501_ctss_fwd Tc:ARPE-19Emt_05hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep2_CNhs14501_13662-147C8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep1_CNhs14500_ctss_rev Tc:ARPE-19Emt_05hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep1_CNhs14500_13661-147C7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep1_CNhs14500_ctss_fwd Tc:ARPE-19Emt_05hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep1_CNhs14500_13661-147C7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep3_CNhs14499_ctss_rev Tc:ARPE-19Emt_04hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep3_CNhs14499_13660-147C6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep3_CNhs14499_ctss_fwd Tc:ARPE-19Emt_04hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep3_CNhs14499_13660-147C6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep2_CNhs14498_ctss_rev Tc:ARPE-19Emt_04hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep2_CNhs14498_13659-147C5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep2_CNhs14498_ctss_fwd Tc:ARPE-19Emt_04hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep2_CNhs14498_13659-147C5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep1_CNhs14497_ctss_rev Tc:ARPE-19Emt_04hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep1_CNhs14497_13658-147C4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep1_CNhs14497_ctss_fwd Tc:ARPE-19Emt_04hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep1_CNhs14497_13658-147C4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep3_CNhs14496_ctss_rev Tc:ARPE-19Emt_03hr30minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep3_CNhs14496_13657-147C3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep3_CNhs14496_ctss_fwd Tc:ARPE-19Emt_03hr30minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep3_CNhs14496_13657-147C3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep2_CNhs14495_ctss_rev Tc:ARPE-19Emt_03hr30minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep2_CNhs14495_13656-147C2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep2_CNhs14495_ctss_fwd Tc:ARPE-19Emt_03hr30minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep2_CNhs14495_13656-147C2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep1_CNhs14494_ctss_rev Tc:ARPE-19Emt_03hr30minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep1_CNhs14494_13655-147C1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep1_CNhs14494_ctss_fwd Tc:ARPE-19Emt_03hr30minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep1_CNhs14494_13655-147C1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep3_CNhs14493_ctss_rev Tc:ARPE-19Emt_03hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep3_CNhs14493_13654-147B9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep3_CNhs14493_ctss_fwd Tc:ARPE-19Emt_03hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep3_CNhs14493_13654-147B9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep2_CNhs14492_ctss_rev Tc:ARPE-19Emt_03hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep2_CNhs14492_13653-147B8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep2_CNhs14492_ctss_fwd Tc:ARPE-19Emt_03hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep2_CNhs14492_13653-147B8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep1_CNhs14491_ctss_rev Tc:ARPE-19Emt_03hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep1_CNhs14491_13652-147B7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep1_CNhs14491_ctss_fwd Tc:ARPE-19Emt_03hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep1_CNhs14491_13652-147B7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep3_CNhs14490_ctss_rev Tc:ARPE-19Emt_02hr30minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep3_CNhs14490_13651-147B6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep3_CNhs14490_ctss_fwd Tc:ARPE-19Emt_02hr30minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep3_CNhs14490_13651-147B6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep2_CNhs14489_ctss_rev Tc:ARPE-19Emt_02hr30minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep2_CNhs14489_13650-147B5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep2_CNhs14489_ctss_fwd Tc:ARPE-19Emt_02hr30minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep2_CNhs14489_13650-147B5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep1_CNhs14488_ctss_rev Tc:ARPE-19Emt_02hr30minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep1_CNhs14488_13649-147B4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep1_CNhs14488_ctss_fwd Tc:ARPE-19Emt_02hr30minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep1_CNhs14488_13649-147B4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep3_CNhs14487_ctss_rev Tc:ARPE-19Emt_02hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep3_CNhs14487_13648-147B3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep3_CNhs14487_ctss_fwd Tc:ARPE-19Emt_02hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep3_CNhs14487_13648-147B3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep2_CNhs14486_ctss_rev Tc:ARPE-19Emt_02hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep2_CNhs14486_13647-147B2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep2_CNhs14486_ctss_fwd Tc:ARPE-19Emt_02hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep2_CNhs14486_13647-147B2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep1_CNhs14485_ctss_rev Tc:ARPE-19Emt_02hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep1_CNhs14485_13646-147B1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep1_CNhs14485_ctss_fwd Tc:ARPE-19Emt_02hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep1_CNhs14485_13646-147B1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep3_CNhs14484_ctss_rev Tc:ARPE-19Emt_01hr40minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep3_CNhs14484_13645-147A9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep3_CNhs14484_ctss_fwd Tc:ARPE-19Emt_01hr40minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep3_CNhs14484_13645-147A9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep2_CNhs14483_ctss_rev Tc:ARPE-19Emt_01hr40minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep2_CNhs14483_13644-147A8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep2_CNhs14483_ctss_fwd Tc:ARPE-19Emt_01hr40minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep2_CNhs14483_13644-147A8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep1_CNhs14482_ctss_rev Tc:ARPE-19Emt_01hr40minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep1_CNhs14482_13643-147A7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep1_CNhs14482_ctss_fwd Tc:ARPE-19Emt_01hr40minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep1_CNhs14482_13643-147A7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep3_CNhs14480_ctss_rev Tc:ARPE-19Emt_01hr20minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep3_CNhs14480_13642-147A6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep3_CNhs14480_ctss_fwd Tc:ARPE-19Emt_01hr20minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep3_CNhs14480_13642-147A6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep2_CNhs14479_ctss_rev Tc:ARPE-19Emt_01hr20minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep2_CNhs14479_13641-147A5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep2_CNhs14479_ctss_fwd Tc:ARPE-19Emt_01hr20minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep2_CNhs14479_13641-147A5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep1_CNhs14478_ctss_rev Tc:ARPE-19Emt_01hr20minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep1_CNhs14478_13640-147A4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep1_CNhs14478_ctss_fwd Tc:ARPE-19Emt_01hr20minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep1_CNhs14478_13640-147A4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep3_CNhs14477_ctss_rev Tc:ARPE-19Emt_01hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep3_CNhs14477_13639-147A3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep3_CNhs14477_ctss_fwd Tc:ARPE-19Emt_01hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep3_CNhs14477_13639-147A3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep2_CNhs14476_ctss_rev Tc:ARPE-19Emt_01hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep2_CNhs14476_13638-147A2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep2_CNhs14476_ctss_fwd Tc:ARPE-19Emt_01hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep2_CNhs14476_13638-147A2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep1_CNhs14475_ctss_rev Tc:ARPE-19Emt_01hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep1_CNhs14475_13637-147A1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep1_CNhs14475_ctss_fwd Tc:ARPE-19Emt_01hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep1_CNhs14475_13637-147A1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep3_CNhs14474_ctss_rev Tc:ARPE-19Emt_00hr45minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep3_CNhs14474_13636-146I9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep3_CNhs14474_ctss_fwd Tc:ARPE-19Emt_00hr45minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep3_CNhs14474_13636-146I9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep2_CNhs14473_ctss_rev Tc:ARPE-19Emt_00hr45minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep2_CNhs14473_13635-146I8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep2_CNhs14473_ctss_fwd Tc:ARPE-19Emt_00hr45minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep2_CNhs14473_13635-146I8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep1_CNhs14472_ctss_rev Tc:ARPE-19Emt_00hr45minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep1_CNhs14472_13634-146I7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep1_CNhs14472_ctss_fwd Tc:ARPE-19Emt_00hr45minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep1_CNhs14472_13634-146I7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep3_CNhs14471_ctss_rev Tc:ARPE-19Emt_00hr30minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep3_CNhs14471_13633-146I6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep3_CNhs14471_ctss_fwd Tc:ARPE-19Emt_00hr30minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep3_CNhs14471_13633-146I6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep2_CNhs14470_ctss_rev Tc:ARPE-19Emt_00hr30minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep2_CNhs14470_13632-146I5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep2_CNhs14470_ctss_fwd Tc:ARPE-19Emt_00hr30minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep2_CNhs14470_13632-146I5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep1_CNhs14469_ctss_rev Tc:ARPE-19Emt_00hr30minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep1_CNhs14469_13631-146I4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep1_CNhs14469_ctss_fwd Tc:ARPE-19Emt_00hr30minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep1_CNhs14469_13631-146I4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep3_CNhs14468_ctss_rev Tc:ARPE-19Emt_00hr15minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep3_CNhs14468_13630-146I3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep3_CNhs14468_ctss_fwd Tc:ARPE-19Emt_00hr15minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep3_CNhs14468_13630-146I3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep2_CNhs14467_ctss_rev Tc:ARPE-19Emt_00hr15minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep2_CNhs14467_13629-146I2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep2_CNhs14467_ctss_fwd Tc:ARPE-19Emt_00hr15minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep2_CNhs14467_13629-146I2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep1_CNhs14466_ctss_rev Tc:ARPE-19Emt_00hr15minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep1_CNhs14466_13628-146I1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep1_CNhs14466_ctss_fwd Tc:ARPE-19Emt_00hr15minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep1_CNhs14466_13628-146I1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep3_CNhs14465_ctss_rev Tc:ARPE-19Emt_00hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep3_CNhs14465_13627-146H9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep3_CNhs14465_ctss_fwd Tc:ARPE-19Emt_00hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep3_CNhs14465_13627-146H9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep2_CNhs14464_ctss_rev Tc:ARPE-19Emt_00hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep2_CNhs14464_13626-146H8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep2_CNhs14464_ctss_fwd Tc:ARPE-19Emt_00hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep2_CNhs14464_13626-146H8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep1_CNhs14463_ctss_rev Tc:ARPE-19Emt_00hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep1_CNhs14463_13625-146H7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep1_CNhs14463_ctss_fwd Tc:ARPE-19Emt_00hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep1_CNhs14463_13625-146H7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep3H9EB3D41_CNhs12950_ctss_rev H9MelanocyticInduction_Day41Br3- H9 Embryoid body cells, melanocytic induction, day41, biol_rep3 (H9EB-3 d41)_CNhs12950_12836-137B1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep3H9EB3D41_CNhs12950_ctss_fwd H9MelanocyticInduction_Day41Br3+ H9 Embryoid body cells, melanocytic induction, day41, biol_rep3 (H9EB-3 d41)_CNhs12950_12836-137B1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep2H9EB2D41_CNhs12907_ctss_rev H9MelanocyticInduction_Day41Br2- H9 Embryoid body cells, melanocytic induction, day41, biol_rep2 (H9EB-2 d41)_CNhs12907_12738-135I2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep2H9EB2D41_CNhs12907_ctss_fwd H9MelanocyticInduction_Day41Br2+ H9 Embryoid body cells, melanocytic induction, day41, biol_rep2 (H9EB-2 d41)_CNhs12907_12738-135I2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep1H9EB1D41_CNhs12905_ctss_rev H9MelanocyticInduction_Day41Br1- H9 Embryoid body cells, melanocytic induction, day41, biol_rep1 (H9EB-1 d41)_CNhs12905_12640-134G3_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep1H9EB1D41_CNhs12905_ctss_fwd H9MelanocyticInduction_Day41Br1+ H9 Embryoid body cells, melanocytic induction, day41, biol_rep1 (H9EB-1 d41)_CNhs12905_12640-134G3_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep3H9EB3D34_CNhs12919_ctss_rev H9MelanocyticInduction_Day34Br3- H9 Embryoid body cells, melanocytic induction, day34, biol_rep3 (H9EB-3 d34)_CNhs12919_12835-137A9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep3H9EB3D34_CNhs12919_ctss_fwd H9MelanocyticInduction_Day34Br3+ H9 Embryoid body cells, melanocytic induction, day34, biol_rep3 (H9EB-3 d34)_CNhs12919_12835-137A9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep2H9EB2D34_CNhs12906_ctss_rev H9MelanocyticInduction_Day34Br2- H9 Embryoid body cells, melanocytic induction, day34, biol_rep2 (H9EB-2 d34)_CNhs12906_12737-135I1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep2H9EB2D34_CNhs12906_ctss_fwd H9MelanocyticInduction_Day34Br2+ H9 Embryoid body cells, melanocytic induction, day34, biol_rep2 (H9EB-2 d34)_CNhs12906_12737-135I1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep1H9EB1D34_CNhs12904_ctss_rev H9MelanocyticInduction_Day34Br1- H9 Embryoid body cells, melanocytic induction, day34, biol_rep1 (H9EB-1 d34)_CNhs12904_12639-134G2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep1H9EB1D34_CNhs12904_ctss_fwd H9MelanocyticInduction_Day34Br1+ H9 Embryoid body cells, melanocytic induction, day34, biol_rep1 (H9EB-1 d34)_CNhs12904_12639-134G2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep3H9EB3D30_CNhs12918_ctss_rev H9MelanocyticInduction_Day30Br3- H9 Embryoid body cells, melanocytic induction, day30, biol_rep3 (H9EB-3 d30)_CNhs12918_12834-137A8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep3H9EB3D30_CNhs12918_ctss_fwd H9MelanocyticInduction_Day30Br3+ H9 Embryoid body cells, melanocytic induction, day30, biol_rep3 (H9EB-3 d30)_CNhs12918_12834-137A8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep2H9EB2D30_CNhs12836_ctss_rev H9MelanocyticInduction_Day30Br2- H9 Embryoid body cells, melanocytic induction, day30, biol_rep2 (H9EB-2 d30)_CNhs12836_12736-135H9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep2H9EB2D30_CNhs12836_ctss_fwd H9MelanocyticInduction_Day30Br2+ H9 Embryoid body cells, melanocytic induction, day30, biol_rep2 (H9EB-2 d30)_CNhs12836_12736-135H9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep1H9EB1D30_CNhs12903_ctss_rev H9MelanocyticInduction_Day30Br1- H9 Embryoid body cells, melanocytic induction, day30, biol_rep1 (H9EB-1 d30)_CNhs12903_12638-134G1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep1H9EB1D30_CNhs12903_ctss_fwd H9MelanocyticInduction_Day30Br1+ H9 Embryoid body cells, melanocytic induction, day30, biol_rep1 (H9EB-1 d30)_CNhs12903_12638-134G1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep3H9EB3D27_CNhs12917_ctss_rev H9MelanocyticInduction_Day27Br3- H9 Embryoid body cells, melanocytic induction, day27, biol_rep3 (H9EB-3 d27)_CNhs12917_12833-137A7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep3H9EB3D27_CNhs12917_ctss_fwd H9MelanocyticInduction_Day27Br3+ H9 Embryoid body cells, melanocytic induction, day27, biol_rep3 (H9EB-3 d27)_CNhs12917_12833-137A7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep2H9EB2D27_CNhs12835_ctss_rev H9MelanocyticInduction_Day27Br2- H9 Embryoid body cells, melanocytic induction, day27, biol_rep2 (H9EB-2 d27)_CNhs12835_12735-135H8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep2H9EB2D27_CNhs12835_ctss_fwd H9MelanocyticInduction_Day27Br2+ H9 Embryoid body cells, melanocytic induction, day27, biol_rep2 (H9EB-2 d27)_CNhs12835_12735-135H8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep1H9EB1D27_CNhs12902_ctss_rev H9MelanocyticInduction_Day27Br1- H9 Embryoid body cells, melanocytic induction, day27, biol_rep1 (H9EB-1 d27)_CNhs12902_12637-134F9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep1H9EB1D27_CNhs12902_ctss_fwd H9MelanocyticInduction_Day27Br1+ H9 Embryoid body cells, melanocytic induction, day27, biol_rep1 (H9EB-1 d27)_CNhs12902_12637-134F9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep3H9EB3D24_CNhs12916_ctss_rev H9MelanocyticInduction_Day24Br3- H9 Embryoid body cells, melanocytic induction, day24, biol_rep3 (H9EB-3 d24)_CNhs12916_12832-137A6_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep3H9EB3D24_CNhs12916_ctss_fwd H9MelanocyticInduction_Day24Br3+ H9 Embryoid body cells, melanocytic induction, day24, biol_rep3 (H9EB-3 d24)_CNhs12916_12832-137A6_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep2H9EB2D24_CNhs12834_ctss_rev H9MelanocyticInduction_Day24Br2- H9 Embryoid body cells, melanocytic induction, day24, biol_rep2 (H9EB-2 d24)_CNhs12834_12734-135H7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep2H9EB2D24_CNhs12834_ctss_fwd H9MelanocyticInduction_Day24Br2+ H9 Embryoid body cells, melanocytic induction, day24, biol_rep2 (H9EB-2 d24)_CNhs12834_12734-135H7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep1H9EB1D24_CNhs12901_ctss_rev H9MelanocyticInduction_Day24Br1- H9 Embryoid body cells, melanocytic induction, day24, biol_rep1 (H9EB-1 d24)_CNhs12901_12636-134F8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep1H9EB1D24_CNhs12901_ctss_fwd H9MelanocyticInduction_Day24Br1+ H9 Embryoid body cells, melanocytic induction, day24, biol_rep1 (H9EB-1 d24)_CNhs12901_12636-134F8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep3H9EB3D21_CNhs12915_ctss_rev H9MelanocyticInduction_Day21Br3- H9 Embryoid body cells, melanocytic induction, day21, biol_rep3 (H9EB-3 d21)_CNhs12915_12831-137A5_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep3H9EB3D21_CNhs12915_ctss_fwd H9MelanocyticInduction_Day21Br3+ H9 Embryoid body cells, melanocytic induction, day21, biol_rep3 (H9EB-3 d21)_CNhs12915_12831-137A5_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep2H9EB2D21_CNhs12833_ctss_rev H9MelanocyticInduction_Day21Br2- H9 Embryoid body cells, melanocytic induction, day21, biol_rep2 (H9EB-2 d21)_CNhs12833_12733-135H6_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep2H9EB2D21_CNhs12833_ctss_fwd H9MelanocyticInduction_Day21Br2+ H9 Embryoid body cells, melanocytic induction, day21, biol_rep2 (H9EB-2 d21)_CNhs12833_12733-135H6_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep1H9EB1D21_CNhs12900_ctss_rev H9MelanocyticInduction_Day21Br1- H9 Embryoid body cells, melanocytic induction, day21, biol_rep1 (H9EB-1 d21)_CNhs12900_12635-134F7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep1H9EB1D21_CNhs12900_ctss_fwd H9MelanocyticInduction_Day21Br1+ H9 Embryoid body cells, melanocytic induction, day21, biol_rep1 (H9EB-1 d21)_CNhs12900_12635-134F7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep3H9EB3D18_CNhs12914_ctss_rev H9MelanocyticInduction_Day18Br3- H9 Embryoid body cells, melanocytic induction, day18, biol_rep3 (H9EB-3 d18)_CNhs12914_12830-137A4_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep3H9EB3D18_CNhs12914_ctss_fwd H9MelanocyticInduction_Day18Br3+ H9 Embryoid body cells, melanocytic induction, day18, biol_rep3 (H9EB-3 d18)_CNhs12914_12830-137A4_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep2H9EB2D18_CNhs12832_ctss_rev H9MelanocyticInduction_Day18Br2- H9 Embryoid body cells, melanocytic induction, day18, biol_rep2 (H9EB-2 d18)_CNhs12832_12732-135H5_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep2H9EB2D18_CNhs12832_ctss_fwd H9MelanocyticInduction_Day18Br2+ H9 Embryoid body cells, melanocytic induction, day18, biol_rep2 (H9EB-2 d18)_CNhs12832_12732-135H5_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep1H9EB1D18_CNhs12899_ctss_rev H9MelanocyticInduction_Day18Br1- H9 Embryoid body cells, melanocytic induction, day18, biol_rep1 (H9EB-1 d18)_CNhs12899_12634-134F6_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep1H9EB1D18_CNhs12899_ctss_fwd H9MelanocyticInduction_Day18Br1+ H9 Embryoid body cells, melanocytic induction, day18, biol_rep1 (H9EB-1 d18)_CNhs12899_12634-134F6_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep3H9EB3D15_CNhs12912_ctss_rev H9MelanocyticInduction_Day15Br3- H9 Embryoid body cells, melanocytic induction, day15, biol_rep3 (H9EB-3 d15)_CNhs12912_12829-137A3_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep3H9EB3D15_CNhs12912_ctss_fwd H9MelanocyticInduction_Day15Br3+ H9 Embryoid body cells, melanocytic induction, day15, biol_rep3 (H9EB-3 d15)_CNhs12912_12829-137A3_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep2H9EB2D15_CNhs12831_ctss_rev H9MelanocyticInduction_Day15Br2- H9 Embryoid body cells, melanocytic induction, day15, biol_rep2 (H9EB-2 d15)_CNhs12831_12731-135H4_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep2H9EB2D15_CNhs12831_ctss_fwd H9MelanocyticInduction_Day15Br2+ H9 Embryoid body cells, melanocytic induction, day15, biol_rep2 (H9EB-2 d15)_CNhs12831_12731-135H4_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep1H9EB1D15_CNhs12898_ctss_rev H9MelanocyticInduction_Day15Br1- H9 Embryoid body cells, melanocytic induction, day15, biol_rep1 (H9EB-1 d15)_CNhs12898_12633-134F5_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep1H9EB1D15_CNhs12898_ctss_fwd H9MelanocyticInduction_Day15Br1+ H9 Embryoid body cells, melanocytic induction, day15, biol_rep1 (H9EB-1 d15)_CNhs12898_12633-134F5_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep3H9EB3D12_CNhs12995_ctss_rev H9MelanocyticInduction_Day12Br3- H9 Embryoid body cells, melanocytic induction, day12, biol_rep3 (H9EB-3 d12)_CNhs12995_12828-137A2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep3H9EB3D12_CNhs12949_ctss_rev H9MelanocyticInduction_Day12Br3- H9 Embryoid body cells, melanocytic induction, day12, biol_rep3 (H9EB-3 d12)_CNhs12949_12828-137A2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep3H9EB3D12_CNhs12995_ctss_fwd H9MelanocyticInduction_Day12Br3+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep3 (H9EB-3 d12)_CNhs12995_12828-137A2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep3H9EB3D12_CNhs12949_ctss_fwd H9MelanocyticInduction_Day12Br3+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep3 (H9EB-3 d12)_CNhs12949_12828-137A2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep2H9EB2D12_CNhs12830_ctss_rev H9MelanocyticInduction_Day12Br2- H9 Embryoid body cells, melanocytic induction, day12, biol_rep2 (H9EB-2 d12)_CNhs12830_12730-135H3_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep2H9EB2D12_CNhs12830_ctss_fwd H9MelanocyticInduction_Day12Br2+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep2 (H9EB-2 d12)_CNhs12830_12730-135H3_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep1H9EB1D12_CNhs12994_ctss_rev H9MelanocyticInduction_Day12Br1- H9 Embryoid body cells, melanocytic induction, day12, biol_rep1 (H9EB-1 d12)_CNhs12994_12632-134F4_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep1H9EB1D12_CNhs12948_ctss_rev H9MelanocyticInduction_Day12Br1- H9 Embryoid body cells, melanocytic induction, day12, biol_rep1 (H9EB-1 d12)_CNhs12948_12632-134F4_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep1H9EB1D12_CNhs12994_ctss_fwd H9MelanocyticInduction_Day12Br1+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep1 (H9EB-1 d12)_CNhs12994_12632-134F4_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep1H9EB1D12_CNhs12948_ctss_fwd H9MelanocyticInduction_Day12Br1+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep1 (H9EB-1 d12)_CNhs12948_12632-134F4_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep3H9EB3D9_CNhs12951_ctss_rev H9MelanocyticInduction_Day09Br3- H9 Embryoid body cells, melanocytic induction, day09, biol_rep3 (H9EB-3 d9)_CNhs12951_12827-137A1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep3H9EB3D9_CNhs12951_ctss_fwd H9MelanocyticInduction_Day09Br3+ H9 Embryoid body cells, melanocytic induction, day09, biol_rep3 (H9EB-3 d9)_CNhs12951_12827-137A1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep2H9EB2D9_CNhs12829_ctss_rev H9MelanocyticInduction_Day09Br2- H9 Embryoid body cells, melanocytic induction, day09, biol_rep2 (H9EB-2 d9)_CNhs12829_12729-135H2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep2H9EB2D9_CNhs12829_ctss_fwd H9MelanocyticInduction_Day09Br2+ H9 Embryoid body cells, melanocytic induction, day09, biol_rep2 (H9EB-2 d9)_CNhs12829_12729-135H2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep1H9EB1D9_CNhs12897_ctss_rev H9MelanocyticInduction_Day09Br1- H9 Embryoid body cells, melanocytic induction, day09, biol_rep1 (H9EB-1 d9)_CNhs12897_12631-134F3_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep1H9EB1D9_CNhs12897_ctss_fwd H9MelanocyticInduction_Day09Br1+ H9 Embryoid body cells, melanocytic induction, day09, biol_rep1 (H9EB-1 d9)_CNhs12897_12631-134F3_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep3H9EB3D6_CNhs12911_ctss_rev H9MelanocyticInduction_Day06Br3- H9 Embryoid body cells, melanocytic induction, day06, biol_rep3 (H9EB-3 d6)_CNhs12911_12826-136I9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep3H9EB3D6_CNhs12911_ctss_fwd H9MelanocyticInduction_Day06Br3+ H9 Embryoid body cells, melanocytic induction, day06, biol_rep3 (H9EB-3 d6)_CNhs12911_12826-136I9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep2H9EB2D6_CNhs12828_ctss_rev H9MelanocyticInduction_Day06Br2- H9 Embryoid body cells, melanocytic induction, day06, biol_rep2 (H9EB-2 d6)_CNhs12828_12728-135H1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep2H9EB2D6_CNhs12828_ctss_fwd H9MelanocyticInduction_Day06Br2+ H9 Embryoid body cells, melanocytic induction, day06, biol_rep2 (H9EB-2 d6)_CNhs12828_12728-135H1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep1H9EB1D6_CNhs12896_ctss_rev H9MelanocyticInduction_Day06Br1- H9 Embryoid body cells, melanocytic induction, day06, biol_rep1 (H9EB-1 d6)_CNhs12896_12630-134F2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep1H9EB1D6_CNhs12896_ctss_fwd H9MelanocyticInduction_Day06Br1+ H9 Embryoid body cells, melanocytic induction, day06, biol_rep1 (H9EB-1 d6)_CNhs12896_12630-134F2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep3H9EB3D3_CNhs12910_ctss_rev H9MelanocyticInduction_Day03Br3- H9 Embryoid body cells, melanocytic induction, day03, biol_rep3 (H9EB-3 d3)_CNhs12910_12825-136I8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep3H9EB3D3_CNhs12910_ctss_fwd H9MelanocyticInduction_Day03Br3+ H9 Embryoid body cells, melanocytic induction, day03, biol_rep3 (H9EB-3 d3)_CNhs12910_12825-136I8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep2H9EB2D3_CNhs12827_ctss_rev H9MelanocyticInduction_Day03Br2- H9 Embryoid body cells, melanocytic induction, day03, biol_rep2 (H9EB-2 d3)_CNhs12827_12727-135G9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep2H9EB2D3_CNhs12827_ctss_fwd H9MelanocyticInduction_Day03Br2+ H9 Embryoid body cells, melanocytic induction, day03, biol_rep2 (H9EB-2 d3)_CNhs12827_12727-135G9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep1H9EB1D3_CNhs12895_ctss_rev H9MelanocyticInduction_Day03Br1- H9 Embryoid body cells, melanocytic induction, day03, biol_rep1 (H9EB-1 d3)_CNhs12895_12629-134F1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep1H9EB1D3_CNhs12895_ctss_fwd H9MelanocyticInduction_Day03Br1+ H9 Embryoid body cells, melanocytic induction, day03, biol_rep1 (H9EB-1 d3)_CNhs12895_12629-134F1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep3H9EB3D1_CNhs12909_ctss_rev H9MelanocyticInduction_Day01Br3- H9 Embryoid body cells, melanocytic induction, day01, biol_rep3 (H9EB-3 d1)_CNhs12909_12824-136I7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep3H9EB3D1_CNhs12909_ctss_fwd H9MelanocyticInduction_Day01Br3+ H9 Embryoid body cells, melanocytic induction, day01, biol_rep3 (H9EB-3 d1)_CNhs12909_12824-136I7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep2H9EB2D1_CNhs12826_ctss_rev H9MelanocyticInduction_Day01Br2- H9 Embryoid body cells, melanocytic induction, day01, biol_rep2 (H9EB-2 d1)_CNhs12826_12726-135G8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep2H9EB2D1_CNhs12826_ctss_fwd H9MelanocyticInduction_Day01Br2+ H9 Embryoid body cells, melanocytic induction, day01, biol_rep2 (H9EB-2 d1)_CNhs12826_12726-135G8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep1H9EB1D1_CNhs12823_ctss_rev H9MelanocyticInduction_Day01Br1- H9 Embryoid body cells, melanocytic induction, day01, biol_rep1 (H9EB-1 d1)_CNhs12823_12628-134E9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep1H9EB1D1_CNhs12823_ctss_fwd H9MelanocyticInduction_Day01Br1+ H9 Embryoid body cells, melanocytic induction, day01, biol_rep1 (H9EB-1 d1)_CNhs12823_12628-134E9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep3H9EB3D0_CNhs12908_ctss_rev H9MelanocyticInduction_Day00Br3- H9 Embryoid body cells, melanocytic induction, day00, biol_rep3 (H9EB-3 d0)_CNhs12908_12823-136I6_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep3H9EB3D0_CNhs12908_ctss_fwd H9MelanocyticInduction_Day00Br3+ H9 Embryoid body cells, melanocytic induction, day00, biol_rep3 (H9EB-3 d0)_CNhs12908_12823-136I6_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep2H9EB2D0_CNhs12825_ctss_rev H9MelanocyticInduction_Day00Br2- H9 Embryoid body cells, melanocytic induction, day00, biol_rep2 (H9EB-2 d0)_CNhs12825_12725-135G7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep2H9EB2D0_CNhs12825_ctss_fwd H9MelanocyticInduction_Day00Br2+ H9 Embryoid body cells, melanocytic induction, day00, biol_rep2 (H9EB-2 d0)_CNhs12825_12725-135G7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep1H9EB1D0_CNhs12822_ctss_rev H9MelanocyticInduction_Day00Br1- H9 Embryoid body cells, melanocytic induction, day00, biol_rep1 (H9EB-1 d0)_CNhs12822_12627-134E8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep1H9EB1D0_CNhs12822_ctss_fwd H9MelanocyticInduction_Day00Br1+ H9 Embryoid body cells, melanocytic induction, day00, biol_rep1 (H9EB-1 d0)_CNhs12822_12627-134E8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep3_CNhs13736_ctss_rev Hes3-gfpCardiomyocyticInduction_Day12Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep3_CNhs13736_13363-143F6_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep3_CNhs13736_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day12Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep3_CNhs13736_13363-143F6_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep2_CNhs13724_ctss_rev Hes3-gfpCardiomyocyticInduction_Day12Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep2_CNhs13724_13351-143E3_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep2_CNhs13724_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day12Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep2_CNhs13724_13351-143E3_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep1_CNhs13711_ctss_rev Hes3-gfpCardiomyocyticInduction_Day12Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep1_CNhs13711_13339-143C9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep1_CNhs13711_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day12Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep1_CNhs13711_13339-143C9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep3_CNhs13735_ctss_rev Hes3-gfpCardiomyocyticInduction_Day11Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep3_CNhs13735_13362-143F5_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep3_CNhs13735_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day11Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep3_CNhs13735_13362-143F5_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep2_CNhs13723_ctss_rev Hes3-gfpCardiomyocyticInduction_Day11Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep2_CNhs13723_13350-143E2_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep2_CNhs13723_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day11Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep2_CNhs13723_13350-143E2_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep1_CNhs13710_ctss_rev Hes3-gfpCardiomyocyticInduction_Day11Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep1_CNhs13710_13338-143C8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep1_CNhs13710_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day11Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep1_CNhs13710_13338-143C8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep3_CNhs13734_ctss_rev Hes3-gfpCardiomyocyticInduction_Day10Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep3_CNhs13734_13361-143F4_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep3_CNhs13734_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day10Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep3_CNhs13734_13361-143F4_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep2_CNhs13722_ctss_rev Hes3-gfpCardiomyocyticInduction_Day10Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep2_CNhs13722_13349-143E1_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep2_CNhs13722_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day10Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep2_CNhs13722_13349-143E1_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep1_CNhs13662_ctss_rev Hes3-gfpCardiomyocyticInduction_Day10Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep1_CNhs13662_13337-143C7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep1_CNhs13662_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day10Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep1_CNhs13662_13337-143C7_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep3_CNhs13733_ctss_rev Hes3-gfpCardiomyocyticInduction_Day09Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep3_CNhs13733_13360-143F3_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep3_CNhs13733_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day09Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep3_CNhs13733_13360-143F3_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep2_CNhs13721_ctss_rev Hes3-gfpCardiomyocyticInduction_Day09Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep2_CNhs13721_13348-143D9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep2_CNhs13721_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day09Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep2_CNhs13721_13348-143D9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep1_CNhs13661_ctss_rev Hes3-gfpCardiomyocyticInduction_Day09Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep1_CNhs13661_13336-143C6_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep1_CNhs13661_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day09Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep1_CNhs13661_13336-143C6_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep3_CNhs13732_ctss_rev Hes3-gfpCardiomyocyticInduction_Day08Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep3_CNhs13732_13359-143F2_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep3_CNhs13732_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day08Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep3_CNhs13732_13359-143F2_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep2_CNhs13720_ctss_rev Hes3-gfpCardiomyocyticInduction_Day08Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep2_CNhs13720_13347-143D8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep2_CNhs13720_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day08Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep2_CNhs13720_13347-143D8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep1_CNhs13660_ctss_rev Hes3-gfpCardiomyocyticInduction_Day08Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep1_CNhs13660_13335-143C5_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep1_CNhs13660_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day08Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep1_CNhs13660_13335-143C5_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep3_CNhs13731_ctss_rev Hes3-gfpCardiomyocyticInduction_Day07Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep3_CNhs13731_13358-143F1_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep3_CNhs13731_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day07Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep3_CNhs13731_13358-143F1_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep2_CNhs13719_ctss_rev Hes3-gfpCardiomyocyticInduction_Day07Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep2_CNhs13719_13346-143D7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep2_CNhs13719_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day07Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep2_CNhs13719_13346-143D7_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep3_CNhs13730_ctss_rev Hes3-gfpCardiomyocyticInduction_Day06Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep3_CNhs13730_13357-143E9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep3_CNhs13730_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day06Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep3_CNhs13730_13357-143E9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep2_CNhs13718_ctss_rev Hes3-gfpCardiomyocyticInduction_Day06Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep2_CNhs13718_13345-143D6_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep2_CNhs13718_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day06Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep2_CNhs13718_13345-143D6_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep1_CNhs13658_ctss_rev Hes3-gfpCardiomyocyticInduction_Day06Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep1_CNhs13658_13333-143C3_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep1_CNhs13658_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day06Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep1_CNhs13658_13333-143C3_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep3_CNhs13729_ctss_rev Hes3-gfpCardiomyocyticInduction_Day05Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep3_CNhs13729_13356-143E8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep3_CNhs13729_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day05Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep3_CNhs13729_13356-143E8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep2_CNhs13717_ctss_rev Hes3-gfpCardiomyocyticInduction_Day05Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep2_CNhs13717_13344-143D5_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep2_CNhs13717_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day05Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep2_CNhs13717_13344-143D5_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep1_CNhs13657_ctss_rev Hes3-gfpCardiomyocyticInduction_Day05Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep1_CNhs13657_13332-143C2_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep1_CNhs13657_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day05Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep1_CNhs13657_13332-143C2_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep3_CNhs13728_ctss_rev Hes3-gfpCardiomyocyticInduction_Day04Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep3_CNhs13728_13355-143E7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep3_CNhs13728_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day04Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep3_CNhs13728_13355-143E7_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep2_CNhs13716_ctss_rev Hes3-gfpCardiomyocyticInduction_Day04Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep2_CNhs13716_13343-143D4_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep2_CNhs13716_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day04Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep2_CNhs13716_13343-143D4_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep1_CNhs13656_ctss_rev Hes3-gfpCardiomyocyticInduction_Day04Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep1_CNhs13656_13331-143C1_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep1_CNhs13656_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day04Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep1_CNhs13656_13331-143C1_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep3_CNhs13727_ctss_rev Hes3-gfpCardiomyocyticInduction_Day03Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep3_CNhs13727_13354-143E6_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep3_CNhs13727_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day03Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep3_CNhs13727_13354-143E6_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep2_CNhs13715_ctss_rev Hes3-gfpCardiomyocyticInduction_Day03Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep2_CNhs13715_13342-143D3_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep2_CNhs13715_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day03Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep2_CNhs13715_13342-143D3_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep1_CNhs13655_ctss_rev Hes3-gfpCardiomyocyticInduction_Day03Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep1_CNhs13655_13330-143B9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep1_CNhs13655_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day03Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep1_CNhs13655_13330-143B9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep3_CNhs13726_ctss_rev Hes3-gfpCardiomyocyticInduction_Day02Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep3_CNhs13726_13353-143E5_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep3_CNhs13726_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day02Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep3_CNhs13726_13353-143E5_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep2_CNhs13714_ctss_rev Hes3-gfpCardiomyocyticInduction_Day02Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep2_CNhs13714_13341-143D2_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep2_CNhs13714_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day02Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep2_CNhs13714_13341-143D2_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep1_CNhs13654_ctss_rev Hes3-gfpCardiomyocyticInduction_Day02Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep1_CNhs13654_13329-143B8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep1_CNhs13654_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day02Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep1_CNhs13654_13329-143B8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep3_CNhs13725_ctss_rev Hes3-gfpCardiomyocyticInduction_Day01Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep3_CNhs13725_13352-143E4_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep3_CNhs13725_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day01Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep3_CNhs13725_13352-143E4_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep2_CNhs13712_ctss_rev Hes3-gfpCardiomyocyticInduction_Day01Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep2_CNhs13712_13340-143D1_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep2_CNhs13712_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day01Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep2_CNhs13712_13340-143D1_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep1_CNhs13653_ctss_rev Hes3-gfpCardiomyocyticInduction_Day01Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep1_CNhs13653_13328-143B7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep1_CNhs13653_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day01Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep1_CNhs13653_13328-143B7_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep3UH3_CNhs13738_ctss_rev Hes3-gfpCardiomyocyticInduction_Day00Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep3 (UH-3)_CNhs13738_13366-143F9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep3UH3_CNhs13738_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day00Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep3 (UH-3)_CNhs13738_13366-143F9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep2UH2_CNhs13695_ctss_rev Hes3-gfpCardiomyocyticInduction_Day00Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep2 (UH-2)_CNhs13695_13365-143F8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep2UH2_CNhs13695_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day00Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep2 (UH-2)_CNhs13695_13365-143F8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep1UH1_CNhs13694_ctss_rev Hes3-gfpCardiomyocyticInduction_Day00Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep1 (UH-1)_CNhs13694_13364-143F7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep1UH1_CNhs13694_ctss_fwd Hes3-gfpCardiomyocyticInduction_Day00Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep1 (UH-1)_CNhs13694_13364-143F7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep3LK60_CNhs13586_ctss_rev AorticSmsToIL1b_06hrBr3- Aortic smooth muscle cell response to IL1b, 06hr, biol_rep3 (LK60)_CNhs13586_12857-137D4_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep3LK60_CNhs13586_ctss_fwd AorticSmsToIL1b_06hrBr3+ Aortic smooth muscle cell response to IL1b, 06hr, biol_rep3 (LK60)_CNhs13586_12857-137D4_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep2LK59_CNhs13378_ctss_rev AorticSmsToIL1b_06hrBr2- Aortic smooth muscle cell response to IL1b, 06hr, biol_rep2 (LK59)_CNhs13378_12759-136B5_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep2LK59_CNhs13378_ctss_fwd AorticSmsToIL1b_06hrBr2+ Aortic smooth muscle cell response to IL1b, 06hr, biol_rep2 (LK59)_CNhs13378_12759-136B5_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_ctss_rev AorticSmsToIL1b_06hrBr1- Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_ctss_fwd AorticSmsToIL1b_06hrBr1+ Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_ctss_rev AorticSmsToIL1b_05hrBr2- Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_ctss_fwd AorticSmsToIL1b_05hrBr2+ Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_ctss_rev AorticSmsToIL1b_05hrBr1- Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_ctss_fwd AorticSmsToIL1b_05hrBr1+ Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_ctss_rev AorticSmsToIL1b_04hrBr3- Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_ctss_fwd AorticSmsToIL1b_04hrBr3+ Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_ctss_rev AorticSmsToIL1b_04hrBr2- Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_ctss_fwd AorticSmsToIL1b_04hrBr2+ Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_ctss_rev AorticSmsToIL1b_04hrBr1- Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_ctss_fwd AorticSmsToIL1b_04hrBr1+ Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_ctss_rev AorticSmsToIL1b_03hrBr2- Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_ctss_fwd AorticSmsToIL1b_03hrBr2+ Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_ctss_rev AorticSmsToIL1b_03hrBr1- Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_ctss_fwd AorticSmsToIL1b_03hrBr1+ Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_ctss_rev AorticSmsToIL1b_02hrBr3- Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_ctss_fwd AorticSmsToIL1b_02hrBr3+ Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_ctss_rev AorticSmsToIL1b_02hrBr2- Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_ctss_fwd AorticSmsToIL1b_02hrBr2+ Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_ctss_rev AorticSmsToIL1b_01hrBr2- Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_ctss_fwd AorticSmsToIL1b_01hrBr2+ Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_ctss_rev AorticSmsToIL1b_01hrBr1- Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_ctss_fwd AorticSmsToIL1b_01hrBr1+ Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_ctss_rev AorticSmsToIL1b_00hr45minBr3- Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_ctss_fwd AorticSmsToIL1b_00hr45minBr3+ Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_ctss_rev AorticSmsToIL1b_00hr45minBr2- Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_ctss_fwd AorticSmsToIL1b_00hr45minBr2+ Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_ctss_rev AorticSmsToIL1b_00hr45minBr1- Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_ctss_fwd AorticSmsToIL1b_00hr45minBr1+ Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_ctss_rev AorticSmsToIL1b_00hr30minBr3- Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_ctss_fwd AorticSmsToIL1b_00hr30minBr3+ Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_ctss_rev AorticSmsToIL1b_00hr30minBr2- Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_ctss_fwd AorticSmsToIL1b_00hr30minBr2+ Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_ctss_rev AorticSmsToIL1b_00hr30minBr1- Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_ctss_fwd AorticSmsToIL1b_00hr30minBr1+ Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_ctss_rev AorticSmsToIL1b_00hr15minBr3- Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_ctss_fwd AorticSmsToIL1b_00hr15minBr3+ Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_ctss_rev AorticSmsToIL1b_00hr15minBr2- Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_ctss_fwd AorticSmsToIL1b_00hr15minBr2+ Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_ctss_rev AorticSmsToIL1b_00hr15minBr1- Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_ctss_fwd AorticSmsToIL1b_00hr15minBr1+ Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_ctss_rev AorticSmsToIL1b_00hr00minBr3- Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_ctss_fwd AorticSmsToIL1b_00hr00minBr3+ Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_ctss_rev AorticSmsToIL1b_00hr00minBr2- Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_ctss_fwd AorticSmsToIL1b_00hr00minBr2+ Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_ctss_rev AorticSmsToIL1b_00hr00minBr1- Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_ctss_fwd AorticSmsToIL1b_00hr00minBr1+ Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_forward Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_ctss_rev AorticSmsToFgf2_06hrBr3- Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_ctss_fwd AorticSmsToFgf2_06hrBr3+ Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_forward Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_ctss_rev AorticSmsToFgf2_06hrBr2- Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_ctss_fwd AorticSmsToFgf2_06hrBr2+ Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_forward Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_ctss_rev AorticSmsToFgf2_06hrBr1- Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_ctss_fwd AorticSmsToFgf2_06hrBr1+ Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_forward Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_ctss_rev AorticSmsToFgf2_05hrBr3- Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_ctss_fwd AorticSmsToFgf2_05hrBr3+ Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_forward Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_ctss_rev AorticSmsToFgf2_05hrBr2- Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_ctss_fwd AorticSmsToFgf2_05hrBr2+ Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_forward Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_ctss_rev AorticSmsToFgf2_05hrBr1- Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_ctss_fwd AorticSmsToFgf2_05hrBr1+ Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_forward Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_ctss_rev AorticSmsToFgf2_03hrBr3- Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_ctss_fwd AorticSmsToFgf2_03hrBr3+ Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_forward Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep2LK20_CNhs13364_ctss_rev AorticSmsToFgf2_03hrBr2- Aortic smooth muscle cell response to FGF2, 03hr, biol_rep2 (LK20)_CNhs13364_12746-136A1_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep2LK20_CNhs13364_ctss_fwd AorticSmsToFgf2_03hrBr2+ Aortic smooth muscle cell response to FGF2, 03hr, biol_rep2 (LK20)_CNhs13364_12746-136A1_forward Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep1LK19_CNhs13345_ctss_rev AorticSmsToFgf2_03hrBr1- Aortic smooth muscle cell response to FGF2, 03hr, biol_rep1 (LK19)_CNhs13345_12648-134H2_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep1LK19_CNhs13345_ctss_fwd AorticSmsToFgf2_03hrBr1+ Aortic smooth muscle cell response to FGF2, 03hr, biol_rep1 (LK19)_CNhs13345_12648-134H2_forward Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep3LK18_CNhs13572_ctss_rev AorticSmsToFgf2_02hrBr3- Aortic smooth muscle cell response to FGF2, 02hr, biol_rep3 (LK18)_CNhs13572_12843-137B8_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep3LK18_CNhs13572_ctss_fwd AorticSmsToFgf2_02hrBr3+ Aortic smooth muscle cell response to FGF2, 02hr, biol_rep3 (LK18)_CNhs13572_12843-137B8_forward Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep2LK17_CNhs13363_ctss_rev AorticSmsToFgf2_02hrBr2- Aortic smooth muscle cell response to FGF2, 02hr, biol_rep2 (LK17)_CNhs13363_12745-135I9_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep2LK17_CNhs13363_ctss_fwd AorticSmsToFgf2_02hrBr2+ Aortic smooth muscle cell response to FGF2, 02hr, biol_rep2 (LK17)_CNhs13363_12745-135I9_forward Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep1LK16_CNhs13344_ctss_rev AorticSmsToFgf2_02hrBr1- Aortic smooth muscle cell response to FGF2, 02hr, biol_rep1 (LK16)_CNhs13344_12647-134H1_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep1LK16_CNhs13344_ctss_fwd AorticSmsToFgf2_02hrBr1+ Aortic smooth muscle cell response to FGF2, 02hr, biol_rep1 (LK16)_CNhs13344_12647-134H1_forward Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep3LK15_CNhs13683_ctss_rev AorticSmsToFgf2_01hrBr3- Aortic smooth muscle cell response to FGF2, 01hr, biol_rep3 (LK15)_CNhs13683_12842-137B7_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep3LK15_CNhs13683_ctss_fwd AorticSmsToFgf2_01hrBr3+ Aortic smooth muscle cell response to FGF2, 01hr, biol_rep3 (LK15)_CNhs13683_12842-137B7_forward Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep1LK13_CNhs12741_ctss_rev AorticSmsToFgf2_01hrBr1- Aortic smooth muscle cell response to FGF2, 01hr, biol_rep1 (LK13)_CNhs12741_12646-134G9_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep1LK13_CNhs12741_ctss_fwd AorticSmsToFgf2_01hrBr1+ Aortic smooth muscle cell response to FGF2, 01hr, biol_rep1 (LK13)_CNhs12741_12646-134G9_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep3LK12_CNhs13571_ctss_rev AorticSmsToFgf2_00hr45minBr3- Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep3 (LK12)_CNhs13571_12841-137B6_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep3LK12_CNhs13571_ctss_fwd AorticSmsToFgf2_00hr45minBr3+ Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep3 (LK12)_CNhs13571_12841-137B6_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep2LK11_CNhs13361_ctss_rev AorticSmsToFgf2_00hr45minBr2- Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep2 (LK11)_CNhs13361_12743-135I7_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep2LK11_CNhs13361_ctss_fwd AorticSmsToFgf2_00hr45minBr2+ Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep2 (LK11)_CNhs13361_12743-135I7_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep1LK10_CNhs13343_ctss_rev AorticSmsToFgf2_00hr45minBr1- Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep1 (LK10)_CNhs13343_12645-134G8_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep1LK10_CNhs13343_ctss_fwd AorticSmsToFgf2_00hr45minBr1+ Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep1 (LK10)_CNhs13343_12645-134G8_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep3LK9_CNhs13569_ctss_rev AorticSmsToFgf2_00hr30minBr3- Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep3 (LK9)_CNhs13569_12840-137B5_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep3LK9_CNhs13569_ctss_fwd AorticSmsToFgf2_00hr30minBr3+ Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep3 (LK9)_CNhs13569_12840-137B5_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep2LK8_CNhs13360_ctss_rev AorticSmsToFgf2_00hr30minBr2- Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep2 (LK8)_CNhs13360_12742-135I6_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep2LK8_CNhs13360_ctss_fwd AorticSmsToFgf2_00hr30minBr2+ Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep2 (LK8)_CNhs13360_12742-135I6_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep1LK7_CNhs13341_ctss_rev AorticSmsToFgf2_00hr30minBr1- Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep1 (LK7)_CNhs13341_12644-134G7_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep1LK7_CNhs13341_ctss_fwd AorticSmsToFgf2_00hr30minBr1+ Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep1 (LK7)_CNhs13341_12644-134G7_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep3LK6_CNhs13568_ctss_rev AorticSmsToFgf2_00hr15minBr3- Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep3 (LK6)_CNhs13568_12839-137B4_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep3LK6_CNhs13568_ctss_fwd AorticSmsToFgf2_00hr15minBr3+ Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep3 (LK6)_CNhs13568_12839-137B4_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_ctss_rev AorticSmsToFgf2_00hr15minBr2- Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_ctss_fwd AorticSmsToFgf2_00hr15minBr2+ Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_ctss_rev AorticSmsToFgf2_00hr15minBr1- Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_ctss_fwd AorticSmsToFgf2_00hr15minBr1+ Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep2LK2_CNhs13358_ctss_rev AorticSmsToFgf2_00hr00minBr2- Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep2LK2_CNhs13358_ctss_fwd AorticSmsToFgf2_00hr00minBr2+ Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_ctss_rev AorticSmsToFgf2_00hr00minBr1- Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_ctss_fwd AorticSmsToFgf2_00hr00minBr1+ Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_forward Regulation 
cpgIslandExtUnmasked Unmasked CpG CpG Islands on All Sequence (Islands < 300 Bases are Light Green) Regulation Description CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. By default, only the masked version of the track is displayed. To view the unmasked version, change the visibility settings in the track controls at the top of this page. Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. The track CpG Islands is constructed on the sequence after all masked sequence is removed. The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula (cited in Gardiner-Garden et al. (1987)): Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. The calculation of the track data is performed by the following command sequence: twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \ | cpg_lh /dev/stdin 2&gt; cpg_lh.err \ | awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2; printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \ | sort -k1,1 -k2,2n &gt; cpgIsland.bed The unmasked track data is constructed from twoBitToFa -noMask output for the twoBitToFa command. Data access CpG islands and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/. The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447 
covidHgiGwas COVID GWAS v3 GWAS meta-analyses from the COVID-19 Host Genetics Initiative Phenotype and Literature Description This track set shows GWAS meta-analyses from the COVID-19 Host Genetics Initiative (HGI): a collaborative effort to facilitate the generation, analysis and sharing of COVID-19 host genetics research. The COVID-19 HGI organizes meta-analyses across multiple studies contributed by partners world-wide to identify the genetic determinants of SARS-CoV-2 infection susceptibility and disease severity and outcomes. Moreover, the COVID-19 HGI also aims to provide a platform for study partners to share analytical results in the form of summary statistics and/or individual level data where possible. The specific phenotypes studied by the COVID-19 HGI are those that benefit from maximal sample size: primary analysis on disease severity. Two meta-analyses are represented in this track: ANA_C2_V2: covid vs. population (6696 cases from 18 studies) ANA_B2_V2: hospitalized covid vs. population (3199 cases from 8 studies) Display Conventions Displayed items are colored by GWAS effect: red for positive, blue for negative. The height of the item reflects the effect size. The effect size, defined as the contribution of a SNP to the genetic variance of the trait, was measured as beta coefficient (beta). The higher the absolute value of the beta coefficient, the stronger the effect. The color saturation indicates statistical significance: p-values smaller than 1e-5 are brightly colored (bright red &nbsp;&nbsp; , bright blue &nbsp;&nbsp; ), those with less significance (p >= 1e-5) are paler (light red &nbsp;&nbsp; , light blue &nbsp;&nbsp; ). For better visualization of the data, only SNPs with p-values smaller than 1e-3 are displayed by default. Each track has separate display controls and data can be filtered according to the number of studies, minimum -log10 p-value, and the effect size (beta coefficient), using the track Configure options. Mouseover on items shows the rs ID (or chrom:pos if none assigned), both the non-effect and effect alleles, the effect size (beta coefficient), the p-value, and the number of studies. Additional information on each variant can be found on the details page by clicking on the item. Methods COVID-19 Host Genetics Initiative (HGI) GWAS meta-analysis round 3 (July 2020) results were used in this study. Each participating study partner submitted GWAS summary statistics for up to four of the COVID-19 phenotype definitions. Data were generated from genome-wide SNP array and whole exome and genome sequencing, leveraging the impact of both common and rare variants. The statistical analysis performed takes into account differences between sex, ancestry, and date of sample collection. Alleles were harmonized across studies and reported allele frequencies are based on gnomAD version 3.0 reference data. Most study partners used the SAIGE GWAS pipeline in order to generate summary statistics used for the COVID-19 HGI meta-analysis. The summary statistics of individual studies were manually examined for inflation, deflation, and excessive number of false positives. Qualifying summary statistics were filtered for INFO > 0.6 and MAF > 0.0001 prior to meta-analyzing the entirety of the data. The meta-analysis was done using inverse variance weighting of effects method, accounting for strand differences and allele flips in the individual studies. The meta-analysis results of variants appearing in at least three studies (analysis C2) or two studies (all other analyses) were made publicly available. The meta-analysis software and workflow are available here. More information about the prospective studies, processing pipeline, results and data sharing can be found here. Data Access The data underlying these tracks and summary statistics results are publicly available in COVID19-hg Release 3 (June 2020). The raw data can be explored interactively with the Table Browser, or the Data Integrator. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Credits Thanks to the COVID-19 Host Genetics Initiative contributors and project leads for making these data available, and in particular to Rachel Liao, Juha Karjalainen, and Kumar Veerapen at the Broad Institute for their review and input during browser track development. References COVID-19 Host Genetics Initiative. The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic. Eur J Hum Genet. 2020 Jun;28(6):715-718. PMID: 32404885; PMC: PMC7220587 
covidHgiGwasB2 Hosp COVID GWAS Hospitalized COVID GWAS from the COVID-19 Host Genetics Initiative (3199 cases, 8 studies) Phenotype and Literature 
covidHgiGwasC2 COVID GWAS COVID GWAS from the COVID-19 Host Genetics Initiative (6696 cases, 18 studies) Phenotype and Literature 
covidMuts COVID Rare Harmful Var Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort Phenotype and Literature Description This track shows rare variants associated with monogenic congenital defects of immunity to the SARS-CoV-2 virus identified by the COVID Human Genetic Effort. This international consortium aims to discover truly causative variations: those underlying severe forms of COVID-19 in previously healthy individuals, and those that make certain individuals resistant to infection by the SARS-CoV2 virus despite repeated exposure. The major feature of the small set of variants in this track is that they are functionally tested to be deleterious and genetically tested to be disease-causing. Specifically, rare variants were predicted to be loss-of-function at human loci known to govern interferon (IFN) immunity to influenza virus in patients with life-threatening COVID-19 pneumonia, relative to subjects with asymptomatic or benign infection. These genetic defects display incomplete penetrance for influenza respiratory distress and only appear clinically upon infection with the more virulent SARS-CoV-2. Display Conventions Only eight genes with 23 variants are contained in this track. Use the links below to navigate to the gene of interest or view all eight genes together using the following sessions for hg38 or hg19. Gene Name Human GRCh37/hg19 Assembly Human GRCh38/hg38 Assembly TLR3 chr4:186990309-187006252 chr4:186069152-186088069 IRF7 chr11:612555-615999 chr11:612591-615970 UNC93B1 chr11:67758575-67771593 chr11:67991100-68004097 TBK1 chr12:64845840-64895899 chr12:64452120-64502114 TICAM1 chr19:4815936-4831754 chr19:4815932-4831704 IRF3 chr19:50162826-50169132 chr19:49659570-49665875 IFNAR1 chr21:34697214-34732128 chr21:33324970-33359864 IFNAR2 chr21:34602231-34636820 chr21:33229974-33264525 Methods This track uses variant calls in autosomal IFN-related genes from whole exome and genome data with a MAF lower than 0.001 (gnomAD v2.1.1) and experimental demonstration of loss-of-function. The patient population studied consisted of 659 patients with life-threatening COVID-19 pneumonia relative to 534 subjects with asymptomatic or benign infection of varying ethnicities. Variants underlying autosomal-recessive or autosomal-dominant deficiencies were identified in 23 patients (3.5%) 17 to 77 years of age. The proportion of individuals carrying at least one variant was compared between severe cases and control cases by means of logistic regression with the likelihood ratio test. Principal Component Analysis (PCA) was conducted with Plink v1.9 software on whole exome and genome sequencing data with the 1000 Genomes (1kG) Project phase 3 public database as reference. Analysis of enrichment in rare synonymous variants of the genes was performed to check the calibration of the burden test. The odds ratio was also estimated by logistic regression and adjusted for ethnic heterogeneity. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Credits Thanks to the COVID Human Genetic Effort contributors for making these data available, and in particular to Qian Zhang at the Rockefeller University for review and input during browser track development. References Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M, Chen J, Ogishi M, Sabli IKD, Hodeib S, Korol C et al. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science. 2020 Sep 24;. PMID: 32972995 
metaDome MetaDome MetaDome - Tolerance Landscape score Phenotype and Literature Description The "Constraint scores" container track includes several subtracks showing the results of constraint prediction algorithms. These try to find regions of negative selection, where variations likely have functional impact. The algorithms do not use multi-species alignments to derive evolutionary constraint, but use primarily human variation, usually from variants collected by gnomAD (see the gnomAD V2 or V3 tracks on hg19 and hg38) or TOPMED (contained in our dbSNP tracks and available as a filter). One of the subtracks is based on UK Biobank variants, which are not available publicly, so we have no track with the raw data. The number of human genomes that are used as the input for these scores are 76k, 53k and 110k for gnomAD, TOPMED and UK Biobank, respectively. Note that another important constraint score, gnomAD constraint, is not part of this container track but can be found in the hg38 gnomAD track. The algorithms included in this track are: JARVIS - "Junk" Annotation genome-wide Residual Variation Intolerance Score: JARVIS scores were created by first scanning the entire genome with a sliding-window approach (using a 1-nucleotide step), recording the number of all TOPMED variants and common variants, irrespective of their predicted effect, within each window, to eventually calculate a single-nucleotide resolution genome-wide residual variation intolerance score (gwRVIS). That score, gwRVIS was then combined with primary genomic sequence context, and additional genomic annotations with a multi-module deep learning framework to infer pathogenicity of noncoding regions that still remains naive to existing phylogenetic conservation metrics. The higher the score, the more deleterious the prediction. This score covers the entire genome, except the gaps. HMC - Homologous Missense Constraint: Homologous Missense Constraint (HMC) is a amino acid level measure of genetic intolerance of missense variants within human populations. For all assessable amino-acid positions in Pfam domains, the number of missense substitutions directly observed in gnomAD (Observed) was counted and compared to the expected value under a neutral evolution model (Expected). The upper limit of a 95% confidence interval for the Observed/Expected ratio is defined as the HMC score. Missense variants disrupting the amino-acid positions with HMC&lt;0.8 are predicted to be likely deleterious. This score only covers PFAM domains within coding regions. MetaDome - Tolerance Landscape Score (hg19 only): MetaDome Tolerance Landscape scores are computed as a missense over synonymous variant count ratio, which is calculated in a sliding window (with a size of 21 codons/residues) to provide a per-position indication of regional tolerance to missense variation. The variant database was gnomAD and the score corrected for codon composition. Scores &lt;0.7 are considered intolerant. This score covers only coding regions. MTR - Missense Tolerance Ratio (hg19 only): Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence. It is estimated across sliding windows of 31 codons (default) and uses observed standing variation data from the WES component of gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores were computed using Ensembl v95 release. The number of gnomAD 2 exomes used here is higher than the number of gnomAD 3 samples (125 exoms versus 76k full genomes), but this score only covers coding regions. UK Biobank depletion rank score (hg38 only): Halldorsson et al. tabulated the number of UK Biobank variants in each 500bp window of the genome and compared this number to an expected number given the heptamer nucleotide composition of the window and the fraction of heptamers with a sequence variant across the genome and their mutational classes. A variant depletion score was computed for every overlapping set of 500-bp windows in the genome with a 50-bp step size. They then assigned a rank (depletion rank (DR)) from 0 (most depletion) to 100 (least depletion) for each 500-bp window. Since the windows are overlapping, we plot the value only in the central 50bp of the 500bp window, following advice from the author of the score, Hakon Jonsson, deCODE Genetics. He suggested that the value of the central window, rather than the worst possible score of all overlapping windows, is the most informative for a position. This score covers almost the entire genome, only very few regions were excluded, where the genome sequence had too many gap characters. Display Conventions and Configuration JARVIS JARVIS scores are shown as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The scores were downloaded and converted to a single bigWig file. Move the mouse over the bars to display the exact values. A horizontal line is shown at the 0.733 value which signifies the 90th percentile. See hg19 makeDoc and hg38 makeDoc. Interpretation: The authors offer a suggested guideline of > 0.9998 for identifying higher confidence calls and minimizing false positives. In addition to that strict threshold, the following two more relaxed cutoffs can be used to explore additional hits. Note that these thresholds are offered as guidelines and are not necessarily representative of pathogenicity. PercentileJARVIS score threshold 99th0.9998 95th0.9826 90th0.7338 HMC HMC scores are displayed as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The highly-constrained cutoff of 0.8 is indicated with a line. Interpretation: A protein residue with HMC score &lt;1 indicates that missense variants affecting the homologous residues are significantly under negative selection (P-value &lt; 0.05) and likely to be deleterious. A more stringent score threshold of HMC&lt;0.8 is recommended to prioritize predicted disease-associated variants. MetaDome MetaDome data can be found on two tracks, MetaDome and MetaDome All Data. The MetaDome track should be used by default for data exploration. In this track the raw data containing the MetaDome tolerance scores were converted into a signal ("wiggle") track. Since this data was computed on the proteome, there was a small amount of coordinate overlap, roughly 0.42%. In these regions the lowest possible score was chosen for display in the track to maintain sensitivity. For this reason, if a protein variant is being evaluated, the MetaDome All Data track can be used to validate the score. More information on this data can be found in the MetaDome FAQ. Interpretation: The authors suggest the following guidelines for evaluating intolerance. By default, the MetaDome track displays a horizontal line at 0.7 which signifies the first intolerant bin. For more information see the MetaDome publication. ClassificationMetaDome Tolerance Score Highly intolerant&le; 0.175 Intolerant&le; 0.525 Slightly intolerant&le; 0.7 MTR MTR data can be found on two tracks, MTR All data and MTR Scores. In the MTR Scores track the data has been converted into 4 separate signal tracks representing each base pair mutation, with the lowest possible score shown when multiple transcripts overlap at a position. Overlaps can happen since this score is derived from transcripts and multiple transcripts can overlap. A horizontal line is drawn on the 0.8 score line to roughly represent the 25th percentile, meaning the items below may be of particular interest. It is recommended that the data be explored using this version of the track, as it condenses the information substantially while retaining the magnitude of the data. Any specific point mutations of interest can then be researched in the MTR All data track. This track contains all of the information from MTRV2 including more than 3 possible scores per base when transcripts overlap. A mouse-over on this track shows the ref and alt allele, as well as the MTR score and the MTR score percentile. Filters are available for MTR score, False Discovery Rate (FDR), MTR percentile, and variant consequence. By default, only items in the bottom 25 percentile are shown. Items in the track are colored according to their MTR percentile: Green items MTR percentiles over 75 Black items MTR percentiles between 25 and 75 Red items MTR percentiles below 25 Blue items No MTR score Interpretation: Regions with low MTR scores were seen to be enriched with pathogenic variants. For example, ClinVar pathogenic variants were seen to have an average score of 0.77 whereas ClinVar benign variants had an average score of 0.92. Further validation using the FATHMM cancer-associated training dataset saw that scores less than 0.5 contained 8.6% of the pathogenic variants while only containing 0.9% of neutral variants. In summary, lower scores are more likely to represent pathogenic variants whereas higher scores could be pathogenic, but have a higher chance to be a false positive. For more information see the MTR-Viewer publication. Methods JARVIS Scores were downloaded and converted to a single bigWig file. See the hg19 makeDoc and the hg38 makeDoc for more info. HMC Scores were downloaded and converted to .bedGraph files with a custom Python script. The bedGraph files were then converted to bigWig files, as documented in our makeDoc hg19 build log. MetaDome The authors provided a bed file containing codon coordinates along with the scores. This file was parsed with a python script to create the two tracks. For the first track the scores were aggregated for each coordinate, then the lowest score chosen for any overlaps and the result written out to bedGraph format. The file was then converted to bigWig with the bedGraphToBigWig utility. For the second track the file was reorganized into a bed 4+3 and conveted to bigBed with the bedToBigBed utility. See the hg19 makeDoc for details including the build script. The raw MetaDome data can also be accessed via their Zenodo handle. MTR V2 file was downloaded and columns were reshuffled as well as itemRgb added for the MTR All data track. For the MTR Scores track the file was parsed with a python script to pull out the highest possible MTR score for each of the 3 possible mutations at each base pair and 4 tracks built out of these values representing each mutation. See the hg19 makeDoc entry on MTR for more info. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/hmc/hmc.bw stdout Please refer to our Data Access FAQ for more information. Credits Thanks to Jean-Madeleine Desainteagathe (APHP Paris, France) for suggesting the JARVIS, MTR, HMC tracks. Thanks to Xialei Zhang for providing the HMC data file and to Dimitrios Vitsios and Slave Petrovski for helping clean up the hg38 JARVIS files for providing guidance on interpretation. Additional thanks to Laurens van de Wiel for providing the MetaDome data as well as guidance on the track development and interpretation. References Vitsios D, Dhindsa RS, Middleton L, Gussow AB, Petrovski S. Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. Nat Commun. 2021 Mar 8;12(1):1504. PMID: 33686085; PMC: PMC7940646 Xiaolei Zhang, Pantazis I. Theotokis, Nicholas Li, the SHaRe Investigators, Caroline F. Wright, Kaitlin E. Samocha, Nicola Whiffin, James S. Ware Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery. Medrxiv 2022.02.16.22271023 Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat. 2019 Aug;40(8):1030-1038. PMID: 31116477; PMC: PMC6772141 Silk M, Petrovski S, Ascher DB. MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 2019 Jul 2;47(W1):W121-W126. PMID: 31170280; PMC: PMC6602522 Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO et al. The sequences of 150,119 genomes in the UK Biobank. Nature. 2022 Jul;607(7920):732-740. PMID: 35859178; PMC: PMC9329122 
wgEncodeAwgDnaseMasterSites Master DNaseI HS DnaseSeq ENCODE Jan 2011 Freeze wgEncodeAwgDnaseMasterSites DNaseI HS Sequencing DNaseI Hypersensitive Site Master List (125 cell types) from ENCODE/Analysis Regulation Description DNaseI hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. This track displays an extensive map of human DHSs (~2.9 million) identified through genome-wide profiling in 125 diverse cell and tissue types by the ENCODE Consortium between September 2007 and January 2011, with follow-on analysis and results reported in September 2012. This master list track represents a summary of the 125 separate cell type DHSs. Each master list element consists of a DHS from at least one of the 125 cell types, and every DHS from a given cell type overlaps at least one master list DHS. For further details see the final paragraph of the Methods section below. The data underlying this track was produced by two ENCODE production groups (University of Washington and Duke University). Uniform processing of the individual experiments was performed by the ENCODE Analysis Working Group, and is displayed in the ENCODE Uniform DNaseI HS browser track. The DNaseI HS Clusters track provides another view of this data. Display Conventions and Configuration The display for this track shows DHS locations and score as grayscale-colored items where higher scores correspond to darker-colored blocks. The label displayed to the left of each item indicates the number of cell types with DnaseI sensitivity detected at the site. Clicking on a displayed block shows a details page that lists the cell types. Methods DNaseI hypersensitivity mapping was performed using protocols developed by Duke University or University of Washington. Data sets were sequenced on Illumina instruments to an average depth of 30 million uniquely mapping sequence tags (27bp for University of Washington and 20bp for Duke University) per replicate. For uniformity of analysis, some cell-type data sets that exceeded 40M tag depth were randomly subsampled to a depth of 30 million tags. Sequence reads were mapped using the Bowtie aligner, allowing a maximum of two mismatches. Only reads mapping uniquely to the genome were used in the analyses. Mappings were to male or female versions of hg19/GRCh37, depending on cell type, with random regions omitted. Data were analysed jointly using a single algorithm to identify sites. The hotspot algorithm (John et. al 2011) was applied uniformly to datasets from both protocols. Briefly, hotspot is a scan statistic that uses the binomial distribution to gauge enrichment of tags based on a local background model estimated around every tag. General-sized regions of enrichment are identified as hotspots, and then 150-bp peaks within hotspots are called by looking for local maxima in the tag density profile (sliding window tag count in 150-bp windows, stepping every 20 bp). Further stringencies are applied to the local maxima detection to prevent over calling of spurious peaks. The hotspot program also includes an FDR (false discovery rate) estimation procedure for thresholding hotspots and peaks, based on a simulation approach. Random reads are generated at the same sequencing depth as the target sample, hotspots are called on the simulated data, and the random and observed hotspots are compared via their z-scores (based on the binomial model) to estimate the FDR. Using this procedure, DHSs were identified at an FDR of 1%. The DHSs called on individual cell-types were consolidated into a master list of 2,890,742 unique, non-overlapping DHS positions by first merging the FDR 1% peaks across all cell-types. Then, for each resulting interval of merged sites, the DHS with the highest z-score was selected for the master list. Any DHSs overlapping the peaks selected for the master list were then discarded. The remaining DHSs were then merged and the process repeated until each original DHS was either in the master list, or discarded. Of these DHSs, 970,100 were specific to a single cell type, 1,920,642 were active in 2 or more cell types, and 3,692 (a small minority) were detected in all cell types. Each master list DHS is annotated with the number of cell-types whose original DHSs overlap the master list DHS. Credits The master list was generated by the University of Washington ENCODE group on behalf of the ENCODE Analysis Working Group, based on uniformly processed DNaseI peaks (ENCODE Uniform DNaseI HS). Credits for the primary data underlying this track and the uniform peak calls are included in track description pages listed in the Description section of the Uniform DNaseI HS track. Contact: Robert Thurman (University of Washington) References Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B et al. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. PMID: 22955617; PMC: PMC3721348 John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet. 2011 Mar;43(3):264-8. PMID: 21258342 See also the references and credit sections in the related ENCODE Uniform DnaseI HS, ENCODE UW DnaseI HS and ENCODE Duke DnaseI HS tracks. 
wgEncodeDNAseSuper ENC DNase/FAIRE ENCODE Open Chromatin by DNaseI HS and FAIRE Regulation Description These tracks display evidence of open chromatin in ENCODE cell types. Open chromatin describes segments of DNA that are unpacked and accessible to the regulatory factors, enzymes, and smaller molecules in the cell. This is in contrast to closed chromatin, which is packed and inaccessible. Transcriptionally-active chromatin tends to be more open, while condensed, densely-packed chromatin tends to be silent. Open chromatin was identified using complementary methods including: DNaseI hypersensitivity (HS), Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE), and chromatin immunoprecipitation (ChIP) for select regulatory factors. DNaseI HS: DNaseI is an enzyme that has long been used to map general chromatin accessibility, and DNaseI "hyperaccessibility" or "hypersensitivity" is a feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, silencers, insulators, promotors, locus control regions and novel elements. DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome. FAIRE: FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) is a method to isolate and identify nucleosome-depleted regions of the genome. FAIRE was initially discovered in yeast and subsequently shown to identify active regulatory elements in human cells (Giresi et al., 2007). Although less well-characterized than DNase, FAIRE also appears to identify functional regulatory elements that include enhancers, silencers, insulators, promotors, locus control regions and novel elements. ChIP: ChIP (Chromatin Immunoprecipitation) is a method to identify the specific location of proteins that are directly or indirectly bound to genomic DNA. By identifying the binding location of sequence-specific transcription factors, general transcription machinery components, and chromatin factors, ChIP can help in the functional annotation of the open chromatin regions identified by DNaseI HS mapping and FAIRE. Display Conventions These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Ho L, Crabtree GR. Chromatin remodelling during development. Nature. 2010 Jan 28;463(7280):474-84. Geiman TM, Robertson KD. Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together? J Cell Biochem. 2002;87(2):117-25. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
metaDomeAllScores MetaDome All Data MetaDome - Tolerance Landscape score all annotations Phenotype and Literature Description The "Constraint scores" container track includes several subtracks showing the results of constraint prediction algorithms. These try to find regions of negative selection, where variations likely have functional impact. The algorithms do not use multi-species alignments to derive evolutionary constraint, but use primarily human variation, usually from variants collected by gnomAD (see the gnomAD V2 or V3 tracks on hg19 and hg38) or TOPMED (contained in our dbSNP tracks and available as a filter). One of the subtracks is based on UK Biobank variants, which are not available publicly, so we have no track with the raw data. The number of human genomes that are used as the input for these scores are 76k, 53k and 110k for gnomAD, TOPMED and UK Biobank, respectively. Note that another important constraint score, gnomAD constraint, is not part of this container track but can be found in the hg38 gnomAD track. The algorithms included in this track are: JARVIS - "Junk" Annotation genome-wide Residual Variation Intolerance Score: JARVIS scores were created by first scanning the entire genome with a sliding-window approach (using a 1-nucleotide step), recording the number of all TOPMED variants and common variants, irrespective of their predicted effect, within each window, to eventually calculate a single-nucleotide resolution genome-wide residual variation intolerance score (gwRVIS). That score, gwRVIS was then combined with primary genomic sequence context, and additional genomic annotations with a multi-module deep learning framework to infer pathogenicity of noncoding regions that still remains naive to existing phylogenetic conservation metrics. The higher the score, the more deleterious the prediction. This score covers the entire genome, except the gaps. HMC - Homologous Missense Constraint: Homologous Missense Constraint (HMC) is a amino acid level measure of genetic intolerance of missense variants within human populations. For all assessable amino-acid positions in Pfam domains, the number of missense substitutions directly observed in gnomAD (Observed) was counted and compared to the expected value under a neutral evolution model (Expected). The upper limit of a 95% confidence interval for the Observed/Expected ratio is defined as the HMC score. Missense variants disrupting the amino-acid positions with HMC&lt;0.8 are predicted to be likely deleterious. This score only covers PFAM domains within coding regions. MetaDome - Tolerance Landscape Score (hg19 only): MetaDome Tolerance Landscape scores are computed as a missense over synonymous variant count ratio, which is calculated in a sliding window (with a size of 21 codons/residues) to provide a per-position indication of regional tolerance to missense variation. The variant database was gnomAD and the score corrected for codon composition. Scores &lt;0.7 are considered intolerant. This score covers only coding regions. MTR - Missense Tolerance Ratio (hg19 only): Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence. It is estimated across sliding windows of 31 codons (default) and uses observed standing variation data from the WES component of gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores were computed using Ensembl v95 release. The number of gnomAD 2 exomes used here is higher than the number of gnomAD 3 samples (125 exoms versus 76k full genomes), but this score only covers coding regions. UK Biobank depletion rank score (hg38 only): Halldorsson et al. tabulated the number of UK Biobank variants in each 500bp window of the genome and compared this number to an expected number given the heptamer nucleotide composition of the window and the fraction of heptamers with a sequence variant across the genome and their mutational classes. A variant depletion score was computed for every overlapping set of 500-bp windows in the genome with a 50-bp step size. They then assigned a rank (depletion rank (DR)) from 0 (most depletion) to 100 (least depletion) for each 500-bp window. Since the windows are overlapping, we plot the value only in the central 50bp of the 500bp window, following advice from the author of the score, Hakon Jonsson, deCODE Genetics. He suggested that the value of the central window, rather than the worst possible score of all overlapping windows, is the most informative for a position. This score covers almost the entire genome, only very few regions were excluded, where the genome sequence had too many gap characters. Display Conventions and Configuration JARVIS JARVIS scores are shown as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The scores were downloaded and converted to a single bigWig file. Move the mouse over the bars to display the exact values. A horizontal line is shown at the 0.733 value which signifies the 90th percentile. See hg19 makeDoc and hg38 makeDoc. Interpretation: The authors offer a suggested guideline of > 0.9998 for identifying higher confidence calls and minimizing false positives. In addition to that strict threshold, the following two more relaxed cutoffs can be used to explore additional hits. Note that these thresholds are offered as guidelines and are not necessarily representative of pathogenicity. PercentileJARVIS score threshold 99th0.9998 95th0.9826 90th0.7338 HMC HMC scores are displayed as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The highly-constrained cutoff of 0.8 is indicated with a line. Interpretation: A protein residue with HMC score &lt;1 indicates that missense variants affecting the homologous residues are significantly under negative selection (P-value &lt; 0.05) and likely to be deleterious. A more stringent score threshold of HMC&lt;0.8 is recommended to prioritize predicted disease-associated variants. MetaDome MetaDome data can be found on two tracks, MetaDome and MetaDome All Data. The MetaDome track should be used by default for data exploration. In this track the raw data containing the MetaDome tolerance scores were converted into a signal ("wiggle") track. Since this data was computed on the proteome, there was a small amount of coordinate overlap, roughly 0.42%. In these regions the lowest possible score was chosen for display in the track to maintain sensitivity. For this reason, if a protein variant is being evaluated, the MetaDome All Data track can be used to validate the score. More information on this data can be found in the MetaDome FAQ. Interpretation: The authors suggest the following guidelines for evaluating intolerance. By default, the MetaDome track displays a horizontal line at 0.7 which signifies the first intolerant bin. For more information see the MetaDome publication. ClassificationMetaDome Tolerance Score Highly intolerant&le; 0.175 Intolerant&le; 0.525 Slightly intolerant&le; 0.7 MTR MTR data can be found on two tracks, MTR All data and MTR Scores. In the MTR Scores track the data has been converted into 4 separate signal tracks representing each base pair mutation, with the lowest possible score shown when multiple transcripts overlap at a position. Overlaps can happen since this score is derived from transcripts and multiple transcripts can overlap. A horizontal line is drawn on the 0.8 score line to roughly represent the 25th percentile, meaning the items below may be of particular interest. It is recommended that the data be explored using this version of the track, as it condenses the information substantially while retaining the magnitude of the data. Any specific point mutations of interest can then be researched in the MTR All data track. This track contains all of the information from MTRV2 including more than 3 possible scores per base when transcripts overlap. A mouse-over on this track shows the ref and alt allele, as well as the MTR score and the MTR score percentile. Filters are available for MTR score, False Discovery Rate (FDR), MTR percentile, and variant consequence. By default, only items in the bottom 25 percentile are shown. Items in the track are colored according to their MTR percentile: Green items MTR percentiles over 75 Black items MTR percentiles between 25 and 75 Red items MTR percentiles below 25 Blue items No MTR score Interpretation: Regions with low MTR scores were seen to be enriched with pathogenic variants. For example, ClinVar pathogenic variants were seen to have an average score of 0.77 whereas ClinVar benign variants had an average score of 0.92. Further validation using the FATHMM cancer-associated training dataset saw that scores less than 0.5 contained 8.6% of the pathogenic variants while only containing 0.9% of neutral variants. In summary, lower scores are more likely to represent pathogenic variants whereas higher scores could be pathogenic, but have a higher chance to be a false positive. For more information see the MTR-Viewer publication. Methods JARVIS Scores were downloaded and converted to a single bigWig file. See the hg19 makeDoc and the hg38 makeDoc for more info. HMC Scores were downloaded and converted to .bedGraph files with a custom Python script. The bedGraph files were then converted to bigWig files, as documented in our makeDoc hg19 build log. MetaDome The authors provided a bed file containing codon coordinates along with the scores. This file was parsed with a python script to create the two tracks. For the first track the scores were aggregated for each coordinate, then the lowest score chosen for any overlaps and the result written out to bedGraph format. The file was then converted to bigWig with the bedGraphToBigWig utility. For the second track the file was reorganized into a bed 4+3 and conveted to bigBed with the bedToBigBed utility. See the hg19 makeDoc for details including the build script. The raw MetaDome data can also be accessed via their Zenodo handle. MTR V2 file was downloaded and columns were reshuffled as well as itemRgb added for the MTR All data track. For the MTR Scores track the file was parsed with a python script to pull out the highest possible MTR score for each of the 3 possible mutations at each base pair and 4 tracks built out of these values representing each mutation. See the hg19 makeDoc entry on MTR for more info. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/hmc/hmc.bw stdout Please refer to our Data Access FAQ for more information. Credits Thanks to Jean-Madeleine Desainteagathe (APHP Paris, France) for suggesting the JARVIS, MTR, HMC tracks. Thanks to Xialei Zhang for providing the HMC data file and to Dimitrios Vitsios and Slave Petrovski for helping clean up the hg38 JARVIS files for providing guidance on interpretation. Additional thanks to Laurens van de Wiel for providing the MetaDome data as well as guidance on the track development and interpretation. References Vitsios D, Dhindsa RS, Middleton L, Gussow AB, Petrovski S. Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. Nat Commun. 2021 Mar 8;12(1):1504. PMID: 33686085; PMC: PMC7940646 Xiaolei Zhang, Pantazis I. Theotokis, Nicholas Li, the SHaRe Investigators, Caroline F. Wright, Kaitlin E. Samocha, Nicola Whiffin, James S. Ware Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery. Medrxiv 2022.02.16.22271023 Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat. 2019 Aug;40(8):1030-1038. PMID: 31116477; PMC: PMC6772141 Silk M, Petrovski S, Ascher DB. MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 2019 Jul 2;47(W1):W121-W126. PMID: 31170280; PMC: PMC6602522 Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO et al. The sequences of 150,119 genomes in the UK Biobank. Nature. 2022 Jul;607(7920):732-740. PMID: 35859178; PMC: PMC9329122 
wgEncodeAwgDnaseUniform Uniform DNaseI HS DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis Regulation Description The ENCODE Analysis Working Group (AWG) has performed uniform processing on datasets produced by multiple data production groups in the ENCODE Consortium. This track represents a uniform set of open chromatin elements (DNaseI hypersensitive sites) in 125 ENCODE cell types, based on DNase-seq data produced by the &quot;Open Chromatin&quot; (Duke/UNC/UT-A) and University of Washington (UW) ENCODE groups from the project inception in 2007 through the ENCODE January 2011 data freeze. The AWG uniform datasets are used in downstream analysis pipelines by members of the ENCODE Consortium and are one of the primary sources of data referenced in the 2012 ENCODE integrative analysis paper (ENCODE Project Consortium 2012). More information about the ENCODE integrative analysis is here. The primary and lab-processed data (along with methods descriptions, credits and references) on which this track is based are available in the following ENCODE tracks: ENCODE Duke DNaseI HS track ENCODE UW DnaseI HS track Display Conventions and Configuration The display for this track shows site location and signal value as grayscale-colored items where higher signal values correspond to darker-colored blocks. The display can be filtered to higher valued items, using the 'Minimum signal' configuration item. This track is a composite annotation track containing multiple subtracks, one for each cell type. The display mode and filtering of each subtrack can be individually controlled. For more information about track configuration, see Configuring Multi-View Tracks. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. The UCSC Accession listed in the metadata can be used with the File Search tool to retrieve primary data files underlying datasets of interest. In the subtrack selection list, the ENCODE tier (priority) is listed for each cell type. Tier 1 and Tier 2 represent categories with cell types designated for intensive study by the ENCODE investigators. After the January 2011 data freeze, an additional set of cell types were promoted from Tier 3 to Tier 2 to broaden the list of intensively studied cell types. These cell types are listed as Tier 2* in the subtrack list here (and are described as 'newly promoted to tier 2: not in 2011 analysis' on the ENCODE Common Cell Types page). Methods The DNase-seq aligned sequence reads (BAM files) from the primary data tracks listed above were processed using the UW HotSpot pipeline (as described in the UW DnaseI HS track description above). First, &quot;hotspots&quot; (i.e. broad, variable-sized regions of generalized chromatin accessibility) were identified using a relaxed threshold. Then more stringent &quot;narrowPeaks&quot; (False Discovery Rate 1% peaks) were generated by first thresholding hotspots (using random simulation) at FDR 1%, and then (essentially) locating local maxima of the tag density (150 bp window, sliding every 20 bp) within the hotspots. FDR 1% peaks were set to a fixed width of 150 bp. The Duke DNase primary data were pre-processed to reduce variability by combining all replicates for a given cell-type and subsampling at a level of 30 million tags. For the UW data, the replicate 1 calls from the primary UW DNaseI HS data track were used. For the 14 cell types where both groups have data, a collapsed set of FDR 1% peaks were generated by taking a non-overlapping selection of the calls from both centers and giving preference to the peak with the higher z-score when calls overlapped. A collapsed set of hotspots on these cell types was generated by merging the calls from both centers (taking the union interval of overlapping intervals). Credits The processed data for this track were generated by the University of Washington ENCODE group on behalf of the ENCODE Analysis Working Group. Credits for the primary data underlying this track are included in track description pages listed in the Description section above. Contact: Robert Thurman (University of Washington) References ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B et al. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. See also the references in the related ENCODE Duke DNaseI HS and ENCODE UW DnaseI HS tracks. Data Release Policy While primary ENCODE data is subject to a restriction period as described in the ENCODE data release policy, this restriction does not apply to the integrative analysis results. The data in this track are freely available. 
wgEncodeAwgDnaseDuke8988tUniPk 8988T DNase 8988T DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001103 Duke wgEncodeAwgDnaseDuke8988tUniPk None Peaks pancreas adenocarcinoma (PA-TU-8988T), "established in 1985 from the liver metastasis of a primary pancreatic adenocarcinoma from a 64-year-old woman" - DSMZ DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment 8988T DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwWi38tamoxifentamoxifenUniPk WI-38(Tamo) DNase WI-38 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001198 UW wgEncodeAwgDnaseUwWi38tamoxifentamoxifenUniPk 4OHTAM_20nM_72hr Peaks embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Regions of enriched signal in experiment WI-38 (Tamoxifen) DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwWi38UniPk WI-38 DNase WI-38 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001197 UW wgEncodeAwgDnaseUwWi38UniPk None Peaks embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwWerirb1UniPk WERI-Rb-1 DNase WERI-Rb-1 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001190 UW wgEncodeAwgDnaseUwWerirb1UniPk None Peaks retinoblastoma (PMID: 844036) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeUrotheliaut189UniPk Urothel(UT) DNase Urothelia DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001114 Duke wgEncodeAwgDnaseDukeUrotheliaut189UniPk UT189 Peaks primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene DNaseI HS Sequencing Crawford - Duke University UT189 E.Coli treatment 1 hour, followed by 24 hour incubation Regions of enriched signal in experiment Urothelia (UT189) DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeUrotheliaUniPk Urothelia DNase Urothelia DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001113 Duke wgEncodeAwgDnaseDukeUrotheliaUniPk None Peaks primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Urothelia DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwTh2UniPk Th2 DNase Th2 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000491 UW wgEncodeAwgDnaseUwTh2UniPk None Peaks primary Th2 T cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th2 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeTh1UniPk Th1 DNase Th1 DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeTh1UniPk None Peaks primary Th1 T cells DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment Th1 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeTh0UniPk Th0 DNase Adult_CD4_Th0 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH002562 UW wgEncodeAwgDnaseDukeTh0UniPk None Peaks CD4+ cells isolated from human blood and enriched for Th0 populations DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th0 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeT47dUniPk T-47D DNase T-47D DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001109 Duke wgEncodeAwgDnaseDukeT47dUniPk None Peaks epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment T-47D DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeStellateUniPk Stellate DNase Stellate DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001108 Duke wgEncodeAwgDnaseDukeStellateUniPk None Peaks hepatic stellate cells, liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Stellate DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwSkmcUniPk SKMC DNase SKMC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000490 UW wgEncodeAwgDnaseUwSkmcUniPk None Peaks skeletal muscle cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SKMC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwSknshraUniPk SK-N-SH_RA DNase SK-N-SH_RA DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000485 UW wgEncodeAwgDnaseUwSknshraUniPk None Peaks neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwSknmcUniPk SK-N-MC DNase SK-N-MC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001189 UW wgEncodeAwgDnaseUwSknmcUniPk None Peaks neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-MC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwSaecUniPk SAEC DNase SAEC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000501 UW wgEncodeAwgDnaseUwSaecUniPk None Peaks small airway epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeRwpe1UniPk RWPE1 DNase RWPE1 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH002553 Duke wgEncodeAwgDnaseDukeRwpe1UniPk None Peaks prostate epithelial DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment RWPE1 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwRptecUniPk RPTEC DNase RPTEC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001188 UW wgEncodeAwgDnaseUwRptecUniPk None Peaks renal proximal tubule epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeProgfibUniPk ProgFib DNase ProgFib DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000576 Duke wgEncodeAwgDnaseDukeProgfibUniPk None Peaks fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment ProgFib DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwPrecUniPk PrEC DNase PrEC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001888 UW wgEncodeAwgDnaseUwPrecUniPk None Peaks prostate epithelial cell line DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PrEC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukePanisletsUniPk PanIslets DNase PanIslets DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000575 Duke wgEncodeAwgDnaseDukePanisletsUniPk None Peaks pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment PanIslets DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukePanisletdUniPk PanIsletD DNase PanIsletD DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001102 Duke wgEncodeAwgDnaseDukePanisletdUniPk None Peaks dedifferentiated human pancreatic islets from the National Disease Research Interchange (NDRI), same source as PanIslets DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment PanIsletD DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukePhteUniPk pHTE DNase pHTE DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001099 Duke wgEncodeAwgDnaseDukePhteUniPk None Peaks primary tracheal epithelial cells DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment pHTE DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwPanc1UniPk PANC-1 DNase PANC-1 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000500 UW wgEncodeAwgDnaseUwPanc1UniPk None Peaks pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PANC-1 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeOsteoblUniPk Osteobl DNase Osteobl DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001098 Duke wgEncodeAwgDnaseDukeOsteoblUniPk None Peaks osteoblasts (NHOst) DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Osteobl DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwNt2d1UniPk NT2-D1 DNase NT2-D1 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001887 UW wgEncodeAwgDnaseUwNt2d1UniPk None Peaks malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NT2-D1 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwNhlfUniPk NHLF DNase NHLF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000521 UW wgEncodeAwgDnaseUwNhlfUniPk None Peaks lung fibroblasts DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeNhekUniPk NHEK DNase NHEK DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeNhekUniPk None Peaks epidermal keratinocytes DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment NHEK DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwNhdfneoUniPk NHDF-neo DNase NHDF-neo DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000518 UW wgEncodeAwgDnaseUwNhdfneoUniPk None Peaks neonatal dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwNhdfadUniPk NHDF-Ad DNase NHDF-Ad DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001177 UW wgEncodeAwgDnaseUwNhdfadUniPk None Peaks adult dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-Ad DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwNhaUniPk NH-A DNase NH-A DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001179 UW wgEncodeAwgDnaseUwNhaUniPk None Peaks astrocytes (also called Astrocy) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NH-A DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwNb4UniPk NB4 DNase NB4 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000498 UW wgEncodeAwgDnaseUwNb4UniPk None Peaks acute promyelocytic leukemia cell line. (PMID: 1995093) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NB4 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeMyometrUniPk Myometr DNase Myometr DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000603 Duke wgEncodeAwgDnaseDukeMyometrUniPk None Peaks myometrial cells DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Myometr DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeMelanoUniPk Melano DNase Melano DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000602 Duke wgEncodeAwgDnaseDukeMelanoUniPk None Peaks epidermal melanocytes DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Melano DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeMedulloUniPk Medullo DNase Medullo DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000574 Duke wgEncodeAwgDnaseDukeMedulloUniPk None Peaks medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Medullo DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeMcf7hypoxiaUniPk MCF7(Hypox) DNase MCF-7 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001745 Duke wgEncodeAwgDnaseDukeMcf7hypoxiaUniPk Hypoxia_LacAcid Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford - Duke University 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) Regions of enriched signal in experiment MCF-7 (Hypoxia) DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeLncapandrogenUniPk LNCaP(Andr) DNase LNCaP DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001096 Duke wgEncodeAwgDnaseDukeLncapandrogenUniPk androgen Peaks prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Crawford - Duke University 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Regions of enriched signal in experiment LNCaP (Androgen) DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeLncapUniPk LNCaP DNase LNCaP DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeLncapUniPk None Peaks prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment LNCaP DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwJurkatUniPk Jurkat DNase Jurkat DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000497 UW wgEncodeAwgDnaseUwJurkatUniPk None Peaks T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Jurkat DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeIshikawatamoxifenUniPk Ishika(Tam) DNase Ishikawa DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH002552 Duke wgEncodeAwgDnaseDukeIshikawatamoxifenUniPk 4OHTAM_100nM_30m Peaks endometrial adenocarcinoma DNaseI HS Sequencing Crawford - Duke University 30 minutes with 100 nM 4-hydroxytamoxifen (Crawford) Regions of enriched signal in experiment Ishikawa (Tamoxifen) DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeIshikawaestradiolUniPk Ishika(Est) DNase Ishikawa DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH002551 Duke wgEncodeAwgDnaseDukeIshikawaestradiolUniPk Estradiol_100nM_1hr Peaks endometrial adenocarcinoma DNaseI HS Sequencing Crawford - Duke University 1 h with 100 nM Estradiol, hormone treatment (Stam) Regions of enriched signal in experiment Ishikawa (Estradiol) DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeIpsUniPk iPS DNase iPS DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001110 Duke wgEncodeAwgDnaseDukeIpsUniPk None Peaks induced pluripotent stem cell derived from skin fibroblast DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment iPS DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeHuh75UniPk Huh7.5 DNase Huh-7.5 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001112 Duke wgEncodeAwgDnaseDukeHuh75UniPk None Peaks hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Huh7.5 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeHuh7UniPk Huh7 DNase Huh-7 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001111 Duke wgEncodeAwgDnaseDukeHuh7UniPk None Peaks hepatocellular carcinoma DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Huh7 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeHepatocytesUniPk Hepatocytes DNase Hepatocytes DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001107 Duke wgEncodeAwgDnaseDukeHepatocytesUniPk None Peaks primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Hepatocytes DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeHelas3ifna4hUniPk HeLaS3(IFN) DNase HeLa-S3 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000577 Duke wgEncodeAwgDnaseDukeHelas3ifna4hUniPk IFNa4h Peaks cervical carcinoma DNaseI HS Sequencing Crawford - Duke University 4 hours of 500 U/ml Interferon alpha (Crawford) Regions of enriched signal in experiment HeLa-S3 (IFNa) DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHvmfUniPk HVMF DNase HVMF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001176 UW wgEncodeAwgDnaseUwHvmfUniPk None Peaks villous mesenchymal fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeHtr8svnUniPk HTR8svn DNase HTR8svn DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001105 Duke wgEncodeAwgDnaseDukeHtr8svnUniPk None Peaks trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment HTR8svn DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeHsmmtubeUniPk HSMMtube DNase HSMMtube DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeHsmmtubeUniPk None Peaks skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment HSMMtube DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeHsmmembUniPk HSMM_emb DNase HSMM_emb DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH002550 Duke wgEncodeAwgDnaseDukeHsmmembUniPk None Peaks embryonic myoblast DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment HSMM_emb DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeHsmmUniPk HSMM DNase HSMM DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeHsmmUniPk None Peaks skeletal muscle myoblasts DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment HSMM DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHrpepicUniPk HRPEpiC DNase HRPEpiC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000517 UW wgEncodeAwgDnaseUwHrpepicUniPk None Peaks retinal pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHrgecUniPk HRGEC DNase HRGEC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001195 UW wgEncodeAwgDnaseUwHrgecUniPk None Peaks renal glomerular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRGEC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHreUniPk HRE DNase HRE DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000494 UW wgEncodeAwgDnaseUwHreUniPk None Peaks renal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHrcepicUniPk HRCEpiC DNase HRCEpiC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000493 UW wgEncodeAwgDnaseUwHrcepicUniPk None Peaks renal cortical epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRCEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHpdlfUniPk HPdLF DNase HPdLF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001175 UW wgEncodeAwgDnaseUwHpdlfUniPk None Peaks periodontal ligament fibroblasts DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPdLF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHpfUniPk HPF DNase HPF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001174 UW wgEncodeAwgDnaseUwHpfUniPk None Peaks pulmonary fibroblasts isolated from lung tissue DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeHpde6e6e7UniPk HPDE6-E6E7 DNase HPDE6-E6E7 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001106 Duke wgEncodeAwgDnaseDukeHpde6e6e7UniPk None Peaks pancreatic duct cells immortalized with E6E7 gene of HPV DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment HPDE6-E6E7 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHpafUniPk HPAF DNase HPAF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001173 UW wgEncodeAwgDnaseUwHpafUniPk None Peaks pulmonary artery fibroblasts DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHpaecUniPk HPAEC DNase HPAEC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001886 UW wgEncodeAwgDnaseUwHpaecUniPk None Peaks pulmonary artery endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAEC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHnpcepicUniPk HNPCEpiC DNase HNPCEpiC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000516 UW wgEncodeAwgDnaseUwHnpcepicUniPk None Peaks non-pigment ciliary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HNPCEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHmvecdneoUniPk HMVEC-dNeo DNase HMVEC-dNeo DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001172 UW wgEncodeAwgDnaseUwHmvecdneoUniPk None Peaks neonatal microvascular endothelial cells (single donor), dermal-derived DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dNeo DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHmvecdlyneoUniPk HMVEC-dLy-N DNase HMVEC-dLy-Neo DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001171 UW wgEncodeAwgDnaseUwHmvecdlyneoUniPk None Peaks neonatal lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dLy-Neo DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHmvecdlyadUniPk HMVEC-dLy-A DNase HMVEC-dLy-Ad DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001170 UW wgEncodeAwgDnaseUwHmvecdlyadUniPk None Peaks adult lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dLy-Ad DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHmvecdblneoUniPk HMVEC-dBl-N DNase HMVEC-dBl-Neo DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001169 UW wgEncodeAwgDnaseUwHmvecdblneoUniPk None Peaks neonatal blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dBl-Neo DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHmvecdbladUniPk HMVEC-dBl-A HMVEC-dBl-Ad DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001168 UW wgEncodeAwgDnaseUwHmvecdbladUniPk None Peaks adult blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dBl-Ad DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHmvecdadUniPk HMVEC-dAd DNase HMVEC-dAd DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001889 UW wgEncodeAwgDnaseUwHmvecdadUniPk None Peaks adult dermal microvascular endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dAd DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHmvecllyUniPk HMVEC-LLy DNase HMVEC-LLy DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001167 UW wgEncodeAwgDnaseUwHmvecllyUniPk None Peaks lymphatic microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-LLy DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHmveclblUniPk HMVEC-LBl DNase HMVEC-LBl DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001163 UW wgEncodeAwgDnaseUwHmveclblUniPk None Peaks blood microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-LBl DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHmfUniPk HMF DNase HMF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001166 UW wgEncodeAwgDnaseUwHmfUniPk None Peaks mammary fibroblasts DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeHmecUniPk HMEC DNase HMEC DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeHmecUniPk None Peaks mammary epithelial cells DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment HMEC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHl60UniPk HL-60 DNase HL-60 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000489 UW wgEncodeAwgDnaseUwHl60UniPk None Peaks promyelocytic leukemia cells, (PMID: 276884) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHipepicUniPk HIPEpiC DNase HIPEpiC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001184 UW wgEncodeAwgDnaseUwHipepicUniPk None Peaks iris pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HIPEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHgfUniPk HGF DNase HGF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000504 UW wgEncodeAwgDnaseUwHgfUniPk None Peaks gingival fibroblasts DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HGF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHffmycUniPk HFF-Myc DNase HFF-Myc DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001194 UW wgEncodeAwgDnaseUwHffmycUniPk None Peaks foreskin fibroblast cells expressing canine cMyc DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF-Myc DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHffUniPk HFF DNase HFF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001193 UW wgEncodeAwgDnaseUwHffUniPk None Peaks foreskin fibroblast DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHeepicUniPk HEEpiC DNase HEEpiC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000515 UW wgEncodeAwgDnaseUwHeepicUniPk None Peaks esophageal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHconfUniPk HConF DNase HConF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001165 UW wgEncodeAwgDnaseUwHconfUniPk None Peaks conjunctival fibroblast DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HConF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHct116UniPk HCT-116 DNase HCT-116 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001162 UW wgEncodeAwgDnaseUwHct116UniPk None Peaks colorectal carcinoma (PMID: 7214343) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHcpepicUniPk HCPEpiC DNase HCPEpiC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000514 UW wgEncodeAwgDnaseUwHcpepicUniPk None Peaks choroid plexus epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHcmUniPk HCM DNase HCM DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000519 UW wgEncodeAwgDnaseUwHcmUniPk None Peaks cardiac myocytes DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHcfaaUniPk HCFaa DNase HCFaa DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001164 UW wgEncodeAwgDnaseUwHcfaaUniPk None Peaks cardiac fibroblasts- adult atrial DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCFaa DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHcfUniPk HCF DNase HCF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000513 UW wgEncodeAwgDnaseUwHcfUniPk None Peaks cardiac fibroblasts DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHbmecUniPk HBMEC DNase HBMEC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001178 UW wgEncodeAwgDnaseUwHbmecUniPk None Peaks brain microvascular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHacUniPk HAc DNase HAc DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001192 UW wgEncodeAwgDnaseUwHacUniPk None Peaks astrocytes-cerebellar DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHaepicUniPk HAEpiC DNase HAEpiC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000512 UW wgEncodeAwgDnaseUwHaepicUniPk None Peaks amniotic epithelial cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAEpiC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHaspUniPk HA-sp DNase HA-sp DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001183 UW wgEncodeAwgDnaseUwHaspUniPk None Peaks astrocytes spinal cord DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwHahUniPk HA-h DNase HA-h DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001191 UW wgEncodeAwgDnaseUwHahUniPk None Peaks astrocytes-hippocampal DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-h DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeH9esUniPk H9ES DNase H9ES DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000594 Duke wgEncodeAwgDnaseDukeH9esUniPk None Peaks embryonic stem cell (hESC) H9 DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment H9ES DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwH7hescUniPk H7-hESC DNase H7-hESC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000511 UW wgEncodeAwgDnaseUwH7hescUniPk None Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeGlioblaUniPk Gliobla DNase Gliobla DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001100 Duke wgEncodeAwgDnaseDukeGlioblaUniPk None Peaks glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Gliobla DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeGm19240UniPk GM19240 DNase GM19240 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000568 Duke wgEncodeAwgDnaseDukeGm19240UniPk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment GM19240 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeGm19239UniPk GM19239 DNase GM19239 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000567 Duke wgEncodeAwgDnaseDukeGm19239UniPk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment GM19239 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeGm19238UniPk GM19238 DNase GM19238 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000566 Duke wgEncodeAwgDnaseDukeGm19238UniPk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment GM19238 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeGm18507UniPk GM18507 DNase GM18507 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000581 Duke wgEncodeAwgDnaseDukeGm18507UniPk None Peaks lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment GM18507 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeGm12892UniPk GM12892 DNase GM12892 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000565 Duke wgEncodeAwgDnaseDukeGm12892UniPk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment GM12892 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeGm12891UniPk GM12891 DNase GM12891 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000564 Duke wgEncodeAwgDnaseDukeGm12891UniPk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment GM12891 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwGm12865UniPk GM12865 DNase GM12865 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000520 UW wgEncodeAwgDnaseUwGm12865UniPk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwGm12864UniPk GM12864 DNase GM12864 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001182 UW wgEncodeAwgDnaseUwGm12864UniPk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwGm06990UniPk GM06990 DNase GM06990 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000481 UW wgEncodeAwgDnaseUwGm06990UniPk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeFibroblUniPk Fibrobl DNase Fibrobl DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000583 Duke wgEncodeAwgDnaseDukeFibroblUniPk None Peaks child fibroblast DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Fibrobl DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeFibropUniPk FibroP DNase FibroP DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000605 Duke wgEncodeAwgDnaseDukeFibropUniPk None Peaks fibroblasts taken from individuals with Parkinson's disease, AG20443, AG08395 and AG08396 were pooled for this sample DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment FibroP DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeChorionUniPk Chorion DNase Chorion DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000595 Duke wgEncodeAwgDnaseDukeChorionUniPk None Peaks chorion cells (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes. DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment Chorion DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwCaco2UniPk Caco-2 DNase Caco-2 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000486 UW wgEncodeAwgDnaseUwCaco2UniPk None Peaks colorectal adenocarcinoma. (PMID: 1939345) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwCmkUniPk CMK DNase CMK DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000510 UW wgEncodeAwgDnaseUwCmkUniPk None Peaks acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CMK DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeCllUniPk CLL DNase CLL DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001104 Duke wgEncodeAwgDnaseDukeCllUniPk None Peaks chronic lymphocytic leukemia cell, T-cell lymphocyte DNaseI HS Sequencing Crawford - Duke University Regions of enriched signal in experiment CLL DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwCd34mobilizedUniPk CD34+_Mobil DNase CD34+_Mobilized DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001885 UW wgEncodeAwgDnaseUwCd34mobilizedUniPk None Peaks hematopoietic progenitor cells- mobilized, from donor RO01679. DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD34+_Mobilized DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwBjUniPk BJ DNase BJ DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000487 UW wgEncodeAwgDnaseUwBjUniPk None Peaks skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwBe2cUniPk BE2_C DNase BE2_C DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001181 UW wgEncodeAwgDnaseUwBe2cUniPk None Peaks neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2_C DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseDukeAosmcUniPk AoSMC DNase AoSMC DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000601 Duke wgEncodeAwgDnaseDukeAosmcUniPk serum_free_media Peaks aortic smooth muscle cells DNaseI HS Sequencing Crawford - Duke University Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford) Regions of enriched signal in experiment AoSMC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwAoafUniPk AoAF DNase AoAF DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001161 UW wgEncodeAwgDnaseUwAoafUniPk None Peaks aortic adventitial fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwAg10803UniPk AG10803 DNase AG10803 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000509 UW wgEncodeAwgDnaseUwAg10803UniPk None Peaks abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwAg09319UniPk AG09319 DNase AG09319 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000508 UW wgEncodeAwgDnaseUwAg09319UniPk None Peaks gum tissue fibroblasts from apparently heathly 24 year old DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwAg09309UniPk AG09309 DNase AG09309 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000507 UW wgEncodeAwgDnaseUwAg09309UniPk None Peaks adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwAg04450UniPk AG04450 DNase AG04450 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000506 UW wgEncodeAwgDnaseUwAg04450UniPk None Peaks fetal lung fibroblast DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwAg04449UniPk AG04449 DNase AG04449 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH000505 UW wgEncodeAwgDnaseUwAg04449UniPk None Peaks fetal buttock/thigh fibroblast DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwMonocytescd14ro01746UniPk Mcyte-CD14+ DNase Monocytes-CD14+_RO01746 DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001196 UW wgEncodeAwgDnaseUwMonocytescd14ro01746UniPk None Peaks Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Monocytes-CD14+ DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeMcf7UniPk MCF-7 DNase MCF-7 DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeMcf7UniPk None Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment MCF-7 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwCd20UniPk CD20+ DNase CD20+ DnaseSeq ENCODE Jan 2011 Freeze wgEncodeEH001884 UW wgEncodeAwgDnaseUwCd20UniPk None Peaks B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD20+ B cell DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeA549UniPk A549 DNase A549 DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeA549UniPk None Peaks epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment A549 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeHepg2UniPk HepG2 DNase HepG2 DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeHepg2UniPk None Peaks hepatocellular carcinoma DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment HepG2 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeHelas3UniPk HeLa-S3 DNase HeLa-S3 DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeHelas3UniPk None Peaks cervical carcinoma DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment HeLa-S3 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeHuvecUniPk HUVEC DNase HUVEC DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeHuvecUniPk None Peaks umbilical vein endothelial cells DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment HUVEC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeK562UniPk K562 DNase K562 DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeK562UniPk None Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment K562 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeH1hescUniPk H1-hESC DNase H1-hESC DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeH1hescUniPk None Peaks embryonic stem cells DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment H1-hESC DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
wgEncodeAwgDnaseUwdukeGm12878UniPk GM12878 DNase GM12878 DnaseSeq ENCODE Jan 2011 Freeze AWG wgEncodeAwgDnaseUwdukeGm12878UniPk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing ENCODE Analysis Working Group Regions of enriched signal in experiment GM12878 DNaseI HS Uniform Peaks from ENCODE/Analysis Regulation 
encTfChipPk ENCODE 3 TFBS Transcription Factor ChIP-seq Peaks (338 factors in 130 cell types) from ENCODE 3 Regulation Description This track represents a comprehensive set of human transcription factor binding sites based on ChIP-seq experiments generated by production groups in the ENCODE Consortium between February 2011 and November 2018. Transcription factors (TFs) are proteins that bind to DNA and interact with RNA polymerases to regulate gene expression. Some TFs contain a DNA binding domain and can bind directly to specific short DNA sequences ('motifs'); others bind to DNA indirectly through interactions with TFs containing a DNA binding domain. High-throughput antibody capture and sequencing methods (e.g. chromatin immunoprecipitation followed by sequencing, or 'ChIP-seq') can be used to identify regions of TF binding genome-wide. These regions are commonly called ChIP-seq peaks. The related Transcription Factor ChIP-seq Clusters tracks (hg19, hg38) provide summary views of this data. Display and File Conventions and Configuration The display for this track shows site location with the point-source of the peak marked with a colored vertical bar and the level of enrichment at the site indicated by the darkness of the item. The subtracks are colored by UCSC ENCODE 2 cell type color conventions on the hg19 assembly, and by similarity of cell types in DNaseI hypersensitivity assays (as in the DNase Signal) track in the hg38 assembly. The display can be filtered to higher valued items, using the Score range: configuration item. The score values were computed at UCSC based on signal values assigned by the ENCODE pipeline. The input signal values were multiplied by a normalization factor calculated as the ratio of the maximum score value (1000) to the signal value at 1 standard deviation from the mean, with values exceeding 1000 capped at 1000. This has the effect of distributing scores up to mean + 1std across the score range, but assigning all above to the maximum score. Methods The ChIP-seq peaks in this track were generated by the the ENCODE Transcription Factor ChIP-seq Processing Pipeline. Methods documentation and full metadata for each track can be found at the ENCODE project portal, using The ENCODE file accession (ENCFF*) listed in the track label. Credits Thanks to the ENCODE Consortium, the ENCODE ChIP-seq production laboratories, and the ENCODE Data Coordination Center for generating and processing the datasets used here. Special thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI, at the ENCODE Data Analysis Center (ZLab at UMass Medical Center) for providing the peak datasets, metadata, and guidance developing this track. Please check the ZLab ENCODE Public Hubs for the most updated data. References ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222; PMCID: PMC3079585 ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMCID: PMC3439153 Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT et al. ENCODE data at the ENCODE portal. Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. PMID: 26527727; PMC: PMC4702836 Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100. PMID: 22955619 Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep;22(9):1798-812. PMID: 22955990; PMC: PMC3431495 Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. PMID: 23203885; PMC: PMC3531197 Data Use Policy Users may freely download, analyze and publish results based on any ENCODE data without restrictions. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE production laboratory(s) that generated the datasets used, as described in Citing ENCODE. 
encTfChipPkENCFF608UAY vagina POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in vagina from ENCODE 3 (ENCFF608UAY) Regulation 
encTfChipPkENCFF988VKY vagina POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in vagina from ENCODE 3 (ENCFF988VKY) Regulation 
encTfChipPkENCFF362SRJ vagina EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in vagina from ENCODE 3 (ENCFF362SRJ) Regulation 
encTfChipPkENCFF797HPJ vagina EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in vagina from ENCODE 3 (ENCFF797HPJ) Regulation 
encTfChipPkENCFF176MPT vagina CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in vagina from ENCODE 3 (ENCFF176MPT) Regulation 
encTfChipPkENCFF767YMW vagina CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in vagina from ENCODE 3 (ENCFF767YMW) Regulation 
encTfChipPkENCFF164YIY uterus POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in uterus from ENCODE 3 (ENCFF164YIY) Regulation 
encTfChipPkENCFF822OTY uterus POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in uterus from ENCODE 3 (ENCFF822OTY) Regulation 
encTfChipPkENCFF634DDY uterus CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in uterus from ENCODE 3 (ENCFF634DDY) Regulation 
encTfChipPkENCFF282BOE uterus CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in uterus from ENCODE 3 (ENCFF282BOE) Regulation 
encTfChipPkENCFF023MUY lungUpLb POLR2A 4 Transcription Factor ChIP-seq Peaks of POLR2A in upper_lobe_of_left_lung from ENCODE 3 (ENCFF023MUY) Regulation 
encTfChipPkENCFF638MFT lungUpLb POLR2A 3 Transcription Factor ChIP-seq Peaks of POLR2A in upper_lobe_of_left_lung from ENCODE 3 (ENCFF638MFT) Regulation 
encTfChipPkENCFF368ROI lungUpLb POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in upper_lobe_of_left_lung from ENCODE 3 (ENCFF368ROI) Regulation 
encTfChipPkENCFF690LWY lungUpLb POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in upper_lobe_of_left_lung from ENCODE 3 (ENCFF690LWY) Regulation 
encTfChipPkENCFF423CKN lungUpLbe EP300 4 Transcription Factor ChIP-seq Peaks of EP300 in upper_lobe_of_left_lung from ENCODE 3 (ENCFF423CKN) Regulation 
encTfChipPkENCFF700HZX lungUpLbe EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in upper_lobe_of_left_lung from ENCODE 3 (ENCFF700HZX) Regulation 
encTfChipPkENCFF145NMU lungUpLbe EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in upper_lobe_of_left_lung from ENCODE 3 (ENCFF145NMU) Regulation 
encTfChipPkENCFF294RNI lungUpLbe EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in upper_lobe_of_left_lung from ENCODE 3 (ENCFF294RNI) Regulation 
encTfChipPkENCFF781EZZ lungUpLobe CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in upper_lobe_of_left_lung from ENCODE 3 (ENCFF781EZZ) Regulation 
encTfChipPkENCFF984EZB lungUpLobe CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in upper_lobe_of_left_lung from ENCODE 3 (ENCFF984EZB) Regulation 
encTfChipPkENCFF544XZU lungUpLobe CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in upper_lobe_of_left_lung from ENCODE 3 (ENCFF544XZU) Regulation 
encTfChipPkENCFF745NPN lungUpLobe CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in upper_lobe_of_left_lung from ENCODE 3 (ENCFF745NPN) Regulation 
encTfChipPkENCFF911TTD trnsvCln POLR2A 4 Transcription Factor ChIP-seq Peaks of POLR2A in transverse_colon from ENCODE 3 (ENCFF911TTD) Regulation 
encTfChipPkENCFF759UNB trnsvCln POLR2A 3 Transcription Factor ChIP-seq Peaks of POLR2A in transverse_colon from ENCODE 3 (ENCFF759UNB) Regulation 
encTfChipPkENCFF022MCD trnsvCln POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in transverse_colon from ENCODE 3 (ENCFF022MCD) Regulation 
encTfChipPkENCFF382QJG trnsvCln POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in transverse_colon from ENCODE 3 (ENCFF382QJG) Regulation 
encTfChipPkENCFF052QTX transvCln EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in transverse_colon from ENCODE 3 (ENCFF052QTX) Regulation 
encTfChipPkENCFF035UIJ transvCln EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in transverse_colon from ENCODE 3 (ENCFF035UIJ) Regulation 
encTfChipPkENCFF830XLX transvCln EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in transverse_colon from ENCODE 3 (ENCFF830XLX) Regulation 
encTfChipPkENCFF547PLX trnsvColon CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in transverse_colon from ENCODE 3 (ENCFF547PLX) Regulation 
encTfChipPkENCFF251IXD trnsvColon CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in transverse_colon from ENCODE 3 (ENCFF251IXD) Regulation 
encTfChipPkENCFF316LSD trnsvColon CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in transverse_colon from ENCODE 3 (ENCFF316LSD) Regulation 
encTfChipPkENCFF369UWV trnsvColon CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in transverse_colon from ENCODE 3 (ENCFF369UWV) Regulation 
encTfChipPkENCFF823BWT tblNerve POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in tibial_nerve from ENCODE 3 (ENCFF823BWT) Regulation 
encTfChipPkENCFF921JEC tblNerve POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in tibial_nerve from ENCODE 3 (ENCFF921JEC) Regulation 
encTfChipPkENCFF981JOH tbialNerv EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in tibial_nerve from ENCODE 3 (ENCFF981JOH) Regulation 
encTfChipPkENCFF086ABE tbialNerv EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in tibial_nerve from ENCODE 3 (ENCFF086ABE) Regulation 
encTfChipPkENCFF239EJM tibialNerve CTCF Transcription Factor ChIP-seq Peaks of CTCF in tibial_nerve from ENCODE 3 (ENCFF239EJM) Regulation 
encTfChipPkENCFF407FUL tbialNerve CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in tibial_nerve from ENCODE 3 (ENCFF407FUL) Regulation 
encTfChipPkENCFF646ODW tbialNerve CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in tibial_nerve from ENCODE 3 (ENCFF646ODW) Regulation 
encTfChipPkENCFF246QUK tibialArtery CTCF Transcription Factor ChIP-seq Peaks of CTCF in tibial_artery from ENCODE 3 (ENCFF246QUK) Regulation 
encTfChipPkENCFF736DQP thyroid POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in thyroid_gland from ENCODE 3 (ENCFF736DQP) Regulation 
encTfChipPkENCFF957ZLA thyroid POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in thyroid_gland from ENCODE 3 (ENCFF957ZLA) Regulation 
encTfChipPkENCFF401DFB thyroid CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in thyroid_gland from ENCODE 3 (ENCFF401DFB) Regulation 
encTfChipPkENCFF384ALJ thyroid CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in thyroid_gland from ENCODE 3 (ENCFF384ALJ) Regulation 
encTfChipPkENCFF520JZM thyroid CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in thyroid_gland from ENCODE 3 (ENCFF520JZM) Regulation 
encTfChipPkENCFF940TNN testis POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in testis from ENCODE 3 (ENCFF940TNN) Regulation 
encTfChipPkENCFF426BJU testis EP300 Transcription Factor ChIP-seq Peaks of EP300 in testis from ENCODE 3 (ENCFF426BJU) Regulation 
encTfChipPkENCFF432XLE testis CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in testis from ENCODE 3 (ENCFF432XLE) Regulation 
encTfChipPkENCFF885KKQ testis CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in testis from ENCODE 3 (ENCFF885KKQ) Regulation 
encTfChipPkENCFF041MRZ sprpSkin POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in suprapubic_skin from ENCODE 3 (ENCFF041MRZ) Regulation 
encTfChipPkENCFF653ILB sprpSkin POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in suprapubic_skin from ENCODE 3 (ENCFF653ILB) Regulation 
encTfChipPkENCFF963PEH suprpSkin EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in suprapubic_skin from ENCODE 3 (ENCFF963PEH) Regulation 
encTfChipPkENCFF704KAE suprpSkin EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in suprapubic_skin from ENCODE 3 (ENCFF704KAE) Regulation 
encTfChipPkENCFF358ADA suprpSkin EP300 Transcription Factor ChIP-seq Peaks of EP300 in suprapubic_skin from ENCODE 3 (ENCFF358ADA) Regulation 
encTfChipPkENCFF971ILA suprpbSkin CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in suprapubic_skin from ENCODE 3 (ENCFF971ILA) Regulation 
encTfChipPkENCFF148LAV suprpbSkin CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in suprapubic_skin from ENCODE 3 (ENCFF148LAV) Regulation 
encTfChipPkENCFF793HCV subcutAdp EP300 4 Transcription Factor ChIP-seq Peaks of EP300 in subcutaneous_adipose_tissue from ENCODE 3 (ENCFF793HCV) Regulation 
encTfChipPkENCFF269VDY subcutAdp EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in subcutaneous_adipose_tissue from ENCODE 3 (ENCFF269VDY) Regulation 
encTfChipPkENCFF109PJK subcutAdp EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in subcutaneous_adipose_tissue from ENCODE 3 (ENCFF109PJK) Regulation 
encTfChipPkENCFF570FPH subcutAdp EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in subcutaneous_adipose_tissue from ENCODE 3 (ENCFF570FPH) Regulation 
encTfChipPkENCFF051USR subcutAdip CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in subcutaneous_adipose_tissue from ENCODE 3 (ENCFF051USR) Regulation 
encTfChipPkENCFF973ISL subcutAdip CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in subcutaneous_adipose_tissue from ENCODE 3 (ENCFF973ISL) Regulation 
encTfChipPkENCFF874HRJ stomach POLR2A 4 Transcription Factor ChIP-seq Peaks of POLR2A in stomach from ENCODE 3 (ENCFF874HRJ) Regulation 
encTfChipPkENCFF957WEQ stomach POLR2A 3 Transcription Factor ChIP-seq Peaks of POLR2A in stomach from ENCODE 3 (ENCFF957WEQ) Regulation 
encTfChipPkENCFF849CHG stomach POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in stomach from ENCODE 3 (ENCFF849CHG) Regulation 
encTfChipPkENCFF168HOV stomach POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in stomach from ENCODE 3 (ENCFF168HOV) Regulation 
encTfChipPkENCFF887XGB stomach EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in stomach from ENCODE 3 (ENCFF887XGB) Regulation 
encTfChipPkENCFF408PSW stomach EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in stomach from ENCODE 3 (ENCFF408PSW) Regulation 
encTfChipPkENCFF243XHX stomach EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in stomach from ENCODE 3 (ENCFF243XHX) Regulation 
encTfChipPkENCFF039SAY stomach CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in stomach from ENCODE 3 (ENCFF039SAY) Regulation 
encTfChipPkENCFF828UBR stomach CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in stomach from ENCODE 3 (ENCFF828UBR) Regulation 
encTfChipPkENCFF560VSK stomach CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in stomach from ENCODE 3 (ENCFF560VSK) Regulation 
encTfChipPkENCFF703CWY stomach CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in stomach from ENCODE 3 (ENCFF703CWY) Regulation 
encTfChipPkENCFF799TEQ spleen POLR2A 4 Transcription Factor ChIP-seq Peaks of POLR2A in spleen from ENCODE 3 (ENCFF799TEQ) Regulation 
encTfChipPkENCFF637KHE spleen POLR2A 3 Transcription Factor ChIP-seq Peaks of POLR2A in spleen from ENCODE 3 (ENCFF637KHE) Regulation 
encTfChipPkENCFF423BKD spleen POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in spleen from ENCODE 3 (ENCFF423BKD) Regulation 
encTfChipPkENCFF991SQZ spleen POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in spleen from ENCODE 3 (ENCFF991SQZ) Regulation 
encTfChipPkENCFF459AHK spleen CTCF 5 Transcription Factor ChIP-seq Peaks of CTCF in spleen from ENCODE 3 (ENCFF459AHK) Regulation 
encTfChipPkENCFF003YLJ spleen CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in spleen from ENCODE 3 (ENCFF003YLJ) Regulation 
encTfChipPkENCFF741BED spleen CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in spleen from ENCODE 3 (ENCFF741BED) Regulation 
encTfChipPkENCFF881YDR spleen CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in spleen from ENCODE 3 (ENCFF881YDR) Regulation 
encTfChipPkENCFF396TUD spleen CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in spleen from ENCODE 3 (ENCFF396TUD) Regulation 
encTfChipPkENCFF586TYX smoothMuscle CTCF Transcription Factor ChIP-seq Peaks of CTCF in smooth_muscle_cell from ENCODE 3 (ENCFF586TYX) Regulation 
encTfChipPkENCFF307VSP sigmdCln POLR2A 5 Transcription Factor ChIP-seq Peaks of POLR2A in sigmoid_colon from ENCODE 3 (ENCFF307VSP) Regulation 
encTfChipPkENCFF174RCV sigmdCln POLR2A 4 Transcription Factor ChIP-seq Peaks of POLR2A in sigmoid_colon from ENCODE 3 (ENCFF174RCV) Regulation 
encTfChipPkENCFF844HAN sigmdCln POLR2A 3 Transcription Factor ChIP-seq Peaks of POLR2A in sigmoid_colon from ENCODE 3 (ENCFF844HAN) Regulation 
encTfChipPkENCFF534MPD sigmdCln POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in sigmoid_colon from ENCODE 3 (ENCFF534MPD) Regulation 
encTfChipPkENCFF207KQM sigmdCln POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in sigmoid_colon from ENCODE 3 (ENCFF207KQM) Regulation 
encTfChipPkENCFF885NNA sigmdCln EP300 4 Transcription Factor ChIP-seq Peaks of EP300 in sigmoid_colon from ENCODE 3 (ENCFF885NNA) Regulation 
encTfChipPkENCFF581DTH sigmdCln EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in sigmoid_colon from ENCODE 3 (ENCFF581DTH) Regulation 
encTfChipPkENCFF917PXT sigmdCln EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in sigmoid_colon from ENCODE 3 (ENCFF917PXT) Regulation 
encTfChipPkENCFF531NFE sigmdCln EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in sigmoid_colon from ENCODE 3 (ENCFF531NFE) Regulation 
encTfChipPkENCFF929YZA sigmdColon CTCF 5 Transcription Factor ChIP-seq Peaks of CTCF in sigmoid_colon from ENCODE 3 (ENCFF929YZA) Regulation 
encTfChipPkENCFF230HWI sigmdColon CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in sigmoid_colon from ENCODE 3 (ENCFF230HWI) Regulation 
encTfChipPkENCFF324KGZ sigmdColon CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in sigmoid_colon from ENCODE 3 (ENCFF324KGZ) Regulation 
encTfChipPkENCFF637HAC sigmdColon CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in sigmoid_colon from ENCODE 3 (ENCFF637HAC) Regulation 
encTfChipPkENCFF689ZNH sigmdColon CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in sigmoid_colon from ENCODE 3 (ENCFF689ZNH) Regulation 
encTfChipPkENCFF379TEL liverRLobe CTCF 1 Transcription Factor ChIP-seq Peaks of POLR2A in right_lobe_of_liver from ENCODE 3 (ENCFF379TEL) Regulation 
encTfChipPkENCFF665OBP liverRLobe CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in right_lobe_of_liver from ENCODE 3 (ENCFF665OBP) Regulation 
encTfChipPkENCFF139DOR retinPgmtEpi CTCF Transcription Factor ChIP-seq Peaks of CTCF in retinal_pigment_epithelial_cell from ENCODE 3 (ENCFF139DOR) Regulation 
encTfChipPkENCFF389DLX prostate POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in prostate_gland from ENCODE 3 (ENCFF389DLX) Regulation 
encTfChipPkENCFF678WCZ prostate POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in prostate_gland from ENCODE 3 (ENCFF678WCZ) Regulation 
encTfChipPkENCFF852XQI prostate EP300 Transcription Factor ChIP-seq Peaks of EP300 in prostate_gland from ENCODE 3 (ENCFF852XQI) Regulation 
encTfChipPkENCFF899MQP prostate CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in prostate_gland from ENCODE 3 (ENCFF899MQP) Regulation 
encTfChipPkENCFF846FIG prostate CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in prostate_gland from ENCODE 3 (ENCFF846FIG) Regulation 
encTfChipPkENCFF570SMG ovary POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in ovary from ENCODE 3 (ENCFF570SMG) Regulation 
encTfChipPkENCFF934XEQ ovary EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in ovary from ENCODE 3 (ENCFF934XEQ) Regulation 
encTfChipPkENCFF057IJK ovary EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in ovary from ENCODE 3 (ENCFF057IJK) Regulation 
encTfChipPkENCFF261BWI ovary CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in ovary from ENCODE 3 (ENCFF261BWI) Regulation 
encTfChipPkENCFF522DLJ ovary CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in ovary from ENCODE 3 (ENCFF522DLJ) Regulation 
encTfChipPkENCFF617XKX omntalFat EP300 4 Transcription Factor ChIP-seq Peaks of EP300 in omental_fat_pad from ENCODE 3 (ENCFF617XKX) Regulation 
encTfChipPkENCFF060OVF omntalFat EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in omental_fat_pad from ENCODE 3 (ENCFF060OVF) Regulation 
encTfChipPkENCFF240NSI omntalFat EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in omental_fat_pad from ENCODE 3 (ENCFF240NSI) Regulation 
encTfChipPkENCFF459MDC omntalFat EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in omental_fat_pad from ENCODE 3 (ENCFF459MDC) Regulation 
encTfChipPkENCFF709PEA omentalFat CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in omental_fat_pad from ENCODE 3 (ENCFF709PEA) Regulation 
encTfChipPkENCFF454PSG omentalFat CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in omental_fat_pad from ENCODE 3 (ENCFF454PSG) Regulation 
encTfChipPkENCFF517HGL omentalFat CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in omental_fat_pad from ENCODE 3 (ENCFF517HGL) Regulation 
encTfChipPkENCFF374BNP neutrophil CTCF Transcription Factor ChIP-seq Peaks of CTCF in neutrophil from ENCODE 3 (ENCFF374BNP) Regulation 
encTfChipPkENCFF140MVM neurlProgntr EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in neural_progenitor_cell from ENCODE 3 (ENCFF140MVM) Regulation 
encTfChipPkENCFF072ZEU neurlProgntr CTCF Transcription Factor ChIP-seq Peaks of CTCF in neural_progenitor_cell from ENCODE 3 (ENCFF072ZEU) Regulation 
encTfChipPkENCFF582SHF neuralCell SMC3 Transcription Factor ChIP-seq Peaks of SMC3 in neural_cell from ENCODE 3 (ENCFF582SHF) Regulation 
encTfChipPkENCFF246HIM neuralCell RAD21 Transcription Factor ChIP-seq Peaks of RAD21 in neural_cell from ENCODE 3 (ENCFF246HIM) Regulation 
encTfChipPkENCFF048JWL neuralCell MXI1 Transcription Factor ChIP-seq Peaks of MXI1 in neural_cell from ENCODE 3 (ENCFF048JWL) Regulation 
encTfChipPkENCFF888JDR neuralCell EP300 Transcription Factor ChIP-seq Peaks of EP300 in neural_cell from ENCODE 3 (ENCFF888JDR) Regulation 
encTfChipPkENCFF618DDO neuralCell CTCF Transcription Factor ChIP-seq Peaks of CTCF in neural_cell from ENCODE 3 (ENCFF618DDO) Regulation 
encTfChipPkENCFF448MBM myotube CTCF Transcription Factor ChIP-seq Peaks of CTCF in myotube from ENCODE 3 (ENCFF448MBM) Regulation 
encTfChipPkENCFF874DDR medlblastoma CTCF Transcription Factor ChIP-seq Peaks of CTCF in medulloblastoma from ENCODE 3 (ENCFF874DDR) Regulation 
encTfChipPkENCFF743FCW mammaryEpith EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in mammary_epithelial_cell from ENCODE 3 (ENCFF743FCW) Regulation 
encTfChipPkENCFF288RFS mammaryEpith CTCF Transcription Factor ChIP-seq Peaks of CTCF in mammary_epithelial_cell from ENCODE 3 (ENCFF288RFS) Regulation 
encTfChipPkENCFF818LBB lwrLgSkn POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in lower_leg_skin from ENCODE 3 (ENCFF818LBB) Regulation 
encTfChipPkENCFF034NUV lwrLgSkn POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in lower_leg_skin from ENCODE 3 (ENCFF034NUV) Regulation 
encTfChipPkENCFF054PUP lwrLegSkin CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in lower_leg_skin from ENCODE 3 (ENCFF054PUP) Regulation 
encTfChipPkENCFF637FOR lwrLegSkin CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in lower_leg_skin from ENCODE 3 (ENCFF637FOR) Regulation 
encTfChipPkENCFF751UAF lwrLegSkin CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in lower_leg_skin from ENCODE 3 (ENCFF751UAF) Regulation 
encTfChipPkENCFF733VAF lwrLegSkin CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in lower_leg_skin from ENCODE 3 (ENCFF733VAF) Regulation 
encTfChipPkENCFF189TVG liver ZBTB33 2 Transcription Factor ChIP-seq Peaks of ZBTB33 in liver from ENCODE 3 (ENCFF189TVG) Regulation 
encTfChipPkENCFF688LUP liver ZBTB33 1 Transcription Factor ChIP-seq Peaks of ZBTB33 in liver from ENCODE 3 (ENCFF688LUP) Regulation 
encTfChipPkENCFF851HUJ liver YY1 2 Transcription Factor ChIP-seq Peaks of YY1 in liver from ENCODE 3 (ENCFF851HUJ) Regulation 
encTfChipPkENCFF566WSG liver YY1 1 Transcription Factor ChIP-seq Peaks of YY1 in liver from ENCODE 3 (ENCFF566WSG) Regulation 
encTfChipPkENCFF739PUT liver TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in liver from ENCODE 3 (ENCFF739PUT) Regulation 
encTfChipPkENCFF017YUI liver SP1 2 Transcription Factor ChIP-seq Peaks of SP1 in liver from ENCODE 3 (ENCFF017YUI) Regulation 
encTfChipPkENCFF881EJW liver SP1 1 Transcription Factor ChIP-seq Peaks of SP1 in liver from ENCODE 3 (ENCFF881EJW) Regulation 
encTfChipPkENCFF189HPG liver RXRA 2 Transcription Factor ChIP-seq Peaks of RXRA in liver from ENCODE 3 (ENCFF189HPG) Regulation 
encTfChipPkENCFF651LIG liver RXRA 1 Transcription Factor ChIP-seq Peaks of RXRA in liver from ENCODE 3 (ENCFF651LIG) Regulation 
encTfChipPkENCFF510UBQ liver REST 2 Transcription Factor ChIP-seq Peaks of REST in liver from ENCODE 3 (ENCFF510UBQ) Regulation 
encTfChipPkENCFF334FKO liver REST 1 Transcription Factor ChIP-seq Peaks of REST in liver from ENCODE 3 (ENCFF334FKO) Regulation 
encTfChipPkENCFF108ZTV liver RAD21 3 Transcription Factor ChIP-seq Peaks of RAD21 in liver from ENCODE 3 (ENCFF108ZTV) Regulation 
encTfChipPkENCFF708GMO liver RAD21 2 Transcription Factor ChIP-seq Peaks of RAD21 in liver from ENCODE 3 (ENCFF708GMO) Regulation 
encTfChipPkENCFF233DOW liver RAD21 1 Transcription Factor ChIP-seq Peaks of RAD21 in liver from ENCODE 3 (ENCFF233DOW) Regulation 
encTfChipPkENCFF168INE liver NR2F2 2 Transcription Factor ChIP-seq Peaks of NR2F2 in liver from ENCODE 3 (ENCFF168INE) Regulation 
encTfChipPkENCFF266KLW liver NR2F2 1 Transcription Factor ChIP-seq Peaks of NR2F2 in liver from ENCODE 3 (ENCFF266KLW) Regulation 
encTfChipPkENCFF612TRG liver MAX 2 Transcription Factor ChIP-seq Peaks of MAX in liver from ENCODE 3 (ENCFF612TRG) Regulation 
encTfChipPkENCFF840NOO liver MAX 1 Transcription Factor ChIP-seq Peaks of MAX in liver from ENCODE 3 (ENCFF840NOO) Regulation 
encTfChipPkENCFF693FRV liver JUND 2 Transcription Factor ChIP-seq Peaks of JUND in liver from ENCODE 3 (ENCFF693FRV) Regulation 
encTfChipPkENCFF804UDG liver JUND 1 Transcription Factor ChIP-seq Peaks of JUND in liver from ENCODE 3 (ENCFF804UDG) Regulation 
encTfChipPkENCFF971QHN liver HNF4G Transcription Factor ChIP-seq Peaks of HNF4G in liver from ENCODE 3 (ENCFF971QHN) Regulation 
encTfChipPkENCFF713MCF liver HNF4A 2 Transcription Factor ChIP-seq Peaks of HNF4A in liver from ENCODE 3 (ENCFF713MCF) Regulation 
encTfChipPkENCFF201MOM liver HNF4A 1 Transcription Factor ChIP-seq Peaks of HNF4A in liver from ENCODE 3 (ENCFF201MOM) Regulation 
encTfChipPkENCFF258PIW liver GABPA 2 Transcription Factor ChIP-seq Peaks of GABPA in liver from ENCODE 3 (ENCFF258PIW) Regulation 
encTfChipPkENCFF236XBR liver GABPA 1 Transcription Factor ChIP-seq Peaks of GABPA in liver from ENCODE 3 (ENCFF236XBR) Regulation 
encTfChipPkENCFF786DKS liver FOXA2 2 Transcription Factor ChIP-seq Peaks of FOXA2 in liver from ENCODE 3 (ENCFF786DKS) Regulation 
encTfChipPkENCFF344EDE liver FOXA2 1 Transcription Factor ChIP-seq Peaks of FOXA2 in liver from ENCODE 3 (ENCFF344EDE) Regulation 
encTfChipPkENCFF207YNL liver FOXA1 2 Transcription Factor ChIP-seq Peaks of FOXA1 in liver from ENCODE 3 (ENCFF207YNL) Regulation 
encTfChipPkENCFF126PNX liver FOXA1 1 Transcription Factor ChIP-seq Peaks of FOXA1 in liver from ENCODE 3 (ENCFF126PNX) Regulation 
encTfChipPkENCFF862SRI liver EGR1 2 Transcription Factor ChIP-seq Peaks of EGR1 in liver from ENCODE 3 (ENCFF862SRI) Regulation 
encTfChipPkENCFF831MEQ liver EGR1 1 Transcription Factor ChIP-seq Peaks of EGR1 in liver from ENCODE 3 (ENCFF831MEQ) Regulation 
encTfChipPkENCFF690BYG liver CTCF Transcription Factor ChIP-seq Peaks of CTCF in liver from ENCODE 3 (ENCFF690BYG) Regulation 
encTfChipPkENCFF975PTM liver ATF3 2 Transcription Factor ChIP-seq Peaks of ATF3 in liver from ENCODE 3 (ENCFF975PTM) Regulation 
encTfChipPkENCFF566FVB liver ATF3 1 Transcription Factor ChIP-seq Peaks of ATF3 in liver from ENCODE 3 (ENCFF566FVB) Regulation 
encTfChipPkENCFF168VBK kidneyEpith CTCF Transcription Factor ChIP-seq Peaks of CTCF in kidney_epithelial_cell from ENCODE 3 (ENCFF168VBK) Regulation 
encTfChipPkENCFF226MQR keratinocyte CTCF Transcription Factor ChIP-seq Peaks of CTCF in keratinocyte from ENCODE 3 (ENCFF226MQR) Regulation 
encTfChipPkENCFF743FZS hepatocyte EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in hepatocyte from ENCODE 3 (ENCFF743FZS) Regulation 
encTfChipPkENCFF776XRJ hepatocyte CTCF Transcription Factor ChIP-seq Peaks of CTCF in hepatocyte from ENCODE 3 (ENCFF776XRJ) Regulation 
encTfChipPkENCFF813MTO hrtLfVnt POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in heart_left_ventricle from ENCODE 3 (ENCFF813MTO) Regulation 
encTfChipPkENCFF596FFJ hrtLfVnt POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in heart_left_ventricle from ENCODE 3 (ENCFF596FFJ) Regulation 
encTfChipPkENCFF240UFV heartLftVent CTCF Transcription Factor ChIP-seq Peaks of CTCF in heart_left_ventricle from ENCODE 3 (ENCFF240UFV) Regulation 
encTfChipPkENCFF174FQT gEsphSph POLR2A 3 Transcription Factor ChIP-seq Peaks of POLR2A in gastroesophageal_sphincter from ENCODE 3 (ENCFF174FQT) Regulation 
encTfChipPkENCFF956QVQ gEsphSph POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in gastroesophageal_sphincter from ENCODE 3 (ENCFF956QVQ) Regulation 
encTfChipPkENCFF532PJX gEsphSph POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in gastroesophageal_sphincter from ENCODE 3 (ENCFF532PJX) Regulation 
encTfChipPkENCFF597JRR gsEsphSph EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in gastroesophageal_sphincter from ENCODE 3 (ENCFF597JRR) Regulation 
encTfChipPkENCFF150ABP gsEsphSph EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in gastroesophageal_sphincter from ENCODE 3 (ENCFF150ABP) Regulation 
encTfChipPkENCFF047QFE gsEsphSph EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in gastroesophageal_sphincter from ENCODE 3 (ENCFF047QFE) Regulation 
encTfChipPkENCFF603KUP gstEsphSph CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in gastroesophageal_sphincter from ENCODE 3 (ENCFF603KUP) Regulation 
encTfChipPkENCFF045AYR gstEsphSph CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in gastroesophageal_sphincter from ENCODE 3 (ENCFF045AYR) Regulation 
encTfChipPkENCFF252FBJ gstrcMed POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in gastrocnemius_medialis from ENCODE 3 (ENCFF252FBJ) Regulation 
encTfChipPkENCFF358ZLQ gstrcMed POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in gastrocnemius_medialis from ENCODE 3 (ENCFF358ZLQ) Regulation 
encTfChipPkENCFF985OZU gastrocMed CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in gastrocnemius_medialis from ENCODE 3 (ENCFF985OZU) Regulation 
encTfChipPkENCFF101PDP gastrocMed CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in gastrocnemius_medialis from ENCODE 3 (ENCFF101PDP) Regulation 
encTfChipPkENCFF396NYG gastrocMed CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in gastrocnemius_medialis from ENCODE 3 (ENCFF396NYG) Regulation 
encTfChipPkENCFF459YEI frskinKrtn CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in foreskin_keratinocyte from ENCODE 3 (ENCFF459YEI) Regulation 
encTfChipPkENCFF633IHZ frskinKrtn CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in foreskin_keratinocyte from ENCODE 3 (ENCFF633IHZ) Regulation 
encTfChipPkENCFF250ZAH frskinKrtn CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in foreskin_keratinocyte from ENCODE 3 (ENCFF250ZAH) Regulation 
encTfChipPkENCFF652MLT frsknFibro CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in foreskin_fibroblast from ENCODE 3 (ENCFF652MLT) Regulation 
encTfChipPkENCFF337WIE frsknFibro CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in foreskin_fibroblast from ENCODE 3 (ENCFF337WIE) Regulation 
encTfChipPkENCFF738CXX vlMesenFibro CTCF Transcription Factor ChIP-seq Peaks of CTCF in fibroblast_of_villous_mesenchyme from ENCODE 3 (ENCFF738CXX) Regulation 
encTfChipPkENCFF859PRV aortaAdFibro CTCF Transcription Factor ChIP-seq Peaks of CTCF in fibroblast_of_the_aortic_adventitia from ENCODE 3 (ENCFF859PRV) Regulation 
encTfChipPkENCFF933VBD plArtryFibro CTCF Transcription Factor ChIP-seq Peaks of CTCF in fibroblast_of_pulmonary_artery from ENCODE 3 (ENCFF933VBD) Regulation 
encTfChipPkENCFF438XHB mamryGlFibro CTCF Transcription Factor ChIP-seq Peaks of CTCF in fibroblast_of_mammary_gland from ENCODE 3 (ENCFF438XHB) Regulation 
encTfChipPkENCFF148VQH lungFibro CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in fibroblast_of_lung from ENCODE 3 (ENCFF148VQH) Regulation 
encTfChipPkENCFF570FLB lungFibro CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in fibroblast_of_lung from ENCODE 3 (ENCFF570FLB) Regulation 
encTfChipPkENCFF476MXK esphSqEp POLR2A 4 Transcription Factor ChIP-seq Peaks of POLR2A in esophagus_squamous_epithelium from ENCODE 3 (ENCFF476MXK) Regulation 
encTfChipPkENCFF458RGL esphSqEp POLR2A 3 Transcription Factor ChIP-seq Peaks of POLR2A in esophagus_squamous_epithelium from ENCODE 3 (ENCFF458RGL) Regulation 
encTfChipPkENCFF715AKU esphSqEp POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in esophagus_squamous_epithelium from ENCODE 3 (ENCFF715AKU) Regulation 
encTfChipPkENCFF538YID esphSqEp POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in esophagus_squamous_epithelium from ENCODE 3 (ENCFF538YID) Regulation 
encTfChipPkENCFF761JIU esphSquEpi CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in esophagus_squamous_epithelium from ENCODE 3 (ENCFF761JIU) Regulation 
encTfChipPkENCFF587LBC esphSquEpi CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in esophagus_squamous_epithelium from ENCODE 3 (ENCFF587LBC) Regulation 
encTfChipPkENCFF369LXG esphSquEpi CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in esophagus_squamous_epithelium from ENCODE 3 (ENCFF369LXG) Regulation 
encTfChipPkENCFF470NNW esphSquEpi CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in esophagus_squamous_epithelium from ENCODE 3 (ENCFF470NNW) Regulation 
encTfChipPkENCFF737IOU esophMscMc POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in esophagus_muscularis_mucosa from ENCODE 3 (ENCFF737IOU) Regulation 
encTfChipPkENCFF614IMK esphMscMc EP300 4 Transcription Factor ChIP-seq Peaks of EP300 in esophagus_muscularis_mucosa from ENCODE 3 (ENCFF614IMK) Regulation 
encTfChipPkENCFF469TTI esphMscMc EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in esophagus_muscularis_mucosa from ENCODE 3 (ENCFF469TTI) Regulation 
encTfChipPkENCFF207RWS esphMscMc EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in esophagus_muscularis_mucosa from ENCODE 3 (ENCFF207RWS) Regulation 
encTfChipPkENCFF451VDG esphMscMc EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in esophagus_muscularis_mucosa from ENCODE 3 (ENCFF451VDG) Regulation 
encTfChipPkENCFF735EHK esphMscMuc CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in esophagus_muscularis_mucosa from ENCODE 3 (ENCFF735EHK) Regulation 
encTfChipPkENCFF435EDS esphMscMuc CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in esophagus_muscularis_mucosa from ENCODE 3 (ENCFF435EDS) Regulation 
encTfChipPkENCFF202BAI esphMscMuc CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in esophagus_muscularis_mucosa from ENCODE 3 (ENCFF202BAI) Regulation 
encTfChipPkENCFF957CWW erythblst GATA1 2 Transcription Factor ChIP-seq Peaks of GATA1 in erythroblast from ENCODE 3 (ENCFF957CWW) Regulation 
encTfChipPkENCFF762DRA erythblst GATA1 1 Transcription Factor ChIP-seq Peaks of GATA1 in erythroblast from ENCODE 3 (ENCFF762DRA) Regulation 
encTfChipPkENCFF470PNM proxTublEpi CTCF Transcription Factor ChIP-seq Peaks of CTCF in epithelial_cell_of_proximal_tubule from ENCODE 3 (ENCFF470PNM) Regulation 
encTfChipPkENCFF698WAX prostateEpi CTCF Transcription Factor ChIP-seq Peaks of CTCF in epithelial_cell_of_prostate from ENCODE 3 (ENCFF698WAX) Regulation 
encTfChipPkENCFF528VFN esophagEpi CTCF Transcription Factor ChIP-seq Peaks of CTCF in epithelial_cell_of_esophagus from ENCODE 3 (ENCFF528VFN) Regulation 
encTfChipPkENCFF876VZQ umbilVein POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in endothelial_cell_of_umbilical_vein from ENCODE 3 (ENCFF876VZQ) Regulation 
encTfChipPkENCFF822SAU umbilVein GATA2 Transcription Factor ChIP-seq Peaks of GATA2 in endothelial_cell_of_umbilical_vein from ENCODE 3 (ENCFF822SAU) Regulation 
encTfChipPkENCFF390MXI umbilVeinEndo FOS Transcription Factor ChIP-seq Peaks of FOS in endothelial_cell_of_umbilical_vein from ENCODE 3 (ENCFF390MXI) Regulation 
encTfChipPkENCFF655XWN umbilVenEndo CTCF Transcription Factor ChIP-seq Peaks of CTCF in endothelial_cell_of_umbilical_vein from ENCODE 3 (ENCFF655XWN) Regulation 
encTfChipPkENCFF700ILD chorPlexEpi CTCF Transcription Factor ChIP-seq Peaks of CTCF in choroid_plexus_epithelial_cell from ENCODE 3 (ENCFF700ILD) Regulation 
encTfChipPkENCFF251QXA heartMuscl CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in cardiac_muscle_cell from ENCODE 3 (ENCFF251QXA) Regulation 
encTfChipPkENCFF266GGD heartMuscl CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in cardiac_muscle_cell from ENCODE 3 (ENCFF266GGD) Regulation 
encTfChipPkENCFF344UBE heartFibro CTCF Transcription Factor ChIP-seq Peaks of CTCF in cardiac_fibroblast from ENCODE 3 (ENCFF344UBE) Regulation 
encTfChipPkENCFF433ZKP brestEpi POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in breast_epithelium from ENCODE 3 (ENCFF433ZKP) Regulation 
encTfChipPkENCFF575RKM brestEpi POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in breast_epithelium from ENCODE 3 (ENCFF575RKM) Regulation 
encTfChipPkENCFF804AVM breastEpi EP300 4 Transcription Factor ChIP-seq Peaks of EP300 in breast_epithelium from ENCODE 3 (ENCFF804AVM) Regulation 
encTfChipPkENCFF647SXX breastEpi EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in breast_epithelium from ENCODE 3 (ENCFF647SXX) Regulation 
encTfChipPkENCFF996UFS breastEpi EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in breast_epithelium from ENCODE 3 (ENCFF996UFS) Regulation 
encTfChipPkENCFF079ZWQ breastEpi EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in breast_epithelium from ENCODE 3 (ENCFF079ZWQ) Regulation 
encTfChipPkENCFF722THT breastEpi CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in breast_epithelium from ENCODE 3 (ENCFF722THT) Regulation 
encTfChipPkENCFF782GCQ breastEpi CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in breast_epithelium from ENCODE 3 (ENCFF782GCQ) Regulation 
encTfChipPkENCFF974SIH breastEpi CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in breast_epithelium from ENCODE 3 (ENCFF974SIH) Regulation 
encTfChipPkENCFF065LHJ brainMicEndo CTCF Transcription Factor ChIP-seq Peaks of CTCF in brain_microvascular_endothelial_cell from ENCODE 3 (ENCFF065LHJ) Regulation 
encTfChipPkENCFF386FNQ pancreas POLR2A 4 Transcription Factor ChIP-seq Peaks of POLR2A in body_of_pancreas from ENCODE 3 (ENCFF386FNQ) Regulation 
encTfChipPkENCFF628UBC pancreas POLR2A 3 Transcription Factor ChIP-seq Peaks of POLR2A in body_of_pancreas from ENCODE 3 (ENCFF628UBC) Regulation 
encTfChipPkENCFF665RHY pancreas POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in body_of_pancreas from ENCODE 3 (ENCFF665RHY) Regulation 
encTfChipPkENCFF760CPU pancreas POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in body_of_pancreas from ENCODE 3 (ENCFF760CPU) Regulation 
encTfChipPkENCFF437LBW pancreas CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in body_of_pancreas from ENCODE 3 (ENCFF437LBW) Regulation 
encTfChipPkENCFF156VNT pancreas CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in body_of_pancreas from ENCODE 3 (ENCFF156VNT) Regulation 
encTfChipPkENCFF628TDS pancreas CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in body_of_pancreas from ENCODE 3 (ENCFF628TDS) Regulation 
encTfChipPkENCFF622QGA pancreas CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in body_of_pancreas from ENCODE 3 (ENCFF622QGA) Regulation 
encTfChipPkENCFF537YZK biplNeuron ZEB1 Transcription Factor ChIP-seq Peaks of ZEB1 in bipolar_neuron from ENCODE 3 (ENCFF537YZK) Regulation 
encTfChipPkENCFF501XJA bipNeuron SMARCA4 Transcription Factor ChIP-seq Peaks of SMARCA4 in bipolar_neuron from ENCODE 3 (ENCFF501XJA) Regulation 
encTfChipPkENCFF355OQM biplNeuron CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in bipolar_neuron from ENCODE 3 (ENCFF355OQM) Regulation 
encTfChipPkENCFF693PZH biplNeuron CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in bipolar_neuron from ENCODE 3 (ENCFF693PZH) Regulation 
encTfChipPkENCFF312HCK spinlAstrcyt CTCF Transcription Factor ChIP-seq Peaks of CTCF in astrocyte_of_the_spinal_cord from ENCODE 3 (ENCFF312HCK) Regulation 
encTfChipPkENCFF660HHS cerebAstrcyt CTCF Transcription Factor ChIP-seq Peaks of CTCF in astrocyte_of_the_cerebellum from ENCODE 3 (ENCFF660HHS) Regulation 
encTfChipPkENCFF415WKV astrocyte CTCF Transcription Factor ChIP-seq Peaks of CTCF in astrocyte from ENCODE 3 (ENCFF415WKV) Regulation 
encTfChipPkENCFF147RBN ascendAorta CTCF Transcription Factor ChIP-seq Peaks of CTCF in ascending_aorta from ENCODE 3 (ENCFF147RBN) Regulation 
encTfChipPkENCFF262QIB adrnlGld POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in adrenal_gland from ENCODE 3 (ENCFF262QIB) Regulation 
encTfChipPkENCFF033XFJ adrnlGld POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in adrenal_gland from ENCODE 3 (ENCFF033XFJ) Regulation 
encTfChipPkENCFF985ZJL adrenlGlnd CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in adrenal_gland from ENCODE 3 (ENCFF985ZJL) Regulation 
encTfChipPkENCFF622LJD adrenlGlnd CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in adrenal_gland from ENCODE 3 (ENCFF622LJD) Regulation 
encTfChipPkENCFF215GGE adrenlGlnd CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in adrenal_gland from ENCODE 3 (ENCFF215GGE) Regulation 
encTfChipPkENCFF627DHJ adrenlGlnd CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in adrenal_gland from ENCODE 3 (ENCFF627DHJ) Regulation 
encTfChipPkENCFF445OFX 22Rv1 ZFX Transcription Factor ChIP-seq Peaks of ZFX in 22Rv1 from ENCODE 3 (ENCFF445OFX) Regulation 
encTfChipPkENCFF259XYR 22Rv1 CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in 22Rv1 from ENCODE 3 (ENCFF259XYR) Regulation 
encTfChipPkENCFF030BPR 22Rv1 CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in 22Rv1 from ENCODE 3 (ENCFF030BPR) Regulation 
encTfChipPkENCFF016EUX WI38 CTCF Transcription Factor ChIP-seq Peaks of CTCF in WI38 from ENCODE 3 (ENCFF016EUX) Regulation 
encTfChipPkENCFF924OMX WERI-Rb-1 CTCF Transcription Factor ChIP-seq Peaks of CTCF in WERI-Rb-1 from ENCODE 3 (ENCFF924OMX) Regulation 
encTfChipPkENCFF304IDM VCaP CTCF Transcription Factor ChIP-seq Peaks of CTCF in VCaP from ENCODE 3 (ENCFF304IDM) Regulation 
encTfChipPkENCFF274TYW T47D JUND Transcription Factor ChIP-seq Peaks of JUND in T47D from ENCODE 3 (ENCFF274TYW) Regulation 
encTfChipPkENCFF058XAD T47D GATA3 Transcription Factor ChIP-seq Peaks of GATA3 in T47D from ENCODE 3 (ENCFF058XAD) Regulation 
encTfChipPkENCFF132WOI T47D FOXA1 Transcription Factor ChIP-seq Peaks of FOXA1 in T47D from ENCODE 3 (ENCFF132WOI) Regulation 
encTfChipPkENCFF516GZM T47D ESR1 3 Transcription Factor ChIP-seq Peaks of ESR1 in T47D from ENCODE 3 (ENCFF516GZM) Regulation 
encTfChipPkENCFF499QUE T47D ESR1 2 Transcription Factor ChIP-seq Peaks of ESR1 in T47D from ENCODE 3 (ENCFF499QUE) Regulation 
encTfChipPkENCFF475MKH T47D ESR1 1 Transcription Factor ChIP-seq Peaks of ESR1 in T47D from ENCODE 3 (ENCFF475MKH) Regulation 
encTfChipPkENCFF903ZMF T47D CTCF Transcription Factor ChIP-seq Peaks of CTCF in T47D from ENCODE 3 (ENCFF903ZMF) Regulation 
encTfChipPkENCFF099NBE SU-DHL-6 CTCF Transcription Factor ChIP-seq Peaks of CTCF in SU-DHL-6 from ENCODE 3 (ENCFF099NBE) Regulation 
encTfChipPkENCFF958LUB SK-N-SH YY1 Transcription Factor ChIP-seq Peaks of YY1 in SK-N-SH from ENCODE 3 (ENCFF958LUB) Regulation 
encTfChipPkENCFF617AHB SK-N-SH USF2 Transcription Factor ChIP-seq Peaks of USF2 in SK-N-SH from ENCODE 3 (ENCFF617AHB) Regulation 
encTfChipPkENCFF588NYF SK-N-SH USF1 Transcription Factor ChIP-seq Peaks of USF1 in SK-N-SH from ENCODE 3 (ENCFF588NYF) Regulation 
encTfChipPkENCFF883EGI SK-N-SH TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in SK-N-SH from ENCODE 3 (ENCFF883EGI) Regulation 
encTfChipPkENCFF650GZO SK-N-SH SIN3A Transcription Factor ChIP-seq Peaks of SIN3A in SK-N-SH from ENCODE 3 (ENCFF650GZO) Regulation 
encTfChipPkENCFF849EEH SK-N-SH RFX5 Transcription Factor ChIP-seq Peaks of RFX5 in SK-N-SH from ENCODE 3 (ENCFF849EEH) Regulation 
encTfChipPkENCFF946MYA SK-N-SH REST 2 Transcription Factor ChIP-seq Peaks of REST in SK-N-SH from ENCODE 3 (ENCFF946MYA) Regulation 
encTfChipPkENCFF781PAL SK-N-SH REST 1 Transcription Factor ChIP-seq Peaks of REST in SK-N-SH from ENCODE 3 (ENCFF781PAL) Regulation 
encTfChipPkENCFF814REB SK-N-SH RCOR1 Transcription Factor ChIP-seq Peaks of RCOR1 in SK-N-SH from ENCODE 3 (ENCFF814REB) Regulation 
encTfChipPkENCFF874PNQ SK-N-SH RAD21 Transcription Factor ChIP-seq Peaks of RAD21 in SK-N-SH from ENCODE 3 (ENCFF874PNQ) Regulation 
encTfChipPkENCFF265QRY SK-N-SH MXI1 Transcription Factor ChIP-seq Peaks of MXI1 in SK-N-SH from ENCODE 3 (ENCFF265QRY) Regulation 
encTfChipPkENCFF598ZLV SK-N-SH JUND 2 Transcription Factor ChIP-seq Peaks of JUND in SK-N-SH from ENCODE 3 (ENCFF598ZLV) Regulation 
encTfChipPkENCFF673PTK SK-N-SH JUND 1 Transcription Factor ChIP-seq Peaks of JUND in SK-N-SH from ENCODE 3 (ENCFF673PTK) Regulation 
encTfChipPkENCFF503SZB SK-N-SH IRF3 Transcription Factor ChIP-seq Peaks of IRF3 in SK-N-SH from ENCODE 3 (ENCFF503SZB) Regulation 
encTfChipPkENCFF403SBB SK-N-SH CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in SK-N-SH from ENCODE 3 (ENCFF403SBB) Regulation 
encTfChipPkENCFF861DPF SK-N-SH CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in SK-N-SH from ENCODE 3 (ENCFF861DPF) Regulation 
encTfChipPkENCFF316NHY SK-N-SH CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in SK-N-SH from ENCODE 3 (ENCFF316NHY) Regulation 
encTfChipPkENCFF527RGJ SK-N-SH CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in SK-N-SH from ENCODE 3 (ENCFF527RGJ) Regulation 
encTfChipPkENCFF373JXT SK-N-MC EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in SK-N-MC from ENCODE 3 (ENCFF373JXT) Regulation 
encTfChipPkENCFF269JRM SH-SY5Y GATA3 Transcription Factor ChIP-seq Peaks of GATA3 in SH-SY5Y from ENCODE 3 (ENCFF269JRM) Regulation 
encTfChipPkENCFF220YOA SH-SY5Y GATA2 Transcription Factor ChIP-seq Peaks of GATA2 in SH-SY5Y from ENCODE 3 (ENCFF220YOA) Regulation 
encTfChipPkENCFF241ZTW Raji POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in Raji from ENCODE 3 (ENCFF241ZTW) Regulation 
encTfChipPkENCFF788CHY RWPE2 CTCF Transcription Factor ChIP-seq Peaks of CTCF in RWPE2 from ENCODE 3 (ENCFF788CHY) Regulation 
encTfChipPkENCFF241JKV RWPE1 CTCF Transcription Factor ChIP-seq Peaks of CTCF in RWPE1 from ENCODE 3 (ENCFF241JKV) Regulation 
encTfChipPkENCFF485EPD PeyrPtch POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in Peyer's_patch from ENCODE 3 (ENCFF485EPD) Regulation 
encTfChipPkENCFF721JKB PeyrPtch POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in Peyer's_patch from ENCODE 3 (ENCFF721JKB) Regulation 
encTfChipPkENCFF112ACP PeyerPatch CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in Peyer's_patch from ENCODE 3 (ENCFF112ACP) Regulation 
encTfChipPkENCFF320GJE PeyerPatch CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in Peyer's_patch from ENCODE 3 (ENCFF320GJE) Regulation 
encTfChipPkENCFF414ZTT PeyerPatch CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in Peyer's_patch from ENCODE 3 (ENCFF414ZTT) Regulation 
encTfChipPkENCFF777TZZ PeyerPatch CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in Peyer's_patch from ENCODE 3 (ENCFF777TZZ) Regulation 
encTfChipPkENCFF223CEU parathyAdn CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in Parathyroid_adenoma from ENCODE 3 (ENCFF223CEU) Regulation 
encTfChipPkENCFF980GQH parathyAdn CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in Parathyroid_adenoma from ENCODE 3 (ENCFF980GQH) Regulation 
encTfChipPkENCFF835LPJ Panc1 TCF7L2 Transcription Factor ChIP-seq Peaks of TCF7L2 in Panc1 from ENCODE 3 (ENCFF835LPJ) Regulation 
encTfChipPkENCFF809ECY Panc1 REST Transcription Factor ChIP-seq Peaks of REST in Panc1 from ENCODE 3 (ENCFF809ECY) Regulation 
encTfChipPkENCFF450CNK Panc1 CTCF Transcription Factor ChIP-seq Peaks of CTCF in Panc1 from ENCODE 3 (ENCFF450CNK) Regulation 
encTfChipPkENCFF070SAY PFSK-1 TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in PFSK-1 from ENCODE 3 (ENCFF070SAY) Regulation 
encTfChipPkENCFF474KHR PFSK-1 REST Transcription Factor ChIP-seq Peaks of REST in PFSK-1 from ENCODE 3 (ENCFF474KHR) Regulation 
encTfChipPkENCFF808UCP PC-9 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in PC-9 from ENCODE 3 (ENCFF808UCP) Regulation 
encTfChipPkENCFF032DEW PC-9 CTCF Transcription Factor ChIP-seq Peaks of CTCF in PC-9 from ENCODE 3 (ENCFF032DEW) Regulation 
encTfChipPkENCFF299FOE PC-3 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in PC-3 from ENCODE 3 (ENCFF299FOE) Regulation 
encTfChipPkENCFF258RWN PC-3 CTCF Transcription Factor ChIP-seq Peaks of CTCF in PC-3 from ENCODE 3 (ENCFF258RWN) Regulation 
encTfChipPkENCFF862VFJ OCI-LY7 CTCF Transcription Factor ChIP-seq Peaks of CTCF in OCI-LY7 from ENCODE 3 (ENCFF862VFJ) Regulation 
encTfChipPkENCFF653ZMJ OCI-LY3 CTCF Transcription Factor ChIP-seq Peaks of CTCF in OCI-LY3 from ENCODE 3 (ENCFF653ZMJ) Regulation 
encTfChipPkENCFF007ATC OCI-LY1 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in OCI-LY1 from ENCODE 3 (ENCFF007ATC) Regulation 
encTfChipPkENCFF247GZH OCI-LY1 CTCF Transcription Factor ChIP-seq Peaks of CTCF in OCI-LY1 from ENCODE 3 (ENCFF247GZH) Regulation 
encTfChipPkENCFF102VYH NT2/D1 ZNF274 Transcription Factor ChIP-seq Peaks of ZNF274 in NT2/D1 from ENCODE 3 (ENCFF102VYH) Regulation 
encTfChipPkENCFF924XFS NCI-H929 CTCF Transcription Factor ChIP-seq Peaks of CTCF in NCI-H929 from ENCODE 3 (ENCFF924XFS) Regulation 
encTfChipPkENCFF407MVV NB4 CTCF Transcription Factor ChIP-seq Peaks of CTCF in NB4 from ENCODE 3 (ENCFF407MVV) Regulation 
encTfChipPkENCFF905EBM MM.1S EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in MM.1S from ENCODE 3 (ENCFF905EBM) Regulation 
encTfChipPkENCFF782KFG MM.1S CTCF Transcription Factor ChIP-seq Peaks of CTCF in MM.1S from ENCODE 3 (ENCFF782KFG) Regulation 
encTfChipPkENCFF807JAC MCF_10A STAT3 2 Transcription Factor ChIP-seq Peaks of STAT3 in MCF_10A from ENCODE 3 (ENCFF807JAC) Regulation 
encTfChipPkENCFF255XVM MCF_10A STAT3 1 Transcription Factor ChIP-seq Peaks of STAT3 in MCF_10A from ENCODE 3 (ENCFF255XVM) Regulation 
encTfChipPkENCFF260TYP MCF_10A POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in MCF_10A from ENCODE 3 (ENCFF260TYP) Regulation 
encTfChipPkENCFF755ZCF MCF_10A POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in MCF_10A from ENCODE 3 (ENCFF755ZCF) Regulation 
encTfChipPkENCFF772PCI MCF_10A MYC Transcription Factor ChIP-seq Peaks of MYC in MCF_10A from ENCODE 3 (ENCFF772PCI) Regulation 
encTfChipPkENCFF988HJD MCF_10A FOS 3 Transcription Factor ChIP-seq Peaks of FOS in MCF_10A from ENCODE 3 (ENCFF988HJD) Regulation 
encTfChipPkENCFF111IPG MCF_10A FOS 2 Transcription Factor ChIP-seq Peaks of FOS in MCF_10A from ENCODE 3 (ENCFF111IPG) Regulation 
encTfChipPkENCFF374FKH MCF_10A FOS 1 Transcription Factor ChIP-seq Peaks of FOS in MCF_10A from ENCODE 3 (ENCFF374FKH) Regulation 
encTfChipPkENCFF806GXB MCF-7 ZNF8 Transcription Factor ChIP-seq Peaks of ZNF8 in MCF-7 from ENCODE 3 (ENCFF806GXB) Regulation 
encTfChipPkENCFF955YVT MCF-7 ZNF687 Transcription Factor ChIP-seq Peaks of ZNF687 in MCF-7 from ENCODE 3 (ENCFF955YVT) Regulation 
encTfChipPkENCFF615FIR MCF-7 ZNF592 2 Transcription Factor ChIP-seq Peaks of ZNF592 in MCF-7 from ENCODE 3 (ENCFF615FIR) Regulation 
encTfChipPkENCFF162RSN MCF-7 ZNF592 1 Transcription Factor ChIP-seq Peaks of ZNF592 in MCF-7 from ENCODE 3 (ENCFF162RSN) Regulation 
encTfChipPkENCFF854CXA MCF-7 ZNF579 Transcription Factor ChIP-seq Peaks of ZNF579 in MCF-7 from ENCODE 3 (ENCFF854CXA) Regulation 
encTfChipPkENCFF603ZTG MCF-7 ZNF574 Transcription Factor ChIP-seq Peaks of ZNF574 in MCF-7 from ENCODE 3 (ENCFF603ZTG) Regulation 
encTfChipPkENCFF922QEI MCF-7 ZNF512B 2 Transcription Factor ChIP-seq Peaks of ZNF512B in MCF-7 from ENCODE 3 (ENCFF922QEI) Regulation 
encTfChipPkENCFF346OZB MCF-7 ZNF512B 1 Transcription Factor ChIP-seq Peaks of ZNF512B in MCF-7 from ENCODE 3 (ENCFF346OZB) Regulation 
encTfChipPkENCFF973DWU MCF-7 ZNF507 Transcription Factor ChIP-seq Peaks of ZNF507 in MCF-7 from ENCODE 3 (ENCFF973DWU) Regulation 
encTfChipPkENCFF563AEQ MCF-7 ZNF444 Transcription Factor ChIP-seq Peaks of ZNF444 in MCF-7 from ENCODE 3 (ENCFF563AEQ) Regulation 
encTfChipPkENCFF961BQJ MCF-7 ZNF24 Transcription Factor ChIP-seq Peaks of ZNF24 in MCF-7 from ENCODE 3 (ENCFF961BQJ) Regulation 
encTfChipPkENCFF567MGV MCF-7 ZNF217 2 Transcription Factor ChIP-seq Peaks of ZNF217 in MCF-7 from ENCODE 3 (ENCFF567MGV) Regulation 
encTfChipPkENCFF178LCE MCF-7 ZNF217 1 Transcription Factor ChIP-seq Peaks of ZNF217 in MCF-7 from ENCODE 3 (ENCFF178LCE) Regulation 
encTfChipPkENCFF051JAE MCF-7 ZNF207 Transcription Factor ChIP-seq Peaks of ZNF207 in MCF-7 from ENCODE 3 (ENCFF051JAE) Regulation 
encTfChipPkENCFF353QLW MCF-7 ZKSCAN1 Transcription Factor ChIP-seq Peaks of ZKSCAN1 in MCF-7 from ENCODE 3 (ENCFF353QLW) Regulation 
encTfChipPkENCFF235RIU MCF-7 ZHX2 Transcription Factor ChIP-seq Peaks of ZHX2 in MCF-7 from ENCODE 3 (ENCFF235RIU) Regulation 
encTfChipPkENCFF146HGZ MCF-7 ZFX Transcription Factor ChIP-seq Peaks of ZFX in MCF-7 from ENCODE 3 (ENCFF146HGZ) Regulation 
encTfChipPkENCFF070WUF MCF-7 ZBTB7B Transcription Factor ChIP-seq Peaks of ZBTB7B in MCF-7 from ENCODE 3 (ENCFF070WUF) Regulation 
encTfChipPkENCFF397XTF MCF-7 ZBTB40 Transcription Factor ChIP-seq Peaks of ZBTB40 in MCF-7 from ENCODE 3 (ENCFF397XTF) Regulation 
encTfChipPkENCFF447FPV MCF-7 ZBTB33 Transcription Factor ChIP-seq Peaks of ZBTB33 in MCF-7 from ENCODE 3 (ENCFF447FPV) Regulation 
encTfChipPkENCFF126PJF MCF-7 ZBTB11 Transcription Factor ChIP-seq Peaks of ZBTB11 in MCF-7 from ENCODE 3 (ENCFF126PJF) Regulation 
encTfChipPkENCFF603AWL MCF-7 ZBTB1 Transcription Factor ChIP-seq Peaks of ZBTB1 in MCF-7 from ENCODE 3 (ENCFF603AWL) Regulation 
encTfChipPkENCFF757QEJ MCF-7 TRIM22 Transcription Factor ChIP-seq Peaks of TRIM22 in MCF-7 from ENCODE 3 (ENCFF757QEJ) Regulation 
encTfChipPkENCFF956LMS MCF-7 SUZ12 Transcription Factor ChIP-seq Peaks of SUZ12 in MCF-7 from ENCODE 3 (ENCFF956LMS) Regulation 
encTfChipPkENCFF870CER MCF-7 SREBF1 Transcription Factor ChIP-seq Peaks of SREBF1 in MCF-7 from ENCODE 3 (ENCFF870CER) Regulation 
encTfChipPkENCFF193MKL MCF-7 SP1 Transcription Factor ChIP-seq Peaks of SP1 in MCF-7 from ENCODE 3 (ENCFF193MKL) Regulation 
encTfChipPkENCFF096LRM MCF-7 SMARCE1 Transcription Factor ChIP-seq Peaks of SMARCE1 in MCF-7 from ENCODE 3 (ENCFF096LRM) Regulation 
encTfChipPkENCFF351NCM MCF-7 SMARCA5 Transcription Factor ChIP-seq Peaks of SMARCA5 in MCF-7 from ENCODE 3 (ENCFF351NCM) Regulation 
encTfChipPkENCFF278ODX MCF-7 SIX4 Transcription Factor ChIP-seq Peaks of SIX4 in MCF-7 from ENCODE 3 (ENCFF278ODX) Regulation 
encTfChipPkENCFF580NQL MCF-7 SIN3A Transcription Factor ChIP-seq Peaks of SIN3A in MCF-7 from ENCODE 3 (ENCFF580NQL) Regulation 
encTfChipPkENCFF949QZO MCF-7 RFX5 Transcription Factor ChIP-seq Peaks of RFX5 in MCF-7 from ENCODE 3 (ENCFF949QZO) Regulation 
encTfChipPkENCFF150TBK MCF-7 RFX1 2 Transcription Factor ChIP-seq Peaks of RFX1 in MCF-7 from ENCODE 3 (ENCFF150TBK) Regulation 
encTfChipPkENCFF015PGM MCF-7 RFX1 1 Transcription Factor ChIP-seq Peaks of RFX1 in MCF-7 from ENCODE 3 (ENCFF015PGM) Regulation 
encTfChipPkENCFF065UFF MCF-7 RCOR1 Transcription Factor ChIP-seq Peaks of RCOR1 in MCF-7 from ENCODE 3 (ENCFF065UFF) Regulation 
encTfChipPkENCFF500ZLG MCF-7 RAD51 Transcription Factor ChIP-seq Peaks of RAD51 in MCF-7 from ENCODE 3 (ENCFF500ZLG) Regulation 
encTfChipPkENCFF883LPV MCF-7 POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in MCF-7 from ENCODE 3 (ENCFF883LPV) Regulation 
encTfChipPkENCFF922GXT MCF-7 PKNOX1 Transcription Factor ChIP-seq Peaks of PKNOX1 in MCF-7 from ENCODE 3 (ENCFF922GXT) Regulation 
encTfChipPkENCFF282SXB MCF-7 PAX8 Transcription Factor ChIP-seq Peaks of PAX8 in MCF-7 from ENCODE 3 (ENCFF282SXB) Regulation 
encTfChipPkENCFF651PWG MCF-7 NRF1 Transcription Factor ChIP-seq Peaks of NRF1 in MCF-7 from ENCODE 3 (ENCFF651PWG) Regulation 
encTfChipPkENCFF839EPV MCF-7 NFXL1 Transcription Factor ChIP-seq Peaks of NFXL1 in MCF-7 from ENCODE 3 (ENCFF839EPV) Regulation 
encTfChipPkENCFF446FHX MCF-7 NFRKB Transcription Factor ChIP-seq Peaks of NFRKB in MCF-7 from ENCODE 3 (ENCFF446FHX) Regulation 
encTfChipPkENCFF817RST MCF-7 NFIB 2 Transcription Factor ChIP-seq Peaks of NFIB in MCF-7 from ENCODE 3 (ENCFF817RST) Regulation 
encTfChipPkENCFF879VLB MCF-7 NFIB 1 Transcription Factor ChIP-seq Peaks of NFIB in MCF-7 from ENCODE 3 (ENCFF879VLB) Regulation 
encTfChipPkENCFF587EOD MCF-7 NEUROD1 Transcription Factor ChIP-seq Peaks of NEUROD1 in MCF-7 from ENCODE 3 (ENCFF587EOD) Regulation 
encTfChipPkENCFF821FWZ MCF-7 NCOA3 2 Transcription Factor ChIP-seq Peaks of NCOA3 in MCF-7 from ENCODE 3 (ENCFF821FWZ) Regulation 
encTfChipPkENCFF117ZKS MCF-7 NCOA3 1 Transcription Factor ChIP-seq Peaks of NCOA3 in MCF-7 from ENCODE 3 (ENCFF117ZKS) Regulation 
encTfChipPkENCFF518OUJ MCF-7 NBN Transcription Factor ChIP-seq Peaks of NBN in MCF-7 from ENCODE 3 (ENCFF518OUJ) Regulation 
encTfChipPkENCFF695IQU MCF-7 MYC 3 Transcription Factor ChIP-seq Peaks of MYC in MCF-7 from ENCODE 3 (ENCFF695IQU) Regulation 
encTfChipPkENCFF682AWN MCF-7 MYC 2 Transcription Factor ChIP-seq Peaks of MYC in MCF-7 from ENCODE 3 (ENCFF682AWN) Regulation 
encTfChipPkENCFF021KDL MCF-7 MYC 1 Transcription Factor ChIP-seq Peaks of MYC in MCF-7 from ENCODE 3 (ENCFF021KDL) Regulation 
encTfChipPkENCFF527ALV MCF-7 MTA3 Transcription Factor ChIP-seq Peaks of MTA3 in MCF-7 from ENCODE 3 (ENCFF527ALV) Regulation 
encTfChipPkENCFF997RPK MCF-7 MTA2 Transcription Factor ChIP-seq Peaks of MTA2 in MCF-7 from ENCODE 3 (ENCFF997RPK) Regulation 
encTfChipPkENCFF965ZRH MCF-7 MTA1 Transcription Factor ChIP-seq Peaks of MTA1 in MCF-7 from ENCODE 3 (ENCFF965ZRH) Regulation 
encTfChipPkENCFF628SBD MCF-7 MNT 2 Transcription Factor ChIP-seq Peaks of MNT in MCF-7 from ENCODE 3 (ENCFF628SBD) Regulation 
encTfChipPkENCFF027CYL MCF-7 MNT 1 Transcription Factor ChIP-seq Peaks of MNT in MCF-7 from ENCODE 3 (ENCFF027CYL) Regulation 
encTfChipPkENCFF686LJE MCF-7 MLLT1 Transcription Factor ChIP-seq Peaks of MLLT1 in MCF-7 from ENCODE 3 (ENCFF686LJE) Regulation 
encTfChipPkENCFF474AYD MCF-7 MBD2 Transcription Factor ChIP-seq Peaks of MBD2 in MCF-7 from ENCODE 3 (ENCFF474AYD) Regulation 
encTfChipPkENCFF298VCE MCF-7 MAFK Transcription Factor ChIP-seq Peaks of MAFK in MCF-7 from ENCODE 3 (ENCFF298VCE) Regulation 
encTfChipPkENCFF314KRZ MCF-7 JUN Transcription Factor ChIP-seq Peaks of JUN in MCF-7 from ENCODE 3 (ENCFF314KRZ) Regulation 
encTfChipPkENCFF836HHL MCF-7 HSF1 Transcription Factor ChIP-seq Peaks of HSF1 in MCF-7 from ENCODE 3 (ENCFF836HHL) Regulation 
encTfChipPkENCFF902IMW MCF-7 HES1 Transcription Factor ChIP-seq Peaks of HES1 in MCF-7 from ENCODE 3 (ENCFF902IMW) Regulation 
encTfChipPkENCFF365WFM MCF-7 HCFC1 Transcription Factor ChIP-seq Peaks of HCFC1 in MCF-7 from ENCODE 3 (ENCFF365WFM) Regulation 
encTfChipPkENCFF265NSP MCF-7 GATAD2B 2 Transcription Factor ChIP-seq Peaks of GATAD2B in MCF-7 from ENCODE 3 (ENCFF265NSP) Regulation 
encTfChipPkENCFF231VAA MCF-7 GATAD2B 1 Transcription Factor ChIP-seq Peaks of GATAD2B in MCF-7 from ENCODE 3 (ENCFF231VAA) Regulation 
encTfChipPkENCFF313TUJ MCF-7 GATA3 Transcription Factor ChIP-seq Peaks of GATA3 in MCF-7 from ENCODE 3 (ENCFF313TUJ) Regulation 
encTfChipPkENCFF671BJT MCF-7 FOXK2 Transcription Factor ChIP-seq Peaks of FOXK2 in MCF-7 from ENCODE 3 (ENCFF671BJT) Regulation 
encTfChipPkENCFF596OJV MCF-7 FOXA1 Transcription Factor ChIP-seq Peaks of FOXA1 in MCF-7 from ENCODE 3 (ENCFF596OJV) Regulation 
encTfChipPkENCFF965AIZ MCF-7 FOS Transcription Factor ChIP-seq Peaks of FOS in MCF-7 from ENCODE 3 (ENCFF965AIZ) Regulation 
encTfChipPkENCFF044NEB MCF-7 ESRRA 2 Transcription Factor ChIP-seq Peaks of ESRRA in MCF-7 from ENCODE 3 (ENCFF044NEB) Regulation 
encTfChipPkENCFF193FZK MCF-7 ESRRA 1 Transcription Factor ChIP-seq Peaks of ESRRA in MCF-7 from ENCODE 3 (ENCFF193FZK) Regulation 
encTfChipPkENCFF267FXT MCF-7 ELK1 Transcription Factor ChIP-seq Peaks of ELK1 in MCF-7 from ENCODE 3 (ENCFF267FXT) Regulation 
encTfChipPkENCFF386TTQ MCF-7 ELF1 Transcription Factor ChIP-seq Peaks of ELF1 in MCF-7 from ENCODE 3 (ENCFF386TTQ) Regulation 
encTfChipPkENCFF795QZU MCF-7 E4F1 Transcription Factor ChIP-seq Peaks of E4F1 in MCF-7 from ENCODE 3 (ENCFF795QZU) Regulation 
encTfChipPkENCFF751DRF MCF-7 E2F8 Transcription Factor ChIP-seq Peaks of E2F8 in MCF-7 from ENCODE 3 (ENCFF751DRF) Regulation 
encTfChipPkENCFF812MZB MCF-7 DPF2 Transcription Factor ChIP-seq Peaks of DPF2 in MCF-7 from ENCODE 3 (ENCFF812MZB) Regulation 
encTfChipPkENCFF572YVL MCF-7 CUX1 Transcription Factor ChIP-seq Peaks of CUX1 in MCF-7 from ENCODE 3 (ENCFF572YVL) Regulation 
encTfChipPkENCFF372SHI MCF-7 CTCF 6 Transcription Factor ChIP-seq Peaks of CTCF in MCF-7 from ENCODE 3 (ENCFF372SHI) Regulation 
encTfChipPkENCFF176YNV MCF-7 CTCF 5 Transcription Factor ChIP-seq Peaks of CTCF in MCF-7 from ENCODE 3 (ENCFF176YNV) Regulation 
encTfChipPkENCFF414FWV MCF-7 CTCF 4 Transcription Factor ChIP-seq Peaks of CTCF in MCF-7 from ENCODE 3 (ENCFF414FWV) Regulation 
encTfChipPkENCFF164EJE MCF-7 CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in MCF-7 from ENCODE 3 (ENCFF164EJE) Regulation 
encTfChipPkENCFF586KIH MCF-7 CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in MCF-7 from ENCODE 3 (ENCFF586KIH) Regulation 
encTfChipPkENCFF136BEY MCF-7 CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in MCF-7 from ENCODE 3 (ENCFF136BEY) Regulation 
encTfChipPkENCFF785ZQF MCF-7 CTBP1 Transcription Factor ChIP-seq Peaks of CTBP1 in MCF-7 from ENCODE 3 (ENCFF785ZQF) Regulation 
encTfChipPkENCFF445LQN MCF-7 CREB1 2 Transcription Factor ChIP-seq Peaks of CREB1 in MCF-7 from ENCODE 3 (ENCFF445LQN) Regulation 
encTfChipPkENCFF127RVQ MCF-7 CREB1 1 Transcription Factor ChIP-seq Peaks of CREB1 in MCF-7 from ENCODE 3 (ENCFF127RVQ) Regulation 
encTfChipPkENCFF755DGT MCF-7 COPS2 Transcription Factor ChIP-seq Peaks of COPS2 in MCF-7 from ENCODE 3 (ENCFF755DGT) Regulation 
encTfChipPkENCFF359WMP MCF-7 CLOCK Transcription Factor ChIP-seq Peaks of CLOCK in MCF-7 from ENCODE 3 (ENCFF359WMP) Regulation 
encTfChipPkENCFF362XAG MCF-7 CHD1 Transcription Factor ChIP-seq Peaks of CHD1 in MCF-7 from ENCODE 3 (ENCFF362XAG) Regulation 
encTfChipPkENCFF353CQJ MCF-7 BMI1 Transcription Factor ChIP-seq Peaks of BMI1 in MCF-7 from ENCODE 3 (ENCFF353CQJ) Regulation 
encTfChipPkENCFF343ULZ MCF-7 ATF7 Transcription Factor ChIP-seq Peaks of ATF7 in MCF-7 from ENCODE 3 (ENCFF343ULZ) Regulation 
encTfChipPkENCFF884RAO MCF-7 ARID3A Transcription Factor ChIP-seq Peaks of ARID3A in MCF-7 from ENCODE 3 (ENCFF884RAO) Regulation 
encTfChipPkENCFF988IOQ LNCaP_FGC CTCF Transcription Factor ChIP-seq Peaks of CTCF in LNCaP_clone_FGC from ENCODE 3 (ENCFF988IOQ) Regulation 
encTfChipPkENCFF901BGG LNCAP CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in LNCAP from ENCODE 3 (ENCFF901BGG) Regulation 
encTfChipPkENCFF155SPQ LNCAP CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in LNCAP from ENCODE 3 (ENCFF155SPQ) Regulation 
encTfChipPkENCFF662IOC KMS-11 CTCF Transcription Factor ChIP-seq Peaks of CTCF in KMS-11 from ENCODE 3 (ENCFF662IOC) Regulation 
encTfChipPkENCFF588OLK K562 ZZZ3 Transcription Factor ChIP-seq Peaks of ZZZ3 in K562 from ENCODE 3 (ENCFF588OLK) Regulation 
encTfChipPkENCFF253NXR K562 ZSCAN29 2 Transcription Factor ChIP-seq Peaks of ZSCAN29 in K562 from ENCODE 3 (ENCFF253NXR) Regulation 
encTfChipPkENCFF303PMJ K562 ZSCAN29 1 Transcription Factor ChIP-seq Peaks of ZSCAN29 in K562 from ENCODE 3 (ENCFF303PMJ) Regulation 
encTfChipPkENCFF901AHW K562 ZNF830 2 Transcription Factor ChIP-seq Peaks of ZNF830 in K562 from ENCODE 3 (ENCFF901AHW) Regulation 
encTfChipPkENCFF996IVU K562 ZNF830 1 Transcription Factor ChIP-seq Peaks of ZNF830 in K562 from ENCODE 3 (ENCFF996IVU) Regulation 
encTfChipPkENCFF284PKK K562 ZNF639 2 Transcription Factor ChIP-seq Peaks of ZNF639 in K562 from ENCODE 3 (ENCFF284PKK) Regulation 
encTfChipPkENCFF708BTH K562 ZNF639 1 Transcription Factor ChIP-seq Peaks of ZNF639 in K562 from ENCODE 3 (ENCFF708BTH) Regulation 
encTfChipPkENCFF273TYA K562 ZNF592 Transcription Factor ChIP-seq Peaks of ZNF592 in K562 from ENCODE 3 (ENCFF273TYA) Regulation 
encTfChipPkENCFF932UEC K562 ZNF407 2 Transcription Factor ChIP-seq Peaks of ZNF407 in K562 from ENCODE 3 (ENCFF932UEC) Regulation 
encTfChipPkENCFF602CFZ K562 ZNF407 1 Transcription Factor ChIP-seq Peaks of ZNF407 in K562 from ENCODE 3 (ENCFF602CFZ) Regulation 
encTfChipPkENCFF706SJZ K562 ZNF384 Transcription Factor ChIP-seq Peaks of ZNF384 in K562 from ENCODE 3 (ENCFF706SJZ) Regulation 
encTfChipPkENCFF698MLW K562 ZNF318 2 Transcription Factor ChIP-seq Peaks of ZNF318 in K562 from ENCODE 3 (ENCFF698MLW) Regulation 
encTfChipPkENCFF921WMN K562 ZNF318 1 Transcription Factor ChIP-seq Peaks of ZNF318 in K562 from ENCODE 3 (ENCFF921WMN) Regulation 
encTfChipPkENCFF442ZUF K562 ZNF316 2 Transcription Factor ChIP-seq Peaks of ZNF316 in K562 from ENCODE 3 (ENCFF442ZUF) Regulation 
encTfChipPkENCFF788EBS K562 ZNF316 1 Transcription Factor ChIP-seq Peaks of ZNF316 in K562 from ENCODE 3 (ENCFF788EBS) Regulation 
encTfChipPkENCFF581ZZT K562 ZNF282 Transcription Factor ChIP-seq Peaks of ZNF282 in K562 from ENCODE 3 (ENCFF581ZZT) Regulation 
encTfChipPkENCFF386WKY K562 ZNF280A Transcription Factor ChIP-seq Peaks of ZNF280A in K562 from ENCODE 3 (ENCFF386WKY) Regulation 
encTfChipPkENCFF836LBG K562 ZNF274 2 Transcription Factor ChIP-seq Peaks of ZNF274 in K562 from ENCODE 3 (ENCFF836LBG) Regulation 
encTfChipPkENCFF344QKL K562 ZNF274 1 Transcription Factor ChIP-seq Peaks of ZNF274 in K562 from ENCODE 3 (ENCFF344QKL) Regulation 
encTfChipPkENCFF340PPI K562 ZNF24 3 Transcription Factor ChIP-seq Peaks of ZNF24 in K562 from ENCODE 3 (ENCFF340PPI) Regulation 
encTfChipPkENCFF973LDQ K562 ZNF24 2 Transcription Factor ChIP-seq Peaks of ZNF24 in K562 from ENCODE 3 (ENCFF973LDQ) Regulation 
encTfChipPkENCFF238MYM K562 ZNF24 1 Transcription Factor ChIP-seq Peaks of ZNF24 in K562 from ENCODE 3 (ENCFF238MYM) Regulation 
encTfChipPkENCFF728NEV K562 ZNF184 2 Transcription Factor ChIP-seq Peaks of ZNF184 in K562 from ENCODE 3 (ENCFF728NEV) Regulation 
encTfChipPkENCFF556YCY K562 ZNF184 1 Transcription Factor ChIP-seq Peaks of ZNF184 in K562 from ENCODE 3 (ENCFF556YCY) Regulation 
encTfChipPkENCFF114IWY K562 ZNF143 Transcription Factor ChIP-seq Peaks of ZNF143 in K562 from ENCODE 3 (ENCFF114IWY) Regulation 
encTfChipPkENCFF511QHY K562 ZMYM3 Transcription Factor ChIP-seq Peaks of ZMYM3 in K562 from ENCODE 3 (ENCFF511QHY) Regulation 
encTfChipPkENCFF597DIY K562 ZMIZ1 Transcription Factor ChIP-seq Peaks of ZMIZ1 in K562 from ENCODE 3 (ENCFF597DIY) Regulation 
encTfChipPkENCFF163VUK K562 ZKSCAN1 Transcription Factor ChIP-seq Peaks of ZKSCAN1 in K562 from ENCODE 3 (ENCFF163VUK) Regulation 
encTfChipPkENCFF195ODE K562 ZHX1 Transcription Factor ChIP-seq Peaks of ZHX1 in K562 from ENCODE 3 (ENCFF195ODE) Regulation 
encTfChipPkENCFF396DNK K562 ZFP91 Transcription Factor ChIP-seq Peaks of ZFP91 in K562 from ENCODE 3 (ENCFF396DNK) Regulation 
encTfChipPkENCFF076IFG K562 ZEB2 2 Transcription Factor ChIP-seq Peaks of ZEB2 in K562 from ENCODE 3 (ENCFF076IFG) Regulation 
encTfChipPkENCFF407AOX K562 ZEB2 1 Transcription Factor ChIP-seq Peaks of ZEB2 in K562 from ENCODE 3 (ENCFF407AOX) Regulation 
encTfChipPkENCFF589EVD K562 ZBTB8A Transcription Factor ChIP-seq Peaks of ZBTB8A in K562 from ENCODE 3 (ENCFF589EVD) Regulation 
encTfChipPkENCFF706ISJ K562 ZBTB7A Transcription Factor ChIP-seq Peaks of ZBTB7A in K562 from ENCODE 3 (ENCFF706ISJ) Regulation 
encTfChipPkENCFF394IKH K562 ZBTB5 2 Transcription Factor ChIP-seq Peaks of ZBTB5 in K562 from ENCODE 3 (ENCFF394IKH) Regulation 
encTfChipPkENCFF359QCN K562 ZBTB5 1 Transcription Factor ChIP-seq Peaks of ZBTB5 in K562 from ENCODE 3 (ENCFF359QCN) Regulation 
encTfChipPkENCFF417LEJ K562 ZBTB40 Transcription Factor ChIP-seq Peaks of ZBTB40 in K562 from ENCODE 3 (ENCFF417LEJ) Regulation 
encTfChipPkENCFF408FQC K562 ZBTB33 Transcription Factor ChIP-seq Peaks of ZBTB33 in K562 from ENCODE 3 (ENCFF408FQC) Regulation 
encTfChipPkENCFF561USY K562 ZBTB2 Transcription Factor ChIP-seq Peaks of ZBTB2 in K562 from ENCODE 3 (ENCFF561USY) Regulation 
encTfChipPkENCFF434QZL K562 ZBTB11 Transcription Factor ChIP-seq Peaks of ZBTB11 in K562 from ENCODE 3 (ENCFF434QZL) Regulation 
encTfChipPkENCFF253FON K562 ZBED1 Transcription Factor ChIP-seq Peaks of ZBED1 in K562 from ENCODE 3 (ENCFF253FON) Regulation 
encTfChipPkENCFF328XKC K562 YY1 2 Transcription Factor ChIP-seq Peaks of YY1 in K562 from ENCODE 3 (ENCFF328XKC) Regulation 
encTfChipPkENCFF557DSM K562 YY1 1 Transcription Factor ChIP-seq Peaks of YY1 in K562 from ENCODE 3 (ENCFF557DSM) Regulation 
encTfChipPkENCFF998KKJ K562 XRCC5 Transcription Factor ChIP-seq Peaks of XRCC5 in K562 from ENCODE 3 (ENCFF998KKJ) Regulation 
encTfChipPkENCFF803LEC K562 XRCC3 Transcription Factor ChIP-seq Peaks of XRCC3 in K562 from ENCODE 3 (ENCFF803LEC) Regulation 
encTfChipPkENCFF119SZQ K562 WHSC1 Transcription Factor ChIP-seq Peaks of WHSC1 in K562 from ENCODE 3 (ENCFF119SZQ) Regulation 
encTfChipPkENCFF150VTD K562 USF2 Transcription Factor ChIP-seq Peaks of USF2 in K562 from ENCODE 3 (ENCFF150VTD) Regulation 
encTfChipPkENCFF671DOL K562 UBTF 2 Transcription Factor ChIP-seq Peaks of UBTF in K562 from ENCODE 3 (ENCFF671DOL) Regulation 
encTfChipPkENCFF938IOJ K562 UBTF 1 Transcription Factor ChIP-seq Peaks of UBTF in K562 from ENCODE 3 (ENCFF938IOJ) Regulation 
encTfChipPkENCFF398EQF K562 U2AF2 Transcription Factor ChIP-seq Peaks of U2AF2 in K562 from ENCODE 3 (ENCFF398EQF) Regulation 
encTfChipPkENCFF730URE K562 U2AF1 Transcription Factor ChIP-seq Peaks of U2AF1 in K562 from ENCODE 3 (ENCFF730URE) Regulation 
encTfChipPkENCFF561IZB K562 TRIP13 Transcription Factor ChIP-seq Peaks of TRIP13 in K562 from ENCODE 3 (ENCFF561IZB) Regulation 
encTfChipPkENCFF591BIT K562 TRIM28 3 Transcription Factor ChIP-seq Peaks of TRIM28 in K562 from ENCODE 3 (ENCFF591BIT) Regulation 
encTfChipPkENCFF858QMI K562 TRIM28 2 Transcription Factor ChIP-seq Peaks of TRIM28 in K562 from ENCODE 3 (ENCFF858QMI) Regulation 
encTfChipPkENCFF164HLQ K562 TRIM28 1 Transcription Factor ChIP-seq Peaks of TRIM28 in K562 from ENCODE 3 (ENCFF164HLQ) Regulation 
encTfChipPkENCFF646VQW K562 TRIM24 2 Transcription Factor ChIP-seq Peaks of TRIM24 in K562 from ENCODE 3 (ENCFF646VQW) Regulation 
encTfChipPkENCFF049CRW K562 TRIM24 1 Transcription Factor ChIP-seq Peaks of TRIM24 in K562 from ENCODE 3 (ENCFF049CRW) Regulation 
encTfChipPkENCFF671BFH K562 THRA Transcription Factor ChIP-seq Peaks of THRA in K562 from ENCODE 3 (ENCFF671BFH) Regulation 
encTfChipPkENCFF641LJY K562 THAP1 Transcription Factor ChIP-seq Peaks of THAP1 in K562 from ENCODE 3 (ENCFF641LJY) Regulation 
encTfChipPkENCFF209MQX K562 TEAD4 Transcription Factor ChIP-seq Peaks of TEAD4 in K562 from ENCODE 3 (ENCFF209MQX) Regulation 
encTfChipPkENCFF312RFN K562 TCF7L2 Transcription Factor ChIP-seq Peaks of TCF7L2 in K562 from ENCODE 3 (ENCFF312RFN) Regulation 
encTfChipPkENCFF249EZR K562 TCF7 Transcription Factor ChIP-seq Peaks of TCF7 in K562 from ENCODE 3 (ENCFF249EZR) Regulation 
encTfChipPkENCFF493TZM K562 TCF12 2 Transcription Factor ChIP-seq Peaks of TCF12 in K562 from ENCODE 3 (ENCFF493TZM) Regulation 
encTfChipPkENCFF242IWJ K562 TCF12 1 Transcription Factor ChIP-seq Peaks of TCF12 in K562 from ENCODE 3 (ENCFF242IWJ) Regulation 
encTfChipPkENCFF380FJL K562 TBP Transcription Factor ChIP-seq Peaks of TBP in K562 from ENCODE 3 (ENCFF380FJL) Regulation 
encTfChipPkENCFF626MVT K562 TBL1XR1 2 Transcription Factor ChIP-seq Peaks of TBL1XR1 in K562 from ENCODE 3 (ENCFF626MVT) Regulation 
encTfChipPkENCFF048OBR K562 TBL1XR1 1 Transcription Factor ChIP-seq Peaks of TBL1XR1 in K562 from ENCODE 3 (ENCFF048OBR) Regulation 
encTfChipPkENCFF284LRP K562 TAL1 2 Transcription Factor ChIP-seq Peaks of TAL1 in K562 from ENCODE 3 (ENCFF284LRP) Regulation 
encTfChipPkENCFF482CEV K562 TAL1 1 Transcription Factor ChIP-seq Peaks of TAL1 in K562 from ENCODE 3 (ENCFF482CEV) Regulation 
encTfChipPkENCFF785HXY K562 TAF9B Transcription Factor ChIP-seq Peaks of TAF9B in K562 from ENCODE 3 (ENCFF785HXY) Regulation 
encTfChipPkENCFF034CQR K562 TAF7 Transcription Factor ChIP-seq Peaks of TAF7 in K562 from ENCODE 3 (ENCFF034CQR) Regulation 
encTfChipPkENCFF617CAZ K562 TAF15 Transcription Factor ChIP-seq Peaks of TAF15 in K562 from ENCODE 3 (ENCFF617CAZ) Regulation 
encTfChipPkENCFF966MVC K562 SUZ12 Transcription Factor ChIP-seq Peaks of SUZ12 in K562 from ENCODE 3 (ENCFF966MVC) Regulation 
encTfChipPkENCFF696KPD K562 STAT5A Transcription Factor ChIP-seq Peaks of STAT5A in K562 from ENCODE 3 (ENCFF696KPD) Regulation 
encTfChipPkENCFF714VIT K562 STAT2 Transcription Factor ChIP-seq Peaks of STAT2 in K562 from ENCODE 3 (ENCFF714VIT) Regulation 
encTfChipPkENCFF648NYF K562 STAT1 4 Transcription Factor ChIP-seq Peaks of STAT1 in K562 from ENCODE 3 (ENCFF648NYF) Regulation 
encTfChipPkENCFF290HTJ K562 STAT1 3 Transcription Factor ChIP-seq Peaks of STAT1 in K562 from ENCODE 3 (ENCFF290HTJ) Regulation 
encTfChipPkENCFF254MPF K562 STAT1 2 Transcription Factor ChIP-seq Peaks of STAT1 in K562 from ENCODE 3 (ENCFF254MPF) Regulation 
encTfChipPkENCFF498DOQ K562 STAT1 1 Transcription Factor ChIP-seq Peaks of STAT1 in K562 from ENCODE 3 (ENCFF498DOQ) Regulation 
encTfChipPkENCFF137IBM K562 SRSF9 Transcription Factor ChIP-seq Peaks of SRSF9 in K562 from ENCODE 3 (ENCFF137IBM) Regulation 
encTfChipPkENCFF059WVE K562 SRSF7 Transcription Factor ChIP-seq Peaks of SRSF7 in K562 from ENCODE 3 (ENCFF059WVE) Regulation 
encTfChipPkENCFF985TSH K562 SREBF1 Transcription Factor ChIP-seq Peaks of SREBF1 in K562 from ENCODE 3 (ENCFF985TSH) Regulation 
encTfChipPkENCFF300XUA K562 SP1 Transcription Factor ChIP-seq Peaks of SP1 in K562 from ENCODE 3 (ENCFF300XUA) Regulation 
encTfChipPkENCFF241TBP K562 SOX6 Transcription Factor ChIP-seq Peaks of SOX6 in K562 from ENCODE 3 (ENCFF241TBP) Regulation 
encTfChipPkENCFF033KXY K562 SNRNP70 Transcription Factor ChIP-seq Peaks of SNRNP70 in K562 from ENCODE 3 (ENCFF033KXY) Regulation 
encTfChipPkENCFF041YQC K562 SMC3 Transcription Factor ChIP-seq Peaks of SMC3 in K562 from ENCODE 3 (ENCFF041YQC) Regulation 
encTfChipPkENCFF622RBW K562 SMARCE1 Transcription Factor ChIP-seq Peaks of SMARCE1 in K562 from ENCODE 3 (ENCFF622RBW) Regulation 
encTfChipPkENCFF114PTZ K562 SMARCC2 Transcription Factor ChIP-seq Peaks of SMARCC2 in K562 from ENCODE 3 (ENCFF114PTZ) Regulation 
encTfChipPkENCFF944GJH K562 SMARCB1 Transcription Factor ChIP-seq Peaks of SMARCB1 in K562 from ENCODE 3 (ENCFF944GJH) Regulation 
encTfChipPkENCFF995NIE K562 SMARCA5 Transcription Factor ChIP-seq Peaks of SMARCA5 in K562 from ENCODE 3 (ENCFF995NIE) Regulation 
encTfChipPkENCFF197YHU K562 SMARCA4 3 Transcription Factor ChIP-seq Peaks of SMARCA4 in K562 from ENCODE 3 (ENCFF197YHU) Regulation 
encTfChipPkENCFF710LRU K562 SMARCA4 2 Transcription Factor ChIP-seq Peaks of SMARCA4 in K562 from ENCODE 3 (ENCFF710LRU) Regulation 
encTfChipPkENCFF883TOD K562 SMARCA4 1 Transcription Factor ChIP-seq Peaks of SMARCA4 in K562 from ENCODE 3 (ENCFF883TOD) Regulation 
encTfChipPkENCFF178MOP K562 SMAD5 Transcription Factor ChIP-seq Peaks of SMAD5 in K562 from ENCODE 3 (ENCFF178MOP) Regulation 
encTfChipPkENCFF011KRN K562 SMAD2 Transcription Factor ChIP-seq Peaks of SMAD2 in K562 from ENCODE 3 (ENCFF011KRN) Regulation 
encTfChipPkENCFF315YAF K562 SMAD1 Transcription Factor ChIP-seq Peaks of SMAD1 in K562 from ENCODE 3 (ENCFF315YAF) Regulation 
encTfChipPkENCFF481WGW K562 SKIL Transcription Factor ChIP-seq Peaks of SKIL in K562 from ENCODE 3 (ENCFF481WGW) Regulation 
encTfChipPkENCFF033EBX K562 SIX5 Transcription Factor ChIP-seq Peaks of SIX5 in K562 from ENCODE 3 (ENCFF033EBX) Regulation 
encTfChipPkENCFF671JEN K562 SIRT6 Transcription Factor ChIP-seq Peaks of SIRT6 in K562 from ENCODE 3 (ENCFF671JEN) Regulation 
encTfChipPkENCFF280GTU K562 SIN3B Transcription Factor ChIP-seq Peaks of SIN3B in K562 from ENCODE 3 (ENCFF280GTU) Regulation 
encTfChipPkENCFF803COK K562 SIN3A 2 Transcription Factor ChIP-seq Peaks of SIN3A in K562 from ENCODE 3 (ENCFF803COK) Regulation 
encTfChipPkENCFF191MPD K562 SIN3A 1 Transcription Factor ChIP-seq Peaks of SIN3A in K562 from ENCODE 3 (ENCFF191MPD) Regulation 
encTfChipPkENCFF294EHN K562 SETDB1 2 Transcription Factor ChIP-seq Peaks of SETDB1 in K562 from ENCODE 3 (ENCFF294EHN) Regulation 
encTfChipPkENCFF095WDB K562 SETDB1 1 Transcription Factor ChIP-seq Peaks of SETDB1 in K562 from ENCODE 3 (ENCFF095WDB) Regulation 
encTfChipPkENCFF718NUA K562 SAP30 Transcription Factor ChIP-seq Peaks of SAP30 in K562 from ENCODE 3 (ENCFF718NUA) Regulation 
encTfChipPkENCFF624NUZ K562 SAFB2 Transcription Factor ChIP-seq Peaks of SAFB2 in K562 from ENCODE 3 (ENCFF624NUZ) Regulation 
encTfChipPkENCFF478MPX K562 SAFB Transcription Factor ChIP-seq Peaks of SAFB in K562 from ENCODE 3 (ENCFF478MPX) Regulation 
encTfChipPkENCFF422BXE K562 RUNX1 2 Transcription Factor ChIP-seq Peaks of RUNX1 in K562 from ENCODE 3 (ENCFF422BXE) Regulation 
encTfChipPkENCFF573DRR K562 RUNX1 1 Transcription Factor ChIP-seq Peaks of RUNX1 in K562 from ENCODE 3 (ENCFF573DRR) Regulation 
encTfChipPkENCFF644WLI K562 RNF2 4 Transcription Factor ChIP-seq Peaks of RNF2 in K562 from ENCODE 3 (ENCFF644WLI) Regulation 
encTfChipPkENCFF539WLH K562 RNF2 3 Transcription Factor ChIP-seq Peaks of RNF2 in K562 from ENCODE 3 (ENCFF539WLH) Regulation 
encTfChipPkENCFF987VNY K562 RNF2 2 Transcription Factor ChIP-seq Peaks of RNF2 in K562 from ENCODE 3 (ENCFF987VNY) Regulation 
encTfChipPkENCFF972LPT K562 RNF2 1 Transcription Factor ChIP-seq Peaks of RNF2 in K562 from ENCODE 3 (ENCFF972LPT) Regulation 
encTfChipPkENCFF209HKW K562 RLF Transcription Factor ChIP-seq Peaks of RLF in K562 from ENCODE 3 (ENCFF209HKW) Regulation 
encTfChipPkENCFF716LRI K562 RFX5 Transcription Factor ChIP-seq Peaks of RFX5 in K562 from ENCODE 3 (ENCFF716LRI) Regulation 
encTfChipPkENCFF010UHD K562 RFX1 2 Transcription Factor ChIP-seq Peaks of RFX1 in K562 from ENCODE 3 (ENCFF010UHD) Regulation 
encTfChipPkENCFF237UAN K562 RFX1 1 Transcription Factor ChIP-seq Peaks of RFX1 in K562 from ENCODE 3 (ENCFF237UAN) Regulation 
encTfChipPkENCFF558VPP K562 REST 2 Transcription Factor ChIP-seq Peaks of REST in K562 from ENCODE 3 (ENCFF558VPP) Regulation 
encTfChipPkENCFF895QLA K562 REST 1 Transcription Factor ChIP-seq Peaks of REST in K562 from ENCODE 3 (ENCFF895QLA) Regulation 
encTfChipPkENCFF484CKD K562 RCOR1 Transcription Factor ChIP-seq Peaks of RCOR1 in K562 from ENCODE 3 (ENCFF484CKD) Regulation 
encTfChipPkENCFF209JJD K562 RBM39 Transcription Factor ChIP-seq Peaks of RBM39 in K562 from ENCODE 3 (ENCFF209JJD) Regulation 
encTfChipPkENCFF782GWS K562 RBM34 Transcription Factor ChIP-seq Peaks of RBM34 in K562 from ENCODE 3 (ENCFF782GWS) Regulation 
encTfChipPkENCFF680WBN K562 RBM25 Transcription Factor ChIP-seq Peaks of RBM25 in K562 from ENCODE 3 (ENCFF680WBN) Regulation 
encTfChipPkENCFF522JUV K562 RBM22 Transcription Factor ChIP-seq Peaks of RBM22 in K562 from ENCODE 3 (ENCFF522JUV) Regulation 
encTfChipPkENCFF861YKK K562 RBM17 Transcription Factor ChIP-seq Peaks of RBM17 in K562 from ENCODE 3 (ENCFF861YKK) Regulation 
encTfChipPkENCFF971VJZ K562 RBM15 Transcription Factor ChIP-seq Peaks of RBM15 in K562 from ENCODE 3 (ENCFF971VJZ) Regulation 
encTfChipPkENCFF682SIY K562 RBM14 Transcription Factor ChIP-seq Peaks of RBM14 in K562 from ENCODE 3 (ENCFF682SIY) Regulation 
encTfChipPkENCFF120IDE K562 RBFOX2 Transcription Factor ChIP-seq Peaks of RBFOX2 in K562 from ENCODE 3 (ENCFF120IDE) Regulation 
encTfChipPkENCFF379MPS K562 RBBP5 Transcription Factor ChIP-seq Peaks of RBBP5 in K562 from ENCODE 3 (ENCFF379MPS) Regulation 
encTfChipPkENCFF975IRM K562 RB1 Transcription Factor ChIP-seq Peaks of RB1 in K562 from ENCODE 3 (ENCFF975IRM) Regulation 
encTfChipPkENCFF096XMD K562 RAD51 Transcription Factor ChIP-seq Peaks of RAD51 in K562 from ENCODE 3 (ENCFF096XMD) Regulation 
encTfChipPkENCFF421KIV K562 PYGO2 Transcription Factor ChIP-seq Peaks of PYGO2 in K562 from ENCODE 3 (ENCFF421KIV) Regulation 
encTfChipPkENCFF694BIA K562 PTBP1 Transcription Factor ChIP-seq Peaks of PTBP1 in K562 from ENCODE 3 (ENCFF694BIA) Regulation 
encTfChipPkENCFF785ACI K562 PRPF4 Transcription Factor ChIP-seq Peaks of PRPF4 in K562 from ENCODE 3 (ENCFF785ACI) Regulation 
encTfChipPkENCFF294HEI K562 PRDM10 Transcription Factor ChIP-seq Peaks of PRDM10 in K562 from ENCODE 3 (ENCFF294HEI) Regulation 
encTfChipPkENCFF273EYJ K562 POLR2G Transcription Factor ChIP-seq Peaks of POLR2G in K562 from ENCODE 3 (ENCFF273EYJ) Regulation 
encTfChipPkENCFF853ZMA K562 POLR2A 8 Transcription Factor ChIP-seq Peaks of POLR2A in K562 from ENCODE 3 (ENCFF853ZMA) Regulation 
encTfChipPkENCFF937VZI K562 POLR2A 7 Transcription Factor ChIP-seq Peaks of POLR2A in K562 from ENCODE 3 (ENCFF937VZI) Regulation 
encTfChipPkENCFF270QAB K562 POLR2A 6 Transcription Factor ChIP-seq Peaks of POLR2A in K562 from ENCODE 3 (ENCFF270QAB) Regulation 
encTfChipPkENCFF662YQK K562 POLR2A 5 Transcription Factor ChIP-seq Peaks of POLR2A in K562 from ENCODE 3 (ENCFF662YQK) Regulation 
encTfChipPkENCFF248IWJ K562 POLR2A 4 Transcription Factor ChIP-seq Peaks of POLR2A in K562 from ENCODE 3 (ENCFF248IWJ) Regulation 
encTfChipPkENCFF394LOQ K562 POLR2A 3 Transcription Factor ChIP-seq Peaks of POLR2A in K562 from ENCODE 3 (ENCFF394LOQ) Regulation 
encTfChipPkENCFF206YXX K562 POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in K562 from ENCODE 3 (ENCFF206YXX) Regulation 
encTfChipPkENCFF947KPB K562 POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in K562 from ENCODE 3 (ENCFF947KPB) Regulation 
encTfChipPkENCFF881QBT K562 PML Transcription Factor ChIP-seq Peaks of PML in K562 from ENCODE 3 (ENCFF881QBT) Regulation 
encTfChipPkENCFF544XKC K562 PKNOX1 Transcription Factor ChIP-seq Peaks of PKNOX1 in K562 from ENCODE 3 (ENCFF544XKC) Regulation 
encTfChipPkENCFF626KTJ K562 PHF8 Transcription Factor ChIP-seq Peaks of PHF8 in K562 from ENCODE 3 (ENCFF626KTJ) Regulation 
encTfChipPkENCFF134CUM K562 PHF21A Transcription Factor ChIP-seq Peaks of PHF21A in K562 from ENCODE 3 (ENCFF134CUM) Regulation 
encTfChipPkENCFF948YVM K562 PHF20 Transcription Factor ChIP-seq Peaks of PHF20 in K562 from ENCODE 3 (ENCFF948YVM) Regulation 
encTfChipPkENCFF462FRU K562 PHB2 Transcription Factor ChIP-seq Peaks of PHB2 in K562 from ENCODE 3 (ENCFF462FRU) Regulation 
encTfChipPkENCFF881XQF K562 PCBP2 Transcription Factor ChIP-seq Peaks of PCBP2 in K562 from ENCODE 3 (ENCFF881XQF) Regulation 
encTfChipPkENCFF941RVL K562 PCBP1 Transcription Factor ChIP-seq Peaks of PCBP1 in K562 from ENCODE 3 (ENCFF941RVL) Regulation 
encTfChipPkENCFF289BUU K562 NUFIP1 Transcription Factor ChIP-seq Peaks of NUFIP1 in K562 from ENCODE 3 (ENCFF289BUU) Regulation 
encTfChipPkENCFF493ABN K562 NRF1 3 Transcription Factor ChIP-seq Peaks of NRF1 in K562 from ENCODE 3 (ENCFF493ABN) Regulation 
encTfChipPkENCFF992QZV K562 NRF1 2 Transcription Factor ChIP-seq Peaks of NRF1 in K562 from ENCODE 3 (ENCFF992QZV) Regulation 
encTfChipPkENCFF144PPR K562 NRF1 1 Transcription Factor ChIP-seq Peaks of NRF1 in K562 from ENCODE 3 (ENCFF144PPR) Regulation 
encTfChipPkENCFF784FIE K562 NR3C1 2 Transcription Factor ChIP-seq Peaks of NR3C1 in K562 from ENCODE 3 (ENCFF784FIE) Regulation 
encTfChipPkENCFF583CIY K562 NR3C1 1 Transcription Factor ChIP-seq Peaks of NR3C1 in K562 from ENCODE 3 (ENCFF583CIY) Regulation 
encTfChipPkENCFF712AXK K562 NR2F6 Transcription Factor ChIP-seq Peaks of NR2F6 in K562 from ENCODE 3 (ENCFF712AXK) Regulation 
encTfChipPkENCFF255EOB K562 NR2F2 Transcription Factor ChIP-seq Peaks of NR2F2 in K562 from ENCODE 3 (ENCFF255EOB) Regulation 
encTfChipPkENCFF175IIE K562 NR2F1 Transcription Factor ChIP-seq Peaks of NR2F1 in K562 from ENCODE 3 (ENCFF175IIE) Regulation 
encTfChipPkENCFF594LCH K562 NR2C2 Transcription Factor ChIP-seq Peaks of NR2C2 in K562 from ENCODE 3 (ENCFF594LCH) Regulation 
encTfChipPkENCFF664ZGR K562 NR2C1 Transcription Factor ChIP-seq Peaks of NR2C1 in K562 from ENCODE 3 (ENCFF664ZGR) Regulation 
encTfChipPkENCFF954NAJ K562 NR0B1 Transcription Factor ChIP-seq Peaks of NR0B1 in K562 from ENCODE 3 (ENCFF954NAJ) Regulation 
encTfChipPkENCFF986MHU K562 NFXL1 Transcription Factor ChIP-seq Peaks of NFXL1 in K562 from ENCODE 3 (ENCFF986MHU) Regulation 
encTfChipPkENCFF677OWM K562 NFRKB 2 Transcription Factor ChIP-seq Peaks of NFRKB in K562 from ENCODE 3 (ENCFF677OWM) Regulation 
encTfChipPkENCFF157UUF K562 NFRKB 1 Transcription Factor ChIP-seq Peaks of NFRKB in K562 from ENCODE 3 (ENCFF157UUF) Regulation 
encTfChipPkENCFF370ENX K562 NFIC Transcription Factor ChIP-seq Peaks of NFIC in K562 from ENCODE 3 (ENCFF370ENX) Regulation 
encTfChipPkENCFF495MHZ K562 NFE2 Transcription Factor ChIP-seq Peaks of NFE2 in K562 from ENCODE 3 (ENCFF495MHZ) Regulation 
encTfChipPkENCFF184RRU K562 NFATC3 2 Transcription Factor ChIP-seq Peaks of NFATC3 in K562 from ENCODE 3 (ENCFF184RRU) Regulation 
encTfChipPkENCFF723RSX K562 NFATC3 1 Transcription Factor ChIP-seq Peaks of NFATC3 in K562 from ENCODE 3 (ENCFF723RSX) Regulation 
encTfChipPkENCFF581YKY K562 NEUROD1 Transcription Factor ChIP-seq Peaks of NEUROD1 in K562 from ENCODE 3 (ENCFF581YKY) Regulation 
encTfChipPkENCFF366UBB K562 NCOR1 3 Transcription Factor ChIP-seq Peaks of NCOR1 in K562 from ENCODE 3 (ENCFF366UBB) Regulation 
encTfChipPkENCFF080NBZ K562 NCOR1 2 Transcription Factor ChIP-seq Peaks of NCOR1 in K562 from ENCODE 3 (ENCFF080NBZ) Regulation 
encTfChipPkENCFF165BCW K562 NCOR1 1 Transcription Factor ChIP-seq Peaks of NCOR1 in K562 from ENCODE 3 (ENCFF165BCW) Regulation 
encTfChipPkENCFF322DSX K562 NCOA6 Transcription Factor ChIP-seq Peaks of NCOA6 in K562 from ENCODE 3 (ENCFF322DSX) Regulation 
encTfChipPkENCFF495CSO K562 NCOA4 Transcription Factor ChIP-seq Peaks of NCOA4 in K562 from ENCODE 3 (ENCFF495CSO) Regulation 
encTfChipPkENCFF922TDM K562 NCOA2 2 Transcription Factor ChIP-seq Peaks of NCOA2 in K562 from ENCODE 3 (ENCFF922TDM) Regulation 
encTfChipPkENCFF914RFS K562 NCOA2 1 Transcription Factor ChIP-seq Peaks of NCOA2 in K562 from ENCODE 3 (ENCFF914RFS) Regulation 
encTfChipPkENCFF701NVT K562 NCOA1 3 Transcription Factor ChIP-seq Peaks of NCOA1 in K562 from ENCODE 3 (ENCFF701NVT) Regulation 
encTfChipPkENCFF967IKR K562 NCOA1 2 Transcription Factor ChIP-seq Peaks of NCOA1 in K562 from ENCODE 3 (ENCFF967IKR) Regulation 
encTfChipPkENCFF297JZQ K562 NCOA1 1 Transcription Factor ChIP-seq Peaks of NCOA1 in K562 from ENCODE 3 (ENCFF297JZQ) Regulation 
encTfChipPkENCFF074EZL K562 NBN Transcription Factor ChIP-seq Peaks of NBN in K562 from ENCODE 3 (ENCFF074EZL) Regulation 
encTfChipPkENCFF583DZD K562 MYNN Transcription Factor ChIP-seq Peaks of MYNN in K562 from ENCODE 3 (ENCFF583DZD) Regulation 
encTfChipPkENCFF634AYU K562 MYC 5 Transcription Factor ChIP-seq Peaks of MYC in K562 from ENCODE 3 (ENCFF634AYU) Regulation 
encTfChipPkENCFF387LTN K562 MYC 4 Transcription Factor ChIP-seq Peaks of MYC in K562 from ENCODE 3 (ENCFF387LTN) Regulation 
encTfChipPkENCFF676YJE K562 MYC 3 Transcription Factor ChIP-seq Peaks of MYC in K562 from ENCODE 3 (ENCFF676YJE) Regulation 
encTfChipPkENCFF465JKF K562 MYC 2 Transcription Factor ChIP-seq Peaks of MYC in K562 from ENCODE 3 (ENCFF465JKF) Regulation 
encTfChipPkENCFF099SDW K562 MYC 1 Transcription Factor ChIP-seq Peaks of MYC in K562 from ENCODE 3 (ENCFF099SDW) Regulation 
encTfChipPkENCFF877ANE K562 MYBL2 Transcription Factor ChIP-seq Peaks of MYBL2 in K562 from ENCODE 3 (ENCFF877ANE) Regulation 
encTfChipPkENCFF970LCB K562 MXI1 Transcription Factor ChIP-seq Peaks of MXI1 in K562 from ENCODE 3 (ENCFF970LCB) Regulation 
encTfChipPkENCFF350YXB K562 MTA3 Transcription Factor ChIP-seq Peaks of MTA3 in K562 from ENCODE 3 (ENCFF350YXB) Regulation 
encTfChipPkENCFF662MVX K562 MTA2 2 Transcription Factor ChIP-seq Peaks of MTA2 in K562 from ENCODE 3 (ENCFF662MVX) Regulation 
encTfChipPkENCFF410EDG K562 MTA2 1 Transcription Factor ChIP-seq Peaks of MTA2 in K562 from ENCODE 3 (ENCFF410EDG) Regulation 
encTfChipPkENCFF769GYG K562 MTA1 Transcription Factor ChIP-seq Peaks of MTA1 in K562 from ENCODE 3 (ENCFF769GYG) Regulation 
encTfChipPkENCFF567GSX K562 MNT 3 Transcription Factor ChIP-seq Peaks of MNT in K562 from ENCODE 3 (ENCFF567GSX) Regulation 
encTfChipPkENCFF973OME K562 MNT 2 Transcription Factor ChIP-seq Peaks of MNT in K562 from ENCODE 3 (ENCFF973OME) Regulation 
encTfChipPkENCFF059ONJ K562 MNT 1 Transcription Factor ChIP-seq Peaks of MNT in K562 from ENCODE 3 (ENCFF059ONJ) Regulation 
encTfChipPkENCFF440JJW K562 MLLT1 2 Transcription Factor ChIP-seq Peaks of MLLT1 in K562 from ENCODE 3 (ENCFF440JJW) Regulation 
encTfChipPkENCFF197OGH K562 MLLT1 1 Transcription Factor ChIP-seq Peaks of MLLT1 in K562 from ENCODE 3 (ENCFF197OGH) Regulation 
encTfChipPkENCFF616LVN K562 MITF 2 Transcription Factor ChIP-seq Peaks of MITF in K562 from ENCODE 3 (ENCFF616LVN) Regulation 
encTfChipPkENCFF497XOD K562 MITF 1 Transcription Factor ChIP-seq Peaks of MITF in K562 from ENCODE 3 (ENCFF497XOD) Regulation 
encTfChipPkENCFF365NKO K562 MIER1 Transcription Factor ChIP-seq Peaks of MIER1 in K562 from ENCODE 3 (ENCFF365NKO) Regulation 
encTfChipPkENCFF670ZCR K562 MGA Transcription Factor ChIP-seq Peaks of MGA in K562 from ENCODE 3 (ENCFF670ZCR) Regulation 
encTfChipPkENCFF613RNG K562 MEIS2 Transcription Factor ChIP-seq Peaks of MEIS2 in K562 from ENCODE 3 (ENCFF613RNG) Regulation 
encTfChipPkENCFF577UJR K562 MEF2A Transcription Factor ChIP-seq Peaks of MEF2A in K562 from ENCODE 3 (ENCFF577UJR) Regulation 
encTfChipPkENCFF452SVO K562 MCM7 3 Transcription Factor ChIP-seq Peaks of MCM7 in K562 from ENCODE 3 (ENCFF452SVO) Regulation 
encTfChipPkENCFF278ONE K562 MCM7 2 Transcription Factor ChIP-seq Peaks of MCM7 in K562 from ENCODE 3 (ENCFF278ONE) Regulation 
encTfChipPkENCFF399GAE K562 MCM7 1 Transcription Factor ChIP-seq Peaks of MCM7 in K562 from ENCODE 3 (ENCFF399GAE) Regulation 
encTfChipPkENCFF872YNU K562 MCM5 2 Transcription Factor ChIP-seq Peaks of MCM5 in K562 from ENCODE 3 (ENCFF872YNU) Regulation 
encTfChipPkENCFF920RYJ K562 MCM5 1 Transcription Factor ChIP-seq Peaks of MCM5 in K562 from ENCODE 3 (ENCFF920RYJ) Regulation 
encTfChipPkENCFF679ITJ K562 MCM3 Transcription Factor ChIP-seq Peaks of MCM3 in K562 from ENCODE 3 (ENCFF679ITJ) Regulation 
encTfChipPkENCFF067LIW K562 MCM2 2 Transcription Factor ChIP-seq Peaks of MCM2 in K562 from ENCODE 3 (ENCFF067LIW) Regulation 
encTfChipPkENCFF226CZE K562 MCM2 1 Transcription Factor ChIP-seq Peaks of MCM2 in K562 from ENCODE 3 (ENCFF226CZE) Regulation 
encTfChipPkENCFF470MLY K562 MBD2 Transcription Factor ChIP-seq Peaks of MBD2 in K562 from ENCODE 3 (ENCFF470MLY) Regulation 
encTfChipPkENCFF422NGZ K562 MAX 2 Transcription Factor ChIP-seq Peaks of MAX in K562 from ENCODE 3 (ENCFF422NGZ) Regulation 
encTfChipPkENCFF799HIG K562 MAX 1 Transcription Factor ChIP-seq Peaks of MAX in K562 from ENCODE 3 (ENCFF799HIG) Regulation 
encTfChipPkENCFF812QPN K562 MAFK Transcription Factor ChIP-seq Peaks of MAFK in K562 from ENCODE 3 (ENCFF812QPN) Regulation 
encTfChipPkENCFF308IXJ K562 MAFF Transcription Factor ChIP-seq Peaks of MAFF in K562 from ENCODE 3 (ENCFF308IXJ) Regulation 
encTfChipPkENCFF043YZF K562 LEF1 2 Transcription Factor ChIP-seq Peaks of LEF1 in K562 from ENCODE 3 (ENCFF043YZF) Regulation 
encTfChipPkENCFF659WAF K562 LEF1 1 Transcription Factor ChIP-seq Peaks of LEF1 in K562 from ENCODE 3 (ENCFF659WAF) Regulation 
encTfChipPkENCFF314ULQ K562 L3MBTL2 Transcription Factor ChIP-seq Peaks of L3MBTL2 in K562 from ENCODE 3 (ENCFF314ULQ) Regulation 
encTfChipPkENCFF844HBQ K562 KLF16 Transcription Factor ChIP-seq Peaks of KLF16 in K562 from ENCODE 3 (ENCFF844HBQ) Regulation 
encTfChipPkENCFF368TYM K562 KDM5B Transcription Factor ChIP-seq Peaks of KDM5B in K562 from ENCODE 3 (ENCFF368TYM) Regulation 
encTfChipPkENCFF477FYN K562 KDM4B 2 Transcription Factor ChIP-seq Peaks of KDM4B in K562 from ENCODE 3 (ENCFF477FYN) Regulation 
encTfChipPkENCFF042RAK K562 KDM4B 1 Transcription Factor ChIP-seq Peaks of KDM4B in K562 from ENCODE 3 (ENCFF042RAK) Regulation 
encTfChipPkENCFF838COI K562 KDM1A 2 Transcription Factor ChIP-seq Peaks of KDM1A in K562 from ENCODE 3 (ENCFF838COI) Regulation 
encTfChipPkENCFF738WCE K562 KDM1A 1 Transcription Factor ChIP-seq Peaks of KDM1A in K562 from ENCODE 3 (ENCFF738WCE) Regulation 
encTfChipPkENCFF772QPO K562 KAT8 Transcription Factor ChIP-seq Peaks of KAT8 in K562 from ENCODE 3 (ENCFF772QPO) Regulation 
encTfChipPkENCFF185GBT K562 KAT2B Transcription Factor ChIP-seq Peaks of KAT2B in K562 from ENCODE 3 (ENCFF185GBT) Regulation 
encTfChipPkENCFF337DKJ K562 JUND Transcription Factor ChIP-seq Peaks of JUND in K562 from ENCODE 3 (ENCFF337DKJ) Regulation 
encTfChipPkENCFF426DUB K562 JUNB Transcription Factor ChIP-seq Peaks of JUNB in K562 from ENCODE 3 (ENCFF426DUB) Regulation 
encTfChipPkENCFF629BFI K562 JUN 5 Transcription Factor ChIP-seq Peaks of JUN in K562 from ENCODE 3 (ENCFF629BFI) Regulation 
encTfChipPkENCFF573GQX K562 JUN 4 Transcription Factor ChIP-seq Peaks of JUN in K562 from ENCODE 3 (ENCFF573GQX) Regulation 
encTfChipPkENCFF192BTP K562 JUN 3 Transcription Factor ChIP-seq Peaks of JUN in K562 from ENCODE 3 (ENCFF192BTP) Regulation 
encTfChipPkENCFF077UYM K562 JUN 2 Transcription Factor ChIP-seq Peaks of JUN in K562 from ENCODE 3 (ENCFF077UYM) Regulation 
encTfChipPkENCFF417QAJ K562 JUN 1 Transcription Factor ChIP-seq Peaks of JUN in K562 from ENCODE 3 (ENCFF417QAJ) Regulation 
encTfChipPkENCFF384YDT K562 IRF2 Transcription Factor ChIP-seq Peaks of IRF2 in K562 from ENCODE 3 (ENCFF384YDT) Regulation 
encTfChipPkENCFF284VUQ K562 IRF1 4 Transcription Factor ChIP-seq Peaks of IRF1 in K562 from ENCODE 3 (ENCFF284VUQ) Regulation 
encTfChipPkENCFF730RUF K562 IRF1 3 Transcription Factor ChIP-seq Peaks of IRF1 in K562 from ENCODE 3 (ENCFF730RUF) Regulation 
encTfChipPkENCFF908UIY K562 IRF1 2 Transcription Factor ChIP-seq Peaks of IRF1 in K562 from ENCODE 3 (ENCFF908UIY) Regulation 
encTfChipPkENCFF909LKK K562 IRF1 1 Transcription Factor ChIP-seq Peaks of IRF1 in K562 from ENCODE 3 (ENCFF909LKK) Regulation 
encTfChipPkENCFF968JVX K562 IKZF1 2 Transcription Factor ChIP-seq Peaks of IKZF1 in K562 from ENCODE 3 (ENCFF968JVX) Regulation 
encTfChipPkENCFF886VSU K562 IKZF1 1 Transcription Factor ChIP-seq Peaks of IKZF1 in K562 from ENCODE 3 (ENCFF886VSU) Regulation 
encTfChipPkENCFF768TJI K562 HNRNPUL1 Transcription Factor ChIP-seq Peaks of HNRNPUL1 in K562 from ENCODE 3 (ENCFF768TJI) Regulation 
encTfChipPkENCFF122QSN K562 HNRNPLL Transcription Factor ChIP-seq Peaks of HNRNPLL in K562 from ENCODE 3 (ENCFF122QSN) Regulation 
encTfChipPkENCFF010STZ K562 HNRNPL Transcription Factor ChIP-seq Peaks of HNRNPL in K562 from ENCODE 3 (ENCFF010STZ) Regulation 
encTfChipPkENCFF777CWV K562 HNRNPK Transcription Factor ChIP-seq Peaks of HNRNPK in K562 from ENCODE 3 (ENCFF777CWV) Regulation 
encTfChipPkENCFF292JRY K562 HNRNPH1 Transcription Factor ChIP-seq Peaks of HNRNPH1 in K562 from ENCODE 3 (ENCFF292JRY) Regulation 
encTfChipPkENCFF558DSF K562 HMBOX1 Transcription Factor ChIP-seq Peaks of HMBOX1 in K562 from ENCODE 3 (ENCFF558DSF) Regulation 
encTfChipPkENCFF676NPW K562 HES1 Transcription Factor ChIP-seq Peaks of HES1 in K562 from ENCODE 3 (ENCFF676NPW) Regulation 
encTfChipPkENCFF998HOR K562 HDAC6 Transcription Factor ChIP-seq Peaks of HDAC6 in K562 from ENCODE 3 (ENCFF998HOR) Regulation 
encTfChipPkENCFF580DYE K562 HDAC3 Transcription Factor ChIP-seq Peaks of HDAC3 in K562 from ENCODE 3 (ENCFF580DYE) Regulation 
encTfChipPkENCFF562JDH K562 HDAC2 3 Transcription Factor ChIP-seq Peaks of HDAC2 in K562 from ENCODE 3 (ENCFF562JDH) Regulation 
encTfChipPkENCFF490VVG K562 HDAC2 2 Transcription Factor ChIP-seq Peaks of HDAC2 in K562 from ENCODE 3 (ENCFF490VVG) Regulation 
encTfChipPkENCFF657VJX K562 HDAC2 1 Transcription Factor ChIP-seq Peaks of HDAC2 in K562 from ENCODE 3 (ENCFF657VJX) Regulation 
encTfChipPkENCFF605KFA K562 HDAC1 4 Transcription Factor ChIP-seq Peaks of HDAC1 in K562 from ENCODE 3 (ENCFF605KFA) Regulation 
encTfChipPkENCFF019ALY K562 HDAC1 3 Transcription Factor ChIP-seq Peaks of HDAC1 in K562 from ENCODE 3 (ENCFF019ALY) Regulation 
encTfChipPkENCFF357NRL K562 HDAC1 2 Transcription Factor ChIP-seq Peaks of HDAC1 in K562 from ENCODE 3 (ENCFF357NRL) Regulation 
encTfChipPkENCFF996CUX K562 HDAC1 1 Transcription Factor ChIP-seq Peaks of HDAC1 in K562 from ENCODE 3 (ENCFF996CUX) Regulation 
encTfChipPkENCFF474NLG K562 HCFC1 Transcription Factor ChIP-seq Peaks of HCFC1 in K562 from ENCODE 3 (ENCFF474NLG) Regulation 
encTfChipPkENCFF126BCK K562 GMEB1 Transcription Factor ChIP-seq Peaks of GMEB1 in K562 from ENCODE 3 (ENCFF126BCK) Regulation 
encTfChipPkENCFF549KOD K562 GATAD2B Transcription Factor ChIP-seq Peaks of GATAD2B in K562 from ENCODE 3 (ENCFF549KOD) Regulation 
encTfChipPkENCFF253FZN K562 GATAD2A Transcription Factor ChIP-seq Peaks of GATAD2A in K562 from ENCODE 3 (ENCFF253FZN) Regulation 
encTfChipPkENCFF732HOE K562 GATA2 Transcription Factor ChIP-seq Peaks of GATA2 in K562 from ENCODE 3 (ENCFF732HOE) Regulation 
encTfChipPkENCFF632NQI K562 GATA1 Transcription Factor ChIP-seq Peaks of GATA1 in K562 from ENCODE 3 (ENCFF632NQI) Regulation 
encTfChipPkENCFF517KRT K562 GABPB1 Transcription Factor ChIP-seq Peaks of GABPB1 in K562 from ENCODE 3 (ENCFF517KRT) Regulation 
encTfChipPkENCFF833FCO K562 GABPA Transcription Factor ChIP-seq Peaks of GABPA in K562 from ENCODE 3 (ENCFF833FCO) Regulation 
encTfChipPkENCFF142CPK K562 FUS Transcription Factor ChIP-seq Peaks of FUS in K562 from ENCODE 3 (ENCFF142CPK) Regulation 
encTfChipPkENCFF699ZII K562 FOXM1 Transcription Factor ChIP-seq Peaks of FOXM1 in K562 from ENCODE 3 (ENCFF699ZII) Regulation 
encTfChipPkENCFF248VHN K562 FOXK2 2 Transcription Factor ChIP-seq Peaks of FOXK2 in K562 from ENCODE 3 (ENCFF248VHN) Regulation 
encTfChipPkENCFF492GXZ K562 FOXK2 1 Transcription Factor ChIP-seq Peaks of FOXK2 in K562 from ENCODE 3 (ENCFF492GXZ) Regulation 
encTfChipPkENCFF809YFY K562 FOXA1 Transcription Factor ChIP-seq Peaks of FOXA1 in K562 from ENCODE 3 (ENCFF809YFY) Regulation 
encTfChipPkENCFF473GCH K562 FOSL1 Transcription Factor ChIP-seq Peaks of FOSL1 in K562 from ENCODE 3 (ENCFF473GCH) Regulation 
encTfChipPkENCFF883WYX K562 FIP1L1 Transcription Factor ChIP-seq Peaks of FIP1L1 in K562 from ENCODE 3 (ENCFF883WYX) Regulation 
encTfChipPkENCFF820EVZ K562 EWSR1 Transcription Factor ChIP-seq Peaks of EWSR1 in K562 from ENCODE 3 (ENCFF820EVZ) Regulation 
encTfChipPkENCFF545VNY K562 ETV6 2 Transcription Factor ChIP-seq Peaks of ETV6 in K562 from ENCODE 3 (ENCFF545VNY) Regulation 
encTfChipPkENCFF660VPM K562 ETV6 1 Transcription Factor ChIP-seq Peaks of ETV6 in K562 from ENCODE 3 (ENCFF660VPM) Regulation 
encTfChipPkENCFF076YZO K562 ETS1 Transcription Factor ChIP-seq Peaks of ETS1 in K562 from ENCODE 3 (ENCFF076YZO) Regulation 
encTfChipPkENCFF213EPU K562 ESRRA Transcription Factor ChIP-seq Peaks of ESRRA in K562 from ENCODE 3 (ENCFF213EPU) Regulation 
encTfChipPkENCFF925ANU K562 EP400 Transcription Factor ChIP-seq Peaks of EP400 in K562 from ENCODE 3 (ENCFF925ANU) Regulation 
encTfChipPkENCFF549TYR K562 EP300 Transcription Factor ChIP-seq Peaks of EP300 in K562 from ENCODE 3 (ENCFF549TYR) Regulation 
encTfChipPkENCFF019PEL K562 ELK1 Transcription Factor ChIP-seq Peaks of ELK1 in K562 from ENCODE 3 (ENCFF019PEL) Regulation 
encTfChipPkENCFF502KHR K562 ELF4 Transcription Factor ChIP-seq Peaks of ELF4 in K562 from ENCODE 3 (ENCFF502KHR) Regulation 
encTfChipPkENCFF392MUM K562 ELF1 Transcription Factor ChIP-seq Peaks of ELF1 in K562 from ENCODE 3 (ENCFF392MUM) Regulation 
encTfChipPkENCFF806BDC K562 EHMT2 Transcription Factor ChIP-seq Peaks of EHMT2 in K562 from ENCODE 3 (ENCFF806BDC) Regulation 
encTfChipPkENCFF558JBX K562 EGR1 3 Transcription Factor ChIP-seq Peaks of EGR1 in K562 from ENCODE 3 (ENCFF558JBX) Regulation 
encTfChipPkENCFF182QDI K562 EGR1 2 Transcription Factor ChIP-seq Peaks of EGR1 in K562 from ENCODE 3 (ENCFF182QDI) Regulation 
encTfChipPkENCFF004WYV K562 EGR1 1 Transcription Factor ChIP-seq Peaks of EGR1 in K562 from ENCODE 3 (ENCFF004WYV) Regulation 
encTfChipPkENCFF083YCQ K562 E4F1 Transcription Factor ChIP-seq Peaks of E4F1 in K562 from ENCODE 3 (ENCFF083YCQ) Regulation 
encTfChipPkENCFF925DJG K562 E2F8 Transcription Factor ChIP-seq Peaks of E2F8 in K562 from ENCODE 3 (ENCFF925DJG) Regulation 
encTfChipPkENCFF310AGG K562 E2F7 Transcription Factor ChIP-seq Peaks of E2F7 in K562 from ENCODE 3 (ENCFF310AGG) Regulation 
encTfChipPkENCFF917COW K562 E2F6 Transcription Factor ChIP-seq Peaks of E2F6 in K562 from ENCODE 3 (ENCFF917COW) Regulation 
encTfChipPkENCFF998YJY K562 E2F1 2 Transcription Factor ChIP-seq Peaks of E2F1 in K562 from ENCODE 3 (ENCFF998YJY) Regulation 
encTfChipPkENCFF106DAY K562 E2F1 1 Transcription Factor ChIP-seq Peaks of E2F1 in K562 from ENCODE 3 (ENCFF106DAY) Regulation 
encTfChipPkENCFF823SYE K562 DPF2 2 Transcription Factor ChIP-seq Peaks of DPF2 in K562 from ENCODE 3 (ENCFF823SYE) Regulation 
encTfChipPkENCFF774QKS K562 DPF2 1 Transcription Factor ChIP-seq Peaks of DPF2 in K562 from ENCODE 3 (ENCFF774QKS) Regulation 
encTfChipPkENCFF034PQD K562 DNMT1 Transcription Factor ChIP-seq Peaks of DNMT1 in K562 from ENCODE 3 (ENCFF034PQD) Regulation 
encTfChipPkENCFF786WZD K562 DEAF1 Transcription Factor ChIP-seq Peaks of DEAF1 in K562 from ENCODE 3 (ENCFF786WZD) Regulation 
encTfChipPkENCFF526HLP K562 DACH1 Transcription Factor ChIP-seq Peaks of DACH1 in K562 from ENCODE 3 (ENCFF526HLP) Regulation 
encTfChipPkENCFF517YCC K562 CUX1 Transcription Factor ChIP-seq Peaks of CUX1 in K562 from ENCODE 3 (ENCFF517YCC) Regulation 
encTfChipPkENCFF738TKN K562 CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in K562 from ENCODE 3 (ENCFF738TKN) Regulation 
encTfChipPkENCFF085HTY K562 CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in K562 from ENCODE 3 (ENCFF085HTY) Regulation 
encTfChipPkENCFF152VMJ K562 CTBP1 Transcription Factor ChIP-seq Peaks of CTBP1 in K562 from ENCODE 3 (ENCFF152VMJ) Regulation 
encTfChipPkENCFF948TXN K562 CREM Transcription Factor ChIP-seq Peaks of CREM in K562 from ENCODE 3 (ENCFF948TXN) Regulation 
encTfChipPkENCFF369HGX K562 CREBBP Transcription Factor ChIP-seq Peaks of CREBBP in K562 from ENCODE 3 (ENCFF369HGX) Regulation 
encTfChipPkENCFF582YPB K562 CREB3L1 Transcription Factor ChIP-seq Peaks of CREB3L1 in K562 from ENCODE 3 (ENCFF582YPB) Regulation 
encTfChipPkENCFF684MLP K562 COPS2 Transcription Factor ChIP-seq Peaks of COPS2 in K562 from ENCODE 3 (ENCFF684MLP) Regulation 
encTfChipPkENCFF602FRL K562 CHAMP1 2 Transcription Factor ChIP-seq Peaks of CHAMP1 in K562 from ENCODE 3 (ENCFF602FRL) Regulation 
encTfChipPkENCFF859FVX K562 CHAMP1 1 Transcription Factor ChIP-seq Peaks of CHAMP1 in K562 from ENCODE 3 (ENCFF859FVX) Regulation 
encTfChipPkENCFF429XKT K562 CEBPB Transcription Factor ChIP-seq Peaks of CEBPB in K562 from ENCODE 3 (ENCFF429XKT) Regulation 
encTfChipPkENCFF643TEZ K562 CDC5L Transcription Factor ChIP-seq Peaks of CDC5L in K562 from ENCODE 3 (ENCFF643TEZ) Regulation 
encTfChipPkENCFF583GKE K562 CCAR2 Transcription Factor ChIP-seq Peaks of CCAR2 in K562 from ENCODE 3 (ENCFF583GKE) Regulation 
encTfChipPkENCFF874QUM K562 CC2D1A Transcription Factor ChIP-seq Peaks of CC2D1A in K562 from ENCODE 3 (ENCFF874QUM) Regulation 
encTfChipPkENCFF062ARS K562 CBX5 Transcription Factor ChIP-seq Peaks of CBX5 in K562 from ENCODE 3 (ENCFF062ARS) Regulation 
encTfChipPkENCFF455TDM K562 CBX3 2 Transcription Factor ChIP-seq Peaks of CBX3 in K562 from ENCODE 3 (ENCFF455TDM) Regulation 
encTfChipPkENCFF005BKP K562 CBX3 1 Transcription Factor ChIP-seq Peaks of CBX3 in K562 from ENCODE 3 (ENCFF005BKP) Regulation 
encTfChipPkENCFF484DKT K562 CBX1 Transcription Factor ChIP-seq Peaks of CBX1 in K562 from ENCODE 3 (ENCFF484DKT) Regulation 
encTfChipPkENCFF993GXU K562 CBFA2T3 Transcription Factor ChIP-seq Peaks of CBFA2T3 in K562 from ENCODE 3 (ENCFF993GXU) Regulation 
encTfChipPkENCFF642BNC K562 CBFA2T2 Transcription Factor ChIP-seq Peaks of CBFA2T2 in K562 from ENCODE 3 (ENCFF642BNC) Regulation 
encTfChipPkENCFF996ZGL K562 C11orf30 Transcription Factor ChIP-seq Peaks of C11orf30 in K562 from ENCODE 3 (ENCFF996ZGL) Regulation 
encTfChipPkENCFF666LZV K562 BRD9 Transcription Factor ChIP-seq Peaks of BRD9 in K562 from ENCODE 3 (ENCFF666LZV) Regulation 
encTfChipPkENCFF714XHL K562 BRD4 Transcription Factor ChIP-seq Peaks of BRD4 in K562 from ENCODE 3 (ENCFF714XHL) Regulation 
encTfChipPkENCFF549GMO K562 BRCA1 Transcription Factor ChIP-seq Peaks of BRCA1 in K562 from ENCODE 3 (ENCFF549GMO) Regulation 
encTfChipPkENCFF048OIZ K562 BMI1 Transcription Factor ChIP-seq Peaks of BMI1 in K562 from ENCODE 3 (ENCFF048OIZ) Regulation 
encTfChipPkENCFF179NDS K562 BHLHE40 Transcription Factor ChIP-seq Peaks of BHLHE40 in K562 from ENCODE 3 (ENCFF179NDS) Regulation 
encTfChipPkENCFF057ZUY K562 BCOR Transcription Factor ChIP-seq Peaks of BCOR in K562 from ENCODE 3 (ENCFF057ZUY) Regulation 
encTfChipPkENCFF423EMU K562 BACH1 Transcription Factor ChIP-seq Peaks of BACH1 in K562 from ENCODE 3 (ENCFF423EMU) Regulation 
encTfChipPkENCFF868QLL K562 ATF7 Transcription Factor ChIP-seq Peaks of ATF7 in K562 from ENCODE 3 (ENCFF868QLL) Regulation 
encTfChipPkENCFF710IEF K562 ATF4 Transcription Factor ChIP-seq Peaks of ATF4 in K562 from ENCODE 3 (ENCFF710IEF) Regulation 
encTfChipPkENCFF475TQE K562 ATF3 2 Transcription Factor ChIP-seq Peaks of ATF3 in K562 from ENCODE 3 (ENCFF475TQE) Regulation 
encTfChipPkENCFF958KNK K562 ATF3 1 Transcription Factor ChIP-seq Peaks of ATF3 in K562 from ENCODE 3 (ENCFF958KNK) Regulation 
encTfChipPkENCFF968KBN K562 ATF2 Transcription Factor ChIP-seq Peaks of ATF2 in K562 from ENCODE 3 (ENCFF968KBN) Regulation 
encTfChipPkENCFF235ZZP K562 ASH1L Transcription Factor ChIP-seq Peaks of ASH1L in K562 from ENCODE 3 (ENCFF235ZZP) Regulation 
encTfChipPkENCFF507MGL K562 ARNT 3 Transcription Factor ChIP-seq Peaks of ARNT in K562 from ENCODE 3 (ENCFF507MGL) Regulation 
encTfChipPkENCFF471ZTZ K562 ARNT 2 Transcription Factor ChIP-seq Peaks of ARNT in K562 from ENCODE 3 (ENCFF471ZTZ) Regulation 
encTfChipPkENCFF944GZI K562 ARNT 1 Transcription Factor ChIP-seq Peaks of ARNT in K562 from ENCODE 3 (ENCFF944GZI) Regulation 
encTfChipPkENCFF835KAT K562 ARID3A Transcription Factor ChIP-seq Peaks of ARID3A in K562 from ENCODE 3 (ENCFF835KAT) Regulation 
encTfChipPkENCFF332ICQ K562 ARID2 Transcription Factor ChIP-seq Peaks of ARID2 in K562 from ENCODE 3 (ENCFF332ICQ) Regulation 
encTfChipPkENCFF225MPC K562 ARID1B Transcription Factor ChIP-seq Peaks of ARID1B in K562 from ENCODE 3 (ENCFF225MPC) Regulation 
encTfChipPkENCFF010MMQ K562 ARHGAP35 Transcription Factor ChIP-seq Peaks of ARHGAP35 in K562 from ENCODE 3 (ENCFF010MMQ) Regulation 
encTfChipPkENCFF836VRV K562 AGO1 Transcription Factor ChIP-seq Peaks of AGO1 in K562 from ENCODE 3 (ENCFF836VRV) Regulation 
encTfChipPkENCFF360BTO K562 AFF1 2 Transcription Factor ChIP-seq Peaks of AFF1 in K562 from ENCODE 3 (ENCFF360BTO) Regulation 
encTfChipPkENCFF076MSV K562 AFF1 1 Transcription Factor ChIP-seq Peaks of AFF1 in K562 from ENCODE 3 (ENCFF076MSV) Regulation 
encTfChipPkENCFF798SFE Ishikawa POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in Ishikawa from ENCODE 3 (ENCFF798SFE) Regulation 
encTfChipPkENCFF585YYZ Ishikawa NR3C1 2 Transcription Factor ChIP-seq Peaks of NR3C1 in Ishikawa from ENCODE 3 (ENCFF585YYZ) Regulation 
encTfChipPkENCFF750JOB Ishikawa NR3C1 1 Transcription Factor ChIP-seq Peaks of NR3C1 in Ishikawa from ENCODE 3 (ENCFF750JOB) Regulation 
encTfChipPkENCFF078ATU Ishikawa ESR1 3 Transcription Factor ChIP-seq Peaks of ESR1 in Ishikawa from ENCODE 3 (ENCFF078ATU) Regulation 
encTfChipPkENCFF248QIW Ishikawa ESR1 2 Transcription Factor ChIP-seq Peaks of ESR1 in Ishikawa from ENCODE 3 (ENCFF248QIW) Regulation 
encTfChipPkENCFF276MQI Ishikawa ESR1 1 Transcription Factor ChIP-seq Peaks of ESR1 in Ishikawa from ENCODE 3 (ENCFF276MQI) Regulation 
encTfChipPkENCFF296XCF Ishikawa CTCF Transcription Factor ChIP-seq Peaks of CTCF in Ishikawa from ENCODE 3 (ENCFF296XCF) Regulation 
encTfChipPkENCFF759MVB IMR-90 USF2 Transcription Factor ChIP-seq Peaks of USF2 in IMR-90 from ENCODE 3 (ENCFF759MVB) Regulation 
encTfChipPkENCFF116RLU IMR-90 SMC3 Transcription Factor ChIP-seq Peaks of SMC3 in IMR-90 from ENCODE 3 (ENCFF116RLU) Regulation 
encTfChipPkENCFF195CYT IMR-90 RAD21 Transcription Factor ChIP-seq Peaks of RAD21 in IMR-90 from ENCODE 3 (ENCFF195CYT) Regulation 
encTfChipPkENCFF641RNZ IMR-90 NFE2L2 Transcription Factor ChIP-seq Peaks of NFE2L2 in IMR-90 from ENCODE 3 (ENCFF641RNZ) Regulation 
encTfChipPkENCFF593MEB IMR-90 MAFK Transcription Factor ChIP-seq Peaks of MAFK in IMR-90 from ENCODE 3 (ENCFF593MEB) Regulation 
encTfChipPkENCFF359IPV IMR-90 FOS Transcription Factor ChIP-seq Peaks of FOS in IMR-90 from ENCODE 3 (ENCFF359IPV) Regulation 
encTfChipPkENCFF757YVY IMR-90 ELK1 Transcription Factor ChIP-seq Peaks of ELK1 in IMR-90 from ENCODE 3 (ENCFF757YVY) Regulation 
encTfChipPkENCFF453XKM IMR-90 CTCF Transcription Factor ChIP-seq Peaks of CTCF in IMR-90 from ENCODE 3 (ENCFF453XKM) Regulation 
encTfChipPkENCFF441IFB IMR-90 CHD1 Transcription Factor ChIP-seq Peaks of CHD1 in IMR-90 from ENCODE 3 (ENCFF441IFB) Regulation 
encTfChipPkENCFF456GRS IMR-90 CEBPB Transcription Factor ChIP-seq Peaks of CEBPB in IMR-90 from ENCODE 3 (ENCFF456GRS) Regulation 
encTfChipPkENCFF942FBW IMR-90 BHLHE40 Transcription Factor ChIP-seq Peaks of BHLHE40 in IMR-90 from ENCODE 3 (ENCFF942FBW) Regulation 
encTfChipPkENCFF324TBP HepG2 ZNF384 Transcription Factor ChIP-seq Peaks of ZNF384 in HepG2 from ENCODE 3 (ENCFF324TBP) Regulation 
encTfChipPkENCFF266KSD HepG2 ZNF282 Transcription Factor ChIP-seq Peaks of ZNF282 in HepG2 from ENCODE 3 (ENCFF266KSD) Regulation 
encTfChipPkENCFF539NTA HepG2 ZNF24 2 Transcription Factor ChIP-seq Peaks of ZNF24 in HepG2 from ENCODE 3 (ENCFF539NTA) Regulation 
encTfChipPkENCFF443EYO HepG2 ZNF24 1 Transcription Factor ChIP-seq Peaks of ZNF24 in HepG2 from ENCODE 3 (ENCFF443EYO) Regulation 
encTfChipPkENCFF556DEP HepG2 ZNF207 Transcription Factor ChIP-seq Peaks of ZNF207 in HepG2 from ENCODE 3 (ENCFF556DEP) Regulation 
encTfChipPkENCFF177FZU HepG2 ZMYM3 Transcription Factor ChIP-seq Peaks of ZMYM3 in HepG2 from ENCODE 3 (ENCFF177FZU) Regulation 
encTfChipPkENCFF614VFL HepG2 ZKSCAN1 Transcription Factor ChIP-seq Peaks of ZKSCAN1 in HepG2 from ENCODE 3 (ENCFF614VFL) Regulation 
encTfChipPkENCFF974OIC HepG2 ZHX2 Transcription Factor ChIP-seq Peaks of ZHX2 in HepG2 from ENCODE 3 (ENCFF974OIC) Regulation 
encTfChipPkENCFF264LQE HepG2 ZBTB7A Transcription Factor ChIP-seq Peaks of ZBTB7A in HepG2 from ENCODE 3 (ENCFF264LQE) Regulation 
encTfChipPkENCFF598VEK HepG2 ZBTB40 Transcription Factor ChIP-seq Peaks of ZBTB40 in HepG2 from ENCODE 3 (ENCFF598VEK) Regulation 
encTfChipPkENCFF557KGA HepG2 ZBTB33 Transcription Factor ChIP-seq Peaks of ZBTB33 in HepG2 from ENCODE 3 (ENCFF557KGA) Regulation 
encTfChipPkENCFF420KEV HepG2 YY1 Transcription Factor ChIP-seq Peaks of YY1 in HepG2 from ENCODE 3 (ENCFF420KEV) Regulation 
encTfChipPkENCFF845GIK HepG2 XRCC5 Transcription Factor ChIP-seq Peaks of XRCC5 in HepG2 from ENCODE 3 (ENCFF845GIK) Regulation 
encTfChipPkENCFF684BLN HepG2 USF1 Transcription Factor ChIP-seq Peaks of USF1 in HepG2 from ENCODE 3 (ENCFF684BLN) Regulation 
encTfChipPkENCFF038QAU HepG2 U2AF2 Transcription Factor ChIP-seq Peaks of U2AF2 in HepG2 from ENCODE 3 (ENCFF038QAU) Regulation 
encTfChipPkENCFF055MVR HepG2 U2AF1 Transcription Factor ChIP-seq Peaks of U2AF1 in HepG2 from ENCODE 3 (ENCFF055MVR) Regulation 
encTfChipPkENCFF623ALA HepG2 TRIM22 Transcription Factor ChIP-seq Peaks of TRIM22 in HepG2 from ENCODE 3 (ENCFF623ALA) Regulation 
encTfChipPkENCFF712NYW HepG2 TFAP4 Transcription Factor ChIP-seq Peaks of TFAP4 in HepG2 from ENCODE 3 (ENCFF712NYW) Regulation 
encTfChipPkENCFF147MAN HepG2 TCF7 Transcription Factor ChIP-seq Peaks of TCF7 in HepG2 from ENCODE 3 (ENCFF147MAN) Regulation 
encTfChipPkENCFF940BIM HepG2 TCF12 2 Transcription Factor ChIP-seq Peaks of TCF12 in HepG2 from ENCODE 3 (ENCFF940BIM) Regulation 
encTfChipPkENCFF949EAE HepG2 TCF12 1 Transcription Factor ChIP-seq Peaks of TCF12 in HepG2 from ENCODE 3 (ENCFF949EAE) Regulation 
encTfChipPkENCFF574YMJ HepG2 TBX3 2 Transcription Factor ChIP-seq Peaks of TBX3 in HepG2 from ENCODE 3 (ENCFF574YMJ) Regulation 
encTfChipPkENCFF807BXT HepG2 TBX3 1 Transcription Factor ChIP-seq Peaks of TBX3 in HepG2 from ENCODE 3 (ENCFF807BXT) Regulation 
encTfChipPkENCFF584CNF HepG2 TBP Transcription Factor ChIP-seq Peaks of TBP in HepG2 from ENCODE 3 (ENCFF584CNF) Regulation 
encTfChipPkENCFF424KTS HepG2 TBL1XR1 Transcription Factor ChIP-seq Peaks of TBL1XR1 in HepG2 from ENCODE 3 (ENCFF424KTS) Regulation 
encTfChipPkENCFF490ZAU HepG2 TAF15 Transcription Factor ChIP-seq Peaks of TAF15 in HepG2 from ENCODE 3 (ENCFF490ZAU) Regulation 
encTfChipPkENCFF345GZF HepG2 TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in HepG2 from ENCODE 3 (ENCFF345GZF) Regulation 
encTfChipPkENCFF086LMU HepG2 SUZ12 Transcription Factor ChIP-seq Peaks of SUZ12 in HepG2 from ENCODE 3 (ENCFF086LMU) Regulation 
encTfChipPkENCFF868WXR HepG2 SRSF9 Transcription Factor ChIP-seq Peaks of SRSF9 in HepG2 from ENCODE 3 (ENCFF868WXR) Regulation 
encTfChipPkENCFF479TZM HepG2 SRSF4 Transcription Factor ChIP-seq Peaks of SRSF4 in HepG2 from ENCODE 3 (ENCFF479TZM) Regulation 
encTfChipPkENCFF573ALP HepG2 SP1 2 Transcription Factor ChIP-seq Peaks of SP1 in HepG2 from ENCODE 3 (ENCFF573ALP) Regulation 
encTfChipPkENCFF741WKY HepG2 SP1 1 Transcription Factor ChIP-seq Peaks of SP1 in HepG2 from ENCODE 3 (ENCFF741WKY) Regulation 
encTfChipPkENCFF432DIT HepG2 SOX6 Transcription Factor ChIP-seq Peaks of SOX6 in HepG2 from ENCODE 3 (ENCFF432DIT) Regulation 
encTfChipPkENCFF132BFM HepG2 SOX13 Transcription Factor ChIP-seq Peaks of SOX13 in HepG2 from ENCODE 3 (ENCFF132BFM) Regulation 
encTfChipPkENCFF337FIU HepG2 SNRNP70 Transcription Factor ChIP-seq Peaks of SNRNP70 in HepG2 from ENCODE 3 (ENCFF337FIU) Regulation 
encTfChipPkENCFF525EJQ HepG2 SMC3 Transcription Factor ChIP-seq Peaks of SMC3 in HepG2 from ENCODE 3 (ENCFF525EJQ) Regulation 
encTfChipPkENCFF743GXH HepG2 SMARCE1 Transcription Factor ChIP-seq Peaks of SMARCE1 in HepG2 from ENCODE 3 (ENCFF743GXH) Regulation 
encTfChipPkENCFF038MCY HepG2 SMARCC2 Transcription Factor ChIP-seq Peaks of SMARCC2 in HepG2 from ENCODE 3 (ENCFF038MCY) Regulation 
encTfChipPkENCFF363QMG HepG2 SKI Transcription Factor ChIP-seq Peaks of SKI in HepG2 from ENCODE 3 (ENCFF363QMG) Regulation 
encTfChipPkENCFF812UZP HepG2 SIN3B Transcription Factor ChIP-seq Peaks of SIN3B in HepG2 from ENCODE 3 (ENCFF812UZP) Regulation 
encTfChipPkENCFF786HHN HepG2 SIN3A Transcription Factor ChIP-seq Peaks of SIN3A in HepG2 from ENCODE 3 (ENCFF786HHN) Regulation 
encTfChipPkENCFF964JXI HepG2 RXRA Transcription Factor ChIP-seq Peaks of RXRA in HepG2 from ENCODE 3 (ENCFF964JXI) Regulation 
encTfChipPkENCFF355ARZ HepG2 RNF2 Transcription Factor ChIP-seq Peaks of RNF2 in HepG2 from ENCODE 3 (ENCFF355ARZ) Regulation 
encTfChipPkENCFF933GHY HepG2 RFX5 Transcription Factor ChIP-seq Peaks of RFX5 in HepG2 from ENCODE 3 (ENCFF933GHY) Regulation 
encTfChipPkENCFF507RHE HepG2 RFX1 Transcription Factor ChIP-seq Peaks of RFX1 in HepG2 from ENCODE 3 (ENCFF507RHE) Regulation 
encTfChipPkENCFF854KPC HepG2 REST 2 Transcription Factor ChIP-seq Peaks of REST in HepG2 from ENCODE 3 (ENCFF854KPC) Regulation 
encTfChipPkENCFF153JLK HepG2 REST 1 Transcription Factor ChIP-seq Peaks of REST in HepG2 from ENCODE 3 (ENCFF153JLK) Regulation 
encTfChipPkENCFF706RIA HepG2 RCOR1 Transcription Factor ChIP-seq Peaks of RCOR1 in HepG2 from ENCODE 3 (ENCFF706RIA) Regulation 
encTfChipPkENCFF221GWO HepG2 RBM39 Transcription Factor ChIP-seq Peaks of RBM39 in HepG2 from ENCODE 3 (ENCFF221GWO) Regulation 
encTfChipPkENCFF688VHI HepG2 RBM22 Transcription Factor ChIP-seq Peaks of RBM22 in HepG2 from ENCODE 3 (ENCFF688VHI) Regulation 
encTfChipPkENCFF663YBI HepG2 RBFOX2 Transcription Factor ChIP-seq Peaks of RBFOX2 in HepG2 from ENCODE 3 (ENCFF663YBI) Regulation 
encTfChipPkENCFF681NJT HepG2 RAD51 Transcription Factor ChIP-seq Peaks of RAD51 in HepG2 from ENCODE 3 (ENCFF681NJT) Regulation 
encTfChipPkENCFF072UEX HepG2 RAD21 2 Transcription Factor ChIP-seq Peaks of RAD21 in HepG2 from ENCODE 3 (ENCFF072UEX) Regulation 
encTfChipPkENCFF584YYH HepG2 RAD21 1 Transcription Factor ChIP-seq Peaks of RAD21 in HepG2 from ENCODE 3 (ENCFF584YYH) Regulation 
encTfChipPkENCFF908HDA HepG2 PTBP1 Transcription Factor ChIP-seq Peaks of PTBP1 in HepG2 from ENCODE 3 (ENCFF908HDA) Regulation 
encTfChipPkENCFF501NHW HepG2 PRPF4 Transcription Factor ChIP-seq Peaks of PRPF4 in HepG2 from ENCODE 3 (ENCFF501NHW) Regulation 
encTfChipPkENCFF259XQC HepG2 POLR2G Transcription Factor ChIP-seq Peaks of POLR2G in HepG2 from ENCODE 3 (ENCFF259XQC) Regulation 
encTfChipPkENCFF992LSQ HepG2 POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in HepG2 from ENCODE 3 (ENCFF992LSQ) Regulation 
encTfChipPkENCFF948QME HepG2 PLRG1 Transcription Factor ChIP-seq Peaks of PLRG1 in HepG2 from ENCODE 3 (ENCFF948QME) Regulation 
encTfChipPkENCFF060MLS HepG2 PHF8 Transcription Factor ChIP-seq Peaks of PHF8 in HepG2 from ENCODE 3 (ENCFF060MLS) Regulation 
encTfChipPkENCFF449ITJ HepG2 PHB2 Transcription Factor ChIP-seq Peaks of PHB2 in HepG2 from ENCODE 3 (ENCFF449ITJ) Regulation 
encTfChipPkENCFF460OWI HepG2 PCBP2 Transcription Factor ChIP-seq Peaks of PCBP2 in HepG2 from ENCODE 3 (ENCFF460OWI) Regulation 
encTfChipPkENCFF468MIF HepG2 PCBP1 Transcription Factor ChIP-seq Peaks of PCBP1 in HepG2 from ENCODE 3 (ENCFF468MIF) Regulation 
encTfChipPkENCFF972NIR HepG2 NRF1 2 Transcription Factor ChIP-seq Peaks of NRF1 in HepG2 from ENCODE 3 (ENCFF972NIR) Regulation 
encTfChipPkENCFF003GNY HepG2 NRF1 1 Transcription Factor ChIP-seq Peaks of NRF1 in HepG2 from ENCODE 3 (ENCFF003GNY) Regulation 
encTfChipPkENCFF311LEU HepG2 NR2F6 Transcription Factor ChIP-seq Peaks of NR2F6 in HepG2 from ENCODE 3 (ENCFF311LEU) Regulation 
encTfChipPkENCFF132QLW HepG2 NFRKB Transcription Factor ChIP-seq Peaks of NFRKB in HepG2 from ENCODE 3 (ENCFF132QLW) Regulation 
encTfChipPkENCFF297BXM HepG2 NFE2L2 Transcription Factor ChIP-seq Peaks of NFE2L2 in HepG2 from ENCODE 3 (ENCFF297BXM) Regulation 
encTfChipPkENCFF033BDT HepG2 NCOR1 Transcription Factor ChIP-seq Peaks of NCOR1 in HepG2 from ENCODE 3 (ENCFF033BDT) Regulation 
encTfChipPkENCFF075PDC HepG2 NBN Transcription Factor ChIP-seq Peaks of NBN in HepG2 from ENCODE 3 (ENCFF075PDC) Regulation 
encTfChipPkENCFF763GJP HepG2 MNT 2 Transcription Factor ChIP-seq Peaks of MNT in HepG2 from ENCODE 3 (ENCFF763GJP) Regulation 
encTfChipPkENCFF453CYS HepG2 MNT 1 Transcription Factor ChIP-seq Peaks of MNT in HepG2 from ENCODE 3 (ENCFF453CYS) Regulation 
encTfChipPkENCFF922GRD HepG2 MAX Transcription Factor ChIP-seq Peaks of MAX in HepG2 from ENCODE 3 (ENCFF922GRD) Regulation 
encTfChipPkENCFF718CQQ HepG2 MAFK 2 Transcription Factor ChIP-seq Peaks of MAFK in HepG2 from ENCODE 3 (ENCFF718CQQ) Regulation 
encTfChipPkENCFF800XTT HepG2 MAFK 1 Transcription Factor ChIP-seq Peaks of MAFK in HepG2 from ENCODE 3 (ENCFF800XTT) Regulation 
encTfChipPkENCFF684ASX HepG2 MAFF Transcription Factor ChIP-seq Peaks of MAFF in HepG2 from ENCODE 3 (ENCFF684ASX) Regulation 
encTfChipPkENCFF308BSD HepG2 LCORL Transcription Factor ChIP-seq Peaks of LCORL in HepG2 from ENCODE 3 (ENCFF308BSD) Regulation 
encTfChipPkENCFF880BTU HepG2 KDM5A Transcription Factor ChIP-seq Peaks of KDM5A in HepG2 from ENCODE 3 (ENCFF880BTU) Regulation 
encTfChipPkENCFF613LYW HepG2 KDM1A Transcription Factor ChIP-seq Peaks of KDM1A in HepG2 from ENCODE 3 (ENCFF613LYW) Regulation 
encTfChipPkENCFF405GHU HepG2 KAT2B Transcription Factor ChIP-seq Peaks of KAT2B in HepG2 from ENCODE 3 (ENCFF405GHU) Regulation 
encTfChipPkENCFF721HUX HepG2 JUND 2 Transcription Factor ChIP-seq Peaks of JUND in HepG2 from ENCODE 3 (ENCFF721HUX) Regulation 
encTfChipPkENCFF085GOJ HepG2 JUND 1 Transcription Factor ChIP-seq Peaks of JUND in HepG2 from ENCODE 3 (ENCFF085GOJ) Regulation 
encTfChipPkENCFF880SXP HepG2 IKZF1 Transcription Factor ChIP-seq Peaks of IKZF1 in HepG2 from ENCODE 3 (ENCFF880SXP) Regulation 
encTfChipPkENCFF560CMG HepG2 HNRNPUL1 Transcription Factor ChIP-seq Peaks of HNRNPUL1 in HepG2 from ENCODE 3 (ENCFF560CMG) Regulation 
encTfChipPkENCFF883CDF HepG2 HNRNPLL Transcription Factor ChIP-seq Peaks of HNRNPLL in HepG2 from ENCODE 3 (ENCFF883CDF) Regulation 
encTfChipPkENCFF233MID HepG2 HNRNPL Transcription Factor ChIP-seq Peaks of HNRNPL in HepG2 from ENCODE 3 (ENCFF233MID) Regulation 
encTfChipPkENCFF099BZU HepG2 HNRNPK Transcription Factor ChIP-seq Peaks of HNRNPK in HepG2 from ENCODE 3 (ENCFF099BZU) Regulation 
encTfChipPkENCFF937MYV HepG2 HNRNPH1 Transcription Factor ChIP-seq Peaks of HNRNPH1 in HepG2 from ENCODE 3 (ENCFF937MYV) Regulation 
encTfChipPkENCFF140ARE HepG2 HNF4G Transcription Factor ChIP-seq Peaks of HNF4G in HepG2 from ENCODE 3 (ENCFF140ARE) Regulation 
encTfChipPkENCFF884JKW HepG2 HNF4A Transcription Factor ChIP-seq Peaks of HNF4A in HepG2 from ENCODE 3 (ENCFF884JKW) Regulation 
encTfChipPkENCFF227PWE HepG2 HNF1A Transcription Factor ChIP-seq Peaks of HNF1A in HepG2 from ENCODE 3 (ENCFF227PWE) Regulation 
encTfChipPkENCFF847HDW HepG2 HDAC6 Transcription Factor ChIP-seq Peaks of HDAC6 in HepG2 from ENCODE 3 (ENCFF847HDW) Regulation 
encTfChipPkENCFF459DRJ HepG2 HDAC2 2 Transcription Factor ChIP-seq Peaks of HDAC2 in HepG2 from ENCODE 3 (ENCFF459DRJ) Regulation 
encTfChipPkENCFF503AZK HepG2 HDAC2 1 Transcription Factor ChIP-seq Peaks of HDAC2 in HepG2 from ENCODE 3 (ENCFF503AZK) Regulation 
encTfChipPkENCFF384XDG HepG2 HDAC1 Transcription Factor ChIP-seq Peaks of HDAC1 in HepG2 from ENCODE 3 (ENCFF384XDG) Regulation 
encTfChipPkENCFF997AAW HepG2 HCFC1 Transcription Factor ChIP-seq Peaks of HCFC1 in HepG2 from ENCODE 3 (ENCFF997AAW) Regulation 
encTfChipPkENCFF210DMP HepG2 GATA4 Transcription Factor ChIP-seq Peaks of GATA4 in HepG2 from ENCODE 3 (ENCFF210DMP) Regulation 
encTfChipPkENCFF065EPE HepG2 GABPA Transcription Factor ChIP-seq Peaks of GABPA in HepG2 from ENCODE 3 (ENCFF065EPE) Regulation 
encTfChipPkENCFF950KWC HepG2 FUS Transcription Factor ChIP-seq Peaks of FUS in HepG2 from ENCODE 3 (ENCFF950KWC) Regulation 
encTfChipPkENCFF501KPU HepG2 FOXP1 Transcription Factor ChIP-seq Peaks of FOXP1 in HepG2 from ENCODE 3 (ENCFF501KPU) Regulation 
encTfChipPkENCFF144FQA HepG2 FOXK2 Transcription Factor ChIP-seq Peaks of FOXK2 in HepG2 from ENCODE 3 (ENCFF144FQA) Regulation 
encTfChipPkENCFF683KBO HepG2 FOXA2 2 Transcription Factor ChIP-seq Peaks of FOXA2 in HepG2 from ENCODE 3 (ENCFF683KBO) Regulation 
encTfChipPkENCFF002ROJ HepG2 FOXA2 1 Transcription Factor ChIP-seq Peaks of FOXA2 in HepG2 from ENCODE 3 (ENCFF002ROJ) Regulation 
encTfChipPkENCFF675TLS HepG2 FOXA1 3 Transcription Factor ChIP-seq Peaks of FOXA1 in HepG2 from ENCODE 3 (ENCFF675TLS) Regulation 
encTfChipPkENCFF978IWS HepG2 FOXA1 2 Transcription Factor ChIP-seq Peaks of FOXA1 in HepG2 from ENCODE 3 (ENCFF978IWS) Regulation 
encTfChipPkENCFF553PWA HepG2 FOXA1 1 Transcription Factor ChIP-seq Peaks of FOXA1 in HepG2 from ENCODE 3 (ENCFF553PWA) Regulation 
encTfChipPkENCFF395KPJ HepG2 FOSL2 Transcription Factor ChIP-seq Peaks of FOSL2 in HepG2 from ENCODE 3 (ENCFF395KPJ) Regulation 
encTfChipPkENCFF093OUB HepG2 FIP1L1 Transcription Factor ChIP-seq Peaks of FIP1L1 in HepG2 from ENCODE 3 (ENCFF093OUB) Regulation 
encTfChipPkENCFF493FED HepG2 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in HepG2 from ENCODE 3 (ENCFF493FED) Regulation 
encTfChipPkENCFF076NCP HepG2 ETV4 Transcription Factor ChIP-seq Peaks of ETV4 in HepG2 from ENCODE 3 (ENCFF076NCP) Regulation 
encTfChipPkENCFF244ORA HepG2 ETS1 Transcription Factor ChIP-seq Peaks of ETS1 in HepG2 from ENCODE 3 (ENCFF244ORA) Regulation 
encTfChipPkENCFF259JWD HepG2 EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in HepG2 from ENCODE 3 (ENCFF259JWD) Regulation 
encTfChipPkENCFF547POU HepG2 EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in HepG2 from ENCODE 3 (ENCFF547POU) Regulation 
encTfChipPkENCFF747CHL HepG2 ELF1 Transcription Factor ChIP-seq Peaks of ELF1 in HepG2 from ENCODE 3 (ENCFF747CHL) Regulation 
encTfChipPkENCFF609YST HepG2 EHMT2 Transcription Factor ChIP-seq Peaks of EHMT2 in HepG2 from ENCODE 3 (ENCFF609YST) Regulation 
encTfChipPkENCFF237OKO HepG2 CTCF Transcription Factor ChIP-seq Peaks of CTCF in HepG2 from ENCODE 3 (ENCFF237OKO) Regulation 
encTfChipPkENCFF693JHE HepG2 CREM Transcription Factor ChIP-seq Peaks of CREM in HepG2 from ENCODE 3 (ENCFF693JHE) Regulation 
encTfChipPkENCFF161PGD HepG2 CREB1 Transcription Factor ChIP-seq Peaks of CREB1 in HepG2 from ENCODE 3 (ENCFF161PGD) Regulation 
encTfChipPkENCFF069RNV HepG2 CHD4 Transcription Factor ChIP-seq Peaks of CHD4 in HepG2 from ENCODE 3 (ENCFF069RNV) Regulation 
encTfChipPkENCFF319IEF HepG2 CEBPB 2 Transcription Factor ChIP-seq Peaks of CEBPB in HepG2 from ENCODE 3 (ENCFF319IEF) Regulation 
encTfChipPkENCFF471HCD HepG2 CEBPB 1 Transcription Factor ChIP-seq Peaks of CEBPB in HepG2 from ENCODE 3 (ENCFF471HCD) Regulation 
encTfChipPkENCFF671IJY HepG2 CCAR2 Transcription Factor ChIP-seq Peaks of CCAR2 in HepG2 from ENCODE 3 (ENCFF671IJY) Regulation 
encTfChipPkENCFF928KZS HepG2 CBX2 Transcription Factor ChIP-seq Peaks of CBX2 in HepG2 from ENCODE 3 (ENCFF928KZS) Regulation 
encTfChipPkENCFF665CIR HepG2 BRD4 Transcription Factor ChIP-seq Peaks of BRD4 in HepG2 from ENCODE 3 (ENCFF665CIR) Regulation 
encTfChipPkENCFF775PPJ HepG2 BRCA1 Transcription Factor ChIP-seq Peaks of BRCA1 in HepG2 from ENCODE 3 (ENCFF775PPJ) Regulation 
encTfChipPkENCFF108RWG HepG2 BHLHE40 2 Transcription Factor ChIP-seq Peaks of BHLHE40 in HepG2 from ENCODE 3 (ENCFF108RWG) Regulation 
encTfChipPkENCFF028BDC HepG2 BHLHE40 1 Transcription Factor ChIP-seq Peaks of BHLHE40 in HepG2 from ENCODE 3 (ENCFF028BDC) Regulation 
encTfChipPkENCFF950HDR HepG2 ATM Transcription Factor ChIP-seq Peaks of ATM in HepG2 from ENCODE 3 (ENCFF950HDR) Regulation 
encTfChipPkENCFF658YLW HepG2 ATF7 Transcription Factor ChIP-seq Peaks of ATF7 in HepG2 from ENCODE 3 (ENCFF658YLW) Regulation 
encTfChipPkENCFF857YVK HepG2 ATF3 Transcription Factor ChIP-seq Peaks of ATF3 in HepG2 from ENCODE 3 (ENCFF857YVK) Regulation 
encTfChipPkENCFF502ZTC HepG2 ATF2 Transcription Factor ChIP-seq Peaks of ATF2 in HepG2 from ENCODE 3 (ENCFF502ZTC) Regulation 
encTfChipPkENCFF747VMG HepG2 ASH2L Transcription Factor ChIP-seq Peaks of ASH2L in HepG2 from ENCODE 3 (ENCFF747VMG) Regulation 
encTfChipPkENCFF808WQI HepG2 ARNT Transcription Factor ChIP-seq Peaks of ARNT in HepG2 from ENCODE 3 (ENCFF808WQI) Regulation 
encTfChipPkENCFF514OYL HepG2 ARID3A Transcription Factor ChIP-seq Peaks of ARID3A in HepG2 from ENCODE 3 (ENCFF514OYL) Regulation 
encTfChipPkENCFF622VSV HepG2 AGO2 Transcription Factor ChIP-seq Peaks of AGO2 in HepG2 from ENCODE 3 (ENCFF622VSV) Regulation 
encTfChipPkENCFF639TOU HepG2 AGO1 Transcription Factor ChIP-seq Peaks of AGO1 in HepG2 from ENCODE 3 (ENCFF639TOU) Regulation 
encTfChipPkENCFF708OJJ HeLa-S3 ZHX1 Transcription Factor ChIP-seq Peaks of ZHX1 in HeLa-S3 from ENCODE 3 (ENCFF708OJJ) Regulation 
encTfChipPkENCFF675ZHC HeLa-S3 UBTF Transcription Factor ChIP-seq Peaks of UBTF in HeLa-S3 from ENCODE 3 (ENCFF675ZHC) Regulation 
encTfChipPkENCFF305QDB HeLa-S3 TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in HeLa-S3 from ENCODE 3 (ENCFF305QDB) Regulation 
encTfChipPkENCFF612ASR HeLa-S3 SUPT20H Transcription Factor ChIP-seq Peaks of SUPT20H in HeLa-S3 from ENCODE 3 (ENCFF612ASR) Regulation 
encTfChipPkENCFF365ICU HeLa-S3 SREBF2 Transcription Factor ChIP-seq Peaks of SREBF2 in HeLa-S3 from ENCODE 3 (ENCFF365ICU) Regulation 
encTfChipPkENCFF932CSV HeLa-S3 REST Transcription Factor ChIP-seq Peaks of REST in HeLa-S3 from ENCODE 3 (ENCFF932CSV) Regulation 
encTfChipPkENCFF417LLT HeLa-S3 POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in HeLa-S3 from ENCODE 3 (ENCFF417LLT) Regulation 
encTfChipPkENCFF712LMP HeLa-S3 NFE2L2 Transcription Factor ChIP-seq Peaks of NFE2L2 in HeLa-S3 from ENCODE 3 (ENCFF712LMP) Regulation 
encTfChipPkENCFF405BKG HeLa-S3 MAFK Transcription Factor ChIP-seq Peaks of MAFK in HeLa-S3 from ENCODE 3 (ENCFF405BKG) Regulation 
encTfChipPkENCFF411BAO HeLa-S3 MAFF Transcription Factor ChIP-seq Peaks of MAFF in HeLa-S3 from ENCODE 3 (ENCFF411BAO) Regulation 
encTfChipPkENCFF793BVO HeLa-S3 GABPA Transcription Factor ChIP-seq Peaks of GABPA in HeLa-S3 from ENCODE 3 (ENCFF793BVO) Regulation 
encTfChipPkENCFF751GGI HeLa-S3 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in HeLa-S3 from ENCODE 3 (ENCFF751GGI) Regulation 
encTfChipPkENCFF768OPK HeLa-S3 CTCF Transcription Factor ChIP-seq Peaks of CTCF in HeLa-S3 from ENCODE 3 (ENCFF768OPK) Regulation 
encTfChipPkENCFF587OBC HL-60 SPI1 Transcription Factor ChIP-seq Peaks of SPI1 in HL-60 from ENCODE 3 (ENCFF587OBC) Regulation 
encTfChipPkENCFF603MCO HL-60 REST Transcription Factor ChIP-seq Peaks of REST in HL-60 from ENCODE 3 (ENCFF603MCO) Regulation 
encTfChipPkENCFF280GDT HL-60 GABPA Transcription Factor ChIP-seq Peaks of GABPA in HL-60 from ENCODE 3 (ENCFF280GDT) Regulation 
encTfChipPkENCFF041ZEP HL-60 CTCF Transcription Factor ChIP-seq Peaks of CTCF in HL-60 from ENCODE 3 (ENCFF041ZEP) Regulation 
encTfChipPkENCFF282QFS HFF-Myc CTCF Transcription Factor ChIP-seq Peaks of CTCF in HFF-Myc from ENCODE 3 (ENCFF282QFS) Regulation 
encTfChipPkENCFF318QLK HEK293T ZNF384 Transcription Factor ChIP-seq Peaks of ZNF384 in HEK293T from ENCODE 3 (ENCFF318QLK) Regulation 
encTfChipPkENCFF514OOQ HEK293T ZFX Transcription Factor ChIP-seq Peaks of ZFX in HEK293T from ENCODE 3 (ENCFF514OOQ) Regulation 
encTfChipPkENCFF813VLK HEK293T SUZ12 Transcription Factor ChIP-seq Peaks of SUZ12 in HEK293T from ENCODE 3 (ENCFF813VLK) Regulation 
encTfChipPkENCFF240PYU HEK293T SP1 Transcription Factor ChIP-seq Peaks of SP1 in HEK293T from ENCODE 3 (ENCFF240PYU) Regulation 
encTfChipPkENCFF331WKY HEK293T PKNOX1 Transcription Factor ChIP-seq Peaks of PKNOX1 in HEK293T from ENCODE 3 (ENCFF331WKY) Regulation 
encTfChipPkENCFF223YXP HEK293T NFRKB Transcription Factor ChIP-seq Peaks of NFRKB in HEK293T from ENCODE 3 (ENCFF223YXP) Regulation 
encTfChipPkENCFF333UCS HEK293T LEF1 Transcription Factor ChIP-seq Peaks of LEF1 in HEK293T from ENCODE 3 (ENCFF333UCS) Regulation 
encTfChipPkENCFF520CSO HEK293T L3MBTL2 Transcription Factor ChIP-seq Peaks of L3MBTL2 in HEK293T from ENCODE 3 (ENCFF520CSO) Regulation 
encTfChipPkENCFF932EVL HEK293T FOXM1 Transcription Factor ChIP-seq Peaks of FOXM1 in HEK293T from ENCODE 3 (ENCFF932EVL) Regulation 
encTfChipPkENCFF203REX HEK293T FOXK2 Transcription Factor ChIP-seq Peaks of FOXK2 in HEK293T from ENCODE 3 (ENCFF203REX) Regulation 
encTfChipPkENCFF146XEP HEK293T FOXA1 Transcription Factor ChIP-seq Peaks of FOXA1 in HEK293T from ENCODE 3 (ENCFF146XEP) Regulation 
encTfChipPkENCFF545SXB HEK293T ELF4 Transcription Factor ChIP-seq Peaks of ELF4 in HEK293T from ENCODE 3 (ENCFF545SXB) Regulation 
encTfChipPkENCFF523NXP HEK293T CTBP1 Transcription Factor ChIP-seq Peaks of CTBP1 in HEK293T from ENCODE 3 (ENCFF523NXP) Regulation 
encTfChipPkENCFF785FBD HEK293T BHLHE40 Transcription Factor ChIP-seq Peaks of BHLHE40 in HEK293T from ENCODE 3 (ENCFF785FBD) Regulation 
encTfChipPkENCFF550UEU HEK293T ARNT Transcription Factor ChIP-seq Peaks of ARNT in HEK293T from ENCODE 3 (ENCFF550UEU) Regulation 
encTfChipPkENCFF034GYQ HEK293 TRIM28 2 Transcription Factor ChIP-seq Peaks of TRIM28 in HEK293 from ENCODE 3 (ENCFF034GYQ) Regulation 
encTfChipPkENCFF721FYE HEK293 TRIM28 1 Transcription Factor ChIP-seq Peaks of TRIM28 in HEK293 from ENCODE 3 (ENCFF721FYE) Regulation 
encTfChipPkENCFF144BSH HCT116 ZFX Transcription Factor ChIP-seq Peaks of ZFX in HCT116 from ENCODE 3 (ENCFF144BSH) Regulation 
encTfChipPkENCFF088WYS HCT116 JUND Transcription Factor ChIP-seq Peaks of JUND in HCT116 from ENCODE 3 (ENCFF088WYS) Regulation 
encTfChipPkENCFF769NCM HCT116 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in HCT116 from ENCODE 3 (ENCFF769NCM) Regulation 
encTfChipPkENCFF418WAW HCT116 CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in HCT116 from ENCODE 3 (ENCFF418WAW) Regulation 
encTfChipPkENCFF364QXM HCT116 CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in HCT116 from ENCODE 3 (ENCFF364QXM) Regulation 
encTfChipPkENCFF917ZPO HCT116 CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in HCT116 from ENCODE 3 (ENCFF917ZPO) Regulation 
encTfChipPkENCFF909JAZ H54 CTCF Transcription Factor ChIP-seq Peaks of CTCF in H54 from ENCODE 3 (ENCFF909JAZ) Regulation 
encTfChipPkENCFF964BYN H1-hESC ZNF143 Transcription Factor ChIP-seq Peaks of ZNF143 in H1-hESC from ENCODE 3 (ENCFF964BYN) Regulation 
encTfChipPkENCFF686VJY H1-hESC YY1 Transcription Factor ChIP-seq Peaks of YY1 in H1-hESC from ENCODE 3 (ENCFF686VJY) Regulation 
encTfChipPkENCFF749OBU H1-hESC USF2 Transcription Factor ChIP-seq Peaks of USF2 in H1-hESC from ENCODE 3 (ENCFF749OBU) Regulation 
encTfChipPkENCFF358BEF H1-hESC USF1 Transcription Factor ChIP-seq Peaks of USF1 in H1-hESC from ENCODE 3 (ENCFF358BEF) Regulation 
encTfChipPkENCFF274AQE H1-hESC TCF12 Transcription Factor ChIP-seq Peaks of TCF12 in H1-hESC from ENCODE 3 (ENCFF274AQE) Regulation 
encTfChipPkENCFF629MBV H1-hESC TBP Transcription Factor ChIP-seq Peaks of TBP in H1-hESC from ENCODE 3 (ENCFF629MBV) Regulation 
encTfChipPkENCFF963TZI H1-hESC TAF7 Transcription Factor ChIP-seq Peaks of TAF7 in H1-hESC from ENCODE 3 (ENCFF963TZI) Regulation 
encTfChipPkENCFF202SNU H1-hESC TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in H1-hESC from ENCODE 3 (ENCFF202SNU) Regulation 
encTfChipPkENCFF336HCY H1-hESC SUZ12 Transcription Factor ChIP-seq Peaks of SUZ12 in H1-hESC from ENCODE 3 (ENCFF336HCY) Regulation 
encTfChipPkENCFF725LDD H1-hESC SRF Transcription Factor ChIP-seq Peaks of SRF in H1-hESC from ENCODE 3 (ENCFF725LDD) Regulation 
encTfChipPkENCFF317TBZ H1-hESC SP1 Transcription Factor ChIP-seq Peaks of SP1 in H1-hESC from ENCODE 3 (ENCFF317TBZ) Regulation 
encTfChipPkENCFF318SDF H1-hESC SIX5 Transcription Factor ChIP-seq Peaks of SIX5 in H1-hESC from ENCODE 3 (ENCFF318SDF) Regulation 
encTfChipPkENCFF719RAM H1-hESC SIRT6 Transcription Factor ChIP-seq Peaks of SIRT6 in H1-hESC from ENCODE 3 (ENCFF719RAM) Regulation 
encTfChipPkENCFF184HWT H1-hESC SIN3A 2 Transcription Factor ChIP-seq Peaks of SIN3A in H1-hESC from ENCODE 3 (ENCFF184HWT) Regulation 
encTfChipPkENCFF820OMK H1-hESC SIN3A 1 Transcription Factor ChIP-seq Peaks of SIN3A in H1-hESC from ENCODE 3 (ENCFF820OMK) Regulation 
encTfChipPkENCFF361QZZ H1-hESC SAP30 Transcription Factor ChIP-seq Peaks of SAP30 in H1-hESC from ENCODE 3 (ENCFF361QZZ) Regulation 
encTfChipPkENCFF369JAI H1-hESC RXRA Transcription Factor ChIP-seq Peaks of RXRA in H1-hESC from ENCODE 3 (ENCFF369JAI) Regulation 
encTfChipPkENCFF193YAN H1-hESC RNF2 Transcription Factor ChIP-seq Peaks of RNF2 in H1-hESC from ENCODE 3 (ENCFF193YAN) Regulation 
encTfChipPkENCFF447QXT H1-hESC RFX5 Transcription Factor ChIP-seq Peaks of RFX5 in H1-hESC from ENCODE 3 (ENCFF447QXT) Regulation 
encTfChipPkENCFF885KLR H1-hESC REST 2 Transcription Factor ChIP-seq Peaks of REST in H1-hESC from ENCODE 3 (ENCFF885KLR) Regulation 
encTfChipPkENCFF453HPD H1-hESC REST 1 Transcription Factor ChIP-seq Peaks of REST in H1-hESC from ENCODE 3 (ENCFF453HPD) Regulation 
encTfChipPkENCFF135DOZ H1-hESC RBBP5 Transcription Factor ChIP-seq Peaks of RBBP5 in H1-hESC from ENCODE 3 (ENCFF135DOZ) Regulation 
encTfChipPkENCFF824FIL H1-hESC RAD21 2 Transcription Factor ChIP-seq Peaks of RAD21 in H1-hESC from ENCODE 3 (ENCFF824FIL) Regulation 
encTfChipPkENCFF732XGR H1-hESC RAD21 1 Transcription Factor ChIP-seq Peaks of RAD21 in H1-hESC from ENCODE 3 (ENCFF732XGR) Regulation 
encTfChipPkENCFF468LYO H1-hESC POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in H1-hESC from ENCODE 3 (ENCFF468LYO) Regulation 
encTfChipPkENCFF687NII H1-hESC PHF8 Transcription Factor ChIP-seq Peaks of PHF8 in H1-hESC from ENCODE 3 (ENCFF687NII) Regulation 
encTfChipPkENCFF508IBP H1-hESC NRF1 Transcription Factor ChIP-seq Peaks of NRF1 in H1-hESC from ENCODE 3 (ENCFF508IBP) Regulation 
encTfChipPkENCFF379EPK H1-hESC NANOG Transcription Factor ChIP-seq Peaks of NANOG in H1-hESC from ENCODE 3 (ENCFF379EPK) Regulation 
encTfChipPkENCFF569IGP H1-hESC MYC Transcription Factor ChIP-seq Peaks of MYC in H1-hESC from ENCODE 3 (ENCFF569IGP) Regulation 
encTfChipPkENCFF646GCM H1-hESC MAFK Transcription Factor ChIP-seq Peaks of MAFK in H1-hESC from ENCODE 3 (ENCFF646GCM) Regulation 
encTfChipPkENCFF583YFS H1-hESC KDM5A Transcription Factor ChIP-seq Peaks of KDM5A in H1-hESC from ENCODE 3 (ENCFF583YFS) Regulation 
encTfChipPkENCFF838KYH H1-hESC KDM4A Transcription Factor ChIP-seq Peaks of KDM4A in H1-hESC from ENCODE 3 (ENCFF838KYH) Regulation 
encTfChipPkENCFF768BPC H1-hESC KDM1A Transcription Factor ChIP-seq Peaks of KDM1A in H1-hESC from ENCODE 3 (ENCFF768BPC) Regulation 
encTfChipPkENCFF073PCP H1-hESC JUND 2 Transcription Factor ChIP-seq Peaks of JUND in H1-hESC from ENCODE 3 (ENCFF073PCP) Regulation 
encTfChipPkENCFF760AQQ H1-hESC JUND 1 Transcription Factor ChIP-seq Peaks of JUND in H1-hESC from ENCODE 3 (ENCFF760AQQ) Regulation 
encTfChipPkENCFF402ELS H1-hESC JUN Transcription Factor ChIP-seq Peaks of JUN in H1-hESC from ENCODE 3 (ENCFF402ELS) Regulation 
encTfChipPkENCFF012LET H1-hESC HDAC6 Transcription Factor ChIP-seq Peaks of HDAC6 in H1-hESC from ENCODE 3 (ENCFF012LET) Regulation 
encTfChipPkENCFF902CVS H1-hESC HDAC2 2 Transcription Factor ChIP-seq Peaks of HDAC2 in H1-hESC from ENCODE 3 (ENCFF902CVS) Regulation 
encTfChipPkENCFF468CFJ H1-hESC HDAC2 1 Transcription Factor ChIP-seq Peaks of HDAC2 in H1-hESC from ENCODE 3 (ENCFF468CFJ) Regulation 
encTfChipPkENCFF894MNP H1-hESC GABPA Transcription Factor ChIP-seq Peaks of GABPA in H1-hESC from ENCODE 3 (ENCFF894MNP) Regulation 
encTfChipPkENCFF418RZE H1-hESC FOSL1 Transcription Factor ChIP-seq Peaks of FOSL1 in H1-hESC from ENCODE 3 (ENCFF418RZE) Regulation 
encTfChipPkENCFF843SYD H1-hESC EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in H1-hESC from ENCODE 3 (ENCFF843SYD) Regulation 
encTfChipPkENCFF456JEW H1-hESC EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in H1-hESC from ENCODE 3 (ENCFF456JEW) Regulation 
encTfChipPkENCFF220IXP H1-hESC EGR1 Transcription Factor ChIP-seq Peaks of EGR1 in H1-hESC from ENCODE 3 (ENCFF220IXP) Regulation 
encTfChipPkENCFF402JJK H1-hESC CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in H1-hESC from ENCODE 3 (ENCFF402JJK) Regulation 
encTfChipPkENCFF093VEE H1-hESC CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in H1-hESC from ENCODE 3 (ENCFF093VEE) Regulation 
encTfChipPkENCFF628RLE H1-hESC CHD7 Transcription Factor ChIP-seq Peaks of CHD7 in H1-hESC from ENCODE 3 (ENCFF628RLE) Regulation 
encTfChipPkENCFF607EOG H1-hESC CHD1 2 Transcription Factor ChIP-seq Peaks of CHD1 in H1-hESC from ENCODE 3 (ENCFF607EOG) Regulation 
encTfChipPkENCFF617RGJ H1-hESC CHD1 1 Transcription Factor ChIP-seq Peaks of CHD1 in H1-hESC from ENCODE 3 (ENCFF617RGJ) Regulation 
encTfChipPkENCFF485WCF H1-hESC CBX8 Transcription Factor ChIP-seq Peaks of CBX8 in H1-hESC from ENCODE 3 (ENCFF485WCF) Regulation 
encTfChipPkENCFF936JMD H1-hESC CBX5 Transcription Factor ChIP-seq Peaks of CBX5 in H1-hESC from ENCODE 3 (ENCFF936JMD) Regulation 
encTfChipPkENCFF658OOS H1-hESC BRCA1 Transcription Factor ChIP-seq Peaks of BRCA1 in H1-hESC from ENCODE 3 (ENCFF658OOS) Regulation 
encTfChipPkENCFF697OBV H1-hESC BCL11A 2 Transcription Factor ChIP-seq Peaks of BCL11A in H1-hESC from ENCODE 3 (ENCFF697OBV) Regulation 
encTfChipPkENCFF175OER H1-hESC BCL11A 1 Transcription Factor ChIP-seq Peaks of BCL11A in H1-hESC from ENCODE 3 (ENCFF175OER) Regulation 
encTfChipPkENCFF977MDK H1-hESC BACH1 Transcription Factor ChIP-seq Peaks of BACH1 in H1-hESC from ENCODE 3 (ENCFF977MDK) Regulation 
encTfChipPkENCFF305HBV H1-hESC ATF3 Transcription Factor ChIP-seq Peaks of ATF3 in H1-hESC from ENCODE 3 (ENCFF305HBV) Regulation 
encTfChipPkENCFF254HZM H1-hESC ASH2L Transcription Factor ChIP-seq Peaks of ASH2L in H1-hESC from ENCODE 3 (ENCFF254HZM) Regulation 
encTfChipPkENCFF238TOS GM23338 REST Transcription Factor ChIP-seq Peaks of REST in GM23338 from ENCODE 3 (ENCFF238TOS) Regulation 
encTfChipPkENCFF735WFO GM23338 NANOG Transcription Factor ChIP-seq Peaks of NANOG in GM23338 from ENCODE 3 (ENCFF735WFO) Regulation 
encTfChipPkENCFF891UNY GM23338 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in GM23338 from ENCODE 3 (ENCFF891UNY) Regulation 
encTfChipPkENCFF276KYQ GM23338 ETS1 Transcription Factor ChIP-seq Peaks of ETS1 in GM23338 from ENCODE 3 (ENCFF276KYQ) Regulation 
encTfChipPkENCFF765BRD GM23338 CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in GM23338 from ENCODE 3 (ENCFF765BRD) Regulation 
encTfChipPkENCFF760HUV GM23338 CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in GM23338 from ENCODE 3 (ENCFF760HUV) Regulation 
encTfChipPkENCFF221ZIG GM23248 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in GM23248 from ENCODE 3 (ENCFF221ZIG) Regulation 
encTfChipPkENCFF244DQW GM20000 CTCF Transcription Factor ChIP-seq Peaks of CTCF in GM20000 from ENCODE 3 (ENCFF244DQW) Regulation 
encTfChipPkENCFF445ATY GM13977 CTCF Transcription Factor ChIP-seq Peaks of CTCF in GM13977 from ENCODE 3 (ENCFF445ATY) Regulation 
encTfChipPkENCFF667URP GM12892 YY1 Transcription Factor ChIP-seq Peaks of YY1 in GM12892 from ENCODE 3 (ENCFF667URP) Regulation 
encTfChipPkENCFF713IVN GM12892 TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in GM12892 from ENCODE 3 (ENCFF713IVN) Regulation 
encTfChipPkENCFF459QKR GM12892 POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in GM12892 from ENCODE 3 (ENCFF459QKR) Regulation 
encTfChipPkENCFF081JNO GM12891 YY1 Transcription Factor ChIP-seq Peaks of YY1 in GM12891 from ENCODE 3 (ENCFF081JNO) Regulation 
encTfChipPkENCFF195IKR GM12891 TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in GM12891 from ENCODE 3 (ENCFF195IKR) Regulation 
encTfChipPkENCFF526NYA GM12891 SPI1 Transcription Factor ChIP-seq Peaks of SPI1 in GM12891 from ENCODE 3 (ENCFF526NYA) Regulation 
encTfChipPkENCFF809HPK GM12891 POU2F2 Transcription Factor ChIP-seq Peaks of POU2F2 in GM12891 from ENCODE 3 (ENCFF809HPK) Regulation 
encTfChipPkENCFF063IRW GM12891 POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in GM12891 from ENCODE 3 (ENCFF063IRW) Regulation 
encTfChipPkENCFF067QUU GM12891 PAX5 Transcription Factor ChIP-seq Peaks of PAX5 in GM12891 from ENCODE 3 (ENCFF067QUU) Regulation 
encTfChipPkENCFF310XJC GM12878 ZZZ3 Transcription Factor ChIP-seq Peaks of ZZZ3 in GM12878 from ENCODE 3 (ENCFF310XJC) Regulation 
encTfChipPkENCFF455HXN GM12878 ZSCAN29 Transcription Factor ChIP-seq Peaks of ZSCAN29 in GM12878 from ENCODE 3 (ENCFF455HXN) Regulation 
encTfChipPkENCFF643OWO GM12878 ZNF687 Transcription Factor ChIP-seq Peaks of ZNF687 in GM12878 from ENCODE 3 (ENCFF643OWO) Regulation 
encTfChipPkENCFF566YUW GM12878 ZNF592 Transcription Factor ChIP-seq Peaks of ZNF592 in GM12878 from ENCODE 3 (ENCFF566YUW) Regulation 
encTfChipPkENCFF371OGO GM12878 ZNF384 Transcription Factor ChIP-seq Peaks of ZNF384 in GM12878 from ENCODE 3 (ENCFF371OGO) Regulation 
encTfChipPkENCFF103OOV GM12878 ZNF24 Transcription Factor ChIP-seq Peaks of ZNF24 in GM12878 from ENCODE 3 (ENCFF103OOV) Regulation 
encTfChipPkENCFF513RIQ GM12878 ZNF217 Transcription Factor ChIP-seq Peaks of ZNF217 in GM12878 from ENCODE 3 (ENCFF513RIQ) Regulation 
encTfChipPkENCFF273BVT GM12878 ZNF207 Transcription Factor ChIP-seq Peaks of ZNF207 in GM12878 from ENCODE 3 (ENCFF273BVT) Regulation 
encTfChipPkENCFF141SAU GM12878 ZNF143 2 Transcription Factor ChIP-seq Peaks of ZNF143 in GM12878 from ENCODE 3 (ENCFF141SAU) Regulation 
encTfChipPkENCFF544NXC GM12878 ZNF143 1 Transcription Factor ChIP-seq Peaks of ZNF143 in GM12878 from ENCODE 3 (ENCFF544NXC) Regulation 
encTfChipPkENCFF357WYN GM12878 ZBTB40 Transcription Factor ChIP-seq Peaks of ZBTB40 in GM12878 from ENCODE 3 (ENCFF357WYN) Regulation 
encTfChipPkENCFF539CKD GM12878 ZBTB33 2 Transcription Factor ChIP-seq Peaks of ZBTB33 in GM12878 from ENCODE 3 (ENCFF539CKD) Regulation 
encTfChipPkENCFF394CWJ GM12878 ZBTB33 1 Transcription Factor ChIP-seq Peaks of ZBTB33 in GM12878 from ENCODE 3 (ENCFF394CWJ) Regulation 
encTfChipPkENCFF123WEZ GM12878 ZBED1 Transcription Factor ChIP-seq Peaks of ZBED1 in GM12878 from ENCODE 3 (ENCFF123WEZ) Regulation 
encTfChipPkENCFF902HNO GM12878 YY1 2 Transcription Factor ChIP-seq Peaks of YY1 in GM12878 from ENCODE 3 (ENCFF902HNO) Regulation 
encTfChipPkENCFF967ACD GM12878 YY1 1 Transcription Factor ChIP-seq Peaks of YY1 in GM12878 from ENCODE 3 (ENCFF967ACD) Regulation 
encTfChipPkENCFF277VDY GM12878 WRNIP1 Transcription Factor ChIP-seq Peaks of WRNIP1 in GM12878 from ENCODE 3 (ENCFF277VDY) Regulation 
encTfChipPkENCFF372DRC GM12878 USF2 Transcription Factor ChIP-seq Peaks of USF2 in GM12878 from ENCODE 3 (ENCFF372DRC) Regulation 
encTfChipPkENCFF298UPI GM12878 UBTF Transcription Factor ChIP-seq Peaks of UBTF in GM12878 from ENCODE 3 (ENCFF298UPI) Regulation 
encTfChipPkENCFF899JBI GM12878 TRIM22 2 Transcription Factor ChIP-seq Peaks of TRIM22 in GM12878 from ENCODE 3 (ENCFF899JBI) Regulation 
encTfChipPkENCFF241GZK GM12878 TRIM22 1 Transcription Factor ChIP-seq Peaks of TRIM22 in GM12878 from ENCODE 3 (ENCFF241GZK) Regulation 
encTfChipPkENCFF305ICK GM12878 TCF7 Transcription Factor ChIP-seq Peaks of TCF7 in GM12878 from ENCODE 3 (ENCFF305ICK) Regulation 
encTfChipPkENCFF017LZE GM12878 TCF12 2 Transcription Factor ChIP-seq Peaks of TCF12 in GM12878 from ENCODE 3 (ENCFF017LZE) Regulation 
encTfChipPkENCFF160WLU GM12878 TCF12 1 Transcription Factor ChIP-seq Peaks of TCF12 in GM12878 from ENCODE 3 (ENCFF160WLU) Regulation 
encTfChipPkENCFF405NFV GM12878 TBX21 Transcription Factor ChIP-seq Peaks of TBX21 in GM12878 from ENCODE 3 (ENCFF405NFV) Regulation 
encTfChipPkENCFF490VYC GM12878 TBP Transcription Factor ChIP-seq Peaks of TBP in GM12878 from ENCODE 3 (ENCFF490VYC) Regulation 
encTfChipPkENCFF957YRU GM12878 TBL1XR1 Transcription Factor ChIP-seq Peaks of TBL1XR1 in GM12878 from ENCODE 3 (ENCFF957YRU) Regulation 
encTfChipPkENCFF544NRC GM12878 TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in GM12878 from ENCODE 3 (ENCFF544NRC) Regulation 
encTfChipPkENCFF746JPU GM12878 SUZ12 Transcription Factor ChIP-seq Peaks of SUZ12 in GM12878 from ENCODE 3 (ENCFF746JPU) Regulation 
encTfChipPkENCFF492YMU GM12878 STAT5A Transcription Factor ChIP-seq Peaks of STAT5A in GM12878 from ENCODE 3 (ENCFF492YMU) Regulation 
encTfChipPkENCFF014RBU GM12878 STAT3 Transcription Factor ChIP-seq Peaks of STAT3 in GM12878 from ENCODE 3 (ENCFF014RBU) Regulation 
encTfChipPkENCFF817QHW GM12878 STAT1 Transcription Factor ChIP-seq Peaks of STAT1 in GM12878 from ENCODE 3 (ENCFF817QHW) Regulation 
encTfChipPkENCFF199WGD GM12878 SRF 3 Transcription Factor ChIP-seq Peaks of SRF in GM12878 from ENCODE 3 (ENCFF199WGD) Regulation 
encTfChipPkENCFF030NYG GM12878 SRF 2 Transcription Factor ChIP-seq Peaks of SRF in GM12878 from ENCODE 3 (ENCFF030NYG) Regulation 
encTfChipPkENCFF909FRA GM12878 SRF 1 Transcription Factor ChIP-seq Peaks of SRF in GM12878 from ENCODE 3 (ENCFF909FRA) Regulation 
encTfChipPkENCFF686FLD GM12878 SMC3 Transcription Factor ChIP-seq Peaks of SMC3 in GM12878 from ENCODE 3 (ENCFF686FLD) Regulation 
encTfChipPkENCFF478DRD GM12878 SMARCA5 Transcription Factor ChIP-seq Peaks of SMARCA5 in GM12878 from ENCODE 3 (ENCFF478DRD) Regulation 
encTfChipPkENCFF134XDY GM12878 SMAD5 Transcription Factor ChIP-seq Peaks of SMAD5 in GM12878 from ENCODE 3 (ENCFF134XDY) Regulation 
encTfChipPkENCFF632MBO GM12878 SMAD1 Transcription Factor ChIP-seq Peaks of SMAD1 in GM12878 from ENCODE 3 (ENCFF632MBO) Regulation 
encTfChipPkENCFF142EVF GM12878 SKIL Transcription Factor ChIP-seq Peaks of SKIL in GM12878 from ENCODE 3 (ENCFF142EVF) Regulation 
encTfChipPkENCFF606WUV GM12878 SIX5 Transcription Factor ChIP-seq Peaks of SIX5 in GM12878 from ENCODE 3 (ENCFF606WUV) Regulation 
encTfChipPkENCFF778DJD GM12878 SIN3A Transcription Factor ChIP-seq Peaks of SIN3A in GM12878 from ENCODE 3 (ENCFF778DJD) Regulation 
encTfChipPkENCFF461FGJ GM12878 RXRA Transcription Factor ChIP-seq Peaks of RXRA in GM12878 from ENCODE 3 (ENCFF461FGJ) Regulation 
encTfChipPkENCFF248QFF GM12878 RUNX3 Transcription Factor ChIP-seq Peaks of RUNX3 in GM12878 from ENCODE 3 (ENCFF248QFF) Regulation 
encTfChipPkENCFF402FYF GM12878 RFX5 Transcription Factor ChIP-seq Peaks of RFX5 in GM12878 from ENCODE 3 (ENCFF402FYF) Regulation 
encTfChipPkENCFF048JKT GM12878 REST 2 Transcription Factor ChIP-seq Peaks of REST in GM12878 from ENCODE 3 (ENCFF048JKT) Regulation 
encTfChipPkENCFF677KJB GM12878 REST 1 Transcription Factor ChIP-seq Peaks of REST in GM12878 from ENCODE 3 (ENCFF677KJB) Regulation 
encTfChipPkENCFF456FQB GM12878 RELB Transcription Factor ChIP-seq Peaks of RELB in GM12878 from ENCODE 3 (ENCFF456FQB) Regulation 
encTfChipPkENCFF898MUV GM12878 RCOR1 Transcription Factor ChIP-seq Peaks of RCOR1 in GM12878 from ENCODE 3 (ENCFF898MUV) Regulation 
encTfChipPkENCFF814CZI GM12878 RBBP5 Transcription Factor ChIP-seq Peaks of RBBP5 in GM12878 from ENCODE 3 (ENCFF814CZI) Regulation 
encTfChipPkENCFF601XVA GM12878 RB1 Transcription Factor ChIP-seq Peaks of RB1 in GM12878 from ENCODE 3 (ENCFF601XVA) Regulation 
encTfChipPkENCFF445UJF GM12878 RAD51 Transcription Factor ChIP-seq Peaks of RAD51 in GM12878 from ENCODE 3 (ENCFF445UJF) Regulation 
encTfChipPkENCFF753RGL GM12878 RAD21 Transcription Factor ChIP-seq Peaks of RAD21 in GM12878 from ENCODE 3 (ENCFF753RGL) Regulation 
encTfChipPkENCFF120VUT GM12878 POLR2A Transcription Factor ChIP-seq Peaks of POLR2A in GM12878 from ENCODE 3 (ENCFF120VUT) Regulation 
encTfChipPkENCFF020GMZ GM12878 PKNOX1 Transcription Factor ChIP-seq Peaks of PKNOX1 in GM12878 from ENCODE 3 (ENCFF020GMZ) Regulation 
encTfChipPkENCFF717IXP GM12878 PBX3 Transcription Factor ChIP-seq Peaks of PBX3 in GM12878 from ENCODE 3 (ENCFF717IXP) Regulation 
encTfChipPkENCFF455YHJ GM12878 PAX8 Transcription Factor ChIP-seq Peaks of PAX8 in GM12878 from ENCODE 3 (ENCFF455YHJ) Regulation 
encTfChipPkENCFF339KUO GM12878 PAX5 2 Transcription Factor ChIP-seq Peaks of PAX5 in GM12878 from ENCODE 3 (ENCFF339KUO) Regulation 
encTfChipPkENCFF199FYD GM12878 PAX5 1 Transcription Factor ChIP-seq Peaks of PAX5 in GM12878 from ENCODE 3 (ENCFF199FYD) Regulation 
encTfChipPkENCFF931XAL GM12878 NRF1 Transcription Factor ChIP-seq Peaks of NRF1 in GM12878 from ENCODE 3 (ENCFF931XAL) Regulation 
encTfChipPkENCFF810CEL GM12878 NR2F1 Transcription Factor ChIP-seq Peaks of NR2F1 in GM12878 from ENCODE 3 (ENCFF810CEL) Regulation 
encTfChipPkENCFF721FTG GM12878 NR2C2 Transcription Factor ChIP-seq Peaks of NR2C2 in GM12878 from ENCODE 3 (ENCFF721FTG) Regulation 
encTfChipPkENCFF381SBC GM12878 NR2C1 Transcription Factor ChIP-seq Peaks of NR2C1 in GM12878 from ENCODE 3 (ENCFF381SBC) Regulation 
encTfChipPkENCFF467NRS GM12878 NFYB Transcription Factor ChIP-seq Peaks of NFYB in GM12878 from ENCODE 3 (ENCFF467NRS) Regulation 
encTfChipPkENCFF414JLN GM12878 NFYA Transcription Factor ChIP-seq Peaks of NFYA in GM12878 from ENCODE 3 (ENCFF414JLN) Regulation 
encTfChipPkENCFF166FRO GM12878 NFXL1 Transcription Factor ChIP-seq Peaks of NFXL1 in GM12878 from ENCODE 3 (ENCFF166FRO) Regulation 
encTfChipPkENCFF628QJU GM12878 NFIC Transcription Factor ChIP-seq Peaks of NFIC in GM12878 from ENCODE 3 (ENCFF628QJU) Regulation 
encTfChipPkENCFF766ERZ GM12878 NFE2 Transcription Factor ChIP-seq Peaks of NFE2 in GM12878 from ENCODE 3 (ENCFF766ERZ) Regulation 
encTfChipPkENCFF704ZYN GM12878 NFATC3 Transcription Factor ChIP-seq Peaks of NFATC3 in GM12878 from ENCODE 3 (ENCFF704ZYN) Regulation 
encTfChipPkENCFF409QJU GM12878 NFATC1 Transcription Factor ChIP-seq Peaks of NFATC1 in GM12878 from ENCODE 3 (ENCFF409QJU) Regulation 
encTfChipPkENCFF055NJR GM12878 NBN Transcription Factor ChIP-seq Peaks of NBN in GM12878 from ENCODE 3 (ENCFF055NJR) Regulation 
encTfChipPkENCFF215YWS GM12878 MYB Transcription Factor ChIP-seq Peaks of MYB in GM12878 from ENCODE 3 (ENCFF215YWS) Regulation 
encTfChipPkENCFF079ZWK GM12878 MXI1 Transcription Factor ChIP-seq Peaks of MXI1 in GM12878 from ENCODE 3 (ENCFF079ZWK) Regulation 
encTfChipPkENCFF413VUC GM12878 MTA3 Transcription Factor ChIP-seq Peaks of MTA3 in GM12878 from ENCODE 3 (ENCFF413VUC) Regulation 
encTfChipPkENCFF966RPL GM12878 MTA2 Transcription Factor ChIP-seq Peaks of MTA2 in GM12878 from ENCODE 3 (ENCFF966RPL) Regulation 
encTfChipPkENCFF881VZH GM12878 MLLT1 Transcription Factor ChIP-seq Peaks of MLLT1 in GM12878 from ENCODE 3 (ENCFF881VZH) Regulation 
encTfChipPkENCFF261ZWR GM12878 MEF2C Transcription Factor ChIP-seq Peaks of MEF2C in GM12878 from ENCODE 3 (ENCFF261ZWR) Regulation 
encTfChipPkENCFF911BYP GM12878 MEF2B Transcription Factor ChIP-seq Peaks of MEF2B in GM12878 from ENCODE 3 (ENCFF911BYP) Regulation 
encTfChipPkENCFF328QLX GM12878 MEF2A Transcription Factor ChIP-seq Peaks of MEF2A in GM12878 from ENCODE 3 (ENCFF328QLX) Regulation 
encTfChipPkENCFF083KVY GM12878 MAX Transcription Factor ChIP-seq Peaks of MAX in GM12878 from ENCODE 3 (ENCFF083KVY) Regulation 
encTfChipPkENCFF689AXJ GM12878 MAFK Transcription Factor ChIP-seq Peaks of MAFK in GM12878 from ENCODE 3 (ENCFF689AXJ) Regulation 
encTfChipPkENCFF827ZLB GM12878 KLF5 Transcription Factor ChIP-seq Peaks of KLF5 in GM12878 from ENCODE 3 (ENCFF827ZLB) Regulation 
encTfChipPkENCFF996RRT GM12878 KDM1A Transcription Factor ChIP-seq Peaks of KDM1A in GM12878 from ENCODE 3 (ENCFF996RRT) Regulation 
encTfChipPkENCFF556PIY GM12878 JUND Transcription Factor ChIP-seq Peaks of JUND in GM12878 from ENCODE 3 (ENCFF556PIY) Regulation 
encTfChipPkENCFF939TZS GM12878 JUNB Transcription Factor ChIP-seq Peaks of JUNB in GM12878 from ENCODE 3 (ENCFF939TZS) Regulation 
encTfChipPkENCFF100ERQ GM12878 IRF5 Transcription Factor ChIP-seq Peaks of IRF5 in GM12878 from ENCODE 3 (ENCFF100ERQ) Regulation 
encTfChipPkENCFF391DVL GM12878 IRF4 Transcription Factor ChIP-seq Peaks of IRF4 in GM12878 from ENCODE 3 (ENCFF391DVL) Regulation 
encTfChipPkENCFF303TVZ GM12878 IRF3 2 Transcription Factor ChIP-seq Peaks of IRF3 in GM12878 from ENCODE 3 (ENCFF303TVZ) Regulation 
encTfChipPkENCFF341HWZ GM12878 IRF3 1 Transcription Factor ChIP-seq Peaks of IRF3 in GM12878 from ENCODE 3 (ENCFF341HWZ) Regulation 
encTfChipPkENCFF653MIQ GM12878 IKZF2 2 Transcription Factor ChIP-seq Peaks of IKZF2 in GM12878 from ENCODE 3 (ENCFF653MIQ) Regulation 
encTfChipPkENCFF339FFC GM12878 IKZF2 1 Transcription Factor ChIP-seq Peaks of IKZF2 in GM12878 from ENCODE 3 (ENCFF339FFC) Regulation 
encTfChipPkENCFF229YSW GM12878 IKZF1 3 Transcription Factor ChIP-seq Peaks of IKZF1 in GM12878 from ENCODE 3 (ENCFF229YSW) Regulation 
encTfChipPkENCFF809OOE GM12878 IKZF1 2 Transcription Factor ChIP-seq Peaks of IKZF1 in GM12878 from ENCODE 3 (ENCFF809OOE) Regulation 
encTfChipPkENCFF073XZC GM12878 IKZF1 1 Transcription Factor ChIP-seq Peaks of IKZF1 in GM12878 from ENCODE 3 (ENCFF073XZC) Regulation 
encTfChipPkENCFF308ZGG GM12878 HSF1 Transcription Factor ChIP-seq Peaks of HSF1 in GM12878 from ENCODE 3 (ENCFF308ZGG) Regulation 
encTfChipPkENCFF109YBE GM12878 HDAC6 Transcription Factor ChIP-seq Peaks of HDAC6 in GM12878 from ENCODE 3 (ENCFF109YBE) Regulation 
encTfChipPkENCFF107UHX GM12878 HDAC2 Transcription Factor ChIP-seq Peaks of HDAC2 in GM12878 from ENCODE 3 (ENCFF107UHX) Regulation 
encTfChipPkENCFF208TRU GM12878 HCFC1 on Transcription Factor ChIP-seq Peaks of HCFC1 in GM12878 from ENCODE 3 (ENCFF208TRU) Regulation 
encTfChipPkENCFF456YII GM12878 GATAD2B Transcription Factor ChIP-seq Peaks of GATAD2B in GM12878 from ENCODE 3 (ENCFF456YII) Regulation 
encTfChipPkENCFF116EXQ GM12878 GABPA Transcription Factor ChIP-seq Peaks of GABPA in GM12878 from ENCODE 3 (ENCFF116EXQ) Regulation 
encTfChipPkENCFF980KSV GM12878 FOXK2 Transcription Factor ChIP-seq Peaks of FOXK2 in GM12878 from ENCODE 3 (ENCFF980KSV) Regulation 
encTfChipPkENCFF678JII GM12878 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in GM12878 from ENCODE 3 (ENCFF678JII) Regulation 
encTfChipPkENCFF760IFZ GM12878 ETV6 2 Transcription Factor ChIP-seq Peaks of ETV6 in GM12878 from ENCODE 3 (ENCFF760IFZ) Regulation 
encTfChipPkENCFF516AJC GM12878 ETV6 1 Transcription Factor ChIP-seq Peaks of ETV6 in GM12878 from ENCODE 3 (ENCFF516AJC) Regulation 
encTfChipPkENCFF332PGQ GM12878 ETS1 Transcription Factor ChIP-seq Peaks of ETS1 in GM12878 from ENCODE 3 (ENCFF332PGQ) Regulation 
encTfChipPkENCFF195PBG GM12878 ESRRA Transcription Factor ChIP-seq Peaks of ESRRA in GM12878 from ENCODE 3 (ENCFF195PBG) Regulation 
encTfChipPkENCFF302XID GM12878 EP300 3 Transcription Factor ChIP-seq Peaks of EP300 in GM12878 from ENCODE 3 (ENCFF302XID) Regulation 
encTfChipPkENCFF222XPQ GM12878 EP300 2 Transcription Factor ChIP-seq Peaks of EP300 in GM12878 from ENCODE 3 (ENCFF222XPQ) Regulation 
encTfChipPkENCFF462GHD GM12878 EP300 1 Transcription Factor ChIP-seq Peaks of EP300 in GM12878 from ENCODE 3 (ENCFF462GHD) Regulation 
encTfChipPkENCFF556JBS GM12878 ELK1 Transcription Factor ChIP-seq Peaks of ELK1 in GM12878 from ENCODE 3 (ENCFF556JBS) Regulation 
encTfChipPkENCFF807AKG GM12878 ELF1 Transcription Factor ChIP-seq Peaks of ELF1 in GM12878 from ENCODE 3 (ENCFF807AKG) Regulation 
encTfChipPkENCFF618EFD GM12878 EGR1 Transcription Factor ChIP-seq Peaks of EGR1 in GM12878 from ENCODE 3 (ENCFF618EFD) Regulation 
encTfChipPkENCFF242VUO GM12878 EED Transcription Factor ChIP-seq Peaks of EED in GM12878 from ENCODE 3 (ENCFF242VUO) Regulation 
encTfChipPkENCFF868VSY GM12878 EBF1 2 Transcription Factor ChIP-seq Peaks of EBF1 in GM12878 from ENCODE 3 (ENCFF868VSY) Regulation 
encTfChipPkENCFF394DLH GM12878 EBF1 1 Transcription Factor ChIP-seq Peaks of EBF1 in GM12878 from ENCODE 3 (ENCFF394DLH) Regulation 
encTfChipPkENCFF711OSR GM12878 E4F1 Transcription Factor ChIP-seq Peaks of E4F1 in GM12878 from ENCODE 3 (ENCFF711OSR) Regulation 
encTfChipPkENCFF063WXY GM12878 E2F8 Transcription Factor ChIP-seq Peaks of E2F8 in GM12878 from ENCODE 3 (ENCFF063WXY) Regulation 
encTfChipPkENCFF433PFN GM12878 E2F4 Transcription Factor ChIP-seq Peaks of E2F4 in GM12878 from ENCODE 3 (ENCFF433PFN) Regulation 
encTfChipPkENCFF349MPF GM12878 DPF2 Transcription Factor ChIP-seq Peaks of DPF2 in GM12878 from ENCODE 3 (ENCFF349MPF) Regulation 
encTfChipPkENCFF721SDD GM12878 CUX1 Transcription Factor ChIP-seq Peaks of CUX1 in GM12878 from ENCODE 3 (ENCFF721SDD) Regulation 
encTfChipPkENCFF710VEH GM12878 CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in GM12878 from ENCODE 3 (ENCFF710VEH) Regulation 
encTfChipPkENCFF833FTF GM12878 CTCF 1 on Transcription Factor ChIP-seq Peaks of CTCF in GM12878 from ENCODE 3 (ENCFF833FTF) Regulation 
encTfChipPkENCFF534CKB GM12878 CREM Transcription Factor ChIP-seq Peaks of CREM in GM12878 from ENCODE 3 (ENCFF534CKB) Regulation 
encTfChipPkENCFF499ZPP GM12878 CHD4 Transcription Factor ChIP-seq Peaks of CHD4 in GM12878 from ENCODE 3 (ENCFF499ZPP) Regulation 
encTfChipPkENCFF273ULT GM12878 CHD1 Transcription Factor ChIP-seq Peaks of CHD1 in GM12878 from ENCODE 3 (ENCFF273ULT) Regulation 
encTfChipPkENCFF761MGJ GM12878 CEBPB Transcription Factor ChIP-seq Peaks of CEBPB in GM12878 from ENCODE 3 (ENCFF761MGJ) Regulation 
encTfChipPkENCFF420YHY GM12878 CBX5 Transcription Factor ChIP-seq Peaks of CBX5 in GM12878 from ENCODE 3 (ENCFF420YHY) Regulation 
encTfChipPkENCFF141LEI GM12878 CBX3 Transcription Factor ChIP-seq Peaks of CBX3 in GM12878 from ENCODE 3 (ENCFF141LEI) Regulation 
encTfChipPkENCFF788LSH GM12878 CBFB Transcription Factor ChIP-seq Peaks of CBFB in GM12878 from ENCODE 3 (ENCFF788LSH) Regulation 
encTfChipPkENCFF082JDH GM12878 BRCA1 Transcription Factor ChIP-seq Peaks of BRCA1 in GM12878 from ENCODE 3 (ENCFF082JDH) Regulation 
encTfChipPkENCFF809PXE GM12878 BMI1 Transcription Factor ChIP-seq Peaks of BMI1 in GM12878 from ENCODE 3 (ENCFF809PXE) Regulation 
encTfChipPkENCFF095GMM GM12878 BHLHE40 2 Transcription Factor ChIP-seq Peaks of BHLHE40 in GM12878 from ENCODE 3 (ENCFF095GMM) Regulation 
encTfChipPkENCFF853SOB GM12878 BHLHE40 1 Transcription Factor ChIP-seq Peaks of BHLHE40 in GM12878 from ENCODE 3 (ENCFF853SOB) Regulation 
encTfChipPkENCFF625SHY GM12878 BCL3 Transcription Factor ChIP-seq Peaks of BCL3 in GM12878 from ENCODE 3 (ENCFF625SHY) Regulation 
encTfChipPkENCFF468MFY GM12878 BCL11A Transcription Factor ChIP-seq Peaks of BCL11A in GM12878 from ENCODE 3 (ENCFF468MFY) Regulation 
encTfChipPkENCFF593FBF GM12878 BATF Transcription Factor ChIP-seq Peaks of BATF in GM12878 from ENCODE 3 (ENCFF593FBF) Regulation 
encTfChipPkENCFF012JXJ GM12878 BACH1 Transcription Factor ChIP-seq Peaks of BACH1 in GM12878 from ENCODE 3 (ENCFF012JXJ) Regulation 
encTfChipPkENCFF726VEK GM12878 ATF7 Transcription Factor ChIP-seq Peaks of ATF7 in GM12878 from ENCODE 3 (ENCFF726VEK) Regulation 
encTfChipPkENCFF609KOY GM12878 ATF2 2 Transcription Factor ChIP-seq Peaks of ATF2 in GM12878 from ENCODE 3 (ENCFF609KOY) Regulation 
encTfChipPkENCFF127GYQ GM12878 ATF2 1 Transcription Factor ChIP-seq Peaks of ATF2 in GM12878 from ENCODE 3 (ENCFF127GYQ) Regulation 
encTfChipPkENCFF917CXD GM12878 ASH2L Transcription Factor ChIP-seq Peaks of ASH2L in GM12878 from ENCODE 3 (ENCFF917CXD) Regulation 
encTfChipPkENCFF166OZW GM12878 ARNT Transcription Factor ChIP-seq Peaks of ARNT in GM12878 from ENCODE 3 (ENCFF166OZW) Regulation 
encTfChipPkENCFF027VZK GM12878 ARID3A Transcription Factor ChIP-seq Peaks of ARID3A in GM12878 from ENCODE 3 (ENCFF027VZK) Regulation 
encTfChipPkENCFF733YSO GM12875 CTCF Transcription Factor ChIP-seq Peaks of CTCF in GM12875 from ENCODE 3 (ENCFF733YSO) Regulation 
encTfChipPkENCFF446MKT GM12874 CTCF Transcription Factor ChIP-seq Peaks of CTCF in GM12874 from ENCODE 3 (ENCFF446MKT) Regulation 
encTfChipPkENCFF295AWO GM12873 CTCF Transcription Factor ChIP-seq Peaks of CTCF in GM12873 from ENCODE 3 (ENCFF295AWO) Regulation 
encTfChipPkENCFF132AJR GM12865 CTCF Transcription Factor ChIP-seq Peaks of CTCF in GM12865 from ENCODE 3 (ENCFF132AJR) Regulation 
encTfChipPkENCFF671RVI GM12864 CTCF Transcription Factor ChIP-seq Peaks of CTCF in GM12864 from ENCODE 3 (ENCFF671RVI) Regulation 
encTfChipPkENCFF855HSK GM10266 CTCF Transcription Factor ChIP-seq Peaks of CTCF in GM10266 from ENCODE 3 (ENCFF855HSK) Regulation 
encTfChipPkENCFF757CRW GM08714 ZNF274 Transcription Factor ChIP-seq Peaks of ZNF274 in GM08714 from ENCODE 3 (ENCFF757CRW) Regulation 
encTfChipPkENCFF930QUM GM06990 CTCF Transcription Factor ChIP-seq Peaks of CTCF in GM06990 from ENCODE 3 (ENCFF930QUM) Regulation 
encTfChipPkENCFF421PBO DOHH2 CTCF Transcription Factor ChIP-seq Peaks of CTCF in DOHH2 from ENCODE 3 (ENCFF421PBO) Regulation 
encTfChipPkENCFF882YQH Caco-2 CTCF Transcription Factor ChIP-seq Peaks of CTCF in Caco-2 from ENCODE 3 (ENCFF882YQH) Regulation 
encTfChipPkENCFF437LHG CD14+monocyte CTCF Transcription Factor ChIP-seq Peaks of CTCF in CD14-positive_monocyte from ENCODE 3 (ENCFF437LHG) Regulation 
encTfChipPkENCFF842WEF C4-2B ZFX Transcription Factor ChIP-seq Peaks of ZFX in C4-2B from ENCODE 3 (ENCFF842WEF) Regulation 
encTfChipPkENCFF658MKE C4-2B CTCF Transcription Factor ChIP-seq Peaks of CTCF in C4-2B from ENCODE 3 (ENCFF658MKE) Regulation 
encTfChipPkENCFF449NOT B_cell CTCF Transcription Factor ChIP-seq Peaks of CTCF in B_cell from ENCODE 3 (ENCFF449NOT) Regulation 
encTfChipPkENCFF649IRT BJ CTCF Transcription Factor ChIP-seq Peaks of CTCF in BJ from ENCODE 3 (ENCFF649IRT) Regulation 
encTfChipPkENCFF965BBC BE2C CTCF Transcription Factor ChIP-seq Peaks of CTCF in BE2C from ENCODE 3 (ENCFF965BBC) Regulation 
encTfChipPkENCFF746CIL AG10803 CTCF Transcription Factor ChIP-seq Peaks of CTCF in AG10803 from ENCODE 3 (ENCFF746CIL) Regulation 
encTfChipPkENCFF245PXW AG09319 CTCF Transcription Factor ChIP-seq Peaks of CTCF in AG09319 from ENCODE 3 (ENCFF245PXW) Regulation 
encTfChipPkENCFF622DUX AG09309 CTCF Transcription Factor ChIP-seq Peaks of CTCF in AG09309 from ENCODE 3 (ENCFF622DUX) Regulation 
encTfChipPkENCFF681OWQ AG04450 CTCF Transcription Factor ChIP-seq Peaks of CTCF in AG04450 from ENCODE 3 (ENCFF681OWQ) Regulation 
encTfChipPkENCFF970AVM AG04449 CTCF Transcription Factor ChIP-seq Peaks of CTCF in AG04449 from ENCODE 3 (ENCFF970AVM) Regulation 
encTfChipPkENCFF085BBF A673 EZH2 Transcription Factor ChIP-seq Peaks of EZH2 in A673 from ENCODE 3 (ENCFF085BBF) Regulation 
encTfChipPkENCFF947IJX A673 CTCF Transcription Factor ChIP-seq Peaks of CTCF in A673 from ENCODE 3 (ENCFF947IJX) Regulation 
encTfChipPkENCFF639NGJ A549 ZBTB33 Transcription Factor ChIP-seq Peaks of ZBTB33 in A549 from ENCODE 3 (ENCFF639NGJ) Regulation 
encTfChipPkENCFF713ISJ A549 YY1 Transcription Factor ChIP-seq Peaks of YY1 in A549 from ENCODE 3 (ENCFF713ISJ) Regulation 
encTfChipPkENCFF754GUT A549 USF2 Transcription Factor ChIP-seq Peaks of USF2 in A549 from ENCODE 3 (ENCFF754GUT) Regulation 
encTfChipPkENCFF672FQU A549 TCF12 Transcription Factor ChIP-seq Peaks of TCF12 in A549 from ENCODE 3 (ENCFF672FQU) Regulation 
encTfChipPkENCFF747LKL A549 TAF1 Transcription Factor ChIP-seq Peaks of TAF1 in A549 from ENCODE 3 (ENCFF747LKL) Regulation 
encTfChipPkENCFF849UJR A549 SREBF2 Transcription Factor ChIP-seq Peaks of SREBF2 in A549 from ENCODE 3 (ENCFF849UJR) Regulation 
encTfChipPkENCFF315VQM A549 SREBF1 Transcription Factor ChIP-seq Peaks of SREBF1 in A549 from ENCODE 3 (ENCFF315VQM) Regulation 
encTfChipPkENCFF348RKC A549 SP1 Transcription Factor ChIP-seq Peaks of SP1 in A549 from ENCODE 3 (ENCFF348RKC) Regulation 
encTfChipPkENCFF125YHG A549 SMC3 Transcription Factor ChIP-seq Peaks of SMC3 in A549 from ENCODE 3 (ENCFF125YHG) Regulation 
encTfChipPkENCFF165AUR A549 SIX5 Transcription Factor ChIP-seq Peaks of SIX5 in A549 from ENCODE 3 (ENCFF165AUR) Regulation 
encTfChipPkENCFF522RIA A549 SIN3A 2 Transcription Factor ChIP-seq Peaks of SIN3A in A549 from ENCODE 3 (ENCFF522RIA) Regulation 
encTfChipPkENCFF172VGB A549 SIN3A 1 Transcription Factor ChIP-seq Peaks of SIN3A in A549 from ENCODE 3 (ENCFF172VGB) Regulation 
encTfChipPkENCFF626AQW A549 RNF2 Transcription Factor ChIP-seq Peaks of RNF2 in A549 from ENCODE 3 (ENCFF626AQW) Regulation 
encTfChipPkENCFF053TBK A549 RFX5 Transcription Factor ChIP-seq Peaks of RFX5 in A549 from ENCODE 3 (ENCFF053TBK) Regulation 
encTfChipPkENCFF188XRD A549 REST 2 Transcription Factor ChIP-seq Peaks of REST in A549 from ENCODE 3 (ENCFF188XRD) Regulation 
encTfChipPkENCFF136RBA A549 REST 1 Transcription Factor ChIP-seq Peaks of REST in A549 from ENCODE 3 (ENCFF136RBA) Regulation 
encTfChipPkENCFF319HLW A549 RCOR1 Transcription Factor ChIP-seq Peaks of RCOR1 in A549 from ENCODE 3 (ENCFF319HLW) Regulation 
encTfChipPkENCFF958VNQ A549 RAD21 Transcription Factor ChIP-seq Peaks of RAD21 in A549 from ENCODE 3 (ENCFF958VNQ) Regulation 
encTfChipPkENCFF292PSZ A549 POLR2A 2 Transcription Factor ChIP-seq Peaks of POLR2A in A549 from ENCODE 3 (ENCFF292PSZ) Regulation 
encTfChipPkENCFF532MZI A549 POLR2A 1 Transcription Factor ChIP-seq Peaks of POLR2A in A549 from ENCODE 3 (ENCFF532MZI) Regulation 
encTfChipPkENCFF890IRR A549 PHF8 Transcription Factor ChIP-seq Peaks of PHF8 in A549 from ENCODE 3 (ENCFF890IRR) Regulation 
encTfChipPkENCFF841IFL A549 NR3C1 6 Transcription Factor ChIP-seq Peaks of NR3C1 in A549 from ENCODE 3 (ENCFF841IFL) Regulation 
encTfChipPkENCFF495YRW A549 NR3C1 5 Transcription Factor ChIP-seq Peaks of NR3C1 in A549 from ENCODE 3 (ENCFF495YRW) Regulation 
encTfChipPkENCFF150STV A549 NR3C1 4 Transcription Factor ChIP-seq Peaks of NR3C1 in A549 from ENCODE 3 (ENCFF150STV) Regulation 
encTfChipPkENCFF648ZNE A549 NR3C1 3 Transcription Factor ChIP-seq Peaks of NR3C1 in A549 from ENCODE 3 (ENCFF648ZNE) Regulation 
encTfChipPkENCFF913WFD A549 NR3C1 2 Transcription Factor ChIP-seq Peaks of NR3C1 in A549 from ENCODE 3 (ENCFF913WFD) Regulation 
encTfChipPkENCFF080RMP A549 NR3C1 1 Transcription Factor ChIP-seq Peaks of NR3C1 in A549 from ENCODE 3 (ENCFF080RMP) Regulation 
encTfChipPkENCFF654YPN A549 NFE2L2 Transcription Factor ChIP-seq Peaks of NFE2L2 in A549 from ENCODE 3 (ENCFF654YPN) Regulation 
encTfChipPkENCFF502JKO A549 MYC Transcription Factor ChIP-seq Peaks of MYC in A549 from ENCODE 3 (ENCFF502JKO) Regulation 
encTfChipPkENCFF530ZTE A549 MAFK Transcription Factor ChIP-seq Peaks of MAFK in A549 from ENCODE 3 (ENCFF530ZTE) Regulation 
encTfChipPkENCFF397TFF A549 KDM5A Transcription Factor ChIP-seq Peaks of KDM5A in A549 from ENCODE 3 (ENCFF397TFF) Regulation 
encTfChipPkENCFF044XMF A549 KDM1A Transcription Factor ChIP-seq Peaks of KDM1A in A549 from ENCODE 3 (ENCFF044XMF) Regulation 
encTfChipPkENCFF499OUD A549 JUND Transcription Factor ChIP-seq Peaks of JUND in A549 from ENCODE 3 (ENCFF499OUD) Regulation 
encTfChipPkENCFF708LCH A549 JUN Transcription Factor ChIP-seq Peaks of JUN in A549 from ENCODE 3 (ENCFF708LCH) Regulation 
encTfChipPkENCFF415WEH A549 HDAC2 Transcription Factor ChIP-seq Peaks of HDAC2 in A549 from ENCODE 3 (ENCFF415WEH) Regulation 
encTfChipPkENCFF755AXA A549 FOXA1 2 Transcription Factor ChIP-seq Peaks of FOXA1 in A549 from ENCODE 3 (ENCFF755AXA) Regulation 
encTfChipPkENCFF441MEM A549 FOXA1 1 Transcription Factor ChIP-seq Peaks of FOXA1 in A549 from ENCODE 3 (ENCFF441MEM) Regulation 
encTfChipPkENCFF374ZCG A549 FOSL2 Transcription Factor ChIP-seq Peaks of FOSL2 in A549 from ENCODE 3 (ENCFF374ZCG) Regulation 
encTfChipPkENCFF297HAT A549 ETS1 Transcription Factor ChIP-seq Peaks of ETS1 in A549 from ENCODE 3 (ENCFF297HAT) Regulation 
encTfChipPkENCFF266ORV A549 ESRRA Transcription Factor ChIP-seq Peaks of ESRRA in A549 from ENCODE 3 (ENCFF266ORV) Regulation 
encTfChipPkENCFF282AEY A549 ELK1 Transcription Factor ChIP-seq Peaks of ELK1 in A549 from ENCODE 3 (ENCFF282AEY) Regulation 
encTfChipPkENCFF533NIV A549 ELF1 Transcription Factor ChIP-seq Peaks of ELF1 in A549 from ENCODE 3 (ENCFF533NIV) Regulation 
encTfChipPkENCFF071ZMT A549 EHMT2 Transcription Factor ChIP-seq Peaks of EHMT2 in A549 from ENCODE 3 (ENCFF071ZMT) Regulation 
encTfChipPkENCFF543VGD A549 CTCF 3 Transcription Factor ChIP-seq Peaks of CTCF in A549 from ENCODE 3 (ENCFF543VGD) Regulation 
encTfChipPkENCFF300IYQ A549 CTCF 2 Transcription Factor ChIP-seq Peaks of CTCF in A549 from ENCODE 3 (ENCFF300IYQ) Regulation 
encTfChipPkENCFF335GSE A549 CTCF 1 Transcription Factor ChIP-seq Peaks of CTCF in A549 from ENCODE 3 (ENCFF335GSE) Regulation 
encTfChipPkENCFF134CPX A549 CREB1 2 Transcription Factor ChIP-seq Peaks of CREB1 in A549 from ENCODE 3 (ENCFF134CPX) Regulation 
encTfChipPkENCFF716FAV A549 CREB1 1 Transcription Factor ChIP-seq Peaks of CREB1 in A549 from ENCODE 3 (ENCFF716FAV) Regulation 
encTfChipPkENCFF231RXA A549 CHD4 Transcription Factor ChIP-seq Peaks of CHD4 in A549 from ENCODE 3 (ENCFF231RXA) Regulation 
encTfChipPkENCFF243NQJ A549 CEBPB Transcription Factor ChIP-seq Peaks of CEBPB in A549 from ENCODE 3 (ENCFF243NQJ) Regulation 
encTfChipPkENCFF744DTQ A549 CBX8 Transcription Factor ChIP-seq Peaks of CBX8 in A549 from ENCODE 3 (ENCFF744DTQ) Regulation 
encTfChipPkENCFF070KLR A549 CBX2 Transcription Factor ChIP-seq Peaks of CBX2 in A549 from ENCODE 3 (ENCFF070KLR) Regulation 
encTfChipPkENCFF325WAV A549 BCL3 Transcription Factor ChIP-seq Peaks of BCL3 in A549 from ENCODE 3 (ENCFF325WAV) Regulation 
encTfChipPkENCFF913MUA A549 ATF3 Transcription Factor ChIP-seq Peaks of ATF3 in A549 from ENCODE 3 (ENCFF913MUA) Regulation 
wgEncodeAwgTfbsUniform Uniform TFBS Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis Regulation Description This track represents a comprehensive set of human transcription factor binding sites based on ChIP-seq experiments generated by production groups in the ENCODE Consortium from the inception of the project in September 2007, through the March 2012 internal data freeze. The track represents peak calls (regions of enrichment) that were generated by the ENCODE Analysis Working Group (AWG) based on a uniform processing pipeline developed for the ENCODE Integrative Analysis effort and published in a set of coordinated papers in September 2012. Peak calls from that effort, based on datasets from the January 2011 ENCODE data freeze) are available at the ENCODE Analysis Data Hub. This track is an update that includes newer data, and slightly modified methods for the peak calling. This track contains 690 ChIP-seq datasets representing 161 unique regulatory factors (generic and sequence-specific factors). The datasets span 91 human cell types and some are in various treatment conditions. These datasets were generated by the five ENCODE TFBS ChIP-seq production groups: Broad, Stanford/Yale/UC-Davis/Harvard, HudsonAlpha Institute, University of Texas-Austin and University of Washington, and University of Chicago. The University of Chicago ChIP-seq were performed with an alternative epitope-tagged ChIP-seq methodology. The primary and lab-processed data (along with methods descriptions, credits and references) on which this track is based are available in the following ENCODE tracks: HAIB TFBS, SYDH TFBS, UChicago TFBS, UTA TFBS, UW CTCF Binding. These tracks are accessible from the ENC TF Binding Super-track. Display and File Conventions and Configuration The display for this track shows site location with the point-source of the peak marked with a colored vertical bar and the level of enrichment at the site indicated by the darkness of the item. The display can be filtered to higher valued items, using the Score range: configuration item. The score values were computed at UCSC based on signal values assigned by the ENCODE uniform analysis pipeline. The input signal values were multiplied by a normalization factor calculated as the ratio of the maximum score value (1000) to the signal value at 1 standard deviation from the mean, with values exceeding 1000 capped at 1000. This has the effect of distributing scores up to mean + 1std across the score range, but assigning all above to the maximum score. This track is a composite annotation track containing multiple subtracks, one for each cell type. The display mode and filtering of each subtrack can be individually controlled. For more information about track configuration, see Configuring Multi-View Tracks. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. The UCSC Accession listed in the metadata can be used with the File Search tool to retrieve primary data files underlying datasets of interest, by selecting UCSC Accession from the &quot;ENCODE terms&quot; drop down menu option. In the subtrack selection list, the ENCODE tier (priority) is listed for each cell type. Tier 1 and Tier 2 represent categories with cell types designated for intensive study by the ENCODE investigators. After the January 2011 data freeze, an additional set of cell types were promoted from Tier 3 to Tier 2 to broaden the list of intensively studied cell types. These cell types are listed as Tier 2* in the subtrack list here (and are described as 'newly promoted to tier 2: not in 2011 analysis' on the ENCODE Common Cell Types page). Download files for this track are in ENCODE NarrowPeak format. Methods All ChIP-seq experiments were performed at least in duplicate, and were scored against an appropriate control designated by the production groups (either input DNA or DNA obtained from a control immunoprecipitation). Short Read Mapping For each dataset, mapped reads in the form of BAM files were downloaded from the ENCODE UCSC DCC. These BAM files were generated by the ENCODE data production labs (using different mappers and mapping parameters), but all used a standardized version of the GRCh37 (hg19) reference human genome sequence with the following modifications: Mitochondrial sequence was included. Alternate sequences were excluded. Random contigs were excluded. The female version of the genome was represented by the autosomes and chrX, whereas the male genome was represented by the autosomes, chrX, and chrY with the PAR regions masked. In order to standardize the mapping protocol, custom unique-mappability tracks were used to only retain unique mapping reads, i.e. reads that map to exactly one location in the genome. Positional and PCR duplicates were also filtered out. Quality Control A number of quality metrics for individual replicates listed on the ENCODE portal Quality Metrics page, including measures of library complexity and signal enrichment, were calculated and are available for review (Landt et al., 2012; Kundaje et al., 2013a). The Integrated Quality Flag from this quality assessment was used to assign the quality metadata term for each dataset (e.g., Good vs. Caution). Datasets that did not pass the minimum quality control thresholds are not included in this track. Peak Calling Since every ENCODE dataset is represented by at least two biological replicate experiments, a novel measure of consistency and reproducibility of peak calling results between replicates, known as the Irreproducible Discovery Rate (IDR), was used to determine an optimal number of reproducible peaks (Li et al., 2011; Kundaje et al., 2013b). Code and detailed step-by-step instructions to call peaks using the IDR method are available. In brief, the SPP peak caller (Kharchenko et al., 2008) was used with a relaxed peak calling threshold (FDR = 0.9) to obtain a large number of peaks (maximum of 300K) that span true signal as well as noise (false identifications). The IDR method analyzes a pair of replicates, and considers peaks that are present in both replicates to belong to one of two populations : a reproducible signal group or an irreproducible noise group. Peaks from the reproducible group are expected to show relatively higher ranks (ranked based on signal scores) and stronger rank-consistency across the replicates, relative to peaks in the irreproducible groups. Based on these assumptions, a two-component probabilistic copula-mixture model is used to fit the bivariate peak rank distributions from the pairs of replicates. The method adaptively learns the degree of peak-rank consistency in the signal component and the proportion of peaks belonging to each component. The model can then be used to infer an IDR score for every peak that is found in both replicates. The IDR score of a peak represents the expected probability that the peak belongs to the noise component, and is based on its ranks in the two replicates. Hence, low IDR scores represent high-confidence peaks. An IDR score threshold of 0.02 (2%) was used to obtain an optimal peak rank threshold on the replicate peak sets (cross-replicate threshold). If a dataset had more than two replicates, all pairs of replicates were analyzed using the IDR method. The maximum peak rank threshold across all pairwise analyses was used as the final cross-replicate peak rank threshold. Reads from replicate datasets were then pooled and SPP was once again used to call peaks on the pooled data with a relaxed FDR of 0.9. Pooled-data peaks were once again ranked by signal-score. The cross-replicate rank threshold learned from the replicates was used to threshold the ranked set of pooled-data peaks. Any thresholds based on reproducibility of peak calling between biological replicates are bounded by the quality and enrichment of the worst replicate. Valuable signal is lost in cases for which a dataset has one replicate that is significantly worse in data quality than another replicate. A rescue pipeline was used for such cases in order to balance data quality between a set of replicates. Mapped reads were pooled across all replicates of a dataset, and then randomly sampled (without replacement) to generate two pseudo-replicates with equal numbers of reads. This sampling strategy tends to transfer signal from stronger replicates to the weaker replicates, thereby balancing cross-replicate data quality and sequencing depth. These pseudo-replicates were then processed using the IDR method in order to learn a rescue threshold. For datasets with comparable replicates (based on independent measures of data quality), the rescue threshold and cross-replicate thresholds were found to be very similar. However, for datasets with replicates of differing data quality, the rescue thresholds were often higher than the cross-replicate thresholds, and were able to capture true peaks that showed statistically significant and visually compelling ChIP-seq signal in one replicate but not in the other. Ultimately, for each dataset, the best of the cross-replicate and rescue thresholds were used to obtain a final consolidated optimal set of peaks. All peak sets were then screened against a specially curated empirical blacklist of regions in the human genome (wgEncodeDacMapabilityConsensusExcludable.bed.gz) and peaks overlapping the blacklisted regions were discarded (Kundaje et al., 2013b). Briefly, these artifact regions typically show the following characteristics: Unstructured and extreme artifactual high signal in sequenced input-DNA and control datasets, as well as open chromatin datasets irrespective of cell type identity. An extreme ratio of multi-mapping to unique mapping reads from sequencing experiments. Overlap with pathological repeat regions such as centromeric, telomeric and satellite repeats that often have few unique mappable locations interspersed in repeats. Differences from the January 2011 freeze pipeline The January 2011 uniform processing was performed as part of the ENCODE Integrative Analysis reported in coordinated publications in September 2012. The results from this effort are available from the ENCODE Analysis Hub at the EBI. For the March 2012 freeze, only the SPP peak caller was used. SPP and PeakSeq were used for the January 2011 freeze. For March 2012, In the read mapping phase, an extra step was performed to remove all positional duplicates. This was done to avoid low library complexity issues. In January 2011, remove positional duplicates were retained. For March 2012, an IDR threshold of 2% was used for comparing and thresholding the true replicates and the pooled pseudo-replicates. In January 2011, the IDR threshold was set to 1% for the true replicates and 0.25% for the pooled pseudo-replicates. These thresholds were determined to be too stringent. Credits The processed data for this track were generated by Anshul Kundaje on behalf of the ENCODE Analysis Working Group. Credits for the primary data underlying this track are included in track description pages listed in the Description section above. Contact: Anshul Kundaje References ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222; PMCID: PMC3079585 ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMCID: PMC3439153 Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec;26(12):1351-9. PMID: 19029915; PMCID: PMC2597701 Kundaje A, Jung L, Kharchenko PV, Sidow A, Batzoglou S, Park PJ. Assessment of ChIP-seq data quality using strand cross-correlation analysis. (submitted), 2012a. Kundaje A, Li Q, Brown JB, Rozowsky J, Harmanci A, Wilder SP, Batzoglou S, Dunham I, Gerstein M, Birney E, et al. Reproducibility measures for automatic threshold selection and quality control in ChIP-seq datasets. (submitted), 2012b. Li QH, Brown JB, Huang HY, Bickel PJ. Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat. 2011; 5(3):1752-1779. Data Release Policy While primary ENCODE data is subject to a restriction period as described in the ENCODE data release policy, this restriction does not apply to the integrative analysis results. The data in this track are freely available. 
wgEncodeAwgTfbsUwWi38CtcfUniPk WI-38 CTCF CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001902 UW wgEncodeAwgTfbsUwWi38CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwWerirb1CtcfUniPk WERI-Rb-1 CTCF CTCF WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000402 UW wgEncodeAwgTfbsUwWerirb1CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsHaibU87NrsfPcr2xUniPk U87 REST NRSF U87 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001554 HudsonAlpha wgEncodeAwgTfbsHaibU87NrsfPcr2xUniPk None Peaks Neuron-restrictive silencer transcription factor glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment U87 TFBS Uniform Peaks of NRSF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibU87Pol24h8V0416101UniPk U87 POLR2A Pol2-4H8 U87 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001674 HudsonAlpha wgEncodeAwgTfbsHaibU87Pol24h8V0416101UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment U87 TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhU2osSetdb1UcdUniPk U2OS SETDB1 SETDB1 U2OS UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001762 USC wgEncodeAwgTfbsSydhU2osSetdb1UcdUniPk None Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment U2OS TFBS Uniform Peaks of SETDB1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhU2osKap1UcdUniPk U2OS KAP1 KAP1 U2OS UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001776 USC wgEncodeAwgTfbsSydhU2osKap1UcdUniPk None Peaks KRAB Associated Protein 1, helps regulate transcriptional repression. osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment U2OS TFBS Uniform Peaks of KAP1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibT47dGata3sc268V0416102Dm002p1hUniPk T-47D+DMSO GATA3 GATA3_(SC-268) T-47D ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001639 HudsonAlpha wgEncodeAwgTfbsHaibT47dGata3sc268V0416102Dm002p1hUniPk DMSO_0.02pct Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D (DMSO) TFBS Uniform Peaks of GATA3_(SC-268) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibT47dFoxa1sc6553V0416102Dm002p1hUniPk T-47D+DMSO FOXA1 FOXA1_(SC-6553) T-47D ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001588 HudsonAlpha wgEncodeAwgTfbsHaibT47dFoxa1sc6553V0416102Dm002p1hUniPk DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D (DMSO) TFBS Uniform Peaks of FOXA1_(SC-6553) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibT47dEralphaaPcr2xGen1hUniPk T-47D+Genist ESR1 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001556 HudsonAlpha wgEncodeAwgTfbsHaibT47dEralphaaPcr2xGen1hUniPk Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment T-47D (Genistein) TFBS Uniform Peaks of ERalpha_a ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibT47dEralphaaV0416102Est10nm1hUniPk T-47D+Estrad ESR1 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001577 HudsonAlpha wgEncodeAwgTfbsHaibT47dEralphaaV0416102Est10nm1hUniPk Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment T-47D (Estradiol) TFBS Uniform Peaks of ERalpha_a ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibT47dEraaV0416102Bpa1hUniPk T-47D+BPA ESR1 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002299 HudsonAlpha wgEncodeAwgTfbsHaibT47dEraaV0416102Bpa1hUniPk BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment T-47D (BPA) TFBS Uniform Peaks of ERalpha_a from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibT47dP300V0416102Dm002p1hUniPk T-47D+DMSO EP300 p300 T-47D ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001602 HudsonAlpha wgEncodeAwgTfbsHaibT47dP300V0416102Dm002p1hUniPk DMSO_0.02pct Peaks EP300(c-20) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D (DMSO) TFBS Uniform Peaks of p300 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibT47dCtcfsc5916V0416102Dm002p1hUniPk T-47D+DMSO CTCF CTCF_(SC-5916) T-47D ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001656 HudsonAlpha wgEncodeAwgTfbsHaibT47dCtcfsc5916V0416102Dm002p1hUniPk DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D (DMSO) TFBS Uniform Peaks of CTCF_(SC-5916) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshraYy1sc281V0416102UniPk SK-N-SH_RA YY1 YY1_(SC-281) SK-N-SH_RA ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001615 HudsonAlpha wgEncodeAwgTfbsHaibSknshraYy1sc281V0416102UniPk None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH_RA TFBS Uniform Peaks of YY1_(SC-281) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshraUsf1sc8983V0416102UniPk SK-N-SH_RA USF1 USF1_(SC-8983) SK-N-SH_RA ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001621 HudsonAlpha wgEncodeAwgTfbsHaibSknshraUsf1sc8983V0416102UniPk None Peaks This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq). neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH_RA TFBS Uniform Peaks of USF1_(SC-8983) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshraRad21V0416102UniPk SK-N-SH_RA RAD21 Rad21 SK-N-SH_RA ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001614 HudsonAlpha wgEncodeAwgTfbsHaibSknshraRad21V0416102UniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH_RA TFBS Uniform Peaks of Rad21 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshraP300V0416102UniPk SK-N-SH_RA EP300 p300 SK-N-SH_RA ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001616 HudsonAlpha wgEncodeAwgTfbsHaibSknshraP300V0416102UniPk None Peaks EP300(c-20) neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH_RA TFBS Uniform Peaks of p300 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUwSknshraCtcfUniPk SK-N-SH_RA CTCF w CTCF SK-N-SH_RA std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000439 UW wgEncodeAwgTfbsUwSknshraCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshraCtcfV0416102UniPk SK-N-SH_RA CTCF h CTCF SK-N-SH_RA ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001613 HudsonAlpha wgEncodeAwgTfbsHaibSknshraCtcfV0416102UniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH_RA TFBS Uniform Peaks of CTCF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknmcPol24h8V0416101UniPk SK-N-MC POLR2A Pol2-4H8 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002281 HudsonAlpha wgEncodeAwgTfbsHaibSknmcPol24h8V0416101UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-MC TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknmcFoxp2Pcr2xUniPk SK-N-MC FOXP2 FOXP2 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001461 HudsonAlpha wgEncodeAwgTfbsHaibSknmcFoxp2Pcr2xUniPk None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-MC TFBS Uniform Peaks of FOXP2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhShsy5yGata3sc269sc269UcdUniPk SH-SY5Y GATA3 GATA3_(SC-269) SH-SY5Y UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002031 USC wgEncodeAwgTfbsSydhShsy5yGata3sc269sc269UcdUniPk None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment SH-SY5Y TFBS Uniform Peaks of GATA3_(SC-269) from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhShsy5yGata2UcdUniPk SH-SY5Y GATA2 GATA-2 SH-SY5Y UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001770 USC wgEncodeAwgTfbsSydhShsy5yGata2UcdUniPk None Peaks GATA binding protein 2 neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment SH-SY5Y TFBS Uniform Peaks of GATA-2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsUwSaecCtcfUniPk SAEC CTCF CTCF SAEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000437 UW wgEncodeAwgTfbsUwSaecCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwRptecCtcfUniPk RPTEC CTCF CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002059 UW wgEncodeAwgTfbsUwRptecCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsSydhRajiPol2UcdUniPk Raji POLR2A Pol2 Raji UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001761 USC wgEncodeAwgTfbsSydhRajiPol2UcdUniPk None Peaks RNA Polymerase II B lymphocyte, "The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment Raji TFBS Uniform Peaks of Pol2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsUtaProgfibPol2UniPk ProgFib POLR2A Pol2 ProgFib ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000606 UT-A wgEncodeAwgTfbsUtaProgfibPol2UniPk None Peaks RNA Polymerase II fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment ProgFib TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaProgfibCtcfUniPk ProgFib CTCF CTCF ProgFib ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000600 UT-A wgEncodeAwgTfbsUtaProgfibCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment ProgFib TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsHaibPfsk1Taf1V0416101UniPk PFSK-1 TAF1 TAF1 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002309 HudsonAlpha wgEncodeAwgTfbsHaibPfsk1Taf1V0416101UniPk None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment PFSK-1 TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibPfsk1Sin3ak20V0416101UniPk PFSK-1 SIN3AK20 Sin3Ak-20 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002268 HudsonAlpha wgEncodeAwgTfbsHaibPfsk1Sin3ak20V0416101UniPk None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment PFSK-1 TFBS Uniform Peaks of Sin3Ak-20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibPfsk1NrsfPcr2xUniPk PFSK-1 REST NRSF PFSK-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001553 HudsonAlpha wgEncodeAwgTfbsHaibPfsk1NrsfPcr2xUniPk None Peaks Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment PFSK-1 TFBS Uniform Peaks of NRSF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibPfsk1Foxp2Pcr2xUniPk PFSK-1 FOXP2 FOXP2 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001460 HudsonAlpha wgEncodeAwgTfbsHaibPfsk1Foxp2Pcr2xUniPk None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment PFSK-1 TFBS Uniform Peaks of FOXP2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhPbdefetalGata1UcdUniPk PBDEFetal GATA1 GATA-1 PBDEFetal UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001785 USC wgEncodeAwgTfbsSydhPbdefetalGata1UcdUniPk None Peaks GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts from 16-19 week human fetal liver Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment PBDEFetal TFBS Uniform Peaks of GATA-1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhPbdePol2UcdUniPk PBDE POLR2A Pol2 PBDE UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001766 USC wgEncodeAwgTfbsSydhPbdePol2UcdUniPk None Peaks RNA Polymerase II peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment PBDE TFBS Uniform Peaks of Pol2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhPbdeGata1UcdUniPk PBDE GATA1 GATA-1 PBDE UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001765 USC wgEncodeAwgTfbsSydhPbdeGata1UcdUniPk None Peaks GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment PBDE TFBS Uniform Peaks of GATA-1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhPanc1Tcf7l2UcdUniPk PANC-1 TCF7L2 TCF7L2 PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002071 USC wgEncodeAwgTfbsSydhPanc1Tcf7l2UcdUniPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment PANC-1 TFBS Uniform Peaks of TCF7L2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibPanc1Sin3ak20V0416101UniPk PANC-1 SIN3AK20 Sin3Ak-20 PANC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002266 HudsonAlpha wgEncodeAwgTfbsHaibPanc1Sin3ak20V0416101UniPk None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment PANC-1 TFBS Uniform Peaks of Sin3Ak-20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibPanc1NrsfPcr2xUniPk PANC-1 REST NRSF PANC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001552 HudsonAlpha wgEncodeAwgTfbsHaibPanc1NrsfPcr2xUniPk None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment PANC-1 TFBS Uniform Peaks of NRSF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibPanc1Pol24h8V0416101UniPk PANC-1 POLR2A Pol2-4H8 PANC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002265 HudsonAlpha wgEncodeAwgTfbsHaibPanc1Pol24h8V0416101UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment PANC-1 TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadOsteoblCtcfUniPk Osteobl CTCF CTCF Osteobl std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001041 Broad wgEncodeAwgTfbsBroadOsteoblCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment Osteobl TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhNt2d1Znf274UcdUniPk NT2-D1 ZNF274 ZNF274 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001775 USC wgEncodeAwgTfbsSydhNt2d1Znf274UcdUniPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment NT2-D1 TFBS Uniform Peaks of ZNF274 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhNt2d1Yy1UcdUniPk NT2-D1 YY1 YY1 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000653 USC wgEncodeAwgTfbsSydhNt2d1Yy1UcdUniPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment NT2-D1 TFBS Uniform Peaks of YY1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhNt2d1Suz12UcdUniPk NT2-D1 SUZ12 SUZ12 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000652 USC wgEncodeAwgTfbsSydhNt2d1Suz12UcdUniPk None Peaks Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment NT2-D1 TFBS Uniform Peaks of SUZ12 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsBroadNhlfEzh239875UniPk NHLF EZH2 EZH2_(39875) NHLF std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002422 Broad wgEncodeAwgTfbsBroadNhlfEzh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment NHLF TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsUwNhlfCtcfUniPk NHLF CTCF w CTCF NHLF std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002548 UW wgEncodeAwgTfbsUwNhlfCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsBroadNhlfCtcfUniPk NHLF CTCF b CTCF NHLF std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000120 Broad wgEncodeAwgTfbsBroadNhlfCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment NHLF TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadNhekPol2bUniPk NHEK POLR2A Pol2(b) NHEK std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000073 Broad wgEncodeAwgTfbsBroadNhekPol2bUniPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment NHEK TFBS Uniform Peaks of Pol2(b) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadNhekEzh239875UniPk NHEK EZH2 EZH2_(39875) NHEK std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002418 Broad wgEncodeAwgTfbsBroadNhekEzh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment NHEK TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsUwNhekCtcfUniPk NHEK CTCF w CTCF NHEK std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000406 UW wgEncodeAwgTfbsUwNhekCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaNhekCtcfUniPk NHEK CTCF t CTCF NHEK ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000559 UT-A wgEncodeAwgTfbsUtaNhekCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment NHEK TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsBroadNhekCtcfUniPk NHEK CTCF b CTCF NHEK std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000063 Broad wgEncodeAwgTfbsBroadNhekCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment NHEK TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsUwNhdfneoCtcfUniPk NHDF-neo CTCF CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002058 UW wgEncodeAwgTfbsUwNhdfneoCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsBroadNhdfadEzh239875UniPk NHDF-Ad EZH2 EZH2_(39875) NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002438 Broad wgEncodeAwgTfbsBroadNhdfadEzh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadNhdfadCtcfUniPk NHDF-Ad CTCF CTCF NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001048 Broad wgEncodeAwgTfbsBroadNhdfadCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadNhaEzh239875UniPk NH-A EZH2 EZH2_(39875) NH-A std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002425 Broad wgEncodeAwgTfbsBroadNhaEzh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment NH-A TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadNhaCtcfUniPk NH-A CTCF CTCF NH-A std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001026 Broad wgEncodeAwgTfbsBroadNhaCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment NH-A TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhNb4Pol2UniPk NB4 POLR2A Pol2 NB4 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000618 Yale wgEncodeAwgTfbsSydhNb4Pol2UniPk None Peaks RNA Polymerase II acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment NB4 TFBS Uniform Peaks of Pol2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhNb4CmycUniPk NB4 MYC c-Myc NB4 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001807 Stanford wgEncodeAwgTfbsSydhNb4CmycUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment NB4 TFBS Uniform Peaks of c-Myc from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhNb4MaxUniPk NB4 MAX Max NB4 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001806 Stanford wgEncodeAwgTfbsSydhNb4MaxUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment NB4 TFBS Uniform Peaks of Max from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsUwNb4CtcfUniPk NB4 CTCF CTCF NB4 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001898 UW wgEncodeAwgTfbsUwNb4CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NB4 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesStat3Etoh01UniPk MCF10AEr+E1 STAT3 STAT3 MCF10A-Er-Src std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001772 Harvard wgEncodeAwgTfbsSydhMcf10aesStat3Etoh01UniPk EtOH_0.01pct Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A-Er-Src (EtOH .01) TFBS Uniform Peaks of STAT3 ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesStat3TamUniPk MCF10+T36 STAT3 STAT3 MCF10A-Er-Src std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001769 Harvard wgEncodeAwgTfbsSydhMcf10aesStat3TamUniPk 4OHTAM_1uM_36hr Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A-Er-Src (TAM 36h) TFBS Uniform Peaks of STAT3 ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesStat3Tam112hHvdUniPk MCF10+T12 STAT3 STAT3 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002836 Harvard wgEncodeAwgTfbsSydhMcf10aesStat3Tam112hHvdUniPk 4OHTAM_1uM_12hr Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A-Er-Src (TAM 12h) TFBS Uniform Peaks of STAT3 ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesStat3Etoh01bUniPk MCF10+E1/4 STAT3 STAT3 MCF10A-Er-Src std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001871 Harvard wgEncodeAwgTfbsSydhMcf10aesStat3Etoh01bUniPk EtOH_0.01pct_4hr Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University 4 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10AErSrc (EtOH.01 4h) TFBS Uniform Peaks of STAT3 ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesStat3Etoh01cUniPk MCF10+E1/12 STAT3 STAT3 MCF10A-Er-Src std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001868 Harvard wgEncodeAwgTfbsSydhMcf10aesStat3Etoh01cUniPk EtOH_0.01pct_12hr Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University 12 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10AErSrc (EtOH.01 12h) TFBS Uniform Peaks of STAT3 ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesPol2TamUniPk MCF10+T36 POLR2A Pol2 MCF10A-Er-Src std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001768 Harvard wgEncodeAwgTfbsSydhMcf10aesPol2TamUniPk 4OHTAM_1uM_36hr Peaks RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A-Er-Src (TAM 36h) TFBS Uniform Peaks of Pol2 ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesPol2Etoh01UniPk MCF10+E1 POLR2A Pol2 MCF10A-Er-Src std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001771 Harvard wgEncodeAwgTfbsSydhMcf10aesPol2Etoh01UniPk EtOH_0.01pct Peaks RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A-Er-Src (EtOH .01) TFBS Uniform Peaks of Pol2 ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesCmycTam14hHvdUniPk MCF10AEr+T4 MYC c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002840 Harvard wgEncodeAwgTfbsSydhMcf10aesCmycTam14hHvdUniPk 4OHTAM_1uM_4hr Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A-Er-Src (TAM 4h) TFBS Uniform Peaks of c-Myc ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesCmycEtoh01HvdUniPk MCF10AEr+E1 MYC c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002816 Harvard wgEncodeAwgTfbsSydhMcf10aesCmycEtoh01HvdUniPk EtOH_0.01pct Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A-Er-Src (EtOH .01) TFBS Uniform Peaks of c-Myc ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesCfosTam14hHvdUniPk MCF10AEr+T4 FOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002838 Harvard wgEncodeAwgTfbsSydhMcf10aesCfosTam14hHvdUniPk 4OHTAM_1uM_4hr Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A-Er-Src (TAM 4h) TFBS Uniform Peaks of c-Fos ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesCfosTamHvdUniPk MCF10AEr+T36 FOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002839 Harvard wgEncodeAwgTfbsSydhMcf10aesCfosTamHvdUniPk 4OHTAM_1uM_36hr Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A-Er-Src (TAM 36h) TFBS Uniform Peaks of c-Fos ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesCfosTam112hHvdUniPk MCF10AEr+T12 FOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002837 Harvard wgEncodeAwgTfbsSydhMcf10aesCfosTam112hHvdUniPk 4OHTAM_1uM_12hr Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A-Er-Src (TAM 12h) TFBS Uniform Peaks of c-Fos ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesCfosEtoh01HvdUniPk MCF10AEr+Et1 FOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002815 Harvard wgEncodeAwgTfbsSydhMcf10aesCfosEtoh01HvdUniPk EtOH_0.01pct Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A-Er-Src (EtOH .01) TFBS Uniform Peaks of c-Fos ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf10aesE2f4TamHvdUniPk MCF10AEr+T36 E2F4 E2F4 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002835 Harvard wgEncodeAwgTfbsSydhMcf10aesE2f4TamHvdUniPk 4OHTAM_1uM_36hr Peaks mapping at the C-terminus of E2F4 of human origin mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A-Er-Src (TAM 36h) TFBS Uniform Peaks of E2F4 ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsUwHvmfCtcfUniPk HVMF CTCF CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002056 UW wgEncodeAwgTfbsUwHvmfCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsBroadHsmmtEzh239875UniPk HSMMtube EZH2 EZH2_(39875) HSMMtube std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003083 Broad wgEncodeAwgTfbsBroadHsmmtEzh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadHsmmtCtcfUniPk HSMMtube CTCF CTCF HSMMtube std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001000 Broad wgEncodeAwgTfbsBroadHsmmtCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadHsmmEzh239875UniPk HSMM EZH2 EZH2_(39875) HSMM std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002415 Broad wgEncodeAwgTfbsBroadHsmmEzh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HSMM TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadHsmmCtcfUniPk HSMM CTCF CTCF HSMM std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000110 Broad wgEncodeAwgTfbsBroadHsmmCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HSMM TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsUwHrpeCtcfUniPk HRPEpiC CTCF CTCF HRPEpiC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000988 UW wgEncodeAwgTfbsUwHrpeCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpiC TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHreCtcfUniPk HRE CTCF CTCF HRE std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000405 UW wgEncodeAwgTfbsUwHreCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHpfCtcfUniPk HPF CTCF CTCF HPF std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000987 UW wgEncodeAwgTfbsUwHpfCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHpafCtcfUniPk HPAF CTCF CTCF HPAF std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000986 UW wgEncodeAwgTfbsUwHpafCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHmfCtcfUniPk HMF CTCF CTCF HMF std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000985 UW wgEncodeAwgTfbsUwHmfCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsBroadHmecEzh239875UniPk HMEC EZH2 EZH2_(39875) HMEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002412 Broad wgEncodeAwgTfbsBroadHmecEzh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HMEC TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsUwHmecCtcfUniPk HMEC CTCF w CTCF HMEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000419 UW wgEncodeAwgTfbsUwHmecCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsBroadHmecCtcfUniPk HMEC CTCF b CTCF HMEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000075 Broad wgEncodeAwgTfbsBroadHmecCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HMEC TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsUwHl60CtcfUniPk HL-60 CTCF CTCF HL-60 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000397 UW wgEncodeAwgTfbsUwHl60CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHffmycCtcfUniPk HFF-Myc CTCF CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001895 UW wgEncodeAwgTfbsUwHffmycCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF-Myc TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHffCtcfUniPk HFF CTCF CTCF HFF std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002547 UW wgEncodeAwgTfbsUwHffCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsSydhHek293tZnf263UcdUniPk HEK293TREx ZNF263 ZNF263 HEK293-T-REx UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001781 USC wgEncodeAwgTfbsSydhHek293tZnf263UcdUniPk None Peaks ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line, hypotriploid, XXX Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HEK293-T-REx TFBS Uniform Peaks of ZNF263 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHek293Tcf7l2UcdUniPk HEK293 TCF7L2 TCF7L2 HEK293 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002022 USC wgEncodeAwgTfbsSydhHek293Tcf7l2UcdUniPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HEK293 TFBS Uniform Peaks of TCF7L2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHek293Pol2UniPk HEK293 POLR2A Pol2 HEK293 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000632 Yale wgEncodeAwgTfbsSydhHek293Pol2UniPk None Peaks RNA Polymerase II embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment HEK293 TFBS Uniform Peaks of Pol2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhHek293Kap1UcdUniPk HEK293 KAP1 KAP1 HEK293 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001779 USC wgEncodeAwgTfbsSydhHek293Kap1UcdUniPk None Peaks KRAB Associated Protein 1, helps regulate transcriptional repression. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HEK293 TFBS Uniform Peaks of KAP1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHek293Elk4UcdUniPk HEK293 ELK4 ELK4 HEK293 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001773 USC wgEncodeAwgTfbsSydhHek293Elk4UcdUniPk None Peaks This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HEK293 TFBS Uniform Peaks of ELK4 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsUwHek293CtcfUniPk HEK293 CTCF CTCF HEK293 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000396 UW wgEncodeAwgTfbsUwHek293CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEK293 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHeeCtcfUniPk HEEpiC CTCF CTCF HEEpiC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000984 UW wgEncodeAwgTfbsUwHeeCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpiC TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsHaibHct116Zbtb33V0416101UniPk HCT-116 ZBTB33 ZBTB33 HCT-116 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001672 HudsonAlpha wgEncodeAwgTfbsHaibHct116Zbtb33V0416101UniPk None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HCT-116 TFBS Uniform Peaks of ZBTB33 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHct116Yy1sc281V0416101UniPk HCT-116 YY1 YY1_(SC-281) HCT-116 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001671 HudsonAlpha wgEncodeAwgTfbsHaibHct116Yy1sc281V0416101UniPk None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HCT-116 TFBS Uniform Peaks of YY1_(SC-281) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHct116Tcf7l2UcdUniPk HCT-116 TCF7L2 TCF7L2 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000629 USC wgEncodeAwgTfbsSydhHct116Tcf7l2UcdUniPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 TFBS Uniform Peaks of TCF7L2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHct116Pol2UcdUniPk HCT-116 POLR2A c Pol2 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000651 USC wgEncodeAwgTfbsSydhHct116Pol2UcdUniPk None Peaks RNA Polymerase II colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 TFBS Uniform Peaks of Pol2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibHct116Pol24h8V0416101UniPk HCT-116 POLR2A h Pol2-4H8 HCT-116 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001627 HudsonAlpha wgEncodeAwgTfbsHaibHct116Pol24h8V0416101UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HCT-116 TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUwHct116CtcfUniPk HCT-116 CTCF CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002055 UW wgEncodeAwgTfbsUwHct116CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHcpeCtcfUniPk HCPEpiC CTCF CTCF HCPEpiC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000983 UW wgEncodeAwgTfbsUwHcpeCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpiC TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHcmCtcfUniPk HCM CTCF CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001894 UW wgEncodeAwgTfbsUwHcmCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHcfaaCtcfUniPk HCFaa CTCF CTCF HCFaa std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000982 UW wgEncodeAwgTfbsUwHcfaaCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCFaa TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHbmecCtcfUniPk HBMEC CTCF CTCF HBMEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000981 UW wgEncodeAwgTfbsUwHbmecCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHaspCtcfUniPk HA-sp CTCF CTCF HA-sp std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000989 UW wgEncodeAwgTfbsUwHaspCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwHacCtcfUniPk HAc CTCF CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001893 UW wgEncodeAwgTfbsUwHacCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaGm19240CtcfUniPk GM19240 CTCF CTCF GM19240 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000572 UT-A wgEncodeAwgTfbsUtaGm19240CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment GM19240 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaGm19239CtcfUniPk GM19239 CTCF CTCF GM19239 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000571 UT-A wgEncodeAwgTfbsUtaGm19239CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment GM19239 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaGm19238CtcfUniPk GM19238 CTCF CTCF GM19238 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000570 UT-A wgEncodeAwgTfbsUtaGm19238CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment GM19238 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhGm19193NfkbTnfaIggrabUniPk GM19193+TNFa RELA NFKB GM19193 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000718 Stanford wgEncodeAwgTfbsSydhGm19193NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM19193 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm19193Pol2IggmusUniPk GM19193 POLR2A Pol2 GM19193 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000743 Stanford wgEncodeAwgTfbsSydhGm19193Pol2IggmusUniPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM19193 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm19099NfkbTnfaIggrabUniPk GM19099+TNFa RELA NFKB GM19099 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000717 Stanford wgEncodeAwgTfbsSydhGm19099NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM19099 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm19099Pol2IggmusUniPk GM19099 POLR2A Pol2 GM19099 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000741 Stanford wgEncodeAwgTfbsSydhGm19099Pol2IggmusUniPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM19099 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm18951NfkbTnfaIggrabUniPk GM18951+TNFa RELA NFKB GM18951 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000738 Stanford wgEncodeAwgTfbsSydhGm18951NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM18951 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm18951Pol2IggmusUniPk GM18951 POLR2A Pol2 GM18951 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000739 Stanford wgEncodeAwgTfbsSydhGm18951Pol2IggmusUniPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM18951 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm18526NfkbTnfaIggrabUniPk GM18526+TNFa RELA NFKB GM18526 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000716 Stanford wgEncodeAwgTfbsSydhGm18526NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM18526 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm18526Pol2IggmusUniPk GM18526 POLR2A Pol2 GM18526 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000733 Stanford wgEncodeAwgTfbsSydhGm18526Pol2IggmusUniPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM18526 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm18505NfkbTnfaIggrabUniPk GM18505+TNFa RELA NFKB GM18505 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000715 Stanford wgEncodeAwgTfbsSydhGm18505NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM18505 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm18505Pol2IggmusUniPk GM18505 POLR2A Pol2 GM18505 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000731 Stanford wgEncodeAwgTfbsSydhGm18505Pol2IggmusUniPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM18505 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm15510NfkbTnfaIggrabUniPk GM15510+TNFa RELA NFKB GM15510 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000736 Stanford wgEncodeAwgTfbsSydhGm15510NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM15510 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm15510Pol2IggmusUniPk GM15510 POLR2A Pol2 GM15510 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000714 Stanford wgEncodeAwgTfbsSydhGm15510Pol2IggmusUniPk None Peaks RNA Polymerase II lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM15510 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12892Yy1V0416101UniPk GM12892 YY1 YY1 GM12892 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001609 HudsonAlpha wgEncodeAwgTfbsHaibGm12892Yy1V0416101UniPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12892 TFBS Uniform Peaks of YY1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12892Taf1V0416102UniPk GM12892 TAF1 TAF1 GM12892 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001513 HudsonAlpha wgEncodeAwgTfbsHaibGm12892Taf1V0416102UniPk None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12892 TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12892NfkbTnfaIggrabUniPk GM12892+TNFa RELA NFKB GM12892 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000712 Stanford wgEncodeAwgTfbsSydhGm12892NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM12892 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12892Pol2IggmusUniPk GM12892 POLR2A s Pol2 GM12892 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000729 Stanford wgEncodeAwgTfbsSydhGm12892Pol2IggmusUniPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12892 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12892Pol2V0416102UniPk GM12892 POLR2A h2 Pol2 GM12892 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001511 HudsonAlpha wgEncodeAwgTfbsHaibGm12892Pol2V0416102UniPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12892 TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12892Pol24h8V0416102UniPk GM12892 POLR2A h1 Pol2-4H8 GM12892 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001512 HudsonAlpha wgEncodeAwgTfbsHaibGm12892Pol24h8V0416102UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12892 TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12892Pax5c20V0416101UniPk GM12892 PAX5 PAX5-C20 GM12892 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001546 HudsonAlpha wgEncodeAwgTfbsHaibGm12892Pax5c20V0416101UniPk None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12892 TFBS Uniform Peaks of PAX5-C20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUtaGm12892CtcfUniPk GM12892 CTCF CTCF GM12892 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000562 UT-A wgEncodeAwgTfbsUtaGm12892CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12892 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12891Yy1sc281V0416101UniPk GM12891 YY1 YY1_(SC-281) GM12891 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001573 HudsonAlpha wgEncodeAwgTfbsHaibGm12891Yy1sc281V0416101UniPk None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12891 TFBS Uniform Peaks of YY1_(SC-281) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12891Taf1Pcr1xUniPk GM12891 TAF1 TAF1 GM12891 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001524 HudsonAlpha wgEncodeAwgTfbsHaibGm12891Taf1Pcr1xUniPk None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12891 TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12891Pu1Pcr1xUniPk GM12891 SPI1 PU.1 GM12891 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001521 HudsonAlpha wgEncodeAwgTfbsHaibGm12891Pu1Pcr1xUniPk None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12891 TFBS Uniform Peaks of PU.1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12891NfkbTnfaIggrabUniPk GM12891+TNFa RELA NFKB GM12891 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000735 Stanford wgEncodeAwgTfbsSydhGm12891NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM12891 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12891Pou2f2Pcr1xUniPk GM12891 POU2F2 POU2F2 GM12891 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001520 HudsonAlpha wgEncodeAwgTfbsHaibGm12891Pou2f2Pcr1xUniPk None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12891 TFBS Uniform Peaks of POU2F2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12891Pol2IggmusUniPk GM12891 POLR2A s Pol2 GM12891 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000710 Stanford wgEncodeAwgTfbsSydhGm12891Pol2IggmusUniPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12891 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12891Pol2Pcr1xUniPk GM12891 POLR2A h2 Pol2 GM12891 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001522 HudsonAlpha wgEncodeAwgTfbsHaibGm12891Pol2Pcr1xUniPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12891 TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12891Pol24h8Pcr1xUniPk GM12891 POLR2A h1 Pol2-4H8 GM12891 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001523 HudsonAlpha wgEncodeAwgTfbsHaibGm12891Pol24h8Pcr1xUniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12891 TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12891Pax5c20V0416101UniPk GM12891 PAX5 PAX5-C20 GM12891 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001545 HudsonAlpha wgEncodeAwgTfbsHaibGm12891Pax5c20V0416101UniPk None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12891 TFBS Uniform Peaks of PAX5-C20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUtaGm12891CtcfUniPk GM12891 CTCF CTCF GM12891 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000569 UT-A wgEncodeAwgTfbsUtaGm12891CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12891 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUwGm12875CtcfUniPk GM12875 CTCF CTCF GM12875 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000452 UW wgEncodeAwgTfbsUwGm12875CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12875 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwGm12874CtcfUniPk GM12874 CTCF CTCF GM12874 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000451 UW wgEncodeAwgTfbsUwGm12874CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12874 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwGm12873CtcfUniPk GM12873 CTCF CTCF GM12873 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000450 UW wgEncodeAwgTfbsUwGm12873CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12873 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwGm12872CtcfUniPk GM12872 CTCF CTCF GM12872 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000449 UW wgEncodeAwgTfbsUwGm12872CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12872 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwGm12865CtcfUniPk GM12865 CTCF CTCF GM12865 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000448 UW wgEncodeAwgTfbsUwGm12865CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwGm12864CtcfUniPk GM12864 CTCF CTCF GM12864 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000447 UW wgEncodeAwgTfbsUwGm12864CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwGm12801CtcfUniPk GM12801 CTCF CTCF GM12801 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000393 UW wgEncodeAwgTfbsUwGm12801CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12801 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsSydhGm10847NfkbTnfaIggrabUniPk GM10847+TNFa RELA NFKB GM10847 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000734 Stanford wgEncodeAwgTfbsSydhGm10847NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM10847 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm10847Pol2IggmusUniPk GM10847 POLR2A Pol2 GM10847 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000705 Stanford wgEncodeAwgTfbsSydhGm10847Pol2IggmusUniPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM10847 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm08714Znf274UcdUniPk GM08714 ZNF274 ZNF274 GM08714 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002866 USC wgEncodeAwgTfbsSydhGm08714Znf274UcdUniPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. lymphoblastoid cell line, Instability of heterochromatin of chromosomes 1, 9, and 16 with variable combined immunodeficiency; dysmorphic facial features, developmental delay, malabsorption, and recurrent infections; see GM08747 Fibroblast; donor subject is a compound heterozygote: one allele has a G&gt;A transition at nucleotide 1807 (1807G&gt;A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B; the second allele has a G&gt;A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G&gt;A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo. Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment GM08714 TFBS Uniform Peaks of ZNF274 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsUwGm06990CtcfUniPk GM06990 CTCF CTCF GM06990 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000392 UW wgEncodeAwgTfbsUwGm06990CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaGlioblaPol2UniPk Gliobla POLR2A Pol2 Gliobla ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001136 UT-A wgEncodeAwgTfbsUtaGlioblaPol2UniPk None Peaks RNA Polymerase II glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment Gliobla TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaGlioblaCtcfUniPk Gliobla CTCF CTCF Gliobla ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001135 UT-A wgEncodeAwgTfbsUtaGlioblaCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment Gliobla TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaFibroblCtcfUniPk Fibrobl CTCF CTCF Fibrobl ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001127 UT-A wgEncodeAwgTfbsUtaFibroblCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. child fibroblast Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment Fibrobl TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsHaibEcc1Pol2V0416102Dm002p1hUniPk ECC-1+DMSO POLR2A Pol2 ECC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001572 HudsonAlpha wgEncodeAwgTfbsHaibEcc1Pol2V0416102Dm002p1hUniPk DMSO_0.02pct Peaks RNA Polymerase II epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 (DMSO) TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibEcc1GrV0416102Dex100nmUniPk ECC-1+Dx100 NR3C1 GR ECC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001540 HudsonAlpha wgEncodeAwgTfbsHaibEcc1GrV0416102Dex100nmUniPk DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment ECC-1 (DEX_100nM) TFBS Uniform Peaks of GR from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibEcc1Foxa1sc6553V0416102Dm002p1hUniPk ECC-1+DMSO FOXA1 FOXA1_(SC-6553) ECC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001586 HudsonAlpha wgEncodeAwgTfbsHaibEcc1Foxa1sc6553V0416102Dm002p1hUniPk DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 (DMSO) TFBS Uniform Peaks of FOXA1_(SC-6553) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibEcc1EralphaaV0416102Gen1hUniPk ECC-1+Genist ESR1 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001575 HudsonAlpha wgEncodeAwgTfbsHaibEcc1EralphaaV0416102Gen1hUniPk Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment ECC-1 (Genistein) TFBS Uniform Peaks of ERalpha_a ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibEcc1EralphaaV0416102Est10nm1hUniPk ECC-1+Estr ESR1 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001536 HudsonAlpha wgEncodeAwgTfbsHaibEcc1EralphaaV0416102Est10nm1hUniPk Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment ECC-1 (Estradiol) TFBS Uniform Peaks of ERalpha_a ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibEcc1EraaV0416102Bpa1hUniPk ECC-1+BPA ESR1 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002313 HudsonAlpha wgEncodeAwgTfbsHaibEcc1EraaV0416102Bpa1hUniPk BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment ECC-1 (BPA) TFBS Uniform Peaks of ERalpha_a from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibEcc1CtcfcV0416102Dm002p1hUniPk ECC-1+DMSO CTCF CTCF_(SC-5916) ECC-1 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002300 HudsonAlpha wgEncodeAwgTfbsHaibEcc1CtcfcV0416102Dm002p1hUniPk DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 (DMSO) TFBS Uniform Peaks of CTCF_(SC-5916) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadDnd41Ezh239875UniPk Dnd41 EZH2 EZH2_(39875) Dnd41 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003080 Broad wgEncodeAwgTfbsBroadDnd41Ezh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadDnd41CtcfUniPk Dnd41 CTCF CTCF Dnd41 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002402 Broad wgEncodeAwgTfbsBroadDnd41CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsUwCaco2CtcfUniPk Caco-2 CTCF CTCF Caco-2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000404 UW wgEncodeAwgTfbsUwCaco2CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwBjCtcfUniPk BJ CTCF CTCF BJ std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000403 UW wgEncodeAwgTfbsUwBjCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwBe2cCtcfUniPk BE2_C CTCF CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001891 UW wgEncodeAwgTfbsUwBe2cCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2_C TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwAoafCtcfUniPk AoAF CTCF CTCF AoAF std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000980 UW wgEncodeAwgTfbsUwAoafCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwAg10803CtcfUniPk AG10803 CTCF CTCF AG10803 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000979 UW wgEncodeAwgTfbsUwAg10803CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwAg09319CtcfUniPk AG09319 CTCF CTCF AG09319 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000978 UW wgEncodeAwgTfbsUwAg09319CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwAg09309CtcfUniPk AG09309 CTCF CTCF AG09309 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000977 UW wgEncodeAwgTfbsUwAg09309CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwAg04450CtcfUniPk AG04450 CTCF CTCF AG04450 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000976 UW wgEncodeAwgTfbsUwAg04450CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUwAg04449CtcfUniPk AG04449 CTCF CTCF AG04449 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000975 UW wgEncodeAwgTfbsUwAg04449CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshTaf1V0416101UniPk SK-N-SH TAF1 TAF1 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002301 HudsonAlpha wgEncodeAwgTfbsHaibSknshTaf1V0416101UniPk None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshSin3ak20V0416101UniPk SK-N-SH SIN3AK20 Sin3Ak-20 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002271 HudsonAlpha wgEncodeAwgTfbsHaibSknshSin3ak20V0416101UniPk None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH TFBS Uniform Peaks of Sin3Ak-20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshNrsfV0416101UniPk SK-N-SH REST h2 NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002269 HudsonAlpha wgEncodeAwgTfbsHaibSknshNrsfV0416101UniPk None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH TFBS Uniform Peaks of NRSF (P:V0416101) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshNrsfPcr2xUniPk SK-N-SH REST h NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001547 HudsonAlpha wgEncodeAwgTfbsHaibSknshNrsfPcr2xUniPk None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH TFBS Uniform Peaks of NRSF (Ptcl:Pcr2x) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibSknshPol24h8V0416101UniPk SK-N-SH POLR2A Pol2-4H8 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002270 HudsonAlpha wgEncodeAwgTfbsHaibSknshPol24h8V0416101UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment SK-N-SH TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf7Znf217UcdUniPk MCF-7 ZNF217 ZNF217 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002036 USC wgEncodeAwgTfbsSydhMcf7Znf217UcdUniPk None Peaks ZNF217 is an important oncogene based on the high frequency of amplification and overexpression in many cancer types, but its molecular mode of gene regulation is poorly understood. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. ZNF217 contains seven C2H2 zinc finger domains and has been shown to bind to gene promoters mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 TFBS Uniform Peaks of ZNF217 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf7Tcf7l2UcdUniPk MCF-7 TCF7L2 TCF7L2 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002072 USC wgEncodeAwgTfbsSydhMcf7Tcf7l2UcdUniPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 TFBS Uniform Peaks of TCF7L2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7Pol2SerumstvdUniPk MCF-7+strv POLR2A Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003438 UT-A wgEncodeAwgTfbsUtaMcf7Pol2SerumstvdUniPk serum_starved_media Peaks RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Regions of enriched signal in experiment MCF-7 (serum_starved) TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7Pol2SerumstimUniPk MCF-7+stim POLR2A Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003435 UT-A wgEncodeAwgTfbsUtaMcf7Pol2SerumstimUniPk serum_stimulated_media Peaks RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Regions of enriched signal in experiment MCF-7 (serum_stimulated) TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7Pol2UniPk MCF-7 POLR2A Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001130 UT-A wgEncodeAwgTfbsUtaMcf7Pol2UniPk None Peaks RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment MCF-7 TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7CmycVehUniPk MCF-7+vehicle MYC c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001133 UT-A wgEncodeAwgTfbsUtaMcf7CmycVehUniPk vehicle Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Regions of enriched signal in experiment MCF-7 (vehicle) TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7CmycSerumstvdUniPk MCF-7+strv MYC c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003439 UT-A wgEncodeAwgTfbsUtaMcf7CmycSerumstvdUniPk serum_starved_media Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Regions of enriched signal in experiment MCF-7 (serum_starved) TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7CmycSerumstimUniPk MCF-7+stim MYC c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003436 UT-A wgEncodeAwgTfbsUtaMcf7CmycSerumstimUniPk serum_stimulated_media Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Regions of enriched signal in experiment MCF-7 (serum_stimulated) TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7CmycEstroUniPk MCF-7+estrog MYC c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001134 UT-A wgEncodeAwgTfbsUtaMcf7CmycEstroUniPk estrogen Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Regions of enriched signal in experiment MCF-7 (estrogen) TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf7Gata3sc269UcdUniPk MCF-7 GATA3 c2 GATA3_(SC-269) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002812 USC wgEncodeAwgTfbsSydhMcf7Gata3sc269UcdUniPk None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 TFBS Uniform Peaks of GATA3_(SC-269) from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf7Gata3UcdUniPk MCF-7 GATA3 c GATA3_(SC-268) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002035 USC wgEncodeAwgTfbsSydhMcf7Gata3UcdUniPk None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 TFBS Uniform Peaks of GATA3_(SC-268) from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhMcf7Hae2f1UcdUniPk MCF-7 E2F1 HA-E2F1 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000693 USC wgEncodeAwgTfbsSydhMcf7Hae2f1UcdUniPk None Peaks The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 TFBS Uniform Peaks of HA-E2F1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsUwMcf7CtcfUniPk MCF-7 CTCF w CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002057 UW wgEncodeAwgTfbsUwMcf7CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7CtcfVehUniPk MCF-7+vehicl CTCF CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001132 UT-A wgEncodeAwgTfbsUtaMcf7CtcfVehUniPk vehicle Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Regions of enriched signal in experiment MCF-7 (vehicle) TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7CtcfSerumstvdUniPk MCF-7+stv CTCF CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003437 UT-A wgEncodeAwgTfbsUtaMcf7CtcfSerumstvdUniPk serum_starved_media Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Regions of enriched signal in experiment MCF-7 (serum_starved) TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7CtcfSerumstimUniPk MCF-7+stim CTCF CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003434 UT-A wgEncodeAwgTfbsUtaMcf7CtcfSerumstimUniPk serum_stimulated_media Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Regions of enriched signal in experiment MCF-7 (serum_stimulated) TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7CtcfEstroUniPk MCF-7+estrog CTCF CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001131 UT-A wgEncodeAwgTfbsUtaMcf7CtcfEstroUniPk estrogen Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Regions of enriched signal in experiment MCF-7 (estrogen) TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsUtaMcf7CtcfUniPk MCF-7 CTCF t CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000598 UT-A wgEncodeAwgTfbsUtaMcf7CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment MCF-7 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhImr90Rad21IggrabUniPk IMR90 RAD21 Rad21 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002810 Stanford wgEncodeAwgTfbsSydhImr90Rad21IggrabUniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment IMR90 TFBS Uniform Peaks of Rad21 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhImr90Pol2IggrabUniPk IMR90 POLR2A Pol2 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002809 Stanford wgEncodeAwgTfbsSydhImr90Pol2IggrabUniPk None Peaks RNA Polymerase II fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment IMR90 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhImr90MafkIggrabUniPk IMR90 MAFK MafK_(ab50322) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002832 Stanford wgEncodeAwgTfbsSydhImr90MafkIggrabUniPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment IMR90 TFBS Uniform Peaks of MafK_(ab50322) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhImr90CtcfbIggrabUniPk IMR90 CTCF CTCF_(SC-15914) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002831 Stanford wgEncodeAwgTfbsSydhImr90CtcfbIggrabUniPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment IMR90 TFBS Uniform Peaks of CTCF_(SC-15914) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhImr90CebpbIggrabUniPk IMR90 CEBPB CEBPB IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002807 Stanford wgEncodeAwgTfbsSydhImr90CebpbIggrabUniPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment IMR90 TFBS Uniform Peaks of CEBPB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Zbtb33V0422111Etoh02UniPk A549+Et.02 ZBTB33 ZBTB33 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002295 HudsonAlpha wgEncodeAwgTfbsHaibA549Zbtb33V0422111Etoh02UniPk EtOH_0.02pct Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of ZBTB33 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Yy1cV0422111Etoh02UniPk A549+Et.02 YY1 YY1_(SC-281) A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002282 HudsonAlpha wgEncodeAwgTfbsHaibA549Yy1cV0422111Etoh02UniPk EtOH_0.02pct Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of YY1_(SC-281) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Usf1V0422111Etoh02UniPk A549+Et02 USF1 h2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002291 HudsonAlpha wgEncodeAwgTfbsHaibA549Usf1V0422111Etoh02UniPk EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of USF-1 (P:V042) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Usf1Pcr1xEtoh02UniPk A549+Et02 USF1 h1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001539 HudsonAlpha wgEncodeAwgTfbsHaibA549Usf1Pcr1xEtoh02UniPk EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of USF-1 (P:Pcr1) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Usf1Pcr1xDex100nmUniPk A549+Dx100n USF1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001509 HudsonAlpha wgEncodeAwgTfbsHaibA549Usf1Pcr1xDex100nmUniPk DEX_100nM Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 (DEX_100nM) TFBS Uniform Peaks of USF-1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Tcf12V0422111Etoh02UniPk A549+Et.02 TCF12 TCF12 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002312 HudsonAlpha wgEncodeAwgTfbsHaibA549Tcf12V0422111Etoh02UniPk EtOH_0.02pct Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of TCF12 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Taf1V0422111Etoh02UniPk A549+Et.02 TAF1 TAF1 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002275 HudsonAlpha wgEncodeAwgTfbsHaibA549Taf1V0422111Etoh02UniPk EtOH_0.02pct Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Six5V0422111Etoh02UniPk A549+Et.02 SIX5 SIX5 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002341 HudsonAlpha wgEncodeAwgTfbsHaibA549Six5V0422111Etoh02UniPk EtOH_0.02pct Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of SIX5 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Sin3ak20V0422111Etoh02UniPk A549+E2 SIN3AK20 Sin3Ak-20 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002342 HudsonAlpha wgEncodeAwgTfbsHaibA549Sin3ak20V0422111Etoh02UniPk EtOH_0.02pct Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of Sin3Ak-20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549NrsfV0422111Etoh02UniPk A549+Et.02 REST NRSF A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002311 HudsonAlpha wgEncodeAwgTfbsHaibA549NrsfV0422111Etoh02UniPk EtOH_0.02pct Peaks Neuron-restrictive silencer transcription factor epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of NRSF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhA549Rad21IggrabUniPk A549 RAD21 Rad21 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002822 Stanford wgEncodeAwgTfbsSydhA549Rad21IggrabUniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment A549 TFBS Uniform Peaks of Rad21 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsUtaA549Pol2UniPk A549 POLR2A t Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002079 UT-A wgEncodeAwgTfbsUtaA549Pol2UniPk None Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment A549 TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhA549Pol2s2IggrabUniPk A549 POLR2A s Pol2(phosphoS2) A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002821 Stanford wgEncodeAwgTfbsSydhA549Pol2s2IggrabUniPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment A549 TFBS Uniform Peaks of Pol2(phosphoS2) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Pol2Pcr2xEtoh02UniPk A549+Et.02 POLR2A Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001493 HudsonAlpha wgEncodeAwgTfbsHaibA549Pol2Pcr2xEtoh02UniPk EtOH_0.02pct Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Pol2Pcr2xDex100nmUniPk A549+Dx100 POLR2A Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001494 HudsonAlpha wgEncodeAwgTfbsHaibA549Pol2Pcr2xDex100nmUniPk DEX_100nM Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 (DEX_100nM) TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549GrPcr1xDex5nmUniPk A549+Dx5nM NR3C1 GR A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001492 HudsonAlpha wgEncodeAwgTfbsHaibA549GrPcr1xDex5nmUniPk DEX_5nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 5 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 (DEX_5nM) TFBS Uniform Peaks of GR from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549GrPcr1xDex50nmUniPk A549+Dx50nM NR3C1 GR A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001491 HudsonAlpha wgEncodeAwgTfbsHaibA549GrPcr1xDex50nmUniPk DEX_50nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 50 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 (DEX_50nM) TFBS Uniform Peaks of GR from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549GrPcr1xDex500pmUniPk A549+Dx500p NR3C1 GR A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001490 HudsonAlpha wgEncodeAwgTfbsHaibA549GrPcr1xDex500pmUniPk DEX_500pM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 500 pM Dexamethasone (Myers) Regions of enriched signal in experiment A549 (DEX_500pM) TFBS Uniform Peaks of GR from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549GrPcr2xDex100nmUniPk A549+Dx100n NR3C1 GR A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001555 HudsonAlpha wgEncodeAwgTfbsHaibA549GrPcr2xDex100nmUniPk DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 (DEX_100nM) TFBS Uniform Peaks of GR from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhA549MaxIggrabUniPk A549 MAX Max A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002820 Stanford wgEncodeAwgTfbsSydhA549MaxIggrabUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment A549 TFBS Uniform Peaks of Max from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibA549GabpV0422111Etoh02UniPk A549+Et.02 GABPA GABP A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002294 HudsonAlpha wgEncodeAwgTfbsHaibA549GabpV0422111Etoh02UniPk EtOH_0.02pct Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of GABP from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Foxa1V0416102Dex100nmUniPk A549+Dx100n FOXA1 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002293 HudsonAlpha wgEncodeAwgTfbsHaibA549Foxa1V0416102Dex100nmUniPk DEX_100nM Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 (DEX_100nM) TFBS Uniform Peaks of FOXA1_(SC-101058) ENCODE/HudsonA/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Fosl2V0422111Etoh02UniPk A549+Et.02 FOSL2 FOSL2 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002310 HudsonAlpha wgEncodeAwgTfbsHaibA549Fosl2V0422111Etoh02UniPk EtOH_0.02pct Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of FOSL2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Ets1V0422111Etoh02UniPk A549+Et.02 ETS1 ETS1 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002290 HudsonAlpha wgEncodeAwgTfbsHaibA549Ets1V0422111Etoh02UniPk EtOH_0.02pct Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of ETS1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549P300V0422111Etoh02UniPk A549+Et.02 EP300 p300 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002292 HudsonAlpha wgEncodeAwgTfbsHaibA549P300V0422111Etoh02UniPk EtOH_0.02pct Peaks EP300(c-20) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of p300 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Elf1V0422111Etoh02UniPk A549+Et.02 ELF1 ELF1_(SC-631) A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002289 HudsonAlpha wgEncodeAwgTfbsHaibA549Elf1V0422111Etoh02UniPk EtOH_0.02pct Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of ELF1_(SC-631) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUwA549CtcfUniPk A549 CTCF w CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001890 UW wgEncodeAwgTfbsUwA549CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaA549CtcfUniPk A549 CTCF t CTCF A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002078 UT-A wgEncodeAwgTfbsUtaA549CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment A549 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Ctcfsc5916Pcr1xEtoh02UniPk A549+Et.02 CTCF CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001508 HudsonAlpha wgEncodeAwgTfbsHaibA549Ctcfsc5916Pcr1xEtoh02UniPk EtOH_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of CTCF_(SC-5916) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Ctcfsc5916Pcr1xDex100nmUniPk A549+Dx100n CTCF CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001507 HudsonAlpha wgEncodeAwgTfbsHaibA549Ctcfsc5916Pcr1xDex100nmUniPk DEX_100nM Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 (DEX_100nM) TFBS Uniform Peaks of CTCF_(SC-5916) ENCODE/HudsonAlph/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Creb1sc240V0416102Dex100nmUniPk A549+Dx100n CREB1 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002323 HudsonAlpha wgEncodeAwgTfbsHaibA549Creb1sc240V0416102Dex100nmUniPk DEX_100nM Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 (DEX_100nM) TFBS Uniform Peaks of CREB1_(SC-240) ENCODE/HudsonAlph/Analysis Regulation 
wgEncodeAwgTfbsSydhA549CebpbIggrabUniPk A549 CEBPB CEBPB A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002818 Stanford wgEncodeAwgTfbsSydhA549CebpbIggrabUniPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment A549 TFBS Uniform Peaks of CEBPB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhA549Bhlhe40IggrabUniPk A549 BHLHE40 BHLHE40 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002817 Stanford wgEncodeAwgTfbsSydhA549Bhlhe40IggrabUniPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment A549 TFBS Uniform Peaks of BHLHE40 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Bcl3V0422111Etoh02UniPk A549+Et.02 BCL3 BCL3 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002303 HudsonAlpha wgEncodeAwgTfbsHaibA549Bcl3V0422111Etoh02UniPk EtOH_0.02pct Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of BCL3 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibA549Atf3V0422111Etoh02UniPk A549+Et.02 ATF3 ATF3 A549 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002288 HudsonAlpha wgEncodeAwgTfbsHaibA549Atf3V0422111Etoh02UniPk EtOH_0.02pct Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 (EtOH .02) TFBS Uniform Peaks of ATF3 ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUtaHuvecPol2UniPk HUVEC POLR2A t Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000552 UT-A wgEncodeAwgTfbsUtaHuvecPol2UniPk None Peaks RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhHuvecPol2UniPk HUVEC POLR2A s Pol2 HUVEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000702 Stanford wgEncodeAwgTfbsSydhHuvecPol2UniPk None Peaks RNA Polymerase II umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHuvecPol2Pcr1xUniPk HUVEC POLR2A h2 Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002297 HudsonAlpha wgEncodeAwgTfbsHaibHuvecPol2Pcr1xUniPk None Peaks RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHuvecPol24h8V0416101UniPk HUVEC POLR2A h Pol2-4H8 HUVEC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002298 HudsonAlpha wgEncodeAwgTfbsHaibHuvecPol24h8V0416101UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. umbilical vein endothelial cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadHuvecPol2bUniPk HUVEC POLR2A b Pol2(b) HUVEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000061 Broad wgEncodeAwgTfbsBroadHuvecPol2bUniPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of Pol2(b) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsUtaHuvecCmycUniPk HUVEC MYC c-Myc HUVEC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000561 UT-A wgEncodeAwgTfbsUtaHuvecCmycUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease umbilical vein endothelial cells Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhHuvecMaxUniPk HUVEC MAX Max HUVEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000768 Stanford wgEncodeAwgTfbsSydhHuvecMaxUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of Max from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHuvecCjunUniPk HUVEC JUN c-Jun HUVEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000719 Stanford wgEncodeAwgTfbsSydhHuvecCjunUniPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of c-Jun from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHuvecGata2UcdUniPk HUVEC GATA2 GATA-2 HUVEC UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001758 USC wgEncodeAwgTfbsSydhHuvecGata2UcdUniPk None Peaks GATA binding protein 2 umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of GATA-2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHuvecCfosUcdUniPk HUVEC FOS c-Fos HUVEC UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001774 USC wgEncodeAwgTfbsSydhHuvecCfosUcdUniPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of c-Fos from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsBroadHuvecEzh239875UniPk HUVEC EZH2 EZH2_(39875) HUVEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003084 Broad wgEncodeAwgTfbsBroadHuvecEzh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsUwHuvecCtcfUniPk HUVEC CTCF w CTCF HUVEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000410 UW wgEncodeAwgTfbsUwHuvecCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaHuvecCtcfUniPk HUVEC CTCF t CTCF HUVEC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000551 UT-A wgEncodeAwgTfbsUtaHuvecCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsBroadHuvecCtcfUniPk HUVEC CTCF b CTCF HUVEC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000054 Broad wgEncodeAwgTfbsBroadHuvecCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Znf274UcdUniPk HepG2 ZNF274 ZNF274 HepG2 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001755 USC wgEncodeAwgTfbsSydhHepg2Znf274UcdUniPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of ZNF274 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Zbtb7aV0416101UniPk HepG2 ZBTB7A ZBTB7A_(SC-34508) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002296 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Zbtb7aV0416101UniPk None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of ZBTB7A_(SC-34508) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Zbtb33Pcr1xUniPk HepG2 ZBTB33 ZBTB33 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001503 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Zbtb33Pcr1xUniPk None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of ZBTB33 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Yy1sc281V0416101UniPk HepG2 YY1 YY1_(SC-281) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001661 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Yy1sc281V0416101UniPk None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of YY1_(SC-281) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Usf2IggrabUniPk HepG2 USF2 USF2 HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001804 Stanford wgEncodeAwgTfbsSydhHepg2Usf2IggrabUniPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of USF2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Usf1Pcr1xUniPk HepG2 USF1 USF-1 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001472 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Usf1Pcr1xUniPk None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of USF-1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Tead4sc101184V0422111UniPk HepG2 TEAD4 TEAD4_(SC-101184) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002345 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Tead4sc101184V0422111UniPk None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of TEAD4_(SC-101184) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Tcf7l2UcdUniPk HepG2 TCF7L2 TCF7L2 HepG2 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001780 USC wgEncodeAwgTfbsSydhHepg2Tcf7l2UcdUniPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of TCF7L2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Tcf12Pcr1xUniPk HepG2 TCF12 TCF12 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001544 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Tcf12Pcr1xUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of TCF12 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2TbpIggrabUniPk HepG2 TBP TBP HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001793 Stanford wgEncodeAwgTfbsSydhHepg2TbpIggrabUniPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of TBP from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Taf1Pcr2xUniPk HepG2 TAF1 TAF1 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001551 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Taf1Pcr2xUniPk None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2SrfV0416101UniPk HepG2 SRF SRF HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001611 HudsonAlpha wgEncodeAwgTfbsHaibHepg2SrfV0416101UniPk None Peaks Serum response transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of SRF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Srebp1InslnUniPk HepG2+insl SREBP1 SREBP1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000759 Stanford wgEncodeAwgTfbsSydhHepg2Srebp1InslnUniPk insulin Peaks Sterol regulatory element binding transcription factor 1 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder) Regions of enriched signal in experiment HepG2 (insulin) TFBS Uniform Peaks of SREBP1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Sp2V0422111UniPk HepG2 SP2 SP2_(SC-643) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002264 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Sp2V0422111UniPk None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of SP2_(SC-643) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Sp1Pcr1xUniPk HepG2 SP1 SP1 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001561 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Sp1Pcr1xUniPk None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of SP1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Smc3ab9263IggrabUniPk HepG2 SMC3 SMC3_(ab9263) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001861 Stanford wgEncodeAwgTfbsSydhHepg2Smc3ab9263IggrabUniPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of SMC3_(ab9263) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Sin3ak20Pcr1xUniPk HepG2 SIN3AK20 Sin3Ak-20 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001471 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Sin3ak20Pcr1xUniPk None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Sin3Ak-20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2RxraPcr1xUniPk HepG2 RXRA RXRA HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001506 HudsonAlpha wgEncodeAwgTfbsHaibHepg2RxraPcr1xUniPk None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of RXRA from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Rfx5200401194IggrabUniPk HepG2 RFX5 RFX5_(200-401-194) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001843 Stanford wgEncodeAwgTfbsSydhHepg2Rfx5200401194IggrabUniPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of RFX5_(200-401-194) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2NrsfV0416101UniPk HepG2 REST h2 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002263 HudsonAlpha wgEncodeAwgTfbsHaibHepg2NrsfV0416101UniPk None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of NRSF (P:V0415101) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2NrsfPcr2xUniPk HepG2 REST h NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001549 HudsonAlpha wgEncodeAwgTfbsHaibHepg2NrsfPcr2xUniPk None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of NRSF (Ptcl:Pcr2x) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Corestsc30189IggrabUniPk HepG2 RCOR1 COREST_(sc-30189) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002845 Stanford wgEncodeAwgTfbsSydhHepg2Corestsc30189IggrabUniPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of COREST_(sc-30189) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Rad21IggrabUniPk HepG2 RAD21 s Rad21 HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001803 Stanford wgEncodeAwgTfbsSydhHepg2Rad21IggrabUniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Rad21 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Rad21V0416101UniPk HepG2 RAD21 h Rad21 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001608 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Rad21V0416101UniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Rad21 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Pgc1aForsklnUniPk HepG2+forsk PGC1A PGC1A HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000757 Stanford wgEncodeAwgTfbsSydhHepg2Pgc1aForsklnUniPk forskolin Peaks The protein encoded by this gene is a transcriptional coactivator that regulates the genes involved in energy metabolism. This protein interacts with PPARgamma, which permits the interaction of this protein with multiple transcription factors. This protein can interact with, and regulate the activities of, cAMP response element binding protein (CREB) and nuclear respiratory factors (NRFs). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HepG2 (forskolin) TFBS Uniform Peaks of PGC1A from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsUtaHepg2Pol2UniPk HepG2 POLR2A t Pol2 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000554 UT-A wgEncodeAwgTfbsUtaHepg2Pol2UniPk None Peaks RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Pol2ForsklnUniPk HepG2+fors POLR2A Pol2 HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000758 Stanford wgEncodeAwgTfbsSydhHepg2Pol2ForsklnUniPk forskolin Peaks RNA Polymerase II hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HepG2 (forskolin) TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Pol2s2IggrabUniPk HepG2 POLR2A s2 Pol2(phosphoS2) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001860 Stanford wgEncodeAwgTfbsSydhHepg2Pol2s2IggrabUniPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Pol2(phosphoS2) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Pol2IggrabUniPk HepG2 POLR2A s Pol2 HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001792 Stanford wgEncodeAwgTfbsSydhHepg2Pol2IggrabUniPk None Peaks RNA Polymerase II hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Pol2Pcr2xUniPk HepG2 POLR2A h2 Pol2 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001550 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Pol2Pcr2xUniPk None Peaks RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Pol24h8V0416102UniPk HepG2 POLR2A h Pol2-4H8 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002278 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Pol24h8V0416102UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Nrf1IggrabUniPk HepG2 NRF1 Nrf1 HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001802 Stanford wgEncodeAwgTfbsSydhHepg2Nrf1IggrabUniPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Nrf1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Tr4UcdUniPk HepG2 NR2C2 TR4 HepG2 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000675 USC wgEncodeAwgTfbsSydhHepg2Tr4UcdUniPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of TR4 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Nficsc81335V0422111UniPk HepG2 NFIC NFIC_(SC-81335) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002319 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Nficsc81335V0422111UniPk None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of NFIC_(SC-81335) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUtaHepg2CmycUniPk HepG2 MYC c-Myc HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000545 UT-A wgEncodeAwgTfbsUtaHepg2CmycUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease hepatocellular carcinoma Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Mybl2sc81192V0422111UniPk HepG2 MYBL2 MYBL2_(SC-81192) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002344 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Mybl2sc81192V0422111UniPk None Peaks The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of MYBL2_(SC-81192) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Mxi1UniPk HepG2 MXI1 Mxi1_(AF4185) HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002029 Stanford wgEncodeAwgTfbsSydhHepg2Mxi1UniPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Mxi1_(AF4185) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Mbd4sc271530V0422111UniPk HepG2 MBD4 MBD4_(SC-271530) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002318 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Mbd4sc271530V0422111UniPk None Peaks MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of MBD4_(SC-271530) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Mazab85725IggrabUniPk HepG2 MAZ MAZ_(ab85725) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002860 Stanford wgEncodeAwgTfbsSydhHepg2Mazab85725IggrabUniPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of MAZ_(ab85725) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2MaxIggrabUniPk HepG2 MAX Max HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002796 Stanford wgEncodeAwgTfbsSydhHepg2MaxIggrabUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of Max from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Mafksc477IggrabUniPk HepG2 MAFK s2 MafK_(SC-477) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001850 Stanford wgEncodeAwgTfbsSydhHepg2Mafksc477IggrabUniPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of MafK_(SC-477) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Mafkab50322IggrabUniPk HepG2 MAFK s MafK_(ab50322) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001842 Stanford wgEncodeAwgTfbsSydhHepg2Mafkab50322IggrabUniPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of MafK_(ab50322) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Maffm8194IggrabUniPk HepG2 MAFF MafF_(M8194) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001841 Stanford wgEncodeAwgTfbsSydhHepg2Maffm8194IggrabUniPk None Peaks The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of MafF_(M8194) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2JundIggrabUniPk HepG2 JUND s JunD HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001801 Stanford wgEncodeAwgTfbsSydhHepg2JundIggrabUniPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of JunD from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2JundPcr1xUniPk HepG2 JUND h JunD HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001470 HudsonAlpha wgEncodeAwgTfbsHaibHepg2JundPcr1xUniPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of JunD from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2CjunIggrabUniPk HepG2 JUN c-Jun HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001794 Stanford wgEncodeAwgTfbsSydhHepg2CjunIggrabUniPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of c-Jun from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Irf3IggrabUniPk HepG2 IRF3 IRF3 HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001800 Stanford wgEncodeAwgTfbsSydhHepg2Irf3IggrabUniPk None Peaks Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of IRF3 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Hsf1ForsklnUniPk HepG2+forsk HSF1 HSF1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000754 Stanford wgEncodeAwgTfbsSydhHepg2Hsf1ForsklnUniPk forskolin Peaks Epitope corresponding to amino acids 219-529 of heat shock transcription factor 1 (HSF1) of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HepG2 (forskolin) TFBS Uniform Peaks of HSF1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Hnf4gsc6558V0416101UniPk HepG2 HNF4G HNF4G_(SC-6558) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001651 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Hnf4gsc6558V0416101UniPk None Peaks Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of HNF4G_(SC-6558) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Hnf4aForsklnUniPk HepG2+forsk HNF4A HNF4A HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000753 Stanford wgEncodeAwgTfbsSydhHepg2Hnf4aForsklnUniPk forskolin Peaks Epitope mapping at the C-terminus of Rab 11 of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HepG2 (forskolin) TFBS Uniform Peaks of HNF4A from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Hnf4asc8987V0416101UniPk HepG2 HNF4A HNF4A_(SC-8987) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001595 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Hnf4asc8987V0416101UniPk None Peaks The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of HNF4A_(SC-8987) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Hdac2sc6296V0416101UniPk HepG2 HDAC2 HDAC2_(SC-6296) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001618 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Hdac2sc6296V0416101UniPk None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of HDAC2_(SC-6296) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Grp20ForsklnUniPk HepG2+forsk GRp20 GRp20 HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000752 Stanford wgEncodeAwgTfbsSydhHepg2Grp20ForsklnUniPk forskolin Peaks Epitope mapping at the C-terminus of GR alpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HepG2 (forskolin) TFBS Uniform Peaks of GRp20 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2GabpPcr2xUniPk HepG2 GABPA GABP HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001548 HudsonAlpha wgEncodeAwgTfbsHaibHepg2GabpPcr2xUniPk None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of GABP from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Foxa2sc6554V0416101UniPk HepG2 FOXA2 FOXA2_(SC-6554) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001650 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Foxa2sc6554V0416101UniPk None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of FOXA2_(SC-6554) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Foxa1sc6553V0416101UniPk HepG2 FOXA1 h2 FOXA1_(SC-6553) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001594 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Foxa1sc6553V0416101UniPk None Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of FOXA1_(SC-6553) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Foxa1sc101058V0416101UniPk HepG2 FOXA1 h FOXA1_(SC-101058) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001630 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Foxa1sc101058V0416101UniPk None Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of FOXA1_(SC-101058) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Fosl2V0416101UniPk HepG2 FOSL2 FOSL2 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001501 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Fosl2V0416101UniPk None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of FOSL2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadHepg2Ezh239875UniPk HepG2 EZH2 EZH2_(39875) HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002416 Broad wgEncodeAwgTfbsBroadHepg2Ezh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2ErraForsklnUniPk HepG2+forsk ESRRA ERRA HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000751 Stanford wgEncodeAwgTfbsSydhHepg2ErraForsklnUniPk forskolin Peaks Epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HepG2 (forskolin) TFBS Uniform Peaks of ERRA from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2P300sc582IggrabUniPk HepG2 EP300 s p300_(SC-584) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001862 Stanford wgEncodeAwgTfbsSydhHepg2P300sc582IggrabUniPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of p300_(SC-584) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2P300V0416101UniPk HepG2 EP300 h p300 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001612 HudsonAlpha wgEncodeAwgTfbsHaibHepg2P300V0416101UniPk None Peaks EP300(c-20) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of p300 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Elf1sc631V0416101UniPk HepG2 ELF1 ELF1_(SC-631) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001641 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Elf1sc631V0416101UniPk None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of ELF1_(SC-631) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUwHepg2CtcfUniPk HepG2 CTCF w CTCF HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000401 UW wgEncodeAwgTfbsUwHepg2CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaHepg2CtcfUniPk HepG2 CTCF t CTCF HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000543 UT-A wgEncodeAwgTfbsUtaHepg2CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Ctcfsc5916V0416101UniPk HepG2 CTCF h CTCF_(SC-5916) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001516 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Ctcfsc5916V0416101UniPk None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of CTCF_(SC-5916) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadHepg2CtcfUniPk HepG2 CTCF b CTCF HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000080 Broad wgEncodeAwgTfbsBroadHepg2CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Chd2ab68301IggrabUniPk HepG2 CHD2 CHD2_(AB68301) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001840 Stanford wgEncodeAwgTfbsSydhHepg2Chd2ab68301IggrabUniPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of CHD2_(AB68301) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Cebpdsc636V0416101UniPk HepG2 CEBPD h2 CEBPD_(SC-636) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002305 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Cebpdsc636V0416101UniPk None Peaks The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of CEBPD_(SC-636) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2CebpbForsklnUniPk HepG2+forsk CEBPB CEBPB HepG2 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000750 Stanford wgEncodeAwgTfbsSydhHepg2CebpbForsklnUniPk forskolin Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HepG2 (forskolin) TFBS Uniform Peaks of CEBPB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2CebpbIggrabUniPk HepG2 CEBPB s CEBPB HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001829 Stanford wgEncodeAwgTfbsSydhHepg2CebpbIggrabUniPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of CEBPB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Cebpbsc150V0416101UniPk HepG2 CEBPB h CEBPB_(SC-150) HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002304 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Cebpbsc150V0416101UniPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of CEBPB_(SC-150) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Brca1a300IggrabUniPk HepG2 BRCA1 BRCA1_(A300-000A) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001859 Stanford wgEncodeAwgTfbsSydhHepg2Brca1a300IggrabUniPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of BRCA1_(A300-000A) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Bhlhe40cIggrabUniPk HepG2 BHLHE40 s BHLHE40_(NB100-1800) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002032 Stanford wgEncodeAwgTfbsSydhHepg2Bhlhe40cIggrabUniPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of BHLHE40_(NB100-1800) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Bhlhe40V0416101UniPk HepG2 BHLHE40 h BHLHE40 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001515 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Bhlhe40V0416101UniPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of BHLHE40 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibHepg2Atf3V0416101UniPk HepG2 ATF3 ATF3 HepG2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001568 HudsonAlpha wgEncodeAwgTfbsHaibHepg2Atf3V0416101UniPk None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. hepatocellular carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of ATF3 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHepg2Arid3anb100279IggrabUniPk HepG2 ARID3A ARID3A_(NB100-279) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002858 Stanford wgEncodeAwgTfbsSydhHepg2Arid3anb100279IggrabUniPk None Peaks This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HepG2 TFBS Uniform Peaks of ARID3A_(NB100-279) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Zzz3UniPk HeLa-S3 ZZZ3 ZZZ3 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001872 Harvard wgEncodeAwgTfbsSydhHelas3Zzz3UniPk None Peaks ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of ZZZ3 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Znf274UcdUniPk HeLa-S3 ZNF274 ZNF274 HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001763 USC wgEncodeAwgTfbsSydhHelas3Znf274UcdUniPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of ZNF274 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Znf143IggrabUniPk HeLa-S3 ZNF143 Znf143_(16618-1-AP) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002028 Stanford wgEncodeAwgTfbsSydhHelas3Znf143IggrabUniPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Znf143_(16618-1-AP) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Zkscan1hpa006672IggrabUniPk HeLa-S3 ZKSCAN1 ZKSCAN1_(HPA006672) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002857 Stanford wgEncodeAwgTfbsSydhHelas3Zkscan1hpa006672IggrabUniPk None Peaks The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of ZKSCAN1_(HPA006672) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Usf2IggmusUniPk HeLa-S3 USF2 USF2 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001819 Stanford wgEncodeAwgTfbsSydhHelas3Usf2IggmusUniPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of USF2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Ap2gammaUniPk HeLa-S3 TFAP2C AP-2gamma HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000686 USC wgEncodeAwgTfbsSydhHelas3Ap2gammaUniPk None Peaks Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5'-GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of AP-2gamma from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Ap2alphaUniPk HeLa-S3 TFAP2A AP-2alpha HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000685 USC wgEncodeAwgTfbsSydhHelas3Ap2alphaUniPk None Peaks Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5' -GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. AP-2alpha is the only AP-2 protein required for early morphogenesis of the lens vesicle (by similarity). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of AP-2alpha from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Tcf7l2c9b92565UcdUniPk HeLa-S3 TCF7L2 c2 TCF7L2_C9B9_(2565) HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002813 USC wgEncodeAwgTfbsSydhHelas3Tcf7l2c9b92565UcdUniPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of TCF7L2_C9B9_(2565) from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Tcf7l2UcdUniPk HeLa-S3 TCF7L2 c TCF7L2 HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002069 USC wgEncodeAwgTfbsSydhHelas3Tcf7l2UcdUniPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of TCF7L2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3TbpIggrabUniPk HeLa-S3 TBP TBP HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001790 Stanford wgEncodeAwgTfbsSydhHelas3TbpIggrabUniPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of TBP from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHelas3Taf1Pcr1xUniPk HeLa-S3 TAF1 TAF1 HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001505 HudsonAlpha wgEncodeAwgTfbsHaibHelas3Taf1Pcr1xUniPk None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. cervical carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Stat3IggrabUniPk HeLa-S3 STAT3 STAT3 HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001799 Stanford wgEncodeAwgTfbsSydhHelas3Stat3IggrabUniPk None Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of STAT3 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Stat1Ifng30UniPk HeLa-S3+IFg STAT1 STAT1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000614 Yale wgEncodeAwgTfbsSydhHelas3Stat1Ifng30UniPk IFNg30 Peaks transcription factor, activated by interferon signalling cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment HeLa-S3 (IFNg30) TFBS Uniform Peaks of STAT1 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Smc3ab9263IggrabUniPk HeLa-S3 SMC3 SMC3_(ab9263) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001839 Stanford wgEncodeAwgTfbsSydhHelas3Smc3ab9263IggrabUniPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of SMC3_(ab9263) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Baf170IggmusUniPk HeLa-S3 SMARCC2 BAF170 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000721 Stanford wgEncodeAwgTfbsSydhHelas3Baf170IggmusUniPk None Peaks BAF170 (SMARCC2, Brg1-Associated Factor, 170 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of BAF170 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Baf155IggmusUniPk HeLa-S3 SMARCC1 BAF155 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000720 Stanford wgEncodeAwgTfbsSydhHelas3Baf155IggmusUniPk None Peaks BAF155 (SMARCC1, Brg1-Associated Factor, 155 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of BAF155 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Ini1IggmusUniPk HeLa-S3 SMARCB1 Ini1 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000722 Stanford wgEncodeAwgTfbsSydhHelas3Ini1IggmusUniPk None Peaks Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Ini1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Brg1IggmusUniPk HeLa-S3 SMARCA4 Brg1 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000781 Yale wgEncodeAwgTfbsSydhHelas3Brg1IggmusUniPk None Peaks Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Brg1 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Rpc155UniPk HeLa-S3 RPC155 RPC155 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000766 Harvard wgEncodeAwgTfbsSydhHelas3Rpc155UniPk None Peaks polymerase (RNA) III (DNA directed) polypeptide A, 155kDa cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of RPC155 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Rfx5200401194IggrabUniPk HeLa-S3 RFX5 RFX5_(200-401-194) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001818 Stanford wgEncodeAwgTfbsSydhHelas3Rfx5200401194IggrabUniPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of RFX5_(200-401-194) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHelas3NrsfPcr1xUniPk HeLa-S3 REST NRSF HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001629 HudsonAlpha wgEncodeAwgTfbsHaibHelas3NrsfPcr1xUniPk None Peaks Neuron-restrictive silencer transcription factor cervical carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of NRSF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Corestsc30189IggrabUniPk HeLa-S3 RCOR1 COREST_(sc-30189) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002844 Stanford wgEncodeAwgTfbsSydhHelas3Corestsc30189IggrabUniPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of COREST_(sc-30189) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Rad21IggrabUniPk HeLa-S3 RAD21 Rad21 HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001789 Stanford wgEncodeAwgTfbsSydhHelas3Rad21IggrabUniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Rad21 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Prdm19115IggrabUniPk HeLa-S3 PRDM1 PRDM1_(9115) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001817 Stanford wgEncodeAwgTfbsSydhHelas3Prdm19115IggrabUniPk None Peaks Transcriptional repressor that binds specifically to the PRDI element in the promoter of the beta-interferon gene. Drives the maturation of B-lymphocytes into Ig secreting cells. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of PRDM1_(9115) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Pol2UniPk HeLa-S3 POLR2A y Pol2 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000613 Yale wgEncodeAwgTfbsSydhHelas3Pol2UniPk None Peaks RNA Polymerase II cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Pol2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsUtaHelas3Pol2UniPk HeLa-S3 POLR2A t Pol2 HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000597 UT-A wgEncodeAwgTfbsUtaHelas3Pol2UniPk None Peaks RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Pol2s2IggrabUniPk HeLa-S3 POLR2A s Pol2(phosphoS2) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001838 Stanford wgEncodeAwgTfbsSydhHelas3Pol2s2IggrabUniPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Pol2(phosphoS2) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHelas3Pol2Pcr1xUniPk HeLa-S3 POLR2A h Pol2 HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001474 HudsonAlpha wgEncodeAwgTfbsHaibHelas3Pol2Pcr1xUniPk None Peaks RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadHelas3Pol2bUniPk HeLa-S3 POLR2A b Pol2(b) HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001021 Broad wgEncodeAwgTfbsBroadHelas3Pol2bUniPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Pol2(b) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Nrf1IggmusUniPk HeLa-S3 NRF1 Nrf1 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000723 Stanford wgEncodeAwgTfbsSydhHelas3Nrf1IggmusUniPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Nrf1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Tr4UniPk HeLa-S3 NR2C2 TR4 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000687 USC wgEncodeAwgTfbsSydhHelas3Tr4UniPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of TR4 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3NfybIggrabUniPk HeLa-S3 NFYB NF-YB HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002067 Harvard wgEncodeAwgTfbsSydhHelas3NfybIggrabUniPk None Peaks NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of NF-YB from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3NfyaIggrabUniPk HeLa-S3 NFYA NF-YA HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002066 Harvard wgEncodeAwgTfbsSydhHelas3NfyaIggrabUniPk None Peaks NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of NF-YA from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3CmycUniPk HeLa-S3 MYC y c-Myc HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000648 Yale wgEncodeAwgTfbsSydhHelas3CmycUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of c-Myc from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsUtaHelas3CmycUniPk HeLa-S3 MYC t c-Myc HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000542 UT-A wgEncodeAwgTfbsUtaHelas3CmycUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Mxi1af4185IggrabUniPk HeLa-S3 MXI1 Mxi1_(AF4185) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001826 Stanford wgEncodeAwgTfbsSydhHelas3Mxi1af4185IggrabUniPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Mxi1_(AF4185) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Mazab85725IggrabUniPk HeLa-S3 MAZ MAZ_(ab85725) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002855 Stanford wgEncodeAwgTfbsSydhHelas3Mazab85725IggrabUniPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of MAZ_(ab85725) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3MaxIggrabUniPk HeLa-S3 MAX Max HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002830 Stanford wgEncodeAwgTfbsSydhHelas3MaxIggrabUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of Max from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3MafkIggrabUniPk HeLa-S3 MAFK MafK_(ab50322) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002856 Stanford wgEncodeAwgTfbsSydhHelas3MafkIggrabUniPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of MafK_(ab50322) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3JundIggrabUniPk HeLa-S3 JUND JunD HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000745 Stanford wgEncodeAwgTfbsSydhHelas3JundIggrabUniPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of JunD from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3CjunIggrabUniPk HeLa-S3 JUN c-Jun HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000746 Stanford wgEncodeAwgTfbsSydhHelas3CjunIggrabUniPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of c-Jun from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Irf3IggrabUniPk HeLa-S3 IRF3 IRF3 HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001788 Stanford wgEncodeAwgTfbsSydhHelas3Irf3IggrabUniPk None Peaks Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of IRF3 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Tf3c110UniPk HeLa-S3 GTF3C2 TFIIIC-110 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000747 Harvard wgEncodeAwgTfbsSydhHelas3Tf3c110UniPk None Peaks TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of TFIIIC-110 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Gtf2f1ab28179IggrabUniPk HeLa-S3 GTF2F1 GTF2F1_(AB28179) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001816 Stanford wgEncodeAwgTfbsSydhHelas3Gtf2f1ab28179IggrabUniPk None Peaks RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of GTF2F1_(AB28179) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibHelas3GabpPcr1xUniPk HeLa-S3 GABPA GABP HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001504 HudsonAlpha wgEncodeAwgTfbsHaibHelas3GabpPcr1xUniPk None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. cervical carcinoma Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of GABP from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3CfosUniPk HeLa-S3 FOS c-Fos HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000647 Yale wgEncodeAwgTfbsSydhHelas3CfosUniPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of c-Fos from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Spt20UniPk HeLa-S3 FAM48A SPT20 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001855 Stanford wgEncodeAwgTfbsSydhHelas3Spt20UniPk None Peaks Also known as FAM48A or P38IP. It is a component of SAGA complex. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of SPT20 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsBroadHelas3Ezh239875UniPk HeLa-S3 EZH2 EZH2_(39875) HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003086 Broad wgEncodeAwgTfbsBroadHelas3Ezh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3P300sc584sc584IggrabUniPk HeLa-S3 EP300 p300_(SC-584) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001820 Stanford wgEncodeAwgTfbsSydhHelas3P300sc584sc584IggrabUniPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of p300_(SC-584) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Elk4UcdUniPk HeLa-S3 ELK4 ELK4 HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001753 USC wgEncodeAwgTfbsSydhHelas3Elk4UcdUniPk None Peaks This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of ELK4 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Elk112771IggrabUniPk HeLa-S3 ELK1 ELK1_(1277-1) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002864 Stanford wgEncodeAwgTfbsSydhHelas3Elk112771IggrabUniPk None Peaks Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of ELK1_(1277-1) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3E2f6UniPk HeLa-S3 E2F6 E2F6 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000692 USC wgEncodeAwgTfbsSydhHelas3E2f6UniPk None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of E2F6 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3E2f4UniPk HeLa-S3 E2F4 E2F4 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000689 USC wgEncodeAwgTfbsSydhHelas3E2f4UniPk None Peaks mapping at the C-terminus of E2F4 of human origin cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of E2F4 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Hae2f1UniPk HeLa-S3 E2F1 c2 HA-E2F1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000688 USC wgEncodeAwgTfbsSydhHelas3Hae2f1UniPk None Peaks The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of HA-E2F1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3E2f1UniPk HeLa-S3 E2F1 c1 E2F1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000699 USC wgEncodeAwgTfbsSydhHelas3E2f1UniPk None Peaks E2F1, the original member of the E2F family of transcription factors, was identified as a cellular protein with DNA binding activity associated with the adenovirus E2 gene promoter. E2F1 is cell cycle regulated with very low levels in early G1, then increasing levels as cells move from G1 to S, and highest levels of protein at the G1/S boundary, which is consistent with its role in S-phase entry. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of E2F1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsUwHelas3CtcfUniPk HeLa-S3 CTCF w CTCF HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000398 UW wgEncodeAwgTfbsUwHelas3CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaHelas3CtcfUniPk HeLa-S3 CTCF t CTCF HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000541 UT-A wgEncodeAwgTfbsUtaHelas3CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsBroadHelas3CtcfUniPk HeLa-S3 CTCF b CTCF HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001012 Broad wgEncodeAwgTfbsBroadHelas3CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Chd2IggrabUniPk HeLa-S3 CHD2 CHD2_(AB68301) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002027 Stanford wgEncodeAwgTfbsSydhHelas3Chd2IggrabUniPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of CHD2_(AB68301) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3CebpbIggrabUniPk HeLa-S3 CEBPB CEBPB HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001815 Stanford wgEncodeAwgTfbsSydhHelas3CebpbIggrabUniPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of CEBPB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Brf2UniPk HeLa-S3 BRF2 BRF2 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000765 Harvard wgEncodeAwgTfbsSydhHelas3Brf2UniPk None Peaks Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of BRF2 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Brf1UniPk HeLa-S3 BRF1 BRF1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000764 Harvard wgEncodeAwgTfbsSydhHelas3Brf1UniPk None Peaks 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of BRF1 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Brca1a300IggrabUniPk HeLa-S3 BRCA1 BRCA1_(A300-000A) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001814 Stanford wgEncodeAwgTfbsSydhHelas3Brca1a300IggrabUniPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of BRCA1_(A300-000A) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhHelas3Bdp1UniPk HeLa-S3 BDP1 BDP1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000763 Harvard wgEncodeAwgTfbsSydhHelas3Bdp1UniPk None Peaks 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFBS Uniform Peaks of BDP1 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Znf274m01UcdUniPk K562 ZNF274 c2 ZNF274_(M01) K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002068 USC wgEncodeAwgTfbsSydhK562Znf274m01UcdUniPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ZNF274_(M01) from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Znf274UcdUniPk K562 ZNF274 c ZNF274 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000696 USC wgEncodeAwgTfbsSydhK562Znf274UcdUniPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ZNF274 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Znf263UcdUniPk K562 ZNF263 ZNF263 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000630 USC wgEncodeAwgTfbsSydhK562Znf263UcdUniPk None Peaks ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ZNF263 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Znf143IggrabUniPk K562 ZNF143 Znf143_(16618-1-AP) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002030 Stanford wgEncodeAwgTfbsSydhK562Znf143IggrabUniPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Znf143_(16618-1-AP) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Zbtb7asc34508V0416101UniPk K562 ZBTB7A ZBTB7A_(SC-34508) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001620 HudsonAlpha wgEncodeAwgTfbsHaibK562Zbtb7asc34508V0416101UniPk None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ZBTB7A_(SC-34508) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Zbtb33Pcr1xUniPk K562 ZBTB33 ZBTB33 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001569 HudsonAlpha wgEncodeAwgTfbsHaibK562Zbtb33Pcr1xUniPk None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ZBTB33 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Yy1UcdUniPk K562 YY1 c YY1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000684 USC wgEncodeAwgTfbsSydhK562Yy1UcdUniPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of YY1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Yy1V0416102UniPk K562 YY1 h2 YY1 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001623 HudsonAlpha wgEncodeAwgTfbsHaibK562Yy1V0416102UniPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of YY1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Yy1V0416101UniPk K562 YY1 h YY1_(SC-281) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001584 HudsonAlpha wgEncodeAwgTfbsHaibK562Yy1V0416101UniPk None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of YY1_(SC-281) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Usf2IggrabUniPk K562 USF2 USF2 K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001797 Stanford wgEncodeAwgTfbsSydhK562Usf2IggrabUniPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of USF2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Usf1V0416101UniPk K562 USF1 USF-1 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001583 HudsonAlpha wgEncodeAwgTfbsHaibK562Usf1V0416101UniPk None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of USF-1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Ubtfsab1404509IggmusUniPk K562 UBTF s2 UBTF_(SAB1404509) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002850 Stanford wgEncodeAwgTfbsSydhK562Ubtfsab1404509IggmusUniPk None Peaks Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of UBTF_(SAB1404509) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Ubfsc13125IggmusUniPk K562 UBTF s UBF_(sc-13125) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002863 Stanford wgEncodeAwgTfbsSydhK562Ubfsc13125IggmusUniPk None Peaks Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of UBF_(sc-13125) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Trim28sc81411V0422111UniPk K562 TRIM28 TRIM28_(SC-81411) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003210 HudsonAlpha wgEncodeAwgTfbsHaibK562Trim28sc81411V0422111UniPk None Peaks The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TRIM28_(SC-81411) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Thap1sc98174V0416101UniPk K562 THAP1 THAP1_(SC-98174) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001655 HudsonAlpha wgEncodeAwgTfbsHaibK562Thap1sc98174V0416101UniPk None Peaks The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of THAP1_(SC-98174) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Tead4sc101184V0422111UniPk K562 TEAD4 TEAD4_(SC-101184) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002333 HudsonAlpha wgEncodeAwgTfbsHaibK562Tead4sc101184V0422111UniPk None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TEAD4_(SC-101184) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562TbpIggmusUniPk K562 TBP TBP K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001825 Stanford wgEncodeAwgTfbsSydhK562TbpIggmusUniPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TBP from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Tblr1nb600270IggrabUniPk K562 TBL1XR1 s2 TBLR1_(NB600-270) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002848 Stanford wgEncodeAwgTfbsSydhK562Tblr1nb600270IggrabUniPk None Peaks F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TBLR1_(NB600-270) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Tblr1ab24550IggrabUniPk K562 TBL1XR1 s TBLR1_(ab24550) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002849 Stanford wgEncodeAwgTfbsSydhK562Tblr1ab24550IggrabUniPk None Peaks F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TBLR1_(ab24550) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Tal1sc12984IggmusUniPk K562 TAL1 TAL1_(SC-12984) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001824 Stanford wgEncodeAwgTfbsSydhK562Tal1sc12984IggmusUniPk None Peaks TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TAL1_(SC-12984) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Taf7sc101167V0416101UniPk K562 TAF7 TAF7_(SC-101167) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001654 HudsonAlpha wgEncodeAwgTfbsHaibK562Taf7sc101167V0416101UniPk None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TAF7_(SC-101167) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Taf1V0416101UniPk K562 TAF1 TAF1 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001582 HudsonAlpha wgEncodeAwgTfbsHaibK562Taf1V0416101UniPk None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Stat5asc74442V0422111UniPk K562 STAT5A STAT5A_(SC-74442) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002347 HudsonAlpha wgEncodeAwgTfbsHaibK562Stat5asc74442V0422111UniPk None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of STAT5A_(SC-74442) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Stat2Ifna6hUniPk K562+IFNa6h STAT2 STAT2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000666 Yale wgEncodeAwgTfbsSydhK562Stat2Ifna6hUniPk IFNa6h Peaks peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNa6h) TFBS Uniform Peaks of STAT2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Stat2Ifna30UniPk K562+IFNa30 STAT2 STAT2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000665 Yale wgEncodeAwgTfbsSydhK562Stat2Ifna30UniPk IFNa30 Peaks peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 (IFNa30) TFBS Uniform Peaks of STAT2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Stat1Ifna6hUniPk K562+IFNa6h STAT1 STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000664 Yale wgEncodeAwgTfbsSydhK562Stat1Ifna6hUniPk IFNa6h Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNa6h) TFBS Uniform Peaks of STAT1 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Stat1Ifna30UniPk K562+IFNa30 STAT1 STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000663 Yale wgEncodeAwgTfbsSydhK562Stat1Ifna30UniPk IFNa30 Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 (IFNa30) TFBS Uniform Peaks of STAT1 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Stat1Ifng6hUniPk K562+IFNg6h STAT1 STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000761 Stanford wgEncodeAwgTfbsSydhK562Stat1Ifng6hUniPk IFNg6h Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNg6h) TFBS Uniform Peaks of STAT1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Stat1Ifng30UniPk K562+IFNg30 STAT1 STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000760 Stanford wgEncodeAwgTfbsSydhK562Stat1Ifng30UniPk IFNg30 Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 (IFNg30) TFBS Uniform Peaks of STAT1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562SrfV0416101UniPk K562 SRF SRF K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001600 HudsonAlpha wgEncodeAwgTfbsHaibK562SrfV0416101UniPk None Peaks Serum response transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of SRF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Pu1Pcr1xUniPk K562 SPI1 PU.1 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001482 HudsonAlpha wgEncodeAwgTfbsHaibK562Pu1Pcr1xUniPk None Peaks PU.1 (H-135) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of PU.1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Sp2sc643V0416102UniPk K562 SP2 SP2_(SC-643) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001653 HudsonAlpha wgEncodeAwgTfbsHaibK562Sp2sc643V0416102UniPk None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of SP2_(SC-643) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Sp1Pcr1xUniPk K562 SP1 SP1 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001578 HudsonAlpha wgEncodeAwgTfbsHaibK562Sp1Pcr1xUniPk None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of SP1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Smc3ab9263IggrabUniPk K562 SMC3 SMC3_(ab9263) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001845 Stanford wgEncodeAwgTfbsSydhK562Smc3ab9263IggrabUniPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of SMC3_(ab9263) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Ini1IggmusUniPk K562 SMARCB1 Ini1 K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000725 Stanford wgEncodeAwgTfbsSydhK562Ini1IggmusUniPk None Peaks Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Ini1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Brg1IggmusUniPk K562 SMARCA4 Brg1 K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000724 Stanford wgEncodeAwgTfbsSydhK562Brg1IggmusUniPk None Peaks Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Brg1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Six5Pcr1xUniPk K562 SIX5 SIX5 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001483 HudsonAlpha wgEncodeAwgTfbsHaibK562Six5Pcr1xUniPk None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of SIX5 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Sirt6UniPk K562 SIRT6 SIRT6 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000681 Harvard wgEncodeAwgTfbsSydhK562Sirt6UniPk None Peaks A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of SIRT6 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Sin3ak20V0416101UniPk K562 SIN3AK20 Sin3Ak-20 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001607 HudsonAlpha wgEncodeAwgTfbsHaibK562Sin3ak20V0416101UniPk None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Sin3Ak-20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Setdb1MnasedUcdUniPk K562+MNase SETDB1 SETDB1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000769 USC wgEncodeAwgTfbsSydhK562Setdb1MnasedUcdUniPk MNaseD Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Fragmented using micrococcal nuclease digestion Regions of enriched signal in experiment K562 (MNaseD) TFBS Uniform Peaks of SETDB1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Setdb1UcdUniPk K562 SETDB1 SETDB1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000677 USC wgEncodeAwgTfbsSydhK562Setdb1UcdUniPk None Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of SETDB1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Sap3039731UniPk K562 SAP30 SAP30_(39731) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002094 Broad wgEncodeAwgTfbsBroadK562Sap3039731UniPk None Peaks SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of SAP30_(39731) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Rpc155UniPk K562 RPC155 RPC155 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000680 Harvard wgEncodeAwgTfbsSydhK562Rpc155UniPk None Peaks polymerase (RNA) III (DNA directed) polypeptide A, 155kDa leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of RPC155 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Rfx5IggrabUniPk K562 RFX5 RFX5_(200-401-194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002033 Stanford wgEncodeAwgTfbsSydhK562Rfx5IggrabUniPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of RFX5_(200-401-194) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562NrsfV0416102UniPk K562 REST NRSF K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001638 HudsonAlpha wgEncodeAwgTfbsHaibK562NrsfV0416102UniPk None Peaks Neuron-restrictive silencer transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of NRSF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562NelfeUniPk K562 RDBP NELFe K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000701 Harvard wgEncodeAwgTfbsSydhK562NelfeUniPk None Peaks NELF-E (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of NELFe from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Corestsc30189IggrabUniPk K562 RCOR1 s2 COREST_(sc-30189) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002814 Stanford wgEncodeAwgTfbsSydhK562Corestsc30189IggrabUniPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of COREST_(sc-30189) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Corestab24166IggrabUniPk K562 RCOR1 s COREST_(ab24166) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002847 Stanford wgEncodeAwgTfbsSydhK562Corestab24166IggrabUniPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of COREST_(ab24166) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Rbbp5a300109aUniPk K562 RBBP5 RBBP5_(A300-109A) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002093 Broad wgEncodeAwgTfbsBroadK562Rbbp5a300109aUniPk None Peaks Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of RBBP5_(A300-109A) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Rad21UniPk K562 RAD21 y Rad21 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000649 Yale wgEncodeAwgTfbsSydhK562Rad21UniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Rad21 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Rad21V0416102UniPk K562 RAD21 h Rad21 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001585 HudsonAlpha wgEncodeAwgTfbsHaibK562Rad21V0416102UniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Rad21 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Pol3UniPk K562 POLR3G Pol3 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000694 Stanford wgEncodeAwgTfbsSydhK562Pol3UniPk None Peaks RNA Polymerase III leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Pol3 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Pol2Ifng6hUniPk K562+IFg6h POLR2A Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000662 Yale wgEncodeAwgTfbsSydhK562Pol2Ifng6hUniPk IFNg6h Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNg6h) TFBS Uniform Peaks of Pol2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Pol2Ifna6hUniPk K562+IFa6h POLR2A Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000661 Yale wgEncodeAwgTfbsSydhK562Pol2Ifna6hUniPk IFNa6h Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNa6h) TFBS Uniform Peaks of Pol2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Pol2Ifna30UniPk K562+IFa30 POLR2A Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000660 Yale wgEncodeAwgTfbsSydhK562Pol2Ifna30UniPk IFNa30 Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 (IFNa30) TFBS Uniform Peaks of Pol2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Pol2UniPk K562 POLR2A y Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000616 Yale wgEncodeAwgTfbsSydhK562Pol2UniPk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Pol2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsUtaK562Pol2UniPk K562 POLR2A t Pol2 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000555 UT-A wgEncodeAwgTfbsUtaK562Pol2UniPk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Pol2Ifng30UniPk K562+IFg30 POLR2A Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000704 Stanford wgEncodeAwgTfbsSydhK562Pol2Ifng30UniPk IFNg30 Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 (IFNg30) TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Pol2s2UniPk K562 POLR2A s3 Pol2(phosphoS2) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001805 Stanford wgEncodeAwgTfbsSydhK562Pol2s2UniPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Pol2(phosphoS2) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Pol2s2IggrabUniPk K562 POLR2A s2 Pol2(phosphoS2) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002833 Stanford wgEncodeAwgTfbsSydhK562Pol2s2IggrabUniPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Pol2(phosphoS2) (Iggrab) ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Pol2IggmusUniPk K562 POLR2A s Pol2 K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000727 Stanford wgEncodeAwgTfbsSydhK562Pol2IggmusUniPk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Pol2V0416101UniPk K562 POLR2A h2 Pol2 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001633 HudsonAlpha wgEncodeAwgTfbsHaibK562Pol2V0416101UniPk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Pol24h8V0416101UniPk K562 POLR2A h Pol2-4H8 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001581 HudsonAlpha wgEncodeAwgTfbsHaibK562Pol24h8V0416101UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Pol2bUniPk K562 POLR2A b Pol2(b) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000053 Broad wgEncodeAwgTfbsBroadK562Pol2bUniPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Pol2(b) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Pmlsc71910V0422111UniPk K562 PML PML_(SC-71910) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002320 HudsonAlpha wgEncodeAwgTfbsHaibK562Pmlsc71910V0422111UniPk None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of PML_(SC-71910) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Phf8a301772aUniPk K562 PHF8 PHF8_(A301-772A) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002092 Broad wgEncodeAwgTfbsBroadK562Phf8a301772aUniPk None Peaks PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of PHF8_(A301-772A) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Nrf1IggrabUniPk K562 NRF1 Nrf1 K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001796 Stanford wgEncodeAwgTfbsSydhK562Nrf1IggrabUniPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Nrf1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Nr2f2sc271940V0422111UniPk K562 NR2F2 NR2F2_(SC-271940) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002382 HudsonAlpha wgEncodeAwgTfbsHaibK562Nr2f2sc271940V0422111UniPk None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of NR2F2_(SC-271940) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Tr4UcdUniPk K562 NR2C2 TR4 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000682 USC wgEncodeAwgTfbsSydhK562Tr4UcdUniPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TR4 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhK562NfybUniPk K562 NFYB NF-YB K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002024 Stanford wgEncodeAwgTfbsSydhK562NfybUniPk None Peaks NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of NF-YB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562NfyaUniPk K562 NFYA NF-YA K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002021 Stanford wgEncodeAwgTfbsSydhK562NfyaUniPk None Peaks NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of NF-YA from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Nfe2UniPk K562 NFE2 NF-E2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000624 Yale wgEncodeAwgTfbsSydhK562Nfe2UniPk None Peaks Nuclear factor, erythroid-derived 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of NF-E2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CmycIfng6hUniPk K562+IFNg6h MYC c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000670 Yale wgEncodeAwgTfbsSydhK562CmycIfng6hUniPk IFNg6h Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNg6h) TFBS Uniform Peaks of c-Myc from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CmycIfna6hUniPk K562+IFNa6h MYC c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000669 Yale wgEncodeAwgTfbsSydhK562CmycIfna6hUniPk IFNa6h Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNa6h) TFBS Uniform Peaks of c-Myc from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CmycIfna30UniPk K562+IFNa30 MYC c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000659 Yale wgEncodeAwgTfbsSydhK562CmycIfna30UniPk IFNa30 Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 (IFNa30) TFBS Uniform Peaks of c-Myc from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CmycUniPk K562 MYC y c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000621 Yale wgEncodeAwgTfbsSydhK562CmycUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of c-Myc from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsUtaK562CmycUniPk K562 MYC t c-Myc K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000536 UT-A wgEncodeAwgTfbsUtaK562CmycUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment K562 TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CmycIfng30UniPk K562+IFNg30 MYC c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001867 Stanford wgEncodeAwgTfbsSydhK562CmycIfng30UniPk IFNg30 Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 (IFNg30) TFBS Uniform Peaks of c-Myc from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CmycIggrabUniPk K562 MYC s c-Myc K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002800 Stanford wgEncodeAwgTfbsSydhK562CmycIggrabUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of c-Myc from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Mxi1af4185IggrabUniPk K562 MXI1 Mxi1_(AF4185) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001827 Stanford wgEncodeAwgTfbsSydhK562Mxi1af4185IggrabUniPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Mxi1_(AF4185) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Mef2aV0416101UniPk K562 MEF2A MEF2A K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001663 HudsonAlpha wgEncodeAwgTfbsHaibK562Mef2aV0416101UniPk None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of MEF2A from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Mazab85725IggrabUniPk K562 MAZ MAZ_(ab85725) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002862 Stanford wgEncodeAwgTfbsSydhK562Mazab85725IggrabUniPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of MAZ_(ab85725) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562MaxIggrabUniPk K562 MAX s Max K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002869 Stanford wgEncodeAwgTfbsSydhK562MaxIggrabUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Max from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562MaxV0416102UniPk K562 MAX h Max K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001605 HudsonAlpha wgEncodeAwgTfbsHaibK562MaxV0416102UniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Max from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Mafkab50322IggrabUniPk K562 MAFK MafK_(ab50322) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001844 Stanford wgEncodeAwgTfbsSydhK562Mafkab50322IggrabUniPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of MafK_(ab50322) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562MaffIggrabUniPk K562 MAFF MafF_(M8194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002804 Stanford wgEncodeAwgTfbsSydhK562MaffIggrabUniPk None Peaks The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of MafF_(M8194) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Plu1UniPk K562 KDM5B PLU1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002085 Broad wgEncodeAwgTfbsBroadK562Plu1UniPk None Peaks JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of PLU1 from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Kap1UcdUniPk K562 KAP1 KAP1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001764 USC wgEncodeAwgTfbsSydhK562Kap1UcdUniPk None Peaks KRAB Associated Protein 1, helps regulate transcriptional repression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of KAP1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsUchicagoK562EjundUniPk K562 JUND i eGFP-JunD K562 Control_eGFP-JunD ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001211 UChicago wgEncodeAwgTfbsUchicagoK562EjundUniPk None Peaks JUND leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JUND Chromatin IP Sequencing White - University of Chicago Regions of enriched signal in experiment K562 TFBS Uniform Peaks of eGFP-JunD from ENCODE/UChicago/Analysis Regulation 
wgEncodeAwgTfbsSydhK562JundIggrabUniPk K562 JUND s JunD K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002164 Stanford wgEncodeAwgTfbsSydhK562JundIggrabUniPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of JunD from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsUchicagoK562EjunbUniPk K562 JUNB eGFP-JunB K562 Control_eGFP-JunB ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001210 UChicago wgEncodeAwgTfbsUchicagoK562EjunbUniPk None Peaks JUNB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JunB Chromatin IP Sequencing White - University of Chicago Regions of enriched signal in experiment K562 TFBS Uniform Peaks of eGFP-JunB from ENCODE/UChicago/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CjunIfng6hUniPk K562+IFNg6h JUN c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000668 Yale wgEncodeAwgTfbsSydhK562CjunIfng6hUniPk IFNg6h Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNg6h) TFBS Uniform Peaks of c-Jun from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CjunIfng30UniPk K562+IFNg30 JUN c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000673 Yale wgEncodeAwgTfbsSydhK562CjunIfng30UniPk IFNg30 Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 (IFNg30) TFBS Uniform Peaks of c-Jun from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CjunIfna6hUniPk K562+IFNa6h JUN c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000667 Yale wgEncodeAwgTfbsSydhK562CjunIfna6hUniPk IFNa6h Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNa6h) TFBS Uniform Peaks of c-Jun from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CjunUniPk K562 JUN c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000620 Yale wgEncodeAwgTfbsSydhK562CjunUniPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of c-Jun from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CjunIfna30UniPk K562+IFNa30 JUN c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002805 Stanford wgEncodeAwgTfbsSydhK562CjunIfna30UniPk IFNa30 Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 (IFNa30) TFBS Uniform Peaks of c-Jun from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Irf1Ifng6hUniPk K562+IFNg6h IRF1 IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001866 Stanford wgEncodeAwgTfbsSydhK562Irf1Ifng6hUniPk IFNg6h Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNg6h) TFBS Uniform Peaks of IRF1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Irf1Ifng30UniPk K562+IFNg30 IRF1 IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002799 Stanford wgEncodeAwgTfbsSydhK562Irf1Ifng30UniPk IFNg30 Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 (IFNg30) TFBS Uniform Peaks of IRF1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Irf1Ifna6hUniPk K562+IFNa6h IRF1 IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002798 Stanford wgEncodeAwgTfbsSydhK562Irf1Ifna6hUniPk IFNa6h Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 (IFNa6h) TFBS Uniform Peaks of IRF1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Irf1Ifna30UniPk K562+IFNa30 IRF1 IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001865 Stanford wgEncodeAwgTfbsSydhK562Irf1Ifna30UniPk IFNa30 Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 (IFNa30) TFBS Uniform Peaks of IRF1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Hmgn3UniPk K562 HMGN3 HMGN3 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001863 Harvard wgEncodeAwgTfbsSydhK562Hmgn3UniPk None Peaks HMGN3 is a high-mobility group protein. These proteins are small, 8 to 11 kDa, ubiquitous proteins believed to play a role in chromatin structure. HMGNs bind to nucleosomes between the histone core and DNA and reduce chromatin compaction. As a result HMGNs, HMGN3 included, are believed to increase access to DNA for DNA replication, repair and transcription. HMGN3 has specifically been implicated in the action of Thyroid horomone receptors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of HMGN3 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsUchicagoK562Ehdac8UniPk K562 HDAC8 eGFP-HDAC8 K562 Control_eGFP-HDAC8 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001209 UChicago wgEncodeAwgTfbsUchicagoK562Ehdac8UniPk None Peaks HDAC8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-HDAC8 Chromatin IP Sequencing White - University of Chicago Regions of enriched signal in experiment K562 TFBS Uniform Peaks of eGFP-HDAC8 from ENCODE/UChicago/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Hdac6a301341aUniPk K562 HDAC6 HDAC6_(A301-341A) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003093 Broad wgEncodeAwgTfbsBroadK562Hdac6a301341aUniPk None Peaks Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of HDAC6_(A301-341A) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Hdac2sc6296V0416102UniPk K562 HDAC2 h HDAC2_(SC-6296) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001622 HudsonAlpha wgEncodeAwgTfbsHaibK562Hdac2sc6296V0416102UniPk None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of HDAC2_(SC-6296) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Hdac2a300705aUniPk K562 HDAC2 b HDAC2_(A300-705A) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002091 Broad wgEncodeAwgTfbsBroadK562Hdac2a300705aUniPk None Peaks Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of HDAC2_(A300-705A) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Hdac1sc6298UniPk K562 HDAC1 HDAC1_(SC-6298) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002090 Broad wgEncodeAwgTfbsBroadK562Hdac1sc6298UniPk None Peaks Histone deacetylase 1 (HDAC1) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC1 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC1 include RPD3L1, HD1, GON-10, and DKFZp686H12203. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of HDAC1_(SC-6298) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Tf3c110UniPk K562 GTF3C2 TFIIIC-110 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000748 Harvard wgEncodeAwgTfbsSydhK562Tf3c110UniPk None Peaks TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of TFIIIC-110 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Gtf2f1ab28179IggrabUniPk K562 GTF2F1 GTF2F1_(AB28179) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001823 Stanford wgEncodeAwgTfbsSydhK562Gtf2f1ab28179IggrabUniPk None Peaks RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of GTF2F1_(AB28179) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Gtf2bUniPk K562 GTF2B GTF2B K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000703 Harvard wgEncodeAwgTfbsSydhK562Gtf2bUniPk None Peaks DNA- binding general transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of GTF2B from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Gata2UcdUniPk K562 GATA2 c GATA-2 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000683 USC wgEncodeAwgTfbsSydhK562Gata2UcdUniPk None Peaks GATA binding protein 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of GATA-2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsUchicagoK562Egata2UniPk K562 GATA2 i eGFP-GATA2 K562 Control_eGFP-GATA2 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001208 UChicago wgEncodeAwgTfbsUchicagoK562Egata2UniPk None Peaks GATA2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-GATA2 Chromatin IP Sequencing White - University of Chicago Regions of enriched signal in experiment K562 TFBS Uniform Peaks of eGFP-GATA2 from ENCODE/UChicago/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Gata2sc267Pcr1xUniPk K562 GATA2 h GATA2_(SC-267) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001576 HudsonAlpha wgEncodeAwgTfbsHaibK562Gata2sc267Pcr1xUniPk None Peaks This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of GATA2_(SC-267) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Gata1UcdUniPk K562 GATA1 GATA-1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000638 USC wgEncodeAwgTfbsSydhK562Gata1UcdUniPk None Peaks GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of GATA-1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibK562GabpV0416101UniPk K562 GABPA GABP K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001604 HudsonAlpha wgEncodeAwgTfbsHaibK562GabpV0416101UniPk None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of GABP from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Fosl1sc183V0416101UniPk K562 FOSL1 FOSL1_(SC-183) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001637 HudsonAlpha wgEncodeAwgTfbsHaibK562Fosl1sc183V0416101UniPk None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of FOSL1_(SC-183) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CfosUniPk K562 FOS y c-Fos K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000619 Yale wgEncodeAwgTfbsSydhK562CfosUniPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of c-Fos from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsUchicagoK562EfosUniPk K562 FOS i eGFP-FOS K562 Control_eGFP-FOS ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001207 UChicago wgEncodeAwgTfbsUchicagoK562EfosUniPk None Peaks FOS leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-FOS Chromatin IP Sequencing White - University of Chicago Regions of enriched signal in experiment K562 TFBS Uniform Peaks of eGFP-FOS from ENCODE/UChicago/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Ezh239875UniPk K562 EZH2 EZH2_(39875) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002089 Broad wgEncodeAwgTfbsBroadK562Ezh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Ets1V0416101UniPk K562 ETS1 ETS1 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001580 HudsonAlpha wgEncodeAwgTfbsHaibK562Ets1V0416101UniPk None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ETS1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562P300IggrabUniPk K562 EP300 s p300 K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002834 Stanford wgEncodeAwgTfbsSydhK562P300IggrabUniPk None Peaks EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of p300 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsBroadK562P300UniPk K562 EP300 b p300 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002086 Broad wgEncodeAwgTfbsBroadK562P300UniPk None Peaks EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of p300 from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Elk112771IggrabUniPk K562 ELK1 ELK1_(1277-1) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003356 Stanford wgEncodeAwgTfbsSydhK562Elk112771IggrabUniPk None Peaks Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ELK1_(1277-1) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Elf1sc631V0416102UniPk K562 ELF1 ELF1_(SC-631) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001619 HudsonAlpha wgEncodeAwgTfbsHaibK562Elf1sc631V0416102UniPk None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ELF1_(SC-631) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Egr1V0416101UniPk K562 EGR1 Egr-1 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001646 HudsonAlpha wgEncodeAwgTfbsHaibK562Egr1V0416101UniPk None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Egr-1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562E2f6UcdUniPk K562 E2F6 c E2F6 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000676 USC wgEncodeAwgTfbsSydhK562E2f6UcdUniPk None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of E2F6 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibK562E2f6V0416102UniPk K562 E2F6 h E2F6 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001598 HudsonAlpha wgEncodeAwgTfbsHaibK562E2f6V0416102UniPk None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of E2F6 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562E2f4UcdUniPk K562 E2F4 E2F4 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000671 USC wgEncodeAwgTfbsSydhK562E2f4UcdUniPk None Peaks mapping at the C-terminus of E2F4 of human origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment K562 TFBS Uniform Peaks of E2F4 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Ctcflsc98982V0416101UniPk K562 CTCFL CTCFL_(SC-98982) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001652 HudsonAlpha wgEncodeAwgTfbsHaibK562Ctcflsc98982V0416101UniPk None Peaks CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CTCFL_(SC-98982) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUwK562CtcfUniPk K562 CTCF w CTCF K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000399 UW wgEncodeAwgTfbsUwK562CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaK562CtcfUniPk K562 CTCF t CTCF K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000535 UT-A wgEncodeAwgTfbsUtaK562CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CtcfbIggrabUniPk K562 CTCF s CTCF_(SC-15914) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002797 Stanford wgEncodeAwgTfbsSydhK562CtcfbIggrabUniPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CTCF_(SC-15914) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk K562 CTCF h CTCF_(SC-5916) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002279 HudsonAlpha wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CTCF_(SC-5916) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadK562CtcfUniPk K562 CTCF b CTCF K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000042 Broad wgEncodeAwgTfbsBroadK562CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Chd2ab68301IggrabUniPk K562 CHD2 CHD2_(AB68301) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001822 Stanford wgEncodeAwgTfbsSydhK562Chd2ab68301IggrabUniPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CHD2_(AB68301) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsBroadK562Chd1a301218aUniPk K562 CHD1 CHD1_(A301-218A) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002088 Broad wgEncodeAwgTfbsBroadK562Chd1a301218aUniPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CHD1_(A301-218A) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhK562CebpbIggrabUniPk K562 CEBPB s CEBPB K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001821 Stanford wgEncodeAwgTfbsSydhK562CebpbIggrabUniPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CEBPB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Cebpbsc150V0422111UniPk K562 CEBPB CEBPB_(SC-150) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002346 HudsonAlpha wgEncodeAwgTfbsHaibK562Cebpbsc150V0422111UniPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CEBPB_(SC-150) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Ccnt2UniPk K562 CCNT2 CCNT2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001864 Harvard wgEncodeAwgTfbsSydhK562Ccnt2UniPk None Peaks CycT2 is one of three cyclins that can form a heterodimer with cyclin-dependent kinase 9 (CDK9). The heterodimer is known as positive elongation factor b (P-TEFb) and is responsible for the phosphophorylation of Ser2 of the heptad repeat in the C-terminal domain of RNA polymerase II as well as the negative elongation factors DSIF (hSpt4/hSpt5) and NELF. Phosphorylation of RNA polymerase II and the negative elongation factors by P-TEFb promotes elongation. CycT2 contains a leucine rich domain capable of binding to the C-terminal domain of RNA polymerase II. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CCNT2 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Cbx3sc101004V0422111UniPk K562 CBX3 CBX3_(SC-101004) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002383 HudsonAlpha wgEncodeAwgTfbsHaibK562Cbx3sc101004V0422111UniPk None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of CBX3_(SC-101004) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Brf2UniPk K562 BRF2 BRF2 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000767 Harvard wgEncodeAwgTfbsSydhK562Brf2UniPk None Peaks Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of BRF2 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Brf1UniPk K562 BRF1 BRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000679 Harvard wgEncodeAwgTfbsSydhK562Brf1UniPk None Peaks 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of BRF1 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Bhlhe40nb100IggrabUniPk K562 BHLHE40 BHLHE40_(NB100-1800) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001857 Stanford wgEncodeAwgTfbsSydhK562Bhlhe40nb100IggrabUniPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of BHLHE40_(NB100-1800) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Bdp1UniPk K562 BDP1 BDP1 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000678 Harvard wgEncodeAwgTfbsSydhK562Bdp1UniPk None Peaks 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of BDP1 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Bclaf101388Pcr1xUniPk K562 BCLAF1 BCLAF1_(SC-101388) K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001571 HudsonAlpha wgEncodeAwgTfbsHaibK562Bclaf101388Pcr1xUniPk None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of BCLAF1_(SC-101388) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Bcl3Pcr1xUniPk K562 BCL3 BCL3 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001570 HudsonAlpha wgEncodeAwgTfbsHaibK562Bcl3Pcr1xUniPk None Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of BCL3 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Bach1sc14700IggrabUniPk K562 BACH1 Bach1_(sc-14700) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002846 Stanford wgEncodeAwgTfbsSydhK562Bach1sc14700IggrabUniPk None Peaks This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of Bach1_(sc-14700) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibK562Atf3V0416101UniPk K562 ATF3 h ATF3 K562 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001662 HudsonAlpha wgEncodeAwgTfbsHaibK562Atf3V0416101UniPk None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ATF3 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Atf3UniPk K562 ATF3 v ATF3 K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000700 Harvard wgEncodeAwgTfbsSydhK562Atf3UniPk None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ATF3 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Atf106325UniPk K562 ATF1 ATF1_(06-325) K562 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002865 Harvard wgEncodeAwgTfbsSydhK562Atf106325UniPk None Peaks ATF1 is a bZip transcription factor from the CREB family. ATF1 binds to both cAMP response elements (TGACGTCA). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ATF1_(06-325) from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhK562Arid3asc8821IggrabUniPk K562 ARID3A ARID3A_(sc-8821) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002861 Stanford wgEncodeAwgTfbsSydhK562Arid3asc8821IggrabUniPk None Peaks This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment K562 TFBS Uniform Peaks of ARID3A_(sc-8821) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescZnf143IggrabUniPk H1-hESC ZNF143 Znf143_(16618-1-AP) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002802 Stanford wgEncodeAwgTfbsSydhH1hescZnf143IggrabUniPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Znf143_(16618-1-AP) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescYy1sc281V0416102UniPk H1-hESC YY1 YY1_(SC-281) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001567 HudsonAlpha wgEncodeAwgTfbsHaibH1hescYy1sc281V0416102UniPk None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of YY1_(SC-281) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescUsf2IggrabUniPk H1-hESC USF2 USF2 H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001837 Stanford wgEncodeAwgTfbsSydhH1hescUsf2IggrabUniPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of USF2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescUsf1Pcr1xUniPk H1-hESC USF1 USF-1 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001532 HudsonAlpha wgEncodeAwgTfbsHaibH1hescUsf1Pcr1xUniPk None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of USF-1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescTead4sc101184V0422111UniPk H1-hESC TEAD4 TEAD4_(SC-101184) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003214 HudsonAlpha wgEncodeAwgTfbsHaibH1hescTead4sc101184V0422111UniPk None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of TEAD4_(SC-101184) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescTcf12Pcr1xUniPk H1-hESC TCF12 TCF12 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001531 HudsonAlpha wgEncodeAwgTfbsHaibH1hescTcf12Pcr1xUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of TCF12 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescTbpIggrabUniPk H1-hESC TBP TBP H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001848 Stanford wgEncodeAwgTfbsSydhH1hescTbpIggrabUniPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of TBP from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescTaf7sc101167V0416102UniPk H1-hESC TAF7 TAF7_(SC-101167) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001610 HudsonAlpha wgEncodeAwgTfbsHaibH1hescTaf7sc101167V0416102UniPk None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of TAF7_(SC-101167) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescTaf1V0416102UniPk H1-hESC TAF1 TAF1 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001500 HudsonAlpha wgEncodeAwgTfbsHaibH1hescTaf1V0416102UniPk None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescSuz12UcdUniPk H1-hESC SUZ12 SUZ12 H1-hESC UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001752 USC wgEncodeAwgTfbsSydhH1hescSuz12UcdUniPk None Peaks Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of SUZ12 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescSrfPcr1xUniPk H1-hESC SRF SRF H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001533 HudsonAlpha wgEncodeAwgTfbsHaibH1hescSrfPcr1xUniPk None Peaks Serum response transcription factor embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of SRF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescSp4v20V0422111UniPk H1-hESC SP4 SP4_(V-20) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002317 HudsonAlpha wgEncodeAwgTfbsHaibH1hescSp4v20V0422111UniPk None Peaks Binds to GT and GC boxes promoters elements. Probable transcriptional activator. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of SP4_(V-20) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescSp2V0422111UniPk H1-hESC SP2 SP2_(SC-643) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002302 HudsonAlpha wgEncodeAwgTfbsHaibH1hescSp2V0422111UniPk None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of SP2_(SC-643) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescSp1Pcr1xUniPk H1-hESC SP1 SP1 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001529 HudsonAlpha wgEncodeAwgTfbsHaibH1hescSp1Pcr1xUniPk None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of SP1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescSix5Pcr1xUniPk H1-hESC SIX5 SIX5 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001528 HudsonAlpha wgEncodeAwgTfbsHaibH1hescSix5Pcr1xUniPk None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of SIX5 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescSin3ak20Pcr1xUniPk H1-hESC SIN3AK20 Sin3Ak-20 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001530 HudsonAlpha wgEncodeAwgTfbsHaibH1hescSin3ak20Pcr1xUniPk None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Sin3Ak-20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescSin3anb6001263IggrabUniPk H1-hESC SIN3A SIN3A_(NB600-1263) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002854 Stanford wgEncodeAwgTfbsSydhH1hescSin3anb6001263IggrabUniPk None Peaks Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of SIN3A_(NB600-1263) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescRxraV0416102UniPk H1-hESC RXRA RXRA H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001560 HudsonAlpha wgEncodeAwgTfbsHaibH1hescRxraV0416102UniPk None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of RXRA from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescRfx5200401194IggrabUniPk H1-hESC RFX5 RFX5_(200-401-194) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001835 Stanford wgEncodeAwgTfbsSydhH1hescRfx5200401194IggrabUniPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of RFX5_(200-401-194) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescNrsfV0416102UniPk H1-hESC REST NRSF H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001498 HudsonAlpha wgEncodeAwgTfbsHaibH1hescNrsfV0416102UniPk None Peaks Neuron-restrictive silencer transcription factor embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of NRSF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadH1hescRbbp5a300109aUniPk H1-hESC RBBP5 RBBP5_(A300-109A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002087 Broad wgEncodeAwgTfbsBroadH1hescRbbp5a300109aUniPk None Peaks Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of RBBP5_(A300-109A) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescRad21IggrabUniPk H1-hESC RAD21 s Rad21 H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001836 Stanford wgEncodeAwgTfbsSydhH1hescRad21IggrabUniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Rad21 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescRad21V0416102UniPk H1-hESC RAD21 h Rad21 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001593 HudsonAlpha wgEncodeAwgTfbsHaibH1hescRad21V0416102UniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Rad21 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescPou5f1sc9081V0416102UniPk H1-hESC POU5F1 on POU5F1_(SC-9081) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001636 HudsonAlpha wgEncodeAwgTfbsHaibH1hescPou5f1sc9081V0416102UniPk None Peaks This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of POU5F1_(SC-9081) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUtaH1hescPol2UniPk H1-hESC POLR2A t Pol2 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000563 UT-A wgEncodeAwgTfbsUtaH1hescPol2UniPk None Peaks RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescPol2V0416102UniPk H1-hESC POLR2A h2 Pol2 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001499 HudsonAlpha wgEncodeAwgTfbsHaibH1hescPol2V0416102UniPk None Peaks RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescPol24h8V0416102UniPk H1-hESC POLR2A h Pol2-4H8 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001514 HudsonAlpha wgEncodeAwgTfbsHaibH1hescPol24h8V0416102UniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescNrf1IggrabUniPk H1-hESC NRF1 Nrf1 H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001847 Stanford wgEncodeAwgTfbsSydhH1hescNrf1IggrabUniPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Nrf1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescNanogsc33759V0416102UniPk H1-hESC NANOG NANOG_(SC-33759) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001635 HudsonAlpha wgEncodeAwgTfbsHaibH1hescNanogsc33759V0416102UniPk None Peaks Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of NANOG_(SC-33759) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUtaH1hescCmycUniPk H1-hESC MYC t c-Myc H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000596 UT-A wgEncodeAwgTfbsUtaH1hescCmycUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescCmycIggrabUniPk H1-hESC MYC s c-Myc H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002795 Stanford wgEncodeAwgTfbsSydhH1hescCmycIggrabUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of c-Myc from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescMxi1IggrabUniPk H1-hESC MXI1 Mxi1_(AF4185) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002829 Stanford wgEncodeAwgTfbsSydhH1hescMxi1IggrabUniPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Mxi1_(AF4185) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescMaxUcdUniPk H1-hESC MAX Max H1-hESC UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001757 USC wgEncodeAwgTfbsSydhH1hescMaxUcdUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Max from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescMafkIggrabUniPk H1-hESC MAFK MafK_(ab50322) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002828 Stanford wgEncodeAwgTfbsSydhH1hescMafkIggrabUniPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of MafK_(ab50322) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsBroadH1hescJarid1aab26049UniPk H1-hESC KDM5A JARID1A_(ab26049) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002096 Broad wgEncodeAwgTfbsBroadH1hescJarid1aab26049UniPk None Peaks Histone demethylase that specifically demethylates embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of JARID1A_(ab26049) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescJundIggrabUniPk H1-hESC JUND s JunD H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002023 Stanford wgEncodeAwgTfbsSydhH1hescJundIggrabUniPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of JunD from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescJundV0416102UniPk H1-hESC JUND h JunD H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001579 HudsonAlpha wgEncodeAwgTfbsHaibH1hescJundV0416102UniPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of JunD from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescCjunIggrabUniPk H1-hESC JUN c-Jun H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001854 Stanford wgEncodeAwgTfbsSydhH1hescCjunIggrabUniPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of c-Jun from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescHdac2sc6296V0416102UniPk H1-hESC HDAC2 HDAC2_(SC-6296) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001659 HudsonAlpha wgEncodeAwgTfbsHaibH1hescHdac2sc6296V0416102UniPk None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of HDAC2_(SC-6296) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescGtf2f1IggrabUniPk H1-hESC GTF2F1 GTF2F1_(AB28179) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002843 Stanford wgEncodeAwgTfbsSydhH1hescGtf2f1IggrabUniPk None Peaks RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of GTF2F1_(AB28179) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescGabpPcr1xUniPk H1-hESC GABPA GABP H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001534 HudsonAlpha wgEncodeAwgTfbsHaibH1hescGabpPcr1xUniPk None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of GABP from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescFosl1sc183V0416102UniPk H1-hESC FOSL1 FOSL1_(SC-183) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001660 HudsonAlpha wgEncodeAwgTfbsHaibH1hescFosl1sc183V0416102UniPk None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of FOSL1_(SC-183) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadH1hescEzh239875UniPk H1-hESC EZH2 EZH2_(39875) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003082 Broad wgEncodeAwgTfbsBroadH1hescEzh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescP300V0416102UniPk H1-hESC EP300 p300 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001574 HudsonAlpha wgEncodeAwgTfbsHaibH1hescP300V0416102UniPk None Peaks EP300(c-20) embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of p300 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescEgr1V0416102UniPk H1-hESC EGR1 Egr-1 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001538 HudsonAlpha wgEncodeAwgTfbsHaibH1hescEgr1V0416102UniPk None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Egr-1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUtaH1hescCtcfUniPk H1-hESC CTCF t CTCF H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000560 UT-A wgEncodeAwgTfbsUtaH1hescCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescCtcfsc5916V0416102UniPk H1-hESC CTCF h CTCF_(SC-5916) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001649 HudsonAlpha wgEncodeAwgTfbsHaibH1hescCtcfsc5916V0416102UniPk None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of CTCF_(SC-5916) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsBroadH1hescCtcfUniPk H1-hESC CTCF b CTCF H1-hESC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000085 Broad wgEncodeAwgTfbsBroadH1hescCtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescCtbp2UcdUniPk H1-hESC CTBP2 CtBP2 H1-hESC UCDavis ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001767 USC wgEncodeAwgTfbsSydhH1hescCtbp2UcdUniPk None Peaks C-terminal binding protein 2 embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of CtBP2 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescChd2IggrabUniPk H1-hESC CHD2 CHD2_(AB68301) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002827 Stanford wgEncodeAwgTfbsSydhH1hescChd2IggrabUniPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of CHD2_(AB68301) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescChd1a301218aIggrabUniPk H1-hESC CHD1 s CHD1_(A301-218A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002826 Stanford wgEncodeAwgTfbsSydhH1hescChd1a301218aIggrabUniPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of CHD1_(A301-218A) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsBroadH1hescChd1a301218aUniPk H1-hESC CHD1 b CHD1_(A301-218A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002095 Broad wgEncodeAwgTfbsBroadH1hescChd1a301218aUniPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of CHD1_(A301-218A) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescCebpbIggrabUniPk H1-hESC CEBPB CEBPB H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002825 Stanford wgEncodeAwgTfbsSydhH1hescCebpbIggrabUniPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of CEBPB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescBrca1IggrabUniPk H1-hESC BRCA1 BRCA1_(A300-000A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002801 Stanford wgEncodeAwgTfbsSydhH1hescBrca1IggrabUniPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of BRCA1_(A300-000A) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescBcl11aPcr1xUniPk H1-hESC BCL11A BCL11A H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001527 HudsonAlpha wgEncodeAwgTfbsHaibH1hescBcl11aPcr1xUniPk None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of BCL11A from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhH1hescBach1sc14700IggrabUniPk H1-hESC BACH1 Bach1_(sc-14700) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002842 Stanford wgEncodeAwgTfbsSydhH1hescBach1sc14700IggrabUniPk None Peaks This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of Bach1_(sc-14700) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescAtf3V0416102UniPk H1-hESC ATF3 ATF3 H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001566 HudsonAlpha wgEncodeAwgTfbsHaibH1hescAtf3V0416102UniPk None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of ATF3 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibH1hescAtf2sc81188V0422111UniPk H1-hESC ATF2 ATF2_(SC-81188) H1-hESC ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002316 HudsonAlpha wgEncodeAwgTfbsHaibH1hescAtf2sc81188V0422111UniPk None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment H1-hESC TFBS Uniform Peaks of ATF2_(SC-81188) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Zzz3UniPk GM12878 ZZZ3 ZZZ3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000698 Harvard wgEncodeAwgTfbsSydhGm12878Zzz3UniPk None Peaks ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of ZZZ3 from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Znf274UniPk GM12878 ZNF274 ZNF274 GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001756 USC wgEncodeAwgTfbsSydhGm12878Znf274UniPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of ZNF274 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Znf143166181apUniPk GM12878 ZNF143 Znf143_(16618-1-AP) GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001853 Stanford wgEncodeAwgTfbsSydhGm12878Znf143166181apUniPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Znf143_(16618-1-AP) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Zeb1sc25388V0416102UniPk GM12878 ZEB1 ZEB1_(SC-25388) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001645 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Zeb1sc25388V0416102UniPk None Peaks This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of ZEB1_(SC-25388) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Zbtb33Pcr1xUniPk GM12878 ZBTB33 ZBTB33 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001488 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Zbtb33Pcr1xUniPk None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of ZBTB33 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Yy1UniPk GM12878 YY1 c YY1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000695 USC wgEncodeAwgTfbsSydhGm12878Yy1UniPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of YY1 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Yy1sc281Pcr1xUniPk GM12878 YY1 h YY1_(SC-281) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001657 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Yy1sc281Pcr1xUniPk None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of YY1_(SC-281) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878WhipIggmusUniPk GM12878 WRNIP1 WHIP GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001787 Stanford wgEncodeAwgTfbsSydhGm12878WhipIggmusUniPk None Peaks Interacts with the N-terminal portion of Werner protein containing the exonuclease domain, shows homology to replication factor C family proteins, and is conserved from E. coli to human. Studies in yeast suggest that this gene may influence the aging process. Functions as a modulator for initiation or reinitiation events during DNA polymerase delta-mediated DNA synthesis. Has an intrinsic ATPase activity that functions as a sensor of DNA damage or of arrested replication forks and regulates the extent of DNA synthesis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of WHIP from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Usf2IggmusUniPk GM12878 USF2 USF2 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001812 Stanford wgEncodeAwgTfbsSydhGm12878Usf2IggmusUniPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of USF2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Usf1Pcr2xUniPk GM12878 USF1 USF-1 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001468 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Usf1Pcr2xUniPk None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of USF-1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Tcf3Pcr1xUniPk GM12878 TCF3 TCF3_(SC-349) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002315 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Tcf3Pcr1xUniPk None Peaks Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of TCF3_(SC-349) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Tcf12Pcr1xUniPk GM12878 TCF12 TCF12 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001485 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Tcf12Pcr1xUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of TCF12 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878TbpIggmusUniPk GM12878 TBP TBP GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001798 Stanford wgEncodeAwgTfbsSydhGm12878TbpIggmusUniPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of TBP from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Tblr1ab24550IggmusUniPk GM12878 TBL1XR1 TBLR1_(ab24550) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002853 Stanford wgEncodeAwgTfbsSydhGm12878Tblr1ab24550IggmusUniPk None Peaks F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of TBLR1_(ab24550) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Taf1Pcr1xUniPk GM12878 TAF1 TAF1 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001478 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Taf1Pcr1xUniPk None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of TAF1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Stat5asc74442V0422111UniPk GM12878 STAT5A STAT5A_(SC-74442) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002321 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Stat5asc74442V0422111UniPk None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of STAT5A_(SC-74442) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Stat3IggmusUniPk GM12878 STAT3 STAT3 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001811 Stanford wgEncodeAwgTfbsSydhGm12878Stat3IggmusUniPk None Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of STAT3 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Stat1UniPk GM12878 STAT1 STAT1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001852 Stanford wgEncodeAwgTfbsSydhGm12878Stat1UniPk None Peaks transcription factor, activated by interferon signalling B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of STAT1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878SrfPcr2xUniPk GM12878 SRF SRF GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001464 HudsonAlpha wgEncodeAwgTfbsHaibGm12878SrfPcr2xUniPk None Peaks Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of SRF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Pu1Pcr1xUniPk GM12878 SPI1 PU.1 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001476 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Pu1Pcr1xUniPk None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of PU.1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Sp1Pcr1xUniPk GM12878 SP1 SP1 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001496 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Sp1Pcr1xUniPk None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of SP1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Smc3ab9263IggmusUniPk GM12878 SMC3 SMC3_(ab9263) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001833 Stanford wgEncodeAwgTfbsSydhGm12878Smc3ab9263IggmusUniPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of SMC3_(ab9263) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Six5Pcr1xUniPk GM12878 SIX5 SIX5 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001542 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Six5Pcr1xUniPk None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of SIX5 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Sin3anb6001263IggmusUniPk GM12878 SIN3A SIN3A_(NB600-1263) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002868 Stanford wgEncodeAwgTfbsSydhGm12878Sin3anb6001263IggmusUniPk None Peaks Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of SIN3A_(NB600-1263) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878RxraPcr1xUniPk GM12878 RXRA RXRA GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001541 HudsonAlpha wgEncodeAwgTfbsHaibGm12878RxraPcr1xUniPk None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of RXRA from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Runx3sc101553V0422111UniPk GM12878 RUNX3 RUNX3_(SC-101553) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002330 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Runx3sc101553V0422111UniPk None Peaks This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of RUNX3_(SC-101553) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Rfx5200401194IggmusUniPk GM12878 RFX5 RFX5_(200-401-194) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001810 Stanford wgEncodeAwgTfbsSydhGm12878Rfx5200401194IggmusUniPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of RFX5_(200-401-194) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878NrsfPcr1xUniPk GM12878 REST NRSF GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002314 HudsonAlpha wgEncodeAwgTfbsHaibGm12878NrsfPcr1xUniPk None Peaks Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of NRSF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878NfkbTnfaIggrabUniPk GM12878+TNFa RELA NFKB GM12878 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000690 Stanford wgEncodeAwgTfbsSydhGm12878NfkbTnfaIggrabUniPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM12878 (TNFa) TFBS Uniform Peaks of NFKB from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Corestsc30189IggmusUniPk GM12878 RCOR1 COREST_(sc-30189) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002841 Stanford wgEncodeAwgTfbsSydhGm12878Corestsc30189IggmusUniPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of COREST_(sc-30189) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Rad21IggrabUniPk GM12878 RAD21 s Rad21 GM12878 IgG-rab ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000749 Stanford wgEncodeAwgTfbsSydhGm12878Rad21IggrabUniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Rad21 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Rad21V0416101UniPk GM12878 RAD21 h Rad21 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001640 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Rad21V0416101UniPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Rad21 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Pou2f2Pcr1xUniPk GM12878 POU2F2 POU2F2 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001475 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Pou2f2Pcr1xUniPk None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of POU2F2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Pol3UniPk GM12878 POLR3G Pol3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000645 Yale wgEncodeAwgTfbsSydhGm12878Pol3UniPk None Peaks RNA Polymerase III B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Pol3 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Pol2UniPk GM12878 POLR2A y Pol2 GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000626 Yale wgEncodeAwgTfbsSydhGm12878Pol2UniPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Pol2 from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsUtaGm12878Pol2UniPk GM12878 POLR2A t Pol2 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000592 UT-A wgEncodeAwgTfbsUtaGm12878Pol2UniPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Pol2 from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Pol2s2IggmusUniPk GM12878 POLR2A s2 Pol2(phosphoS2) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001858 Stanford wgEncodeAwgTfbsSydhGm12878Pol2s2IggmusUniPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Pol2(phosphoS2) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Pol2IggmusUniPk GM12878 POLR2A s Pol2 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000708 Stanford wgEncodeAwgTfbsSydhGm12878Pol2IggmusUniPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Pol2 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Pol2Pcr2xUniPk GM12878 POLR2A h2 Pol2 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001463 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Pol2Pcr2xUniPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Pol2 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Pol24h8Pcr1xUniPk GM12878 POLR2A h Pol2-4H8 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001517 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Pol24h8Pcr1xUniPk None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Pol2-4H8 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Pmlsc71910V0422111UniPk GM12878 PML PML_(SC-71910) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002308 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Pmlsc71910V0422111UniPk None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of PML_(SC-71910) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Pbx3Pcr1xUniPk GM12878 PBX3 Pbx3 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001477 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Pbx3Pcr1xUniPk None Peaks Pbx 3 (D-17) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Pbx3 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Pax5n19Pcr1xUniPk GM12878 PAX5 h2 PAX5-N19 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001495 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Pax5n19Pcr1xUniPk None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of PAX5-N19 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Pax5c20Pcr1xUniPk GM12878 PAX5 h PAX5-C20 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001489 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Pax5c20Pcr1xUniPk None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of PAX5-C20 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Nrf1IggmusUniPk GM12878 NRF1 Nrf1 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001846 Stanford wgEncodeAwgTfbsSydhGm12878Nrf1IggmusUniPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Nrf1 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Tr4UniPk GM12878 NR2C2 TR4 GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000697 USC wgEncodeAwgTfbsSydhGm12878Tr4UniPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of TR4 from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878NfybIggmusUniPk GM12878 NFYB NF-YB GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002065 Harvard wgEncodeAwgTfbsSydhGm12878NfybIggmusUniPk None Peaks NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of NF-YB from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878NfyaIggmusUniPk GM12878 NFYA NF-YA GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002064 Harvard wgEncodeAwgTfbsSydhGm12878NfyaIggmusUniPk None Peaks NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Struhl - Harvard University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of NF-YA from ENCODE/Harvard/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Nficsc81335V0422111UniPk GM12878 NFIC NFIC_(SC-81335) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002343 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Nficsc81335V0422111UniPk None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of NFIC_(SC-81335) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Nfe2sc22827UniPk GM12878 NFE2 NF-E2_(SC-22827) GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001808 Stanford wgEncodeAwgTfbsSydhGm12878Nfe2sc22827UniPk None Peaks Transcription factor NFE2 45 kDa subunit is a component of the NFE2 complex and essential for regulating erythroid and megakaryocytic maturation and differentiation. Binds to the hypersensitive site 2 (HS2) of the beta-globin control region (LCR). This subunit (NFE2)recognizes the TCAT/C sequence of the AP-1-like core palindrome present in a number of erythroid and megakaryocytic gene promoters. Requires MAFK or other small MAF proteins for binding to the NFE2 motif. May play a role in all aspects of hemoglobin production from globin and heme synthesis to procurement of iron. NFE2 has been shown to interact with CREB binding protein. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of NF-E2_(SC-22827) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Nfatc1sc17834V0422111UniPk GM12878 NFATC1 NFATC1_(SC-17834) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002307 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Nfatc1sc17834V0422111UniPk None Peaks The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Five transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of NFATC1_(SC-17834) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsUtaGm12878CmycUniPk GM12878 MYC c-Myc GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000547 UT-A wgEncodeAwgTfbsUtaGm12878CmycUniPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of c-Myc from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Mxi1IggmusUniPk GM12878 MXI1 Mxi1_(AF4185) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002026 Stanford wgEncodeAwgTfbsSydhGm12878Mxi1IggmusUniPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Mxi1_(AF4185) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Mta3sc81325V0422111UniPk GM12878 MTA3 MTA3_(SC-81325) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002329 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Mta3sc81325V0422111UniPk None Peaks Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of MTA3_(SC-81325) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Mef2csc13268V0416101UniPk GM12878 MEF2C MEF2C_(SC-13268) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001648 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Mef2csc13268V0416101UniPk None Peaks This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of MEF2C_(SC-13268) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Mef2aPcr1xUniPk GM12878 MEF2A MEF2A GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001565 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Mef2aPcr1xUniPk None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of MEF2A from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Mazab85725IggmusUniPk GM12878 MAZ MAZ_(ab85725) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002852 Stanford wgEncodeAwgTfbsSydhGm12878Mazab85725IggmusUniPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of MAZ_(ab85725) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878MaxIggmusUniPk GM12878 MAX Max GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002806 Stanford wgEncodeAwgTfbsSydhGm12878MaxIggmusUniPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Max from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878JundUniPk GM12878 JUND JunD GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000639 Yale wgEncodeAwgTfbsSydhGm12878JundUniPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of JunD from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Irf4sc6059Pcr1xUniPk GM12878 IRF4 IRF4_(SC-6059) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001484 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Irf4sc6059Pcr1xUniPk None Peaks The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of IRF4_(SC-6059) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Ikzf1iknuclaUniPk GM12878 IKZF1 IKZF1_(IkN)_(UCLA) GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002811 USC wgEncodeAwgTfbsSydhGm12878Ikzf1iknuclaUniPk None Peaks IKAROS family zinc finger 1 (Ikaros or IKZF1) is a C2H2 zinc finger transcription factor that is associated with various chromatin-modifying complexes and is suggested to play a role in the development of lymphocytes, B- and T-cells. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Farnham - University of Southern California Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of IKZF1_(IkN)_(UCLA) from ENCODE/USC/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878GabpPcr2xUniPk GM12878 GABPA GABP GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001462 HudsonAlpha wgEncodeAwgTfbsHaibGm12878GabpPcr2xUniPk None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of GABP from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Foxm1sc502V0422111UniPk GM12878 FOXM1 FOXM1_(SC-502) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002529 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Foxm1sc502V0422111UniPk None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of FOXM1_(SC-502) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878CfosUniPk GM12878 FOS c-Fos GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000622 Yale wgEncodeAwgTfbsSydhGm12878CfosUniPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Yale University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of c-Fos from ENCODE/Yale/Analysis Regulation 
wgEncodeAwgTfbsBroadGm12878Ezh239875UniPk GM12878 EZH2 EZH2_(39875) GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002411 Broad wgEncodeAwgTfbsBroadGm12878Ezh239875UniPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of EZH2_(39875) from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Ets1Pcr1xUniPk GM12878 ETS1 ETS1 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001564 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Ets1Pcr1xUniPk None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of ETS1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878P300bUniPk GM12878 EP300 s2 p300_(SC-584) GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002037 Stanford wgEncodeAwgTfbsSydhGm12878P300bUniPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of p300_(SC-584) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878P300IggmusUniPk GM12878 EP300 s p300 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002824 Stanford wgEncodeAwgTfbsSydhGm12878P300IggmusUniPk None Peaks EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of p300 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878P300Pcr1xUniPk GM12878 EP300 h p300 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001487 HudsonAlpha wgEncodeAwgTfbsHaibGm12878P300Pcr1xUniPk None Peaks EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of p300 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Elk112771IggmusUniPk GM12878 ELK1 ELK1_(1277-1) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002851 Stanford wgEncodeAwgTfbsSydhGm12878Elk112771IggmusUniPk None Peaks Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of ELK1_(1277-1) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Elf1sc631V0416101UniPk GM12878 ELF1 ELF1_(SC-631) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001617 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Elf1sc631V0416101UniPk None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of ELF1_(SC-631) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Egr1Pcr2xUniPk GM12878 EGR1 Egr-1 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002328 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Egr1Pcr2xUniPk None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of Egr-1 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Ebf1sc137065UniPk GM12878 EBF1 s EBF1_(SC-137065) GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001832 Stanford wgEncodeAwgTfbsSydhGm12878Ebf1sc137065UniPk None Peaks Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of EBF1_(SC-137065) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Ebf1sc137065Pcr1xUniPk GM12878 EBF1 h EBF1_(SC-137065) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001480 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Ebf1sc137065Pcr1xUniPk None Peaks Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of EBF1_(SC-137065) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878E2f4IggmusUniPk GM12878 E2F4 E2F4 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002867 Stanford wgEncodeAwgTfbsSydhGm12878E2f4IggmusUniPk None Peaks mapping at the C-terminus of E2F4 of human origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of E2F4 from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsUwGm12878CtcfUniPk GM12878 CTCF w CTCF GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000394 UW wgEncodeAwgTfbsUwGm12878CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of CTCF from ENCODE/UW/Analysis Regulation 
wgEncodeAwgTfbsUtaGm12878CtcfUniPk GM12878 CTCF t CTCF GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000532 UT-A wgEncodeAwgTfbsUtaGm12878CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of CTCF from ENCODE/UT-A/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Ctcfsc15914c20UniPk GM12878 CTCF s CTCF_(SC-15914) GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001851 Stanford wgEncodeAwgTfbsSydhGm12878Ctcfsc15914c20UniPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of CTCF_(SC-15914) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsBroadGm12878CtcfUniPk GM12878 CTCF b CTCF GM12878 std ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH000029 Broad wgEncodeAwgTfbsBroadGm12878CtcfUniPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of CTCF from ENCODE/Broad/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Chd2ab68301IggmusUniPk GM12878 CHD2 CHD2_(AB68301) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001831 Stanford wgEncodeAwgTfbsSydhGm12878Chd2ab68301IggmusUniPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of CHD2_(AB68301) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Chd1a301218aIggmusUniPk GM12878 CHD1 CHD1_(A301-218A) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002823 Stanford wgEncodeAwgTfbsSydhGm12878Chd1a301218aIggmusUniPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of CHD1_(A301-218A) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Cebpbsc150V0422111UniPk GM12878 CEBPB CEBPB_(SC-150) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH003212 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Cebpbsc150V0422111UniPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of CEBPB_(SC-150) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Brca1a300IggmusUniPk GM12878 BRCA1 BRCA1_(A300-000A) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001830 Stanford wgEncodeAwgTfbsSydhGm12878Brca1a300IggmusUniPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of BRCA1_(A300-000A) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsSydhGm12878Bhlhe40cIggmusUniPk GM12878 BHLHE40 BHLHE40_(NB100-1800) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002025 Stanford wgEncodeAwgTfbsSydhGm12878Bhlhe40cIggmusUniPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder - Stanford University Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of BHLHE40_(NB100-1800) from ENCODE/Stanford/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Bclaf101388V0416101UniPk GM12878 BCLAF1 BCLAF1_(SC-101388) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001563 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Bclaf101388V0416101UniPk None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of BCLAF1_(SC-101388) ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Bcl3V0416101UniPk GM12878 BCL3 BCL3 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001658 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Bcl3V0416101UniPk None Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of BCL3 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Bcl11aPcr1xUniPk GM12878 BCL11A BCL11A GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001486 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Bcl11aPcr1xUniPk None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of BCL11A from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878BatfPcr1xUniPk GM12878 BATF BATF GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001479 HudsonAlpha wgEncodeAwgTfbsHaibGm12878BatfPcr1xUniPk None Peaks The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of BATF from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Atf3Pcr1xUniPk GM12878 ATF3 ATF3 GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH001562 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Atf3Pcr1xUniPk None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of ATF3 from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAwgTfbsHaibGm12878Atf2sc81188V0422111UniPk GM12878 ATF2 ATF2_(SC-81188) GM12878 ChipSeq ENCODE Mar 2012 Freeze wgEncodeEH002306 HudsonAlpha wgEncodeAwgTfbsHaibGm12878Atf2sc81188V0422111UniPk None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers - Hudson Alpha Institute for Biotechnology Regions of enriched signal in experiment GM12878 TFBS Uniform Peaks of ATF2_(SC-81188) from ENCODE/HudsonAlpha/Analysis Regulation 
wgEncodeAffyRnaChip Affy RNA Loc RNA Subcellular Localization by Tiling Microarray from ENCODE Affymetrix/CSHL Expression Description This track is produced as part of the ENCODE Transcriptome Project. Transcription of different RNA extracts from different sub-cellular localizations in different cell lines is compared in companion experiments using three different technologies: tiling arrays, RNA-seq using Solexa, and RNA-seq using SOLiD. The tiling array data are shown in this track. The Transfrags data are lifted over from the hg18 assembly. The Raw Transfrags are available for download only. Other views are available on the hg18 assembly. Display Conventions and Configuration To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Transfrags The filtered transfrags view excludes repeats and other known annotations including: tRNAs and rRNAs, mi/snoRNAs, things mapping to the mitochondrial or Y chromosomes, and many predicted snoRNAs and miRNAs. Methods Cells were grown according to the approved ENCODE cell culture protocols. RNA molecules longer than 200 nt and present in RNA population isolated from different subcellular compartments (such as cytosol, nucleus, polysomes and others) were fractionated into polyA+ and polyA- fractions as described in these protocols. Each RNA fraction was converted into double-stranded cDNA using random hexamers, labeled and hybridized to a tiling 91-array set containing probes against the non-repetitive portion of the human genome tiled on average every 5 bp (center-to-center of each consecutive 25-mers). All arrays were scaled to a median array intensity of 330. Within a sliding 61 bp window centered on each probe, an estimate of RNA abundance was found by calculating the median of all pairwise average PM-MM values, where PM is a perfect match and MM is a mismatch. Kapranov et al. (2002), Cheng et al. (2005) , Kapranov et al. (2007), and Cawley et al. (2004) are good references for the experimental methods. Cawley et al. also describes the analytical methods. Verification The reproducibility of the labeling method was assessed separately. Three independent technical replicates were generated from the same RNA pool for each RNA preparation and hybridized to duplicate arrays (two technical replicates) that contain the ENCODE regions. Labeled RNA samples were then pooled and hybridized to the tiling 91-array set spanning the whole genome. Transcribed regions (transfrags; see the Raw Transfrags view) were generated from the Raw Signal by merging genomic positions to which probes are mapped. This merging was based on a 5% false positive rate cutoff in negative bacterial controls, a maximum gap (MaxGap) of 40 base-pairs and minimum run (MinRun) of 40 base-pairs. Release Notes The track data were originally computed on the Human March 2006 assembly (hg18); the coordinates of the Transfrags were transformed to this assembly using UCSC's liftOver program. Credits These data were generated and analyzed by the transcriptome group at Affymetrix and Cold Spring Harbor Laboratories: P. Kapranov, I. Bell, E. Dumais, J. Drenkow, J. Dumais, N. Garg, M. Lubinsky, Carrie A. Davis, Huaien Wang, Kimberly Bell, Jorg Drenkow, Chris Zaleski, and Thomas R. Gingeras. Contact: Tom Gingeras References Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004 Feb 20;116(4):499-509. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 2005 May 20;308(5725):1149-54. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR. Large-scale transcriptional activity in chromosomes 21 and 22. Science. 2002 May 3;296(5569):916-9. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackerm&#252;ller J, Hofacker IL et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007 Jun 8;316(5830):1484-8. Publications Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012;7(1):e28213. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeAffyRnaChipViewFiltTransfrags Transfrags RNA Subcellular Localization by Tiling Microarray from ENCODE Affymetrix/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsProstateCellLongpolya Prostate cell pA+ prostate RnaChip ENCODE Nov 2008 Freeze 2008-11-24 2009-08-24 wgEncodeEH000010 10 Gingeras Affy cell hg18 longPolyA wgEncodeAffyRnaChipFiltTransfragsProstateCellLongpolya FiltTransfrags prostate tissue purchased for CSHL project RNA Protein Interactions Gingeras Gingeras - Affymetrix Whole cell Poly(A)+ RNA longer than 200 nt Filtered transcript fragments Prostate whole cell polyA+ Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsProstateCellLongnonpolya Prostate cell pA- prostate RnaChip ENCODE Nov 2008 Freeze 2008-11-24 2009-08-24 wgEncodeEH000009 9 Gingeras Affy cell hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsProstateCellLongnonpolya FiltTransfrags prostate tissue purchased for CSHL project RNA Protein Interactions Gingeras Gingeras - Affymetrix Whole cell Poly(A)- RNA longer than 200 nt Filtered transcript fragments Prostate whole cell polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsKeratinocyteNucleusLongpolya NHEK nucl pA+ NHEK RnaChip ENCODE July 2009 Freeze 2009-06-12 2010-03-12 wgEncodeEH000023 23 Gingeras Affy nucleus hg18 longPolyA wgEncodeAffyRnaChipFiltTransfragsKeratinocyteNucleusLongpolya FiltTransfrags epidermal keratinocytes RNA Protein Interactions Gingeras Gingeras - Affymetrix Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Filtered transcript fragments NHEK nucleus polyA+ Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsKeratinocyteNucleusLongnonpolya NHEK nucl pA- NHEK RnaChip ENCODE July 2009 Freeze 2009-06-12 2010-03-12 wgEncodeEH000022 22 Gingeras Affy nucleus hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsKeratinocyteNucleusLongnonpolya FiltTransfrags epidermal keratinocytes RNA Protein Interactions Gingeras Gingeras - Affymetrix Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Filtered transcript fragments NHEK nucleus polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsKeratinocyteCytosolLongpolya NHEK cyto pA+ NHEK RnaChip ENCODE July 2009 Freeze 2009-05-27 2010-02-27 wgEncodeEH000021 21 Gingeras Affy cytosol hg18 longPolyA wgEncodeAffyRnaChipFiltTransfragsKeratinocyteCytosolLongpolya FiltTransfrags epidermal keratinocytes RNA Protein Interactions Gingeras Gingeras - Affymetrix The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Filtered transcript fragments NHEK cytosol polyA+ Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsKeratinocyteCytosolLongnonpolya NHEK cyto pA- NHEK RnaChip ENCODE July 2009 Freeze 2009-05-27 2010-02-27 wgEncodeEH000020 20 Gingeras Affy cytosol hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsKeratinocyteCytosolLongnonpolya FiltTransfrags epidermal keratinocytes RNA Protein Interactions Gingeras Gingeras - Affymetrix The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Filtered transcript fragments NHEK cytosol polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsHepg2NucleolusTotal HepG2 nlus tot HepG2 RnaChip ENCODE Sep 2009 Freeze 2009-08-27 2010-05-27 wgEncodeEH000027 27 Gingeras Affy nucleolus hg18 total wgEncodeAffyRnaChipFiltTransfragsHepg2NucleolusTotal FiltTransfrags hepatocellular carcinoma RNA Protein Interactions Gingeras Gingeras - Affymetrix The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Filtered transcript fragments HepG2 nucleolus total Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsHepg2NucleusLongpolya HepG2 nucl pA+ HepG2 RnaChip ENCODE July 2009 Freeze 2009-07-17 2010-04-17 wgEncodeEH000025 25 Gingeras Affy nucleus hg18 longPolyA wgEncodeAffyRnaChipFiltTransfragsHepg2NucleusLongpolya FiltTransfrags hepatocellular carcinoma RNA Protein Interactions Gingeras Gingeras - Affymetrix Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Filtered transcript fragments HepG2 nucleus polyA+ Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsHepg2NucleusLongnonpolya HepG2 nucl pA- HepG2 RnaChip ENCODE July 2009 Freeze 2009-07-17 2010-04-17 wgEncodeEH000024 24 Gingeras Affy nucleus hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsHepg2NucleusLongnonpolya FiltTransfrags hepatocellular carcinoma RNA Protein Interactions Gingeras Gingeras - Affymetrix Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Filtered transcript fragments HepG2 nucleus polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsHepg2CytosolLongpolya HepG2 cyto pA+ HepG2 RnaChip ENCODE July 2009 Freeze 2009-05-27 2010-02-27 wgEncodeEH000019 19 Gingeras Affy cytosol hg18 longPolyA wgEncodeAffyRnaChipFiltTransfragsHepg2CytosolLongpolya FiltTransfrags hepatocellular carcinoma RNA Protein Interactions Gingeras Gingeras - Affymetrix The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Filtered transcript fragments HepG2 cytosol polyA+ Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsHepg2CytosolLongnonpolya HepG2 cyto pA- HepG2 RnaChip ENCODE July 2009 Freeze 2009-05-27 2010-02-27 wgEncodeEH000018 18 Gingeras Affy cytosol hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsHepg2CytosolLongnonpolya FiltTransfrags hepatocellular carcinoma RNA Protein Interactions Gingeras Gingeras - Affymetrix The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Filtered transcript fragments HepG2 cytosol polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsK562NucleolusTotal K562 nlus tot K562 RnaChip ENCODE Feb 2009 Freeze 2009-02-04 2009-11-04 wgEncodeEH000015 15 Gingeras Affy nucleolus hg18 total wgEncodeAffyRnaChipFiltTransfragsK562NucleolusTotal FiltTransfrags leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Protein Interactions Gingeras Gingeras - Affymetrix The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Filtered transcript fragments K562 nucleolus total Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsK562ChromatinTotal K562 chrm tot K562 RnaChip ENCODE Feb 2009 Freeze 2009-01-09 2009-10-09 wgEncodeEH000013 13 Gingeras Affy chromatin hg18 total wgEncodeAffyRnaChipFiltTransfragsK562ChromatinTotal FiltTransfrags leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Protein Interactions Gingeras Gingeras - Affymetrix Nuclear DNA and associated proteins Total RNA extract (longer than 200 nt) Filtered transcript fragments K562 chromatin total Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsK562NucleoplasmTotal K562 nplm tot K562 RnaChip ENCODE Feb 2009 Freeze 2009-03-10 2009-12-10 wgEncodeEH000014 14 Gingeras Affy nucleoplasm hg18 total wgEncodeAffyRnaChipFiltTransfragsK562NucleoplasmTotal FiltTransfrags leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Protein Interactions Gingeras Gingeras - Affymetrix That part of the nuclear content other than the chromosomes or the nucleolus Total RNA extract (longer than 200 nt) Filtered transcript fragments K562 nucleoplasm total Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsK562NucleusLongpolya K562 nucl pA+ K562 RnaChip ENCODE Nov 2008 Freeze 2008-11-22 2009-08-22 wgEncodeEH000008 8 Gingeras Affy nucleus hg18 longPolyA wgEncodeAffyRnaChipFiltTransfragsK562NucleusLongpolya FiltTransfrags leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Protein Interactions Gingeras Gingeras - Affymetrix Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Filtered transcript fragments K562 nucleus polyA+ Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsK562NucleusLongnonpolya K562 nucl pA- K562 RnaChip ENCODE Nov 2008 Freeze 2008-11-22 2009-08-22 wgEncodeEH000007 7 Gingeras Affy nucleus hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsK562NucleusLongnonpolya FiltTransfrags leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Protein Interactions Gingeras Gingeras - Affymetrix Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Filtered transcript fragments K562 nucleus polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsK562PolysomeLongnonpolya K562 psom pA- K562 RnaChip ENCODE Nov 2008 Freeze 2008-11-21 2009-08-21 wgEncodeEH000004 4 Gingeras Affy polysome hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsK562PolysomeLongnonpolya FiltTransfrags leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Protein Interactions Gingeras Gingeras - Affymetrix Strand of mRNA with ribosomes attached Poly(A)- RNA longer than 200 nt Filtered transcript fragments K562 polysome polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsK562CytosolLongpolya K562 cyto pA+ K562 RnaChip ENCODE Nov 2008 Freeze 2008-11-22 2009-08-22 wgEncodeEH000006 6 Gingeras Affy cytosol hg18 longPolyA wgEncodeAffyRnaChipFiltTransfragsK562CytosolLongpolya FiltTransfrags leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Protein Interactions Gingeras Gingeras - Affymetrix The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Filtered transcript fragments K562 cytosol polyA+ Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsK562CytosolLongnonpolya K562 cyto pA- K562 RnaChip ENCODE Nov 2008 Freeze 2008-11-22 2009-08-22 wgEncodeEH000005 5 Gingeras Affy cytosol hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsK562CytosolLongnonpolya FiltTransfrags leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Protein Interactions Gingeras Gingeras - Affymetrix The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Filtered transcript fragments K562 cytosol polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsK562CellTotal K562 cell tot K562 RnaChip ENCODE Nov 2008 Freeze 2008-11-25 2009-08-25 wgEncodeEH000011 11 Gingeras Affy cell hg18 total wgEncodeAffyRnaChipFiltTransfragsK562CellTotal FiltTransfrags leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Protein Interactions Gingeras Gingeras - Affymetrix Whole cell Total RNA extract (longer than 200 nt) Filtered transcript fragments K562 whole cell total Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsGm12878NucleolusTotal GM12878 nlus tot GM12878 RnaChip ENCODE Sep 2009 Freeze 2009-08-27 2010-05-27 wgEncodeEH000026 26 Gingeras Affy nucleolus hg18 total wgEncodeAffyRnaChipFiltTransfragsGm12878NucleolusTotal FiltTransfrags B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Protein Interactions Gingeras Gingeras - Affymetrix The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Filtered transcript fragments GM12878 nucleolus total Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsGm12878NucleusLongpolya GM12878 nucl pA+ GM12878 RnaChip ENCODE Feb 2009 Freeze 2009-04-01 2010-01-01 wgEncodeEH000017 17 Gingeras Affy nucleus hg18 longPolyA wgEncodeAffyRnaChipFiltTransfragsGm12878NucleusLongpolya FiltTransfrags B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Protein Interactions Gingeras Gingeras - Affymetrix Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Filtered transcript fragments GM12878 nucleus polyA+ Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsGm12878NucleusLongnonpolya GM12878 nucl pA- GM12878 RnaChip ENCODE Nov 2008 Freeze 2008-11-21 2009-08-21 wgEncodeEH000003 3 Gingeras Affy nucleus hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsGm12878NucleusLongnonpolya FiltTransfrags B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Protein Interactions Gingeras Gingeras - Affymetrix Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Filtered transcript fragments GM12878 nucleus polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongpolya GM12878 cyto pA+ GM12878 RnaChip ENCODE Nov 2008 Freeze 2008-11-21 2009-08-21 wgEncodeEH000002 2 Gingeras Affy cytosol hg18 longPolyA wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongpolya FiltTransfrags B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Protein Interactions Gingeras Gingeras - Affymetrix The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Filtered transcript fragments GM12878 cytosol polyA+ Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongnonpolya GM12878 cyto pA- GM12878 RnaChip ENCODE Nov 2008 Freeze 2008-12-09 2009-09-09 wgEncodeEH000012 12 Gingeras Affy cytosol hg18 longNonPolyA wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongnonpolya FiltTransfrags B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Protein Interactions Gingeras Gingeras - Affymetrix The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Filtered transcript fragments GM12878 cytosol polyA- Microarray Transfrags from ENCODE Affy/CSHL Expression 
wgEncodeAffyRnaChipFiltTransfragsGm12878CellTotal GM12878 cell tot GM12878 RnaChip ENCODE Feb 2009 Freeze 2009-03-10 2009-12-10 wgEncodeEH000016 16 Gingeras Affy cell hg18 total wgEncodeAffyRnaChipFiltTransfragsGm12878CellTotal FiltTransfrags B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Protein Interactions Gingeras Gingeras - Affymetrix Whole cell Total RNA extract (longer than 200 nt) Filtered transcript fragments GM12878 whole cell total Microarray Transfrags from ENCODE Affy/CSHL Expression 
consIndelsHgMmCanFam Cons Indels MmCf Indel-based Conservation for Human hg19, Mouse mm8 and Dog canFam2 Comparative Genomics Description This track displays regions showing evidence for conservation with respect to mutations involving sequence insertions and deletions (indels). These “indel-purified sequences” (IPSs) were obtained by comparing the predictions of a neutral model of indel evolution with data obtained from human (hg19), mouse (mm8) and dog (camFam2) alignments (Lunter et al., 2006) The evidence for conservation is statistical, and each region is annotated with a posterior probability. It may be interpreted as the probability that the segment shows the paucity of indels by selection, rather than by random chance. Apart from the underlying alignment, these data are independent of the conservation of the nucleotide sequence itself. Any inferred conservation of the sequence, e.g. as shown by phastCons, is therefore independent evidence for selection. It may happen that sequence is conserved with respect to indel mutations without concomitant evidence of conservation of the nucleotide sequence. The opposite may also happen. Display Conventions The score (based on the false discovery rate, FDR) is reflected in the bluescale density gradient coloring the track items. Lighter colours reflect a higher FDR. Methods In the absence of selection, indels have a certain predicted distribution over the genome. The actual distribution shows an over-abundance of ungapped regions, due to selection purifying functional sequence from the deleterious effects of indels. Neutrally evolving sequence, such as (by and large) ancestral repeats, show an exceedingly good fit to the neutral predictions. This accurate fit allows the identification of a good proportion of conserved sequence at a relatively low false discovery rate (FDR). For example, at an FDR of 10%, the predicted sensitivity is 75%. Each identified indel-purified sequence (IPS) is annotated by two numbers: a false discovery rate (FDR), and a posterior probability (p). The FDR refers to a set of segments, not a given segment by itself. In this case, it refers to the minimum FDR of all sets that include the segment of interest. For example, a segment annotated with a 10% FDR also belongs to a set with a 15% FDR, but not a set with a 5% FDR. The posterior probability does refer to the single segment by itself. It has a frequentist interpretation, namely, as the proportion of regions, annotated with the same posterior probability, that have been under purifying selection, rather than showing the observed lack of indels by random chance. The data include segments for a false-discovery rate of up to 50%. The score directly reflects the FDR, through the following formula: score = 90 / (FDR + 0.08) This maps FDR 1% (the most restrictive category) to 999, and FDR 10% to 500. For further details of the Methods, see Lunter et al., 2006. Verification The neutral indel model was calibrated using ancestral repeats, against which it showed an excellent fit. Among the identified IPSs at 10% FDR and predicted sensitivity of 75%, we found 75% of annotated protein-coding exons (weighted by length), and 75% of the 222 microRNAs that were annotated at the time. Ancestral repeats were heavily depleted among the identified segments. Credits These data were generated by Gerton Lunter and Chris Ponting, MRC Functional Genetics Unit, University of Oxford, United Kingdom and Jotun Hein, Department of Statistics, University of Oxford, United Kingdom. References Lunter G, Ponting CP, Hein J. Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol. 2006 Jan;2(1):e5. PMID: 16410828; PMC: PMC1326222 The data may also be browsed here. 
rnaCluster Gene Bounds Gene Boundaries as Defined by RNA and Spliced EST Clusters mRNA and EST Description This track shows the boundaries of genes and the direction of transcription as deduced from clustering spliced ESTs and mRNAs against the genome. When many spliced variants of the same gene exist, this track shows the variant that spans the greatest distance in the genome. Method ESTs and mRNAs from GenBank were aligned against the genome using BLAT. Alignments with less than 97.5% base identity within the aligning blocks were filtered out. When multiple alignments occurred, only those alignments with a percentage identity within 0.2% of the best alignment were kept. The following alignments were also discarded: ESTs that aligned without any introns, blocks smaller than 10 bases, and blocks smaller than 130 bases that were not located next to an intron. The orientations of the ESTs and mRNAs were deduced from the GT/AG splice sites at the introns; ESTs and mRNAs with overlapping blocks on the same strand were merged into clusters. Only the extent and orientation of the clusters are shown in this track. Scores for individual gene boundaries were assigned based on the number of cDNA alignments used: 300 &mdash; based on a single cDNA alignment 600 &mdash; based on two alignments 900 &mdash; based on three alignments 1000 &mdash; based on four or more alignments Credits This track, which was originally developed by Jim Kent, was generated at UCSC and uses data submitted to GenBank by scientists worldwide. References Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32:D23-6. Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. 
omimLocation OMIM Cyto Loci OMIM Cytogenetic Loci Phenotypes - Gene Unknown Phenotype and Literature Description NOTE: OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the OMIM database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. Further, please be sure to click through to omim.org for the very latest, as they are continually updating data. NOTE ABOUT DOWNLOADS: OMIM is the property of Johns Hopkins University and is not available for download or mirroring by any third party without their permission. Please see OMIM for downloads. OMIM is a compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known Mendelian disorders and over 12,000 genes. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. This database was initiated in the early 1960s by Dr. Victor A. McKusick as a catalog of Mendelian traits and disorders, entitled Mendelian Inheritance in Man (MIM). The OMIM data are separated into three separate tracks: OMIM Alellic Variant Phenotypes (OMIM Alleles) &nbsp;&nbsp;&nbsp;&nbsp;Variants in the OMIM database that have associated dbSNP identifiers. OMIM Gene Phenotypes (OMIM Genes) &nbsp;&nbsp;&nbsp;&nbsp;The genomic positions of gene entries in the OMIM database. The coloring indicates the associated OMIM phenotype map key. OMIM Cytogenetic Loci Phenotypes - Gene Unknown (OMIM Cyto Loci) &nbsp;&nbsp;&nbsp;&nbsp;Regions known to be associated with a phenotype, but for which no specific gene is known to be causative. This track also includes known multi-gene syndromes. This track shows the cytogenetic locations of phenotype entries in the Online Mendelian Inheritance in Man (OMIM) database for which the gene is unknown. Display Conventions and Configuration Cytogenetic locations of OMIM entries are displayed as solid blocks. The entries are colored according to the OMIM phenotype map key of associated disorders: Lighter Green for phenotype map key 1 OMIM records - the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known. Light Green for phenotype map key 2 OMIM records - the disorder has been placed on the map by linkage; no mutation has been found. Dark Green for phenotype map key 3 OMIM records - the molecular basis for the disorder is known; a mutation has been found in the gene. Purple for phenotype map key 4 OMIM records - a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype. Gene symbols and disease information, when available, are displayed on the details pages. The descriptions of OMIM entries are shown on the main browser display when Full display mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry. Items displayed can be filtered according to phenotype map key on the track controls page. Methods This track was constructed as follows: The data file genemap.txt from OMIM was loaded into the MySQL table omimGeneMap. Entries in genemap.txt having disorder info were parsed and loaded into the omimPhenotype table. The phenotype map keys (the numbers (1)(2)(3)(4) from the disorder columns) were placed into a separate field. The cytogenetic location data (from the location column in omimGeneMap) were parsed and converted into genomic start and end positions based on the cytoBand table. These genomic positions, together with the corresponding OMIM IDs, were loaded into the omimLocation table. All entries with no associated phenotype map key and all OMIM gene entries as reported in the &quot;OMIM Genes&quot; track were then excluded from the omimLocation table. Data Access Because OMIM has only allowed Data queries within individual chromosomes, no download files are available from the Genome Browser. Full genome datasets can be downloaded directly from the OMIM Downloads page. All genome-wide downloads are freely available from OMIM after registration. If you need the OMIM data in exactly the format of the UCSC Genome Browser, for example if you are running a UCSC Genome Browser local installation (a partial &quot;mirror&quot;), please create a user account on omim.org and contact OMIM via https://omim.org/contact. Send them your OMIM account name and request access to the UCSC Genome Browser 'entitlement'. They will then grant you access to a MySQL/MariaDB data dump that contains all UCSC Genome Browser OMIM tables. UCSC offers queries within chromosomes from Table Browser that include a variety of filtering options and cross-referencing other datasets using our Data Integrator tool. UCSC also has an API that can be used to retrieve data in JSON format from a particular chromosome range. Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information. Credits Thanks to OMIM and NCBI for the use of their data. This track was constructed by Fan Hsu, Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group. References Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. PMID: 18842627; PMC: PMC2686440 Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7. PMID: 15608251; PMC: PMC539987 
TSS_activity_TPM TSS activity (TPM) FANTOM5: TSS activity per sample (TPM) Regulation Description The FANTOM5 track shows mapped transcription start sites (TSS) and their usage in primary cells, cell lines, and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. Display Conventions and Configuration Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Protocol Individual biological states are profiled by HeliScopeCAGE, which is a variation of the CAGE (Cap Analysis Gene Expression) protocol based on a single molecule sequencer. The standard protocol requiring 5 &micro;g of total RNA as a starting material is referred to as hCAGE, and an optimized version for a lower quantity (~ 100 ng) is referred to as LQhCAGE (Kanamori-Katyama et al. 2011). hCAGE LQhCAGE Samples Transcription start sites (TSSs) were mapped and their usage in human and mouse primary cells, cell lines, and tissues was to produce a comprehensive overview of mammalian gene expression across the human body. 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. Individual samples shown in "TSS activity" tracks are grouped as below. Primary cell Tissue Cell Line Time course Fractionation TSS peaks and enhancers TSS (CAGE) peaks across the panel of the biological states (samples) are identified by DPI (decomposition based peak identification, Forrest et al. 2014), where each of the peaks consists of neighboring and related TSSs. The peaks are used as anchors to define promoters and units of promoter-level expression analysis. Two subsets of the peaks are defined based on evidence of read counts, depending on scopes of subsequent analyses, and the first subset (referred as robust set of the peaks, thresholded for expression analysis is shown as TSS peaks. They are named as "p#@GENE_SYMBOL" if associated with 5'-end of known genes, or "p@CHROM:START..END,STRAND" otherwise. The CAGE data is also used to produce an atlas of active, in vivo-transcribed enhancers (Andersson et al. 2014). The summary tracks consist of the TSS (CAGE) peaks, and summary profiles of TSS activities (total and maximum values). The summary track consists of the following tracks. TSS (CAGE) peaks the robust peaks Enhancers TSS summary profiles Total counts and TPM (tags per million) in all the samples Maximum counts and TPM among the samples TSS activity 5&prime;-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million). Categories of individual samples - Cell Line hCAGE - Cell Line LQhCAGE - fractionation hCAGE - Primary cell hCAGE - Primary cell LQhCAGE - Time course hCAGE - Tissue hCAGE FANTOM-NET enhancers A set of enhancers consist of the ones identified by Andersson et al. 2014 and the ones by Hirabayashi et al. 2019 FANTOM CAT FANTOM CAGE associated transcriptome (FANTOM CAT) is a meta-assembly where FANTOM5 CAGE datasets were integrated with transcript models from diverse sources. Transcription Initiation Evidence Score (TIEScore) is a custom metric that evaluates the properties of a pair of CAGE cluster and transcript model to quantify the likelihood that the corresponding CAGE transcription start site (TSS) is genuine. TIEScore was first applied to each of the five transcript model collections separately and then merged into a non-redundant transcript set. Specifically, the transcript models from GENCODEv19 were used as the initial reference to sequentially overlay onto them the transcripts from the other four collections, in sequence of Human BodyMap 2.0, miTranscriptome, ENCODE, and FANTOM5 RNA-seq assembly. For more details, please refer to Hon et al. 2017. Data Access FANTOM5 data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The FANTOM5 reprocessed data can be found and downloaded on the FANTOM website. Credits Thanks to the FANTOM5 consortium, the Large Scale Data Managing Unit and Preventive Medicine and Applied Genomics Unit, Center for Integrative Medical Sciences (IMS), and RIKEN for providing this data and its analysis. References Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. PMID: 24670763; PMC: PMC5215096 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. PMID: 24670764; PMC: PMC4529748 Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet. 2019 Sep;51(9):1369-1379. PMID: 31477927 Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J et al. An atlas of human long non-coding RNAs with accurate 5' ends. Nature. 2017 Mar 9;543(7644):199-204. PMID: 28241135; PMC: PMC6857182 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 2011 Jul;21(7):1150-9. PMID: 21596820; PMC: PMC3129257 Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. PMID: 25723102; PMC: PMC4310165 
VeinAdult_CNhs12844_tpm_rev VeinAdult- vein, adult_CNhs12844_10191-103E2_reverse Regulation 
VeinAdult_CNhs12844_tpm_fwd VeinAdult+ vein, adult_CNhs12844_10191-103E2_forward Regulation 
VaginaAdult_CNhs12854_tpm_rev VaginaAdult- vagina, adult_CNhs12854_10204-103F6_reverse Regulation 
VaginaAdult_CNhs12854_tpm_fwd VaginaAdult+ vagina, adult_CNhs12854_10204-103F6_forward Regulation 
UterusFetalDonor1_CNhs11763_tpm_rev UterusFetalD1- uterus, fetal, donor1_CNhs11763_10055-101H1_reverse Regulation 
UterusFetalDonor1_CNhs11763_tpm_fwd UterusFetalD1+ uterus, fetal, donor1_CNhs11763_10055-101H1_forward Regulation 
UterusAdultPool1_CNhs11676_tpm_rev UterusAdultPl1- uterus, adult, pool1_CNhs11676_10100-102D1_reverse Regulation 
UterusAdultPool1_CNhs11676_tpm_fwd UterusAdultPl1+ uterus, adult, pool1_CNhs11676_10100-102D1_forward Regulation 
UrethraDonor2_CNhs13464_tpm_rev UrethraD2- Urethra, donor2_CNhs13464_10319-105A4_reverse Regulation 
UrethraDonor2_CNhs13464_tpm_fwd UrethraD2+ Urethra, donor2_CNhs13464_10319-105A4_forward Regulation 
UniversalRNAHumanNormalTissuesBiochainPool1_CNhs10612_tpm_rev UniversalRnaNormalTissuesBiochainPl1- Universal RNA - Human Normal Tissues Biochain, pool1_CNhs10612_10007-101B4_reverse Regulation 
UniversalRNAHumanNormalTissuesBiochainPool1_CNhs10612_tpm_fwd UniversalRnaNormalTissuesBiochainPl1+ Universal RNA - Human Normal Tissues Biochain, pool1_CNhs10612_10007-101B4_forward Regulation 
UmbilicalCordFetalDonor1_CNhs11765_tpm_rev UmbilicalCordFetalD1- umbilical cord, fetal, donor1_CNhs11765_10057-101H3_reverse Regulation 
UmbilicalCordFetalDonor1_CNhs11765_tpm_fwd UmbilicalCordFetalD1+ umbilical cord, fetal, donor1_CNhs11765_10057-101H3_forward Regulation 
TracheaFetalDonor1_CNhs11766_tpm_rev TracheaFetalD1- trachea, fetal, donor1_CNhs11766_10058-101H4_reverse Regulation 
TracheaFetalDonor1_CNhs11766_tpm_fwd TracheaFetalD1+ trachea, fetal, donor1_CNhs11766_10058-101H4_forward Regulation 
TracheaAdultPool1_CNhs10635_tpm_rev TracheaAdultPl1- trachea, adult, pool1_CNhs10635_10029-101E2_reverse Regulation 
TracheaAdultPool1_CNhs10635_tpm_fwd TracheaAdultPl1+ trachea, adult, pool1_CNhs10635_10029-101E2_forward Regulation 
TonsilAdultPool1_CNhs10654_tpm_rev TonsilAdultPl1- tonsil, adult, pool1_CNhs10654_10047-101G2_reverse Regulation 
TonsilAdultPool1_CNhs10654_tpm_fwd TonsilAdultPl1+ tonsil, adult, pool1_CNhs10654_10047-101G2_forward Regulation 
TongueFetalDonor1_CNhs11768_tpm_rev TongueFetalD1- tongue, fetal, donor1_CNhs11768_10059-101H5_reverse Regulation 
TongueFetalDonor1_CNhs11768_tpm_fwd TongueFetalD1+ tongue, fetal, donor1_CNhs11768_10059-101H5_forward Regulation 
TongueEpidermisFungiformPapillaeDonor1_CNhs13460_tpm_rev TongueEpidermisD1- tongue epidermis (fungiform papillae), donor1_CNhs13460_10288-104F9_reverse Regulation 
TongueEpidermisFungiformPapillaeDonor1_CNhs13460_tpm_fwd TongueEpidermisD1+ tongue epidermis (fungiform papillae), donor1_CNhs13460_10288-104F9_forward Regulation 
TongueAdult_CNhs12853_tpm_rev TongueAdult- tongue, adult_CNhs12853_10203-103F5_reverse Regulation 
TongueAdult_CNhs12853_tpm_fwd TongueAdult+ tongue, adult_CNhs12853_10203-103F5_forward Regulation 
ThyroidFetalDonor1_CNhs11769_tpm_rev ThyroidFetalD1- thyroid, fetal, donor1_CNhs11769_10060-101H6_reverse Regulation 
ThyroidFetalDonor1_CNhs11769_tpm_fwd ThyroidFetalD1+ thyroid, fetal, donor1_CNhs11769_10060-101H6_forward Regulation 
ThyroidAdultPool1_CNhs10634_tpm_rev ThyroidAdultPl1- thyroid, adult, pool1_CNhs10634_10028-101E1_reverse Regulation 
ThyroidAdultPool1_CNhs10634_tpm_fwd ThyroidAdultPl1+ thyroid, adult, pool1_CNhs10634_10028-101E1_forward Regulation 
ThymusFetalPool1_CNhs10650_tpm_rev ThymusFetalPl1- thymus, fetal, pool1_CNhs10650_10043-101F7_reverse Regulation 
ThymusFetalPool1_CNhs10650_tpm_fwd ThymusFetalPl1+ thymus, fetal, pool1_CNhs10650_10043-101F7_forward Regulation 
ThymusAdultPool1_CNhs10633_tpm_rev ThymusAdultPl1- thymus, adult, pool1_CNhs10633_10027-101D9_reverse Regulation 
ThymusAdultPool1_CNhs10633_tpm_fwd ThymusAdultPl1+ thymus, adult, pool1_CNhs10633_10027-101D9_forward Regulation 
ThroatFetalDonor1_CNhs11770_tpm_rev ThroatFetalD1- throat, fetal, donor1_CNhs11770_10061-101H7_reverse Regulation 
ThroatFetalDonor1_CNhs11770_tpm_fwd ThroatFetalD1+ throat, fetal, donor1_CNhs11770_10061-101H7_forward Regulation 
ThroatAdult_CNhs12858_tpm_rev ThroatAdult- throat, adult_CNhs12858_10209-103G2_reverse Regulation 
ThroatAdult_CNhs12858_tpm_fwd ThroatAdult+ throat, adult_CNhs12858_10209-103G2_forward Regulation 
ThalamusNewbornDonor10223_CNhs14084_tpm_rev ThalamusNbD10223- thalamus, newborn, donor10223_CNhs14084_10366-105F6_reverse Regulation 
ThalamusNewbornDonor10223_CNhs14084_tpm_fwd ThalamusNbD10223+ thalamus, newborn, donor10223_CNhs14084_10366-105F6_forward Regulation 
ThalamusAdultDonor10258TechRep2_CNhs14551_tpm_rev ThalamusAdultD10258Tr2- thalamus, adult, donor10258, tech_rep2_CNhs14551_10370-105G1_reverse Regulation 
ThalamusAdultDonor10258TechRep2_CNhs14551_tpm_fwd ThalamusAdultD10258Tr2+ thalamus, adult, donor10258, tech_rep2_CNhs14551_10370-105G1_forward Regulation 
ThalamusAdultDonor10258TechRep1_CNhs14223_tpm_rev ThalamusAdultD10258Tr1- thalamus, adult, donor10258, tech_rep1_CNhs14223_10370-105G1_reverse Regulation 
ThalamusAdultDonor10258TechRep1_CNhs14223_tpm_fwd ThalamusAdultD10258Tr1+ thalamus, adult, donor10258, tech_rep1_CNhs14223_10370-105G1_forward Regulation 
ThalamusAdultDonor10252_CNhs12314_tpm_rev ThalamusAdultD10252- thalamus, adult, donor10252_CNhs12314_10154-103A1_reverse Regulation 
ThalamusAdultDonor10252_CNhs12314_tpm_fwd ThalamusAdultD10252+ thalamus, adult, donor10252_CNhs12314_10154-103A1_forward Regulation 
ThalamusAdultDonor10196_CNhs13794_tpm_rev ThalamusAdultD10196- thalamus - adult, donor10196_CNhs13794_10168-103B6_reverse Regulation 
ThalamusAdultDonor10196_CNhs13794_tpm_fwd ThalamusAdultD10196+ thalamus - adult, donor10196_CNhs13794_10168-103B6_forward Regulation 
TestisAdultPool2_CNhs12998_tpm_rev TestisAdultPl2- testis, adult, pool2_CNhs12998_10096-102C6_reverse Regulation 
TestisAdultPool2_CNhs12998_tpm_fwd TestisAdultPl2+ testis, adult, pool2_CNhs12998_10096-102C6_forward Regulation 
TestisAdultPool1_CNhs10632_tpm_rev TestisAdultPl1- testis, adult, pool1_CNhs10632_10026-101D8_reverse Regulation 
TestisAdultPool1_CNhs10632_tpm_fwd TestisAdultPl1+ testis, adult, pool1_CNhs10632_10026-101D8_forward Regulation 
TemporalLobeFetalDonor1TechRep2_CNhs12996_tpm_rev TemporalLobeFetalD1Tr2- temporal lobe, fetal, donor1, tech_rep2_CNhs12996_10063-101H9_reverse Regulation 
TemporalLobeFetalDonor1TechRep2_CNhs12996_tpm_fwd TemporalLobeFetalD1Tr2+ temporal lobe, fetal, donor1, tech_rep2_CNhs12996_10063-101H9_forward Regulation 
TemporalLobeFetalDonor1TechRep1_CNhs11772_tpm_rev TemporalLobeFetalD1Tr1- temporal lobe, fetal, donor1, tech_rep1_CNhs11772_10063-101H9_reverse Regulation 
TemporalLobeFetalDonor1TechRep1_CNhs11772_tpm_fwd TemporalLobeFetalD1Tr1+ temporal lobe, fetal, donor1, tech_rep1_CNhs11772_10063-101H9_forward Regulation 
TemporalLobeAdultPool1_CNhs10637_tpm_rev TemporalLobeAdultPl1- temporal lobe, adult, pool1_CNhs10637_10031-101E4_reverse Regulation 
TemporalLobeAdultPool1_CNhs10637_tpm_fwd TemporalLobeAdultPl1+ temporal lobe, adult, pool1_CNhs10637_10031-101E4_forward Regulation 
SubstantiaNigraNewbornDonor10223_CNhs14076_tpm_rev SubstantiaNigraNbD10223- substantia nigra, newborn, donor10223_CNhs14076_10358-105E7_reverse Regulation 
SubstantiaNigraNewbornDonor10223_CNhs14076_tpm_fwd SubstantiaNigraNbD10223+ substantia nigra, newborn, donor10223_CNhs14076_10358-105E7_forward Regulation 
SubstantiaNigraAdultDonor10258_CNhs14224_tpm_rev SubstantiaNigraAdultD10258- substantia nigra, adult, donor10258_CNhs14224_10371-105G2_reverse Regulation 
SubstantiaNigraAdultDonor10258_CNhs14224_tpm_fwd SubstantiaNigraAdultD10258+ substantia nigra, adult, donor10258_CNhs14224_10371-105G2_forward Regulation 
SubstantiaNigraAdultDonor10252_CNhs12318_tpm_rev SubstantiaNigraAdultD10252- substantia nigra, adult, donor10252_CNhs12318_10158-103A5_reverse Regulation 
SubstantiaNigraAdultDonor10252_CNhs12318_tpm_fwd SubstantiaNigraAdultD10252+ substantia nigra, adult, donor10252_CNhs12318_10158-103A5_forward Regulation 
SubstantiaNigraAdultDonor10196_CNhs13803_tpm_rev SubstantiaNigraAdultD10196- substantia nigra - adult, donor10196_CNhs13803_10178-103C7_reverse Regulation 
SubstantiaNigraAdultDonor10196_CNhs13803_tpm_fwd SubstantiaNigraAdultD10196+ substantia nigra - adult, donor10196_CNhs13803_10178-103C7_forward Regulation 
SubmaxillaryGlandAdult_CNhs12852_tpm_rev SubmaxillaryGlandAdult- submaxillary gland, adult_CNhs12852_10202-103F4_reverse Regulation 
SubmaxillaryGlandAdult_CNhs12852_tpm_fwd SubmaxillaryGlandAdult+ submaxillary gland, adult_CNhs12852_10202-103F4_forward Regulation 
StomachFetalDonor1_CNhs11771_tpm_rev StomachFetalD1- stomach, fetal, donor1_CNhs11771_10062-101H8_reverse Regulation 
StomachFetalDonor1_CNhs11771_tpm_fwd StomachFetalD1+ stomach, fetal, donor1_CNhs11771_10062-101H8_forward Regulation 
SpleenFetalPool1_CNhs10651_tpm_rev SpleenFetalPl1- spleen, fetal, pool1_CNhs10651_10044-101F8_reverse Regulation 
SpleenFetalPool1_CNhs10651_tpm_fwd SpleenFetalPl1+ spleen, fetal, pool1_CNhs10651_10044-101F8_forward Regulation 
SpleenAdultPool1_CNhs10631_tpm_rev SpleenAdultPl1- spleen, adult, pool1_CNhs10631_10025-101D7_reverse Regulation 
SpleenAdultPool1_CNhs10631_tpm_fwd SpleenAdultPl1+ spleen, adult, pool1_CNhs10631_10025-101D7_forward Regulation 
SpinalCordNewbornDonor10223_CNhs14077_tpm_rev SpinalCordNbD10223- spinal cord, newborn, donor10223_CNhs14077_10359-105E8_reverse Regulation 
SpinalCordNewbornDonor10223_CNhs14077_tpm_fwd SpinalCordNbD10223+ spinal cord, newborn, donor10223_CNhs14077_10359-105E8_forward Regulation 
SpinalCordFetalDonor1_CNhs11764_tpm_rev SpinalCordFetalD1- spinal cord, fetal, donor1_CNhs11764_10056-101H2_reverse Regulation 
SpinalCordFetalDonor1_CNhs11764_tpm_fwd SpinalCordFetalD1+ spinal cord, fetal, donor1_CNhs11764_10056-101H2_forward Regulation 
SpinalCordAdultDonor10258_CNhs14222_tpm_rev SpinalCordAdultD10258- spinal cord, adult, donor10258_CNhs14222_10369-105F9_reverse Regulation 
SpinalCordAdultDonor10258_CNhs14222_tpm_fwd SpinalCordAdultD10258+ spinal cord, adult, donor10258_CNhs14222_10369-105F9_forward Regulation 
SpinalCordAdultDonor10252_CNhs12227_tpm_rev SpinalCordAdultD10252- spinal cord, adult, donor10252_CNhs12227_10159-103A6_reverse Regulation 
SpinalCordAdultDonor10252_CNhs12227_tpm_fwd SpinalCordAdultD10252+ spinal cord, adult, donor10252_CNhs12227_10159-103A6_forward Regulation 
SpinalCordAdultDonor10196_CNhs13807_tpm_rev SpinalCordAdultD10196- spinal cord - adult, donor10196_CNhs13807_10181-103D1_reverse Regulation 
SpinalCordAdultDonor10196_CNhs13807_tpm_fwd SpinalCordAdultD10196+ spinal cord - adult, donor10196_CNhs13807_10181-103D1_forward Regulation 
SmoothMuscleAdultPool1_CNhs11755_tpm_rev SmoothMuscleAdultPl1- smooth muscle, adult, pool1_CNhs11755_10048-101G3_reverse Regulation 
SmoothMuscleAdultPool1_CNhs11755_tpm_fwd SmoothMuscleAdultPl1+ smooth muscle, adult, pool1_CNhs11755_10048-101G3_forward Regulation 
SmallIntestineFetalDonor1_CNhs11773_tpm_rev SmallIntestineFetalD1- small intestine, fetal, donor1_CNhs11773_10064-101I1_reverse Regulation 
SmallIntestineFetalDonor1_CNhs11773_tpm_fwd SmallIntestineFetalD1+ small intestine, fetal, donor1_CNhs11773_10064-101I1_forward Regulation 
SmallIntestineAdultPool1_CNhs10630_tpm_rev SmallIntestineAdultPl1- small intestine, adult, pool1_CNhs10630_10024-101D6_reverse Regulation 
SmallIntestineAdultPool1_CNhs10630_tpm_fwd SmallIntestineAdultPl1+ small intestine, adult, pool1_CNhs10630_10024-101D6_forward Regulation 
SkinPalmDonor1_CNhs13458_tpm_rev SkinPalmD1- Skin - palm, donor1_CNhs13458_10286-104F7_reverse Regulation 
SkinPalmDonor1_CNhs13458_tpm_fwd SkinPalmD1+ Skin - palm, donor1_CNhs13458_10286-104F7_forward Regulation 
SkinFetalDonor1_CNhs11774_tpm_rev SkinFetalD1- skin, fetal, donor1_CNhs11774_10065-101I2_reverse Regulation 
SkinFetalDonor1_CNhs11774_tpm_fwd SkinFetalD1+ skin, fetal, donor1_CNhs11774_10065-101I2_forward Regulation 
SkinAdultDonor1_CNhs11785_tpm_rev SkinAdultD1- skin, adult, donor1_CNhs11785_10074-102A2_reverse Regulation 
SkinAdultDonor1_CNhs11785_tpm_fwd SkinAdultD1+ skin, adult, donor1_CNhs11785_10074-102A2_forward Regulation 
SkeletalMuscleSoleusMuscleDonor1_CNhs13454_tpm_rev SkeletalMuscleSoleusMuscleD1- skeletal muscle - soleus muscle, donor1_CNhs13454_10282-104F3_reverse Regulation 
SkeletalMuscleSoleusMuscleDonor1_CNhs13454_tpm_fwd SkeletalMuscleSoleusMuscleD1+ skeletal muscle - soleus muscle, donor1_CNhs13454_10282-104F3_forward Regulation 
SkeletalMuscleFetalDonor1_CNhs11776_tpm_rev SkeletalMuscleFetalD1- skeletal muscle, fetal, donor1_CNhs11776_10066-101I3_reverse Regulation 
SkeletalMuscleFetalDonor1_CNhs11776_tpm_fwd SkeletalMuscleFetalD1+ skeletal muscle, fetal, donor1_CNhs11776_10066-101I3_forward Regulation 
SkeletalMuscleAdultPool1_CNhs10629_tpm_rev SkeletalMuscleAdultPl1- skeletal muscle, adult, pool1_CNhs10629_10023-101D5_reverse Regulation 
SkeletalMuscleAdultPool1_CNhs10629_tpm_fwd SkeletalMuscleAdultPl1+ skeletal muscle, adult, pool1_CNhs10629_10023-101D5_forward Regulation 
SeminalVesicleAdult_CNhs12851_tpm_rev SeminalVesicleAdult- seminal vesicle, adult_CNhs12851_10201-103F3_reverse Regulation 
SeminalVesicleAdult_CNhs12851_tpm_fwd SeminalVesicleAdult+ seminal vesicle, adult_CNhs12851_10201-103F3_forward Regulation 
SalivaryGlandAdultPool1_CNhs11677_tpm_rev SalivaryGlandAdultPl1- salivary gland, adult, pool1_CNhs11677_10093-102C3_reverse Regulation 
SalivaryGlandAdultPool1_CNhs11677_tpm_fwd SalivaryGlandAdultPl1+ salivary gland, adult, pool1_CNhs11677_10093-102C3_forward Regulation 
SABiosciencesXpressRefHumanUniversalTotalRNAPool1_CNhs10610_tpm_rev SabiosciencesXpressrefUniversalPl1- SABiosciences XpressRef Human Universal Total RNA, pool1_CNhs10610_10002-101A5_reverse Regulation 
SABiosciencesXpressRefHumanUniversalTotalRNAPool1_CNhs10610_tpm_fwd SabiosciencesXpressrefUniversalPl1+ SABiosciences XpressRef Human Universal Total RNA, pool1_CNhs10610_10002-101A5_forward Regulation 
RetinaAdultPool1_CNhs10636_tpm_rev RetinaAdultPl1- retina, adult, pool1_CNhs10636_10030-101E3_reverse Regulation 
RetinaAdultPool1_CNhs10636_tpm_fwd RetinaAdultPl1+ retina, adult, pool1_CNhs10636_10030-101E3_forward Regulation 
RectumFetalDonor1_CNhs11777_tpm_rev RectumFetalD1- rectum, fetal, donor1_CNhs11777_10067-101I4_reverse Regulation 
RectumFetalDonor1_CNhs11777_tpm_fwd RectumFetalD1+ rectum, fetal, donor1_CNhs11777_10067-101I4_forward Regulation 
PutamenNewbornDonor10223_CNhs14083_tpm_rev PutamenNbD10223- putamen, newborn, donor10223_CNhs14083_10365-105F5_reverse Regulation 
PutamenNewbornDonor10223_CNhs14083_tpm_fwd PutamenNbD10223+ putamen, newborn, donor10223_CNhs14083_10365-105F5_forward Regulation 
PutamenAdultDonor10258TechRep2_CNhs14618_tpm_rev PutamenAdultD10258Tr2- putamen, adult, donor10258, tech_rep2_CNhs14618_10372-105G3_reverse Regulation 
PutamenAdultDonor10258TechRep2_CNhs14618_tpm_fwd PutamenAdultD10258Tr2+ putamen, adult, donor10258, tech_rep2_CNhs14618_10372-105G3_forward Regulation 
PutamenAdultDonor10258TechRep1_CNhs14225_tpm_rev PutamenAdultD10258Tr1- putamen, adult, donor10258, tech_rep1_CNhs14225_10372-105G3_reverse Regulation 
PutamenAdultDonor10258TechRep1_CNhs14225_tpm_fwd PutamenAdultD10258Tr1+ putamen, adult, donor10258, tech_rep1_CNhs14225_10372-105G3_forward Regulation 
PutamenAdultDonor10252_CNhs13912_tpm_rev PutamenAdultD10252- putamen, adult, donor10252_CNhs13912_10152-102I8_reverse Regulation 
PutamenAdultDonor10252_CNhs13912_tpm_fwd PutamenAdultD10252+ putamen, adult, donor10252_CNhs13912_10152-102I8_forward Regulation 
PutamenAdultDonor10196_CNhs12324_tpm_rev PutamenAdultD10196- putamen, adult, donor10196_CNhs12324_10176-103C5_reverse Regulation 
PutamenAdultDonor10196_CNhs12324_tpm_fwd PutamenAdultD10196+ putamen, adult, donor10196_CNhs12324_10176-103C5_forward Regulation 
ProstateAdultPool1_CNhs10628_tpm_rev ProstateAdultPl1- prostate, adult, pool1_CNhs10628_10022-101D4_reverse Regulation 
ProstateAdultPool1_CNhs10628_tpm_fwd ProstateAdultPl1+ prostate, adult, pool1_CNhs10628_10022-101D4_forward Regulation 
PostcentralGyrusAdultPool1_CNhs10638_tpm_rev PostcentralGyrusAdultPl1- postcentral gyrus, adult, pool1_CNhs10638_10032-101E5_reverse Regulation 
PostcentralGyrusAdultPool1_CNhs10638_tpm_fwd PostcentralGyrusAdultPl1+ postcentral gyrus, adult, pool1_CNhs10638_10032-101E5_forward Regulation 
PonsAdultPool1_CNhs10640_tpm_rev PonsAdultPl1- pons, adult, pool1_CNhs10640_10033-101E6_reverse Regulation 
PonsAdultPool1_CNhs10640_tpm_fwd PonsAdultPl1+ pons, adult, pool1_CNhs10640_10033-101E6_forward Regulation 
PlacentaAdultPool1_CNhs10627_tpm_rev PlacentaAdultPl1- placenta, adult, pool1_CNhs10627_10021-101D3_reverse Regulation 
PlacentaAdultPool1_CNhs10627_tpm_fwd PlacentaAdultPl1+ placenta, adult, pool1_CNhs10627_10021-101D3_forward Regulation 
PituitaryGlandAdultDonor10258_CNhs14231_tpm_rev PituitaryGlandAdultD10258- pituitary gland, adult, donor10258_CNhs14231_10378-105G9_reverse Regulation 
PituitaryGlandAdultDonor10258_CNhs14231_tpm_fwd PituitaryGlandAdultD10258+ pituitary gland, adult, donor10258_CNhs14231_10378-105G9_forward Regulation 
PituitaryGlandAdultDonor10252_CNhs12229_tpm_rev PituitaryGlandAdultD10252- pituitary gland, adult, donor10252_CNhs12229_10162-103A9_reverse Regulation 
PituitaryGlandAdultDonor10252_CNhs12229_tpm_fwd PituitaryGlandAdultD10252+ pituitary gland, adult, donor10252_CNhs12229_10162-103A9_forward Regulation 
PituitaryGlandAdultDonor10196_CNhs13805_tpm_rev PituitaryGlandAdultD10196- pituitary gland - adult, donor10196_CNhs13805_10180-103C9_reverse Regulation 
PituitaryGlandAdultDonor10196_CNhs13805_tpm_fwd PituitaryGlandAdultD10196+ pituitary gland - adult, donor10196_CNhs13805_10180-103C9_forward Regulation 
PinealGlandAdultDonor10258_CNhs14230_tpm_rev PinealGlandAdultD10258- pineal gland, adult, donor10258_CNhs14230_10377-105G8_reverse Regulation 
PinealGlandAdultDonor10258_CNhs14230_tpm_fwd PinealGlandAdultD10258+ pineal gland, adult, donor10258_CNhs14230_10377-105G8_forward Regulation 
PinealGlandAdultDonor10252_CNhs12228_tpm_rev PinealGlandAdultD10252- pineal gland, adult, donor10252_CNhs12228_10160-103A7_reverse Regulation 
PinealGlandAdultDonor10252_CNhs12228_tpm_fwd PinealGlandAdultD10252+ pineal gland, adult, donor10252_CNhs12228_10160-103A7_forward Regulation 
PinealGlandAdultDonor10196_CNhs13804_tpm_rev PinealGlandAdultD10196- pineal gland - adult, donor10196_CNhs13804_10179-103C8_reverse Regulation 
PinealGlandAdultDonor10196_CNhs13804_tpm_fwd PinealGlandAdultD10196+ pineal gland - adult, donor10196_CNhs13804_10179-103C8_forward Regulation 
PenisAdult_CNhs12850_tpm_rev PenisAdult- penis, adult_CNhs12850_10200-103F2_reverse Regulation 
PenisAdult_CNhs12850_tpm_fwd PenisAdult+ penis, adult_CNhs12850_10200-103F2_forward Regulation 
ParotidGlandAdult_CNhs12849_tpm_rev ParotidGlandAdult- parotid gland, adult_CNhs12849_10199-103F1_reverse Regulation 
ParotidGlandAdult_CNhs12849_tpm_fwd ParotidGlandAdult+ parotid gland, adult_CNhs12849_10199-103F1_forward Regulation 
ParietalLobeNewbornDonor10223_CNhs14074_tpm_rev ParietalLobeNbD10223- parietal lobe, newborn, donor10223_CNhs14074_10356-105E5_reverse Regulation 
ParietalLobeNewbornDonor10223_CNhs14074_tpm_fwd ParietalLobeNbD10223+ parietal lobe, newborn, donor10223_CNhs14074_10356-105E5_forward Regulation 
ParietalLobeFetalDonor1_CNhs11782_tpm_rev ParietalLobeFetalD1- parietal lobe, fetal, donor1_CNhs11782_10072-101I9_reverse Regulation 
ParietalLobeFetalDonor1_CNhs11782_tpm_fwd ParietalLobeFetalD1+ parietal lobe, fetal, donor1_CNhs11782_10072-101I9_forward Regulation 
ParietalLobeAdultPool1_CNhs10641_tpm_rev ParietalLobeAdultPl1- parietal lobe, adult, pool1_CNhs10641_10034-101E7_reverse Regulation 
ParietalLobeAdultPool1_CNhs10641_tpm_fwd ParietalLobeAdultPl1+ parietal lobe, adult, pool1_CNhs10641_10034-101E7_forward Regulation 
ParietalLobeAdultDonor10252_CNhs12317_tpm_rev ParietalLobeAdultD10252- parietal lobe, adult, donor10252_CNhs12317_10157-103A4_reverse Regulation 
ParietalLobeAdultDonor10252_CNhs12317_tpm_fwd ParietalLobeAdultD10252+ parietal lobe, adult, donor10252_CNhs12317_10157-103A4_forward Regulation 
ParietalLobeAdultDonor10196_CNhs13797_tpm_rev ParietalLobeAdultD10196- parietal lobe - adult, donor10196_CNhs13797_10171-103B9_reverse Regulation 
ParietalLobeAdultDonor10196_CNhs13797_tpm_fwd ParietalLobeAdultD10196+ parietal lobe - adult, donor10196_CNhs13797_10171-103B9_forward Regulation 
ParietalCortexAdultDonor10258_CNhs14226_tpm_rev ParietalCortexAdultD10258- parietal cortex, adult, donor10258_CNhs14226_10373-105G4_reverse Regulation 
ParietalCortexAdultDonor10258_CNhs14226_tpm_fwd ParietalCortexAdultD10258+ parietal cortex, adult, donor10258_CNhs14226_10373-105G4_forward Regulation 
ParacentralGyrusAdultPool1_CNhs10642_tpm_rev ParacentralGyrusAdultPl1- paracentral gyrus, adult, pool1_CNhs10642_10035-101E8_reverse Regulation 
ParacentralGyrusAdultPool1_CNhs10642_tpm_fwd ParacentralGyrusAdultPl1+ paracentral gyrus, adult, pool1_CNhs10642_10035-101E8_forward Regulation 
PancreasAdultDonor1_CNhs11756_tpm_rev PancreasAdultD1- pancreas, adult, donor1_CNhs11756_10049-101G4_reverse Regulation 
PancreasAdultDonor1_CNhs11756_tpm_fwd PancreasAdultD1+ pancreas, adult, donor1_CNhs11756_10049-101G4_forward Regulation 
OvaryAdultPool1_CNhs10626_tpm_rev OvaryAdultPl1- ovary, adult, pool1_CNhs10626_10020-101D2_reverse Regulation 
OvaryAdultPool1_CNhs10626_tpm_fwd OvaryAdultPl1+ ovary, adult, pool1_CNhs10626_10020-101D2_forward Regulation 
OpticNerveDonor1_CNhs13449_tpm_rev OpticNerveD1- optic nerve, donor1_CNhs13449_10277-104E7_reverse Regulation 
OpticNerveDonor1_CNhs13449_tpm_fwd OpticNerveD1+ optic nerve, donor1_CNhs13449_10277-104E7_forward Regulation 
OlfactoryRegionAdult_CNhs12611_tpm_rev OlfactoryRegionAdult- olfactory region, adult_CNhs12611_10195-103E6_reverse Regulation 
OlfactoryRegionAdult_CNhs12611_tpm_fwd OlfactoryRegionAdult+ olfactory region, adult_CNhs12611_10195-103E6_forward Regulation 
OccipitalPoleAdultPool1_CNhs10643_tpm_rev OccipitalPoleAdultPl1- occipital pole, adult, pool1_CNhs10643_10036-101E9_reverse Regulation 
OccipitalPoleAdultPool1_CNhs10643_tpm_fwd OccipitalPoleAdultPl1+ occipital pole, adult, pool1_CNhs10643_10036-101E9_forward Regulation 
OccipitalLobeFetalDonor1_CNhs11784_tpm_rev OccipitalLobeFetalD1- occipital lobe, fetal, donor1_CNhs11784_10073-102A1_reverse Regulation 
OccipitalLobeFetalDonor1_CNhs11784_tpm_fwd OccipitalLobeFetalD1+ occipital lobe, fetal, donor1_CNhs11784_10073-102A1_forward Regulation 
OccipitalLobeAdultDonor1_CNhs11787_tpm_rev OccipitalLobeAdultD1- occipital lobe, adult, donor1_CNhs11787_10076-102A4_reverse Regulation 
OccipitalLobeAdultDonor1_CNhs11787_tpm_fwd OccipitalLobeAdultD1+ occipital lobe, adult, donor1_CNhs11787_10076-102A4_forward Regulation 
OccipitalCortexNewbornDonor10223_CNhs14073_tpm_rev OccipitalCortexNbD10223- occipital cortex, newborn, donor10223_CNhs14073_10355-105E4_reverse Regulation 
OccipitalCortexNewbornDonor10223_CNhs14073_tpm_fwd OccipitalCortexNbD10223+ occipital cortex, newborn, donor10223_CNhs14073_10355-105E4_forward Regulation 
OccipitalCortexAdultDonor10252_CNhs12320_tpm_rev OccipitalCortexAdultD10252- occipital cortex, adult, donor10252_CNhs12320_10163-103B1_reverse Regulation 
OccipitalCortexAdultDonor10252_CNhs12320_tpm_fwd OccipitalCortexAdultD10252+ occipital cortex, adult, donor10252_CNhs12320_10163-103B1_forward Regulation 
OccipitalCortexAdultDonor10196_CNhs13798_tpm_rev OccipitalCortexAdultD10196- occipital cortex - adult, donor10196_CNhs13798_10172-103C1_reverse Regulation 
OccipitalCortexAdultDonor10196_CNhs13798_tpm_fwd OccipitalCortexAdultD10196+ occipital cortex - adult, donor10196_CNhs13798_10172-103C1_forward Regulation 
NucleusAccumbensAdultPool1_CNhs10644_tpm_rev NucleusAccumbensAdultPl1- nucleus accumbens, adult, pool1_CNhs10644_10037-101F1_reverse Regulation 
NucleusAccumbensAdultPool1_CNhs10644_tpm_fwd NucleusAccumbensAdultPl1+ nucleus accumbens, adult, pool1_CNhs10644_10037-101F1_forward Regulation 
MedullaOblongataNewbornDonor10223_CNhs14079_tpm_rev MedullaOblongataNbD10223- medulla oblongata, newborn, donor10223_CNhs14079_10361-105F1_reverse Regulation 
MedullaOblongataNewbornDonor10223_CNhs14079_tpm_fwd MedullaOblongataNbD10223+ medulla oblongata, newborn, donor10223_CNhs14079_10361-105F1_forward Regulation 
MedullaOblongataAdultPool1_CNhs10645_tpm_rev MedullaOblongataAdultPl1- medulla oblongata, adult, pool1_CNhs10645_10038-101F2_reverse Regulation 
MedullaOblongataAdultPool1_CNhs10645_tpm_fwd MedullaOblongataAdultPl1+ medulla oblongata, adult, pool1_CNhs10645_10038-101F2_forward Regulation 
MedullaOblongataAdultDonor10252_CNhs12315_tpm_rev MedullaOblongataAdultD10252- medulla oblongata, adult, donor10252_CNhs12315_10155-103A2_reverse Regulation 
MedullaOblongataAdultDonor10252_CNhs12315_tpm_fwd MedullaOblongataAdultD10252+ medulla oblongata, adult, donor10252_CNhs12315_10155-103A2_forward Regulation 
MedullaOblongataAdultDonor10196_CNhs13800_tpm_rev MedullaOblongataAdultD10196- medulla oblongata - adult, donor10196_CNhs13800_10174-103C3_reverse Regulation 
MedullaOblongataAdultDonor10196_CNhs13800_tpm_fwd MedullaOblongataAdultD10196+ medulla oblongata - adult, donor10196_CNhs13800_10174-103C3_forward Regulation 
MedialTemporalGyrusNewbornDonor10223_CNhs14070_tpm_rev MedialTemporalGyrusNbD10223- medial temporal gyrus, newborn, donor10223_CNhs14070_10353-105E2_reverse Regulation 
MedialTemporalGyrusNewbornDonor10223_CNhs14070_tpm_fwd MedialTemporalGyrusNbD10223+ medial temporal gyrus, newborn, donor10223_CNhs14070_10353-105E2_forward Regulation 
MedialTemporalGyrusAdultDonor10258TechRep2_CNhs14552_tpm_rev MedialTemporalGyrusAdultD10258Tr2- medial temporal gyrus, adult, donor10258, tech_rep2_CNhs14552_10376-105G7_reverse Regulation 
MedialTemporalGyrusAdultDonor10258TechRep2_CNhs14552_tpm_fwd MedialTemporalGyrusAdultD10258Tr2+ medial temporal gyrus, adult, donor10258, tech_rep2_CNhs14552_10376-105G7_forward Regulation 
MedialTemporalGyrusAdultDonor10258TechRep1_CNhs14229_tpm_rev MedialTemporalGyrusAdultD10258Tr1- medial temporal gyrus, adult, donor10258, tech_rep1_CNhs14229_10376-105G7_reverse Regulation 
MedialTemporalGyrusAdultDonor10258TechRep1_CNhs14229_tpm_fwd MedialTemporalGyrusAdultD10258Tr1+ medial temporal gyrus, adult, donor10258, tech_rep1_CNhs14229_10376-105G7_forward Regulation 
MedialTemporalGyrusAdultDonor10252_CNhs12316_tpm_rev MedialTemporalGyrusAdultD10252- medial temporal gyrus, adult, donor10252_CNhs12316_10156-103A3_reverse Regulation 
MedialTemporalGyrusAdultDonor10252_CNhs12316_tpm_fwd MedialTemporalGyrusAdultD10252+ medial temporal gyrus, adult, donor10252_CNhs12316_10156-103A3_forward Regulation 
MedialTemporalGyrusAdultDonor10196_CNhs13809_tpm_rev MedialTemporalGyrusAdultD10196- medial temporal gyrus - adult, donor10196_CNhs13809_10183-103D3_reverse Regulation 
MedialTemporalGyrusAdultDonor10196_CNhs13809_tpm_fwd MedialTemporalGyrusAdultD10196+ medial temporal gyrus - adult, donor10196_CNhs13809_10183-103D3_forward Regulation 
MedialFrontalGyrusNewbornDonor10223_CNhs14069_tpm_rev MedialFrontalGyrusNbD10223- medial frontal gyrus, newborn, donor10223_CNhs14069_10352-105E1_reverse Regulation 
MedialFrontalGyrusNewbornDonor10223_CNhs14069_tpm_fwd MedialFrontalGyrusNbD10223+ medial frontal gyrus, newborn, donor10223_CNhs14069_10352-105E1_forward Regulation 
MedialFrontalGyrusAdultDonor10258_CNhs14221_tpm_rev MedialFrontalGyrusAdultD10258- medial frontal gyrus, adult, donor10258_CNhs14221_10368-105F8_reverse Regulation 
MedialFrontalGyrusAdultDonor10258_CNhs14221_tpm_fwd MedialFrontalGyrusAdultD10258+ medial frontal gyrus, adult, donor10258_CNhs14221_10368-105F8_forward Regulation 
MedialFrontalGyrusAdultDonor10252_CNhs12310_tpm_rev MedialFrontalGyrusAdultD10252- medial frontal gyrus, adult, donor10252_CNhs12310_10150-102I6_reverse Regulation 
MedialFrontalGyrusAdultDonor10252_CNhs12310_tpm_fwd MedialFrontalGyrusAdultD10252+ medial frontal gyrus, adult, donor10252_CNhs12310_10150-102I6_forward Regulation 
MedialFrontalGyrusAdultDonor10196_CNhs13796_tpm_rev MedialFrontalGyrusAdultD10196- medial frontal gyrus - adult, donor10196_CNhs13796_10170-103B8_reverse Regulation 
MedialFrontalGyrusAdultDonor10196_CNhs13796_tpm_fwd MedialFrontalGyrusAdultD10196+ medial frontal gyrus - adult, donor10196_CNhs13796_10170-103B8_forward Regulation 
LymphNodeAdultDonor1_CNhs11788_tpm_rev LymphNodeAdultD1- lymph node, adult, donor1_CNhs11788_10077-102A5_reverse Regulation 
LymphNodeAdultDonor1_CNhs11788_tpm_fwd LymphNodeAdultD1+ lymph node, adult, donor1_CNhs11788_10077-102A5_forward Regulation 
LungRightLowerLobeAdultDonor1_CNhs11786_tpm_rev LungRightLowerLobeAdultD1- lung, right lower lobe, adult, donor1_CNhs11786_10075-102A3_reverse Regulation 
LungRightLowerLobeAdultDonor1_CNhs11786_tpm_fwd LungRightLowerLobeAdultD1+ lung, right lower lobe, adult, donor1_CNhs11786_10075-102A3_forward Regulation 
LungFetalDonor1_CNhs11680_tpm_rev LungFetalD1- lung, fetal, donor1_CNhs11680_10068-101I5_reverse Regulation 
LungFetalDonor1_CNhs11680_tpm_fwd LungFetalD1+ lung, fetal, donor1_CNhs11680_10068-101I5_forward Regulation 
LungAdultPool1_CNhs10625_tpm_rev LungAdultPl1- lung, adult, pool1_CNhs10625_10019-101D1_reverse Regulation 
LungAdultPool1_CNhs10625_tpm_fwd LungAdultPl1+ lung, adult, pool1_CNhs10625_10019-101D1_forward Regulation 
LocusCoeruleusNewbornDonor10223_CNhs14080_tpm_rev LocusCoeruleusNbD10223- locus coeruleus, newborn, donor10223_CNhs14080_10362-105F2_reverse Regulation 
LocusCoeruleusNewbornDonor10223_CNhs14080_tpm_fwd LocusCoeruleusNbD10223+ locus coeruleus, newborn, donor10223_CNhs14080_10362-105F2_forward Regulation 
LocusCoeruleusAdultDonor10258_CNhs14550_tpm_rev LocusCoeruleusAdultD10258- locus coeruleus, adult, donor10258_CNhs14550_10375-105G6_reverse Regulation 
LocusCoeruleusAdultDonor10258_CNhs14550_tpm_fwd LocusCoeruleusAdultD10258+ locus coeruleus, adult, donor10258_CNhs14550_10375-105G6_forward Regulation 
LocusCoeruleusAdultDonor10252_CNhs12322_tpm_rev LocusCoeruleusAdultD10252- locus coeruleus, adult, donor10252_CNhs12322_10165-103B3_reverse Regulation 
LocusCoeruleusAdultDonor10252_CNhs12322_tpm_fwd LocusCoeruleusAdultD10252+ locus coeruleus, adult, donor10252_CNhs12322_10165-103B3_forward Regulation 
LocusCoeruleusAdultDonor10196_CNhs13808_tpm_rev LocusCoeruleusAdultD10196- locus coeruleus - adult, donor10196_CNhs13808_10182-103D2_reverse Regulation 
LocusCoeruleusAdultDonor10196_CNhs13808_tpm_fwd LocusCoeruleusAdultD10196+ locus coeruleus - adult, donor10196_CNhs13808_10182-103D2_forward Regulation 
LiverFetalPool1_CNhs11798_tpm_rev LiverFetalPl1- liver, fetal, pool1_CNhs11798_10086-102B5_reverse Regulation 
LiverFetalPool1_CNhs11798_tpm_fwd LiverFetalPl1+ liver, fetal, pool1_CNhs11798_10086-102B5_forward Regulation 
LiverAdultPool1_CNhs10624_tpm_rev LiverAdultPl1- liver, adult, pool1_CNhs10624_10018-101C9_reverse Regulation 
LiverAdultPool1_CNhs10624_tpm_fwd LiverAdultPl1+ liver, adult, pool1_CNhs10624_10018-101C9_forward Regulation 
LeftVentricleAdultDonor1_CNhs11789_tpm_rev LeftVentricleAdultD1- left ventricle, adult, donor1_CNhs11789_10078-102A6_reverse Regulation 
LeftVentricleAdultDonor1_CNhs11789_tpm_fwd LeftVentricleAdultD1+ left ventricle, adult, donor1_CNhs11789_10078-102A6_forward Regulation 
LeftAtriumAdultDonor1_CNhs11790_tpm_rev LeftAtriumAdultD1- left atrium, adult, donor1_CNhs11790_10079-102A7_reverse Regulation 
LeftAtriumAdultDonor1_CNhs11790_tpm_fwd LeftAtriumAdultD1+ left atrium, adult, donor1_CNhs11790_10079-102A7_forward Regulation 
KidneyFetalPool1_CNhs10652_tpm_rev KidneyFetalPl1- kidney, fetal, pool1_CNhs10652_10045-101F9_reverse Regulation 
KidneyFetalPool1_CNhs10652_tpm_fwd KidneyFetalPl1+ kidney, fetal, pool1_CNhs10652_10045-101F9_forward Regulation 
KidneyAdultPool1_CNhs10622_tpm_rev KidneyAdultPl1- kidney, adult, pool1_CNhs10622_10017-101C8_reverse Regulation 
KidneyAdultPool1_CNhs10622_tpm_fwd KidneyAdultPl1+ kidney, adult, pool1_CNhs10622_10017-101C8_forward Regulation 
InsulaAdultPool1_CNhs10646_tpm_rev InsulaAdultPl1- insula, adult, pool1_CNhs10646_10039-101F3_reverse Regulation 
InsulaAdultPool1_CNhs10646_tpm_fwd InsulaAdultPl1+ insula, adult, pool1_CNhs10646_10039-101F3_forward Regulation 
HippocampusNewbornDonor10223_CNhs14081_tpm_rev HippocampusNbD10223- hippocampus, newborn, donor10223_CNhs14081_10363-105F3_reverse Regulation 
HippocampusNewbornDonor10223_CNhs14081_tpm_fwd HippocampusNbD10223+ hippocampus, newborn, donor10223_CNhs14081_10363-105F3_forward Regulation 
HippocampusAdultDonor10258_CNhs14227_tpm_rev HippocampusAdultD10258- hippocampus, adult, donor10258_CNhs14227_10374-105G5_reverse Regulation 
HippocampusAdultDonor10258_CNhs14227_tpm_fwd HippocampusAdultD10258+ hippocampus, adult, donor10258_CNhs14227_10374-105G5_forward Regulation 
HippocampusAdultDonor10252_CNhs12312_tpm_rev HippocampusAdultD10252- hippocampus, adult, donor10252_CNhs12312_10153-102I9_reverse Regulation 
HippocampusAdultDonor10252_CNhs12312_tpm_fwd HippocampusAdultD10252+ hippocampus, adult, donor10252_CNhs12312_10153-102I9_forward Regulation 
HippocampusAdultDonor10196_CNhs13795_tpm_rev HippocampusAdultD10196- hippocampus - adult, donor10196_CNhs13795_10169-103B7_reverse Regulation 
HippocampusAdultDonor10196_CNhs13795_tpm_fwd HippocampusAdultD10196+ hippocampus - adult, donor10196_CNhs13795_10169-103B7_forward Regulation 
HeartTricuspidValveAdult_CNhs12857_tpm_rev HeartTricuspidValveAdult- heart - tricuspid valve, adult_CNhs12857_10207-103F9_reverse Regulation 
HeartTricuspidValveAdult_CNhs12857_tpm_fwd HeartTricuspidValveAdult+ heart - tricuspid valve, adult_CNhs12857_10207-103F9_forward Regulation 
HeartPulmonicValveAdult_CNhs12856_tpm_rev HeartPulmonicValveAdult- heart - pulmonic valve, adult_CNhs12856_10206-103F8_reverse Regulation 
HeartPulmonicValveAdult_CNhs12856_tpm_fwd HeartPulmonicValveAdult+ heart - pulmonic valve, adult_CNhs12856_10206-103F8_forward Regulation 
HeartMitralValveAdult_CNhs12855_tpm_rev HeartMitralValveAdult- heart - mitral valve, adult_CNhs12855_10205-103F7_reverse Regulation 
HeartMitralValveAdult_CNhs12855_tpm_fwd HeartMitralValveAdult+ heart - mitral valve, adult_CNhs12855_10205-103F7_forward Regulation 
HeartFetalPool1_CNhs10653_tpm_rev HeartFetalPl1- heart, fetal, pool1_CNhs10653_10046-101G1_reverse Regulation 
HeartFetalPool1_CNhs10653_tpm_fwd HeartFetalPl1+ heart, fetal, pool1_CNhs10653_10046-101G1_forward Regulation 
HeartAdultPool1_CNhs10621_tpm_rev HeartAdultPl1- heart, adult, pool1_CNhs10621_10016-101C7_reverse Regulation 
HeartAdultPool1_CNhs10621_tpm_fwd HeartAdultPl1+ heart, adult, pool1_CNhs10621_10016-101C7_forward Regulation 
HeartAdultDiseasedPostinfarctionDonor1_CNhs11757_tpm_rev HeartAdultDiseasedPost-infarctionD1- heart, adult, diseased post-infarction, donor1_CNhs11757_10050-101G5_reverse Regulation 
HeartAdultDiseasedPostinfarctionDonor1_CNhs11757_tpm_fwd HeartAdultDiseasedPost-infarctionD1+ heart, adult, diseased post-infarction, donor1_CNhs11757_10050-101G5_forward Regulation 
HeartAdultDiseasedDonor1_CNhs11758_tpm_rev HeartAdultDiseasedD1- heart, adult, diseased, donor1_CNhs11758_10051-101G6_reverse Regulation 
HeartAdultDiseasedDonor1_CNhs11758_tpm_fwd HeartAdultDiseasedD1+ heart, adult, diseased, donor1_CNhs11758_10051-101G6_forward Regulation 
GlobusPallidusNewbornDonor10223_CNhs14082_tpm_rev GlobusPallidusNbD10223- globus pallidus, newborn, donor10223_CNhs14082_10364-105F4_reverse Regulation 
GlobusPallidusNewbornDonor10223_CNhs14082_tpm_fwd GlobusPallidusNbD10223+ globus pallidus, newborn, donor10223_CNhs14082_10364-105F4_forward Regulation 
GlobusPallidusAdultDonor10258_CNhs14549_tpm_rev GlobusPallidusAdultD10258- globus pallidus, adult, donor10258_CNhs14549_10367-105F7_reverse Regulation 
GlobusPallidusAdultDonor10258_CNhs14549_tpm_fwd GlobusPallidusAdultD10258+ globus pallidus, adult, donor10258_CNhs14549_10367-105F7_forward Regulation 
GlobusPallidusAdultDonor10252_CNhs12319_tpm_rev GlobusPallidusAdultD10252- globus pallidus, adult, donor10252_CNhs12319_10161-103A8_reverse Regulation 
GlobusPallidusAdultDonor10252_CNhs12319_tpm_fwd GlobusPallidusAdultD10252+ globus pallidus, adult, donor10252_CNhs12319_10161-103A8_forward Regulation 
GlobusPallidusAdultDonor10196_CNhs13801_tpm_rev GlobusPallidusAdultD10196- globus pallidus - adult, donor10196_CNhs13801_10175-103C4_reverse Regulation 
GlobusPallidusAdultDonor10196_CNhs13801_tpm_fwd GlobusPallidusAdultD10196+ globus pallidus - adult, donor10196_CNhs13801_10175-103C4_forward Regulation 
GallBladderAdult_CNhs12848_tpm_rev GallBladderAdult- gall bladder, adult_CNhs12848_10198-103E9_reverse Regulation 
GallBladderAdult_CNhs12848_tpm_fwd GallBladderAdult+ gall bladder, adult_CNhs12848_10198-103E9_forward Regulation 
FrontalLobeAdultPool1_CNhs10647_tpm_rev FrontalLobeAdultPl1- frontal lobe, adult, pool1_CNhs10647_10040-101F4_reverse Regulation 
FrontalLobeAdultPool1_CNhs10647_tpm_fwd FrontalLobeAdultPl1+ frontal lobe, adult, pool1_CNhs10647_10040-101F4_forward Regulation 
FingernailIncludingNailPlateEponychiumAndHyponychiumDonor2_CNhs13445_tpm_rev FingernailD2- Fingernail (including nail plate, eponychium and hyponychium), donor2_CNhs13445_10301-104H4_reverse Regulation 
FingernailIncludingNailPlateEponychiumAndHyponychiumDonor2_CNhs13445_tpm_fwd FingernailD2+ Fingernail (including nail plate, eponychium and hyponychium), donor2_CNhs13445_10301-104H4_forward Regulation 
EyeVitreousHumorDonor1_CNhs13440_tpm_rev EyeVitreousHumorD1- eye - vitreous humor, donor1_CNhs13440_10268-104D7_reverse Regulation 
EyeVitreousHumorDonor1_CNhs13440_tpm_fwd EyeVitreousHumorD1+ eye - vitreous humor, donor1_CNhs13440_10268-104D7_forward Regulation 
EyeMuscleSuperiorDonor2_CNhs13441_tpm_rev EyeMuscleSuperiorD2- eye - muscle superior, donor2_CNhs13441_10297-104G9_reverse Regulation 
EyeMuscleSuperiorDonor2_CNhs13441_tpm_fwd EyeMuscleSuperiorD2+ eye - muscle superior, donor2_CNhs13441_10297-104G9_forward Regulation 
EyeMuscleMedialDonor2_CNhs13443_tpm_rev EyeMuscleMedialD2- eye - muscle medial, donor2_CNhs13443_10299-104H2_reverse Regulation 
EyeMuscleMedialDonor2_CNhs13443_tpm_fwd EyeMuscleMedialD2+ eye - muscle medial, donor2_CNhs13443_10299-104H2_forward Regulation 
EyeMuscleLateralDonor2_CNhs13442_tpm_rev EyeMuscleLateralD2- eye - muscle lateral, donor2_CNhs13442_10298-104H1_reverse Regulation 
EyeMuscleLateralDonor2_CNhs13442_tpm_fwd EyeMuscleLateralD2+ eye - muscle lateral, donor2_CNhs13442_10298-104H1_forward Regulation 
EyeMuscleInferiorRectusDonor1_CNhs13444_tpm_rev EyeMuscleInferiorRectusD1- eye - muscle inferior rectus, donor1_CNhs13444_10272-104E2_reverse Regulation 
EyeMuscleInferiorRectusDonor1_CNhs13444_tpm_fwd EyeMuscleInferiorRectusD1+ eye - muscle inferior rectus, donor1_CNhs13444_10272-104E2_forward Regulation 
EyeFetalDonor1_CNhs11762_tpm_rev EyeFetalD1- eye, fetal, donor1_CNhs11762_10054-101G9_reverse Regulation 
EyeFetalDonor1_CNhs11762_tpm_fwd EyeFetalD1+ eye, fetal, donor1_CNhs11762_10054-101G9_forward Regulation 
EsophagusAdultPool1_CNhs10620_tpm_rev EsophagusAdultPl1- esophagus, adult, pool1_CNhs10620_10015-101C6_reverse Regulation 
EsophagusAdultPool1_CNhs10620_tpm_fwd EsophagusAdultPl1+ esophagus, adult, pool1_CNhs10620_10015-101C6_forward Regulation 
EpididymisAdult_CNhs12847_tpm_rev EpididymisAdult- epididymis, adult_CNhs12847_10197-103E8_reverse Regulation 
EpididymisAdult_CNhs12847_tpm_fwd EpididymisAdult+ epididymis, adult_CNhs12847_10197-103E8_forward Regulation 
DuraMaterAdultDonor1_CNhs10648_tpm_rev DuraMaterAdultD1- dura mater, adult, donor1_CNhs10648_10041-101F5_reverse Regulation 
DuraMaterAdultDonor1_CNhs10648_tpm_fwd DuraMaterAdultD1+ dura mater, adult, donor1_CNhs10648_10041-101F5_forward Regulation 
DuodenumFetalDonor1TechRep2_CNhs12997_tpm_rev DuodenumFetalD1Tr2- duodenum, fetal, donor1, tech_rep2_CNhs12997_10071-101I8_reverse Regulation 
DuodenumFetalDonor1TechRep2_CNhs12997_tpm_fwd DuodenumFetalD1Tr2+ duodenum, fetal, donor1, tech_rep2_CNhs12997_10071-101I8_forward Regulation 
DuodenumFetalDonor1TechRep1_CNhs11781_tpm_rev DuodenumFetalD1Tr1- duodenum, fetal, donor1, tech_rep1_CNhs11781_10071-101I8_reverse Regulation 
DuodenumFetalDonor1TechRep1_CNhs11781_tpm_fwd DuodenumFetalD1Tr1+ duodenum, fetal, donor1, tech_rep1_CNhs11781_10071-101I8_forward Regulation 
DuctusDeferensAdult_CNhs12846_tpm_rev DuctusDeferensAdult- ductus deferens, adult_CNhs12846_10196-103E7_reverse Regulation 
DuctusDeferensAdult_CNhs12846_tpm_fwd DuctusDeferensAdult+ ductus deferens, adult_CNhs12846_10196-103E7_forward Regulation 
DiencephalonAdult_CNhs12610_tpm_rev DiencephalonAdult- diencephalon, adult_CNhs12610_10193-103E4_reverse Regulation 
DiencephalonAdult_CNhs12610_tpm_fwd DiencephalonAdult+ diencephalon, adult_CNhs12610_10193-103E4_forward Regulation 
DiaphragmFetalDonor1_CNhs11779_tpm_rev DiaphragmFetalD1- diaphragm, fetal, donor1_CNhs11779_10069-101I6_reverse Regulation 
DiaphragmFetalDonor1_CNhs11779_tpm_fwd DiaphragmFetalD1+ diaphragm, fetal, donor1_CNhs11779_10069-101I6_forward Regulation 
CruciateLigamentDonor2_CNhs13439_tpm_rev CruciateLigamentD2- cruciate ligament, donor2_CNhs13439_10295-104G7_reverse Regulation 
CruciateLigamentDonor2_CNhs13439_tpm_fwd CruciateLigamentD2+ cruciate ligament, donor2_CNhs13439_10295-104G7_forward Regulation 
CorpusCallosumAdultPool1_CNhs10649_tpm_rev CorpusCallosumAdultPl1- corpus callosum, adult, pool1_CNhs10649_10042-101F6_reverse Regulation 
CorpusCallosumAdultPool1_CNhs10649_tpm_fwd CorpusCallosumAdultPl1+ corpus callosum, adult, pool1_CNhs10649_10042-101F6_forward Regulation 
ColonFetalDonor1_CNhs11780_tpm_rev ColonFetalD1- colon, fetal, donor1_CNhs11780_10070-101I7_reverse Regulation 
ColonFetalDonor1_CNhs11780_tpm_fwd ColonFetalD1+ colon, fetal, donor1_CNhs11780_10070-101I7_forward Regulation 
ColonAdultPool1_CNhs10619_tpm_rev ColonAdultPl1- colon, adult, pool1_CNhs10619_10014-101C5_reverse Regulation 
ColonAdultPool1_CNhs10619_tpm_fwd ColonAdultPl1+ colon, adult, pool1_CNhs10619_10014-101C5_forward Regulation 
ColonAdultDonor1_CNhs11794_tpm_rev ColonAdultD1- colon, adult, donor1_CNhs11794_10082-102B1_reverse Regulation 
ColonAdultDonor1_CNhs11794_tpm_fwd ColonAdultD1+ colon, adult, donor1_CNhs11794_10082-102B1_forward Regulation 
ClontechHumanUniversalReferenceTotalRNAPool1_CNhs10608_tpm_rev ClontechUniversalReferencePl1- Clontech Human Universal Reference Total RNA, pool1_CNhs10608_10000-101A1_reverse Regulation 
ClontechHumanUniversalReferenceTotalRNAPool1_CNhs10608_tpm_fwd ClontechUniversalReferencePl1+ Clontech Human Universal Reference Total RNA, pool1_CNhs10608_10000-101A1_forward Regulation 
CervixAdultPool1_CNhs10618_tpm_rev CervixAdultPl1- cervix, adult, pool1_CNhs10618_10013-101C4_reverse Regulation 
CervixAdultPool1_CNhs10618_tpm_fwd CervixAdultPl1+ cervix, adult, pool1_CNhs10618_10013-101C4_forward Regulation 
CerebrospinalFluidDonor2_CNhs13437_tpm_rev CerebrospinalFluidD2- cerebrospinal fluid, donor2_CNhs13437_10294-104G6_reverse Regulation 
CerebrospinalFluidDonor2_CNhs13437_tpm_fwd CerebrospinalFluidD2+ cerebrospinal fluid, donor2_CNhs13437_10294-104G6_forward Regulation 
CerebralMeningesAdult_CNhs12840_tpm_rev CerebralMeningesAdult- cerebral meninges, adult_CNhs12840_10188-103D8_reverse Regulation 
CerebralMeningesAdult_CNhs12840_tpm_fwd CerebralMeningesAdult+ cerebral meninges, adult_CNhs12840_10188-103D8_forward Regulation 
CerebellumNewbornDonor10223_CNhs14075_tpm_rev CerebellumNbD10223- cerebellum, newborn, donor10223_CNhs14075_10357-105E6_reverse Regulation 
CerebellumNewbornDonor10223_CNhs14075_tpm_fwd CerebellumNbD10223+ cerebellum, newborn, donor10223_CNhs14075_10357-105E6_forward Regulation 
CerebellumAdultPool1_CNhs11795_tpm_rev CerebellumAdultPl1- cerebellum, adult, pool1_CNhs11795_10083-102B2_reverse Regulation 
CerebellumAdultPool1_CNhs11795_tpm_fwd CerebellumAdultPl1+ cerebellum, adult, pool1_CNhs11795_10083-102B2_forward Regulation 
CerebellumAdultDonor10252_CNhs12323_tpm_rev CerebellumAdultD10252- cerebellum, adult, donor10252_CNhs12323_10166-103B4_reverse Regulation 
CerebellumAdultDonor10252_CNhs12323_tpm_fwd CerebellumAdultD10252+ cerebellum, adult, donor10252_CNhs12323_10166-103B4_forward Regulation 
CerebellumAdultDonor10196_CNhs13799_tpm_rev CerebellumAdultD10196- cerebellum - adult, donor10196_CNhs13799_10173-103C2_reverse Regulation 
CerebellumAdultDonor10196_CNhs13799_tpm_fwd CerebellumAdultD10196+ cerebellum - adult, donor10196_CNhs13799_10173-103C2_forward Regulation 
CaudateNucleusNewbornDonor10223_CNhs14071_tpm_rev CaudateNucleusNbD10223- caudate nucleus, newborn, donor10223_CNhs14071_10354-105E3_reverse Regulation 
CaudateNucleusNewbornDonor10223_CNhs14071_tpm_fwd CaudateNucleusNbD10223+ caudate nucleus, newborn, donor10223_CNhs14071_10354-105E3_forward Regulation 
CaudateNucleusAdultDonor10258_CNhs14232_tpm_rev CaudateNucleusAdultD10258- caudate nucleus, adult, donor10258_CNhs14232_10379-105H1_reverse Regulation 
CaudateNucleusAdultDonor10258_CNhs14232_tpm_fwd CaudateNucleusAdultD10258+ caudate nucleus, adult, donor10258_CNhs14232_10379-105H1_forward Regulation 
CaudateNucleusAdultDonor10252_CNhs12321_tpm_rev CaudateNucleusAdultD10252- caudate nucleus, adult, donor10252_CNhs12321_10164-103B2_reverse Regulation 
CaudateNucleusAdultDonor10252_CNhs12321_tpm_fwd CaudateNucleusAdultD10252+ caudate nucleus, adult, donor10252_CNhs12321_10164-103B2_forward Regulation 
CaudateNucleusAdultDonor10196_CNhs13802_tpm_rev CaudateNucleusAdultD10196- caudate nucleus - adult, donor10196_CNhs13802_10177-103C6_reverse Regulation 
CaudateNucleusAdultDonor10196_CNhs13802_tpm_fwd CaudateNucleusAdultD10196+ caudate nucleus - adult, donor10196_CNhs13802_10177-103C6_forward Regulation 
BreastAdultDonor1_CNhs11792_tpm_rev BreastAdultD1- breast, adult, donor1_CNhs11792_10080-102A8_reverse Regulation 
BreastAdultDonor1_CNhs11792_tpm_fwd BreastAdultD1+ breast, adult, donor1_CNhs11792_10080-102A8_forward Regulation 
BrainFetalPool1_CNhs11797_tpm_rev BrainFetalPl1- brain, fetal, pool1_CNhs11797_10085-102B4_reverse Regulation 
BrainFetalPool1_CNhs11797_tpm_fwd BrainFetalPl1+ brain, fetal, pool1_CNhs11797_10085-102B4_forward Regulation 
BrainAdultPool1_CNhs10617_tpm_rev BrainAdultPl1- brain, adult, pool1_CNhs10617_10012-101C3_reverse Regulation 
BrainAdultPool1_CNhs10617_tpm_fwd BrainAdultPl1+ brain, adult, pool1_CNhs10617_10012-101C3_forward Regulation 
BrainAdultDonor1_CNhs11796_tpm_rev BrainAdultD1- brain, adult, donor1_CNhs11796_10084-102B3_reverse Regulation 
BrainAdultDonor1_CNhs11796_tpm_fwd BrainAdultD1+ brain, adult, donor1_CNhs11796_10084-102B3_forward Regulation 
BoneMarrowAdult_CNhs12845_tpm_rev BoneMarrowAdult- bone marrow, adult_CNhs12845_10192-103E3_reverse Regulation 
BoneMarrowAdult_CNhs12845_tpm_fwd BoneMarrowAdult+ bone marrow, adult_CNhs12845_10192-103E3_forward Regulation 
BloodAdultPool1_CNhs11761_tpm_rev BloodAdultPl1- blood, adult, pool1_CNhs11761_10053-101G8_reverse Regulation 
BloodAdultPool1_CNhs11761_tpm_fwd BloodAdultPl1+ blood, adult, pool1_CNhs11761_10053-101G8_forward Regulation 
BladderAdultPool1_CNhs10616_tpm_rev BladderAdultPl1- bladder, adult, pool1_CNhs10616_10011-101C2_reverse Regulation 
BladderAdultPool1_CNhs10616_tpm_fwd BladderAdultPl1+ bladder, adult, pool1_CNhs10616_10011-101C2_forward Regulation 
ArteryAdult_CNhs12843_tpm_rev ArteryAdult- artery, adult_CNhs12843_10190-103E1_reverse Regulation 
ArteryAdult_CNhs12843_tpm_fwd ArteryAdult+ artery, adult_CNhs12843_10190-103E1_forward Regulation 
AppendixAdult_CNhs12842_tpm_rev AppendixAdult- appendix, adult_CNhs12842_10189-103D9_reverse Regulation 
AppendixAdult_CNhs12842_tpm_fwd AppendixAdult+ appendix, adult_CNhs12842_10189-103D9_forward Regulation 
AortaAdultPool1_CNhs11760_tpm_rev AortaAdultPl1- aorta, adult, pool1_CNhs11760_10052-101G7_reverse Regulation 
AortaAdultPool1_CNhs11760_tpm_fwd AortaAdultPl1+ aorta, adult, pool1_CNhs11760_10052-101G7_forward Regulation 
AmygdalaNewbornDonor10223_CNhs14078_tpm_rev AmygdalaNbD1D10223- amygdala, newborn, donor10223_CNhs14078_10360-105E9_reverse Regulation 
AmygdalaNewbornDonor10223_CNhs14078_tpm_fwd AmygdalaNbD1D10223+ amygdala, newborn, donor10223_CNhs14078_10360-105E9_forward Regulation 
AmygdalaAdultDonor10252_CNhs12311_tpm_rev AmygdalaAdultD10252- amygdala, adult, donor10252_CNhs12311_10151-102I7_reverse Regulation 
AmygdalaAdultDonor10252_CNhs12311_tpm_fwd AmygdalaAdultD10252+ amygdala, adult, donor10252_CNhs12311_10151-102I7_forward Regulation 
AmygdalaAdultDonor10196_CNhs13793_tpm_rev AmygdalaAdultD10196- amygdala - adult, donor10196_CNhs13793_10167-103B5_reverse Regulation 
AmygdalaAdultDonor10196_CNhs13793_tpm_fwd AmygdalaAdultD10196+ amygdala - adult, donor10196_CNhs13793_10167-103B5_forward Regulation 
AdrenalGlandAdultPool1_CNhs11793_tpm_rev AdrenalGlandAdultPl1- adrenal gland, adult, pool1_CNhs11793_10081-102A9_reverse Regulation 
AdrenalGlandAdultPool1_CNhs11793_tpm_fwd AdrenalGlandAdultPl1+ adrenal gland, adult, pool1_CNhs11793_10081-102A9_forward Regulation 
AdiposeTissueAdultPool1_CNhs10615_tpm_rev AdiposeTissueAdultPl1- adipose tissue, adult, pool1_CNhs10615_10010-101C1_reverse Regulation 
AdiposeTissueAdultPool1_CNhs10615_tpm_fwd AdiposeTissueAdultPl1+ adipose tissue, adult, pool1_CNhs10615_10010-101C1_forward Regulation 
AdiposeDonor4_CNhs13975_tpm_rev AdiposeD4- adipose, donor4_CNhs13975_10187-103D7_reverse Regulation 
AdiposeDonor4_CNhs13975_tpm_fwd AdiposeD4+ adipose, donor4_CNhs13975_10187-103D7_forward Regulation 
AdiposeDonor3_CNhs13974_tpm_rev AdiposeD3- adipose, donor3_CNhs13974_10186-103D6_reverse Regulation 
AdiposeDonor3_CNhs13974_tpm_fwd AdiposeD3+ adipose, donor3_CNhs13974_10186-103D6_forward Regulation 
AdiposeDonor2_CNhs13973_tpm_rev AdiposeD2- adipose, donor2_CNhs13973_10185-103D5_reverse Regulation 
AdiposeDonor2_CNhs13973_tpm_fwd AdiposeD2+ adipose, donor2_CNhs13973_10185-103D5_forward Regulation 
AdiposeDonor1_CNhs13972_tpm_rev AdiposeD1- adipose, donor1_CNhs13972_10184-103D4_reverse Regulation 
AdiposeDonor1_CNhs13972_tpm_fwd AdiposeD1+ adipose, donor1_CNhs13972_10184-103D4_forward Regulation 
AchillesTendonDonor2_CNhs13435_tpm_rev AchillesTendonD2- achilles tendon, donor2_CNhs13435_10292-104G4_reverse Regulation 
AchillesTendonDonor2_CNhs13435_tpm_fwd AchillesTendonD2+ achilles tendon, donor2_CNhs13435_10292-104G4_forward Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep3B3T17_CNhs14196_tpm_rev Tc:Saos-2Untreated_Day28Br3- Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep3 (B3 T17)_CNhs14196_12893-137H4_reverse Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep3B3T17_CNhs14196_tpm_fwd Tc:Saos-2Untreated_Day28Br3+ Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep3 (B3 T17)_CNhs14196_12893-137H4_forward Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep2B2T17_CNhs14195_tpm_rev Tc:Saos-2Untreated_Day28Br2- Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep2 (B2 T17)_CNhs14195_12795-136F5_reverse Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep2B2T17_CNhs14195_tpm_fwd Tc:Saos-2Untreated_Day28Br2+ Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep2 (B2 T17)_CNhs14195_12795-136F5_forward Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep1B1T17_CNhs14194_tpm_rev Tc:Saos-2Untreated_Day28Br1- Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep1 (B1 T17)_CNhs14194_12697-135D6_reverse Regulation 
Saos2OsteosarcomaCellLineUntreatedControlDay28BiolRep1B1T17_CNhs14194_tpm_fwd Tc:Saos-2Untreated_Day28Br1+ Saos-2 osteosarcoma cell line, untreated control, day28, biol_rep1 (B1 T17)_CNhs14194_12697-135D6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep3_CNhs13634_tpm_rev Tc:MscToAdiposeUndiffBr3- mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep3_CNhs13634_13282-142F6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep3_CNhs13634_tpm_fwd Tc:MscToAdiposeUndiffBr3+ mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep3_CNhs13634_13282-142F6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep2_CNhs13633_tpm_rev Tc:MscToAdiposeUndiffBr2- mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep2_CNhs13633_13281-142F5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep2_CNhs13633_tpm_fwd Tc:MscToAdiposeUndiffBr2+ mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep2_CNhs13633_13281-142F5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep1_CNhs13692_tpm_rev Tc:MscToAdiposeUndiffBr1- mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep1_CNhs13692_13280-142F4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedUndifferentiatedControlBiolRep1_CNhs13692_tpm_fwd Tc:MscToAdiposeUndiffBr1+ mesenchymal stem cells (adipose derived), undifferentiated control, biol_rep1_CNhs13692_13280-142F4_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor1868_121MI_0h_CNhs13637_tpm_rev Tc:MdmToMock_00hr00minD1- Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor1 (868_121:MI_0h)_CNhs13637_13304-142I1_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor1868_121MI_0h_CNhs13637_tpm_fwd Tc:MdmToMock_00hr00minD1+ Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor1 (868_121:MI_0h)_CNhs13637_13304-142I1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor1T20Subject1_CNhs12930_tpm_rev Tc:MdmToLps_16hrD1- Monocyte-derived macrophages response to LPS, 16hr, donor1 (t20 Subject1)_CNhs12930_12717-135F8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor1T20Subject1_CNhs12930_tpm_fwd Tc:MdmToLps_16hrD1+ Monocyte-derived macrophages response to LPS, 16hr, donor1 (t20 Subject1)_CNhs12930_12717-135F8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor1T17Subject1_CNhs12928_tpm_rev Tc:MdmToLps_10hrD1- Monocyte-derived macrophages response to LPS, 10hr, donor1 (t17 Subject1)_CNhs12928_12714-135F5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor1T17Subject1_CNhs12928_tpm_fwd Tc:MdmToLps_10hrD1+ Monocyte-derived macrophages response to LPS, 10hr, donor1 (t17 Subject1)_CNhs12928_12714-135F5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor3T15Subject3_CNhs13325_tpm_rev Tc:MdmToLps_07hrD3- Monocyte-derived macrophages response to LPS, 07hr, donor3 (t15 Subject3)_CNhs13325_12908-138A1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor3T15Subject3_CNhs13325_tpm_fwd Tc:MdmToLps_07hrD3+ Monocyte-derived macrophages response to LPS, 07hr, donor3 (t15 Subject3)_CNhs13325_12908-138A1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor2T15Subject2_CNhs13394_tpm_rev Tc:MdmToLps_07hrD2- Monocyte-derived macrophages response to LPS, 07hr, donor2 (t15 Subject2)_CNhs13394_12810-136H2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor2T15Subject2_CNhs13394_tpm_fwd Tc:MdmToLps_07hrD2+ Monocyte-derived macrophages response to LPS, 07hr, donor2 (t15 Subject2)_CNhs13394_12810-136H2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor1T15Subject1_CNhs12926_tpm_rev Tc:MdmToLps_07hrD1- Monocyte-derived macrophages response to LPS, 07hr, donor1 (t15 Subject1)_CNhs12926_12712-135F3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS07hrDonor1T15Subject1_CNhs12926_tpm_fwd Tc:MdmToLps_07hrD1+ Monocyte-derived macrophages response to LPS, 07hr, donor1 (t15 Subject1)_CNhs12926_12712-135F3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor3T14Subject3_CNhs13187_tpm_rev Tc:MdmToLps_06hrD3- Monocyte-derived macrophages response to LPS, 06hr, donor3 (t14 Subject3)_CNhs13187_12907-137I9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor3T14Subject3_CNhs13187_tpm_fwd Tc:MdmToLps_06hrD3+ Monocyte-derived macrophages response to LPS, 06hr, donor3 (t14 Subject3)_CNhs13187_12907-137I9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor2T14Subject2_CNhs13393_tpm_rev Tc:MdmToLps_06hrD2- Monocyte-derived macrophages response to LPS, 06hr, donor2 (t14 Subject2)_CNhs13393_12809-136H1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor2T14Subject2_CNhs13393_tpm_fwd Tc:MdmToLps_06hrD2+ Monocyte-derived macrophages response to LPS, 06hr, donor2 (t14 Subject2)_CNhs13393_12809-136H1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor1T14Subject1_CNhs12925_tpm_rev Tc:MdmToLps_06hrD1- Monocyte-derived macrophages response to LPS, 06hr, donor1 (t14 Subject1)_CNhs12925_12711-135F2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS06hrDonor1T14Subject1_CNhs12925_tpm_fwd Tc:MdmToLps_06hrD1+ Monocyte-derived macrophages response to LPS, 06hr, donor1 (t14 Subject1)_CNhs12925_12711-135F2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor1T12Subject1_CNhs13154_tpm_rev Tc:MdmToLps_04hrD1- Monocyte-derived macrophages response to LPS, 04hr, donor1 (t12 Subject1)_CNhs13154_12709-135E9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor1T12Subject1_CNhs13154_tpm_fwd Tc:MdmToLps_04hrD1+ Monocyte-derived macrophages response to LPS, 04hr, donor1 (t12 Subject1)_CNhs13154_12709-135E9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor1T11Subject1_CNhs13153_tpm_rev Tc:MdmToLps_03hr30minD1- Monocyte-derived macrophages response to LPS, 03hr30min, donor1 (t11 Subject1)_CNhs13153_12708-135E8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor1T11Subject1_CNhs13153_tpm_fwd Tc:MdmToLps_03hr30minD1+ Monocyte-derived macrophages response to LPS, 03hr30min, donor1 (t11 Subject1)_CNhs13153_12708-135E8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor1T8Subject1_CNhs13151_tpm_rev Tc:MdmToLps_02hr00minD1- Monocyte-derived macrophages response to LPS, 02hr00min, donor1 (t8 Subject1)_CNhs13151_12705-135E5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor1T8Subject1_CNhs13151_tpm_fwd Tc:MdmToLps_02hr00minD1+ Monocyte-derived macrophages response to LPS, 02hr00min, donor1 (t8 Subject1)_CNhs13151_12705-135E5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor3T7Subject3_CNhs13180_tpm_rev Tc:MdmToLps_01hr40minD3- Monocyte-derived macrophages response to LPS, 01hr40min, donor3 (t7 Subject3)_CNhs13180_12900-137I2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor3T7Subject3_CNhs13180_tpm_fwd Tc:MdmToLps_01hr40minD3+ Monocyte-derived macrophages response to LPS, 01hr40min, donor3 (t7 Subject3)_CNhs13180_12900-137I2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor2T7Subject2_CNhs13385_tpm_rev Tc:MdmToLps_01hr40minD2- Monocyte-derived macrophages response to LPS, 01hr40min, donor2 (t7 Subject2)_CNhs13385_12802-136G3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor2T7Subject2_CNhs13385_tpm_fwd Tc:MdmToLps_01hr40minD2+ Monocyte-derived macrophages response to LPS, 01hr40min, donor2 (t7 Subject2)_CNhs13385_12802-136G3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor1T7Subject1_CNhs13150_tpm_rev Tc:MdmToLps_01hr40minD1- Monocyte-derived macrophages response to LPS, 01hr40min, donor1 (t7 Subject1)_CNhs13150_12704-135E4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr40minDonor1T7Subject1_CNhs13150_tpm_fwd Tc:MdmToLps_01hr40minD1+ Monocyte-derived macrophages response to LPS, 01hr40min, donor1 (t7 Subject1)_CNhs13150_12704-135E4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor1T6Subject1_CNhs13149_tpm_rev Tc:MdmToLps_01hr20minD1- Monocyte-derived macrophages response to LPS, 01hr20min, donor1 (t6 Subject1)_CNhs13149_12703-135E3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor1T6Subject1_CNhs13149_tpm_fwd Tc:MdmToLps_01hr20minD1+ Monocyte-derived macrophages response to LPS, 01hr20min, donor1 (t6 Subject1)_CNhs13149_12703-135E3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor1T5Subject1_CNhs13148_tpm_rev Tc:MdmToLps_01hr00minD1- Monocyte-derived macrophages response to LPS, 01hr00min, donor1 (t5 Subject1)_CNhs13148_12702-135E2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor1T5Subject1_CNhs13148_tpm_fwd Tc:MdmToLps_01hr00minD1+ Monocyte-derived macrophages response to LPS, 01hr00min, donor1 (t5 Subject1)_CNhs13148_12702-135E2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor1T4Subject1_CNhs13147_tpm_rev Tc:MdmToLps_00hr45minD1- Monocyte-derived macrophages response to LPS, 00hr45min, donor1 (t4 Subject1)_CNhs13147_12701-135E1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor1T4Subject1_CNhs13147_tpm_fwd Tc:MdmToLps_00hr45minD1+ Monocyte-derived macrophages response to LPS, 00hr45min, donor1 (t4 Subject1)_CNhs13147_12701-135E1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor1T3Subject1_CNhs13146_tpm_rev Tc:MdmToLps_00hr30minD1- Monocyte-derived macrophages response to LPS, 00hr30min, donor1 (t3 Subject1)_CNhs13146_12700-135D9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor1T3Subject1_CNhs13146_tpm_fwd Tc:MdmToLps_00hr30minD1+ Monocyte-derived macrophages response to LPS, 00hr30min, donor1 (t3 Subject1)_CNhs13146_12700-135D9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor1T2Subject1_CNhs13145_tpm_rev Tc:MdmToLps_00hr15minD1- Monocyte-derived macrophages response to LPS, 00hr15min, donor1 (t2 Subject1)_CNhs13145_12699-135D8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor1T2Subject1_CNhs13145_tpm_fwd Tc:MdmToLps_00hr15minD1+ Monocyte-derived macrophages response to LPS, 00hr15min, donor1 (t2 Subject1)_CNhs13145_12699-135D8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep3_CNhs12804_tpm_rev Tc:K562ToHemin_Day04Br3- K562 erythroblastic leukemia response to hemin, day04, biol_rep3_CNhs12804_13228-141I6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep3_CNhs12804_tpm_fwd Tc:K562ToHemin_Day04Br3+ K562 erythroblastic leukemia response to hemin, day04, biol_rep3_CNhs12804_13228-141I6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep2_CNhs12702_tpm_rev Tc:K562ToHemin_Day04Br2- K562 erythroblastic leukemia response to hemin, day04, biol_rep2_CNhs12702_13162-141B3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep2_CNhs12702_tpm_fwd Tc:K562ToHemin_Day04Br2+ K562 erythroblastic leukemia response to hemin, day04, biol_rep2_CNhs12702_13162-141B3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep1_CNhs12474_tpm_rev Tc:K562ToHemin_Day04Br1- K562 erythroblastic leukemia response to hemin, day04, biol_rep1_CNhs12474_13096-140C9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay04BiolRep1_CNhs12474_tpm_fwd Tc:K562ToHemin_Day04Br1+ K562 erythroblastic leukemia response to hemin, day04, biol_rep1_CNhs12474_13096-140C9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep3_CNhs12803_tpm_rev Tc:K562ToHemin_Day03Br3- K562 erythroblastic leukemia response to hemin, day03, biol_rep3_CNhs12803_13227-141I5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep3_CNhs12803_tpm_fwd Tc:K562ToHemin_Day03Br3+ K562 erythroblastic leukemia response to hemin, day03, biol_rep3_CNhs12803_13227-141I5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep2_CNhs12701_tpm_rev Tc:K562ToHemin_Day03Br2- K562 erythroblastic leukemia response to hemin, day03, biol_rep2_CNhs12701_13161-141B2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep2_CNhs12701_tpm_fwd Tc:K562ToHemin_Day03Br2+ K562 erythroblastic leukemia response to hemin, day03, biol_rep2_CNhs12701_13161-141B2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep1_CNhs12473_tpm_rev Tc:K562ToHemin_Day03Br1- K562 erythroblastic leukemia response to hemin, day03, biol_rep1_CNhs12473_13095-140C8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay03BiolRep1_CNhs12473_tpm_fwd Tc:K562ToHemin_Day03Br1+ K562 erythroblastic leukemia response to hemin, day03, biol_rep1_CNhs12473_13095-140C8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep3_CNhs12802_tpm_rev Tc:K562ToHemin_Day02Br3- K562 erythroblastic leukemia response to hemin, day02, biol_rep3_CNhs12802_13226-141I4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep3_CNhs12802_tpm_fwd Tc:K562ToHemin_Day02Br3+ K562 erythroblastic leukemia response to hemin, day02, biol_rep3_CNhs12802_13226-141I4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep2_CNhs12700_tpm_rev Tc:K562ToHemin_Day02Br2- K562 erythroblastic leukemia response to hemin, day02, biol_rep2_CNhs12700_13160-141B1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep2_CNhs12700_tpm_fwd Tc:K562ToHemin_Day02Br2+ K562 erythroblastic leukemia response to hemin, day02, biol_rep2_CNhs12700_13160-141B1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep1_CNhs12472_tpm_rev Tc:K562ToHemin_Day02Br1- K562 erythroblastic leukemia response to hemin, day02, biol_rep1_CNhs12472_13094-140C7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHeminDay02BiolRep1_CNhs12472_tpm_fwd Tc:K562ToHemin_Day02Br1+ K562 erythroblastic leukemia response to hemin, day02, biol_rep1_CNhs12472_13094-140C7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep3_CNhs12801_tpm_rev Tc:K562ToHemin_24hrBr3- K562 erythroblastic leukemia response to hemin, 24hr, biol_rep3_CNhs12801_13225-141I3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep3_CNhs12801_tpm_fwd Tc:K562ToHemin_24hrBr3+ K562 erythroblastic leukemia response to hemin, 24hr, biol_rep3_CNhs12801_13225-141I3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep2_CNhs12699_tpm_rev Tc:K562ToHemin_24hrBr2- K562 erythroblastic leukemia response to hemin, 24hr, biol_rep2_CNhs12699_13159-141A9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep2_CNhs12699_tpm_fwd Tc:K562ToHemin_24hrBr2+ K562 erythroblastic leukemia response to hemin, 24hr, biol_rep2_CNhs12699_13159-141A9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep1_CNhs12471_tpm_rev Tc:K562ToHemin_24hrBr1- K562 erythroblastic leukemia response to hemin, 24hr, biol_rep1_CNhs12471_13093-140C6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin24hrBiolRep1_CNhs12471_tpm_fwd Tc:K562ToHemin_24hrBr1+ K562 erythroblastic leukemia response to hemin, 24hr, biol_rep1_CNhs12471_13093-140C6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep3_CNhs12800_tpm_rev Tc:K562ToHemin_12hrBr3- K562 erythroblastic leukemia response to hemin, 12hr, biol_rep3_CNhs12800_13224-141I2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep3_CNhs12800_tpm_fwd Tc:K562ToHemin_12hrBr3+ K562 erythroblastic leukemia response to hemin, 12hr, biol_rep3_CNhs12800_13224-141I2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep2_CNhs12698_tpm_rev Tc:K562ToHemin_12hrBr2- K562 erythroblastic leukemia response to hemin, 12hr, biol_rep2_CNhs12698_13158-141A8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep2_CNhs12698_tpm_fwd Tc:K562ToHemin_12hrBr2+ K562 erythroblastic leukemia response to hemin, 12hr, biol_rep2_CNhs12698_13158-141A8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep1_CNhs12470_tpm_rev Tc:K562ToHemin_12hrBr1- K562 erythroblastic leukemia response to hemin, 12hr, biol_rep1_CNhs12470_13092-140C5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin12hrBiolRep1_CNhs12470_tpm_fwd Tc:K562ToHemin_12hrBr1+ K562 erythroblastic leukemia response to hemin, 12hr, biol_rep1_CNhs12470_13092-140C5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep3_CNhs12799_tpm_rev Tc:K562ToHemin_06hrBr3- K562 erythroblastic leukemia response to hemin, 06hr, biol_rep3_CNhs12799_13223-141I1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep3_CNhs12799_tpm_fwd Tc:K562ToHemin_06hrBr3+ K562 erythroblastic leukemia response to hemin, 06hr, biol_rep3_CNhs12799_13223-141I1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep2_CNhs12697_tpm_rev Tc:K562ToHemin_06hrBr2- K562 erythroblastic leukemia response to hemin, 06hr, biol_rep2_CNhs12697_13157-141A7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep2_CNhs12697_tpm_fwd Tc:K562ToHemin_06hrBr2+ K562 erythroblastic leukemia response to hemin, 06hr, biol_rep2_CNhs12697_13157-141A7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep1_CNhs12469_tpm_rev Tc:K562ToHemin_06hrBr1- K562 erythroblastic leukemia response to hemin, 06hr, biol_rep1_CNhs12469_13091-140C4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin06hrBiolRep1_CNhs12469_tpm_fwd Tc:K562ToHemin_06hrBr1+ K562 erythroblastic leukemia response to hemin, 06hr, biol_rep1_CNhs12469_13091-140C4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep3_CNhs12798_tpm_rev Tc:K562ToHemin_04hrBr3- K562 erythroblastic leukemia response to hemin, 04hr, biol_rep3_CNhs12798_13222-141H9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep3_CNhs12798_tpm_fwd Tc:K562ToHemin_04hrBr3+ K562 erythroblastic leukemia response to hemin, 04hr, biol_rep3_CNhs12798_13222-141H9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep2_CNhs12696_tpm_rev Tc:K562ToHemin_04hrBr2- K562 erythroblastic leukemia response to hemin, 04hr, biol_rep2_CNhs12696_13156-141A6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep2_CNhs12696_tpm_fwd Tc:K562ToHemin_04hrBr2+ K562 erythroblastic leukemia response to hemin, 04hr, biol_rep2_CNhs12696_13156-141A6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep1_CNhs12468_tpm_rev Tc:K562ToHemin_04hrBr1- K562 erythroblastic leukemia response to hemin, 04hr, biol_rep1_CNhs12468_13090-140C3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin04hrBiolRep1_CNhs12468_tpm_fwd Tc:K562ToHemin_04hrBr1+ K562 erythroblastic leukemia response to hemin, 04hr, biol_rep1_CNhs12468_13090-140C3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep3_CNhs12797_tpm_rev Tc:K562ToHemin_03hr30minBr3- K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep3_CNhs12797_13221-141H8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep3_CNhs12797_tpm_fwd Tc:K562ToHemin_03hr30minBr3+ K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep3_CNhs12797_13221-141H8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep2_CNhs12695_tpm_rev Tc:K562ToHemin_03hr30minBr2- K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep2_CNhs12695_13155-141A5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep2_CNhs12695_tpm_fwd Tc:K562ToHemin_03hr30minBr2+ K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep2_CNhs12695_13155-141A5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep1_CNhs12467_tpm_rev Tc:K562ToHemin_03hr30minBr1- K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep1_CNhs12467_13089-140C2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr30minBiolRep1_CNhs12467_tpm_fwd Tc:K562ToHemin_03hr30minBr1+ K562 erythroblastic leukemia response to hemin, 03hr30min, biol_rep1_CNhs12467_13089-140C2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep3_CNhs12796_tpm_rev Tc:K562ToHemin_03hr00minBr3- K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep3_CNhs12796_13220-141H7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep3_CNhs12796_tpm_fwd Tc:K562ToHemin_03hr00minBr3+ K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep3_CNhs12796_13220-141H7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep2_CNhs12694_tpm_rev Tc:K562ToHemin_03hr00minBr2- K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep2_CNhs12694_13154-141A4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep2_CNhs12694_tpm_fwd Tc:K562ToHemin_03hr00minBr2+ K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep2_CNhs12694_13154-141A4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep1_CNhs12466_tpm_rev Tc:K562ToHemin_03hr00minBr1- K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep1_CNhs12466_13088-140C1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin03hr00minBiolRep1_CNhs12466_tpm_fwd Tc:K562ToHemin_03hr00minBr1+ K562 erythroblastic leukemia response to hemin, 03hr00min, biol_rep1_CNhs12466_13088-140C1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep3_CNhs12795_tpm_rev Tc:K562ToHemin_02hr30minBr3- K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep3_CNhs12795_13219-141H6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep3_CNhs12795_tpm_fwd Tc:K562ToHemin_02hr30minBr3+ K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep3_CNhs12795_13219-141H6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep2_CNhs12693_tpm_rev Tc:K562ToHemin_02hr30minBr2- K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep2_CNhs12693_13153-141A3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep2_CNhs12693_tpm_fwd Tc:K562ToHemin_02hr30minBr2+ K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep2_CNhs12693_13153-141A3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep1_CNhs12465_tpm_rev Tc:K562ToHemin_02hr30minBr1- K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep1_CNhs12465_13087-140B9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr30minBiolRep1_CNhs12465_tpm_fwd Tc:K562ToHemin_02hr30minBr1+ K562 erythroblastic leukemia response to hemin, 02hr30min, biol_rep1_CNhs12465_13087-140B9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep3_CNhs12794_tpm_rev Tc:K562ToHemin_02hr00minBr3- K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep3_CNhs12794_13218-141H5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep3_CNhs12794_tpm_fwd Tc:K562ToHemin_02hr00minBr3+ K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep3_CNhs12794_13218-141H5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep2_CNhs12692_tpm_rev Tc:K562ToHemin_02hr00minBr2- K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep2_CNhs12692_13152-141A2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep2_CNhs12692_tpm_fwd Tc:K562ToHemin_02hr00minBr2+ K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep2_CNhs12692_13152-141A2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep1_CNhs12737_tpm_rev Tc:K562ToHemin_02hr00minBr1- K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep1_CNhs12737_13086-140B8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin02hr00minBiolRep1_CNhs12737_tpm_fwd Tc:K562ToHemin_02hr00minBr1+ K562 erythroblastic leukemia response to hemin, 02hr00min, biol_rep1_CNhs12737_13086-140B8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep3_CNhs12792_tpm_rev Tc:K562ToHemin_01hr40minBr3- K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep3_CNhs12792_13217-141H4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep3_CNhs12792_tpm_fwd Tc:K562ToHemin_01hr40minBr3+ K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep3_CNhs12792_13217-141H4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep2_CNhs12691_tpm_rev Tc:K562ToHemin_01hr40minBr2- K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep2_CNhs12691_13151-141A1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep2_CNhs12691_tpm_fwd Tc:K562ToHemin_01hr40minBr2+ K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep2_CNhs12691_13151-141A1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep1_CNhs12464_tpm_rev Tc:K562ToHemin_01hr40minBr1- K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep1_CNhs12464_13085-140B7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr40minBiolRep1_CNhs12464_tpm_fwd Tc:K562ToHemin_01hr40minBr1+ K562 erythroblastic leukemia response to hemin, 01hr40min, biol_rep1_CNhs12464_13085-140B7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep3_CNhs12791_tpm_rev Tc:K562ToHemin_01hr20minBr3- K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep3_CNhs12791_13216-141H3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep3_CNhs12791_tpm_fwd Tc:K562ToHemin_01hr20minBr3+ K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep3_CNhs12791_13216-141H3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep2_CNhs12690_tpm_rev Tc:K562ToHemin_01hr20minBr2- K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep2_CNhs12690_13150-140I9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep2_CNhs12690_tpm_fwd Tc:K562ToHemin_01hr20minBr2+ K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep2_CNhs12690_13150-140I9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep1_CNhs12463_tpm_rev Tc:K562ToHemin_01hr20minBr1- K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep1_CNhs12463_13084-140B6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr20minBiolRep1_CNhs12463_tpm_fwd Tc:K562ToHemin_01hr20minBr1+ K562 erythroblastic leukemia response to hemin, 01hr20min, biol_rep1_CNhs12463_13084-140B6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep3_CNhs12790_tpm_rev Tc:K562ToHemin_01hr00minBr3- K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep3_CNhs12790_13215-141H2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep3_CNhs12790_tpm_fwd Tc:K562ToHemin_01hr00minBr3+ K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep3_CNhs12790_13215-141H2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep2_CNhs12689_tpm_rev Tc:K562ToHemin_01hr00minBr2- K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep2_CNhs12689_13149-140I8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep2_CNhs12689_tpm_fwd Tc:K562ToHemin_01hr00minBr2+ K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep2_CNhs12689_13149-140I8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep1_CNhs12462_tpm_rev Tc:K562ToHemin_01hr00minBr1- K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep1_CNhs12462_13083-140B5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin01hr00minBiolRep1_CNhs12462_tpm_fwd Tc:K562ToHemin_01hr00minBr1+ K562 erythroblastic leukemia response to hemin, 01hr00min, biol_rep1_CNhs12462_13083-140B5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep3_CNhs12789_tpm_rev Tc:K562ToHemin_00hr45minBr3- K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep3_CNhs12789_13214-141H1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep3_CNhs12789_tpm_fwd Tc:K562ToHemin_00hr45minBr3+ K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep3_CNhs12789_13214-141H1_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep2_CNhs12688_tpm_rev Tc:K562ToHemin_00hr45minBr2- K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep2_CNhs12688_13148-140I7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep2_CNhs12688_tpm_fwd Tc:K562ToHemin_00hr45minBr2+ K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep2_CNhs12688_13148-140I7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep1_CNhs12461_tpm_rev Tc:K562ToHemin_00hr45minBr1- K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep1_CNhs12461_13082-140B4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr45minBiolRep1_CNhs12461_tpm_fwd Tc:K562ToHemin_00hr45minBr1+ K562 erythroblastic leukemia response to hemin, 00hr45min, biol_rep1_CNhs12461_13082-140B4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep3_CNhs12788_tpm_rev Tc:K562ToHemin_00hr30minBr3- K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep3_CNhs12788_13213-141G9_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep3_CNhs12788_tpm_fwd Tc:K562ToHemin_00hr30minBr3+ K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep3_CNhs12788_13213-141G9_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep2_CNhs12687_tpm_rev Tc:K562ToHemin_00hr30minBr2- K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep2_CNhs12687_13147-140I6_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep2_CNhs12687_tpm_fwd Tc:K562ToHemin_00hr30minBr2+ K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep2_CNhs12687_13147-140I6_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep1_CNhs12460_tpm_rev Tc:K562ToHemin_00hr30minBr1- K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep1_CNhs12460_13081-140B3_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr30minBiolRep1_CNhs12460_tpm_fwd Tc:K562ToHemin_00hr30minBr1+ K562 erythroblastic leukemia response to hemin, 00hr30min, biol_rep1_CNhs12460_13081-140B3_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep3_CNhs12787_tpm_rev Tc:K562ToHemin_00hr15minBr3- K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep3_CNhs12787_13212-141G8_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep3_CNhs12787_tpm_fwd Tc:K562ToHemin_00hr15minBr3+ K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep3_CNhs12787_13212-141G8_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep2_CNhs12686_tpm_rev Tc:K562ToHemin_00hr15minBr2- K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep2_CNhs12686_13146-140I5_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep2_CNhs12686_tpm_fwd Tc:K562ToHemin_00hr15minBr2+ K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep2_CNhs12686_13146-140I5_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep1_CNhs12459_tpm_rev Tc:K562ToHemin_00hr15minBr1- K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep1_CNhs12459_13080-140B2_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr15minBiolRep1_CNhs12459_tpm_fwd Tc:K562ToHemin_00hr15minBr1+ K562 erythroblastic leukemia response to hemin, 00hr15min, biol_rep1_CNhs12459_13080-140B2_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep3_CNhs12786_tpm_rev Tc:K562ToHemin_00hr00minBr3- K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep3_CNhs12786_13211-141G7_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep3_CNhs12786_tpm_fwd Tc:K562ToHemin_00hr00minBr3+ K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep3_CNhs12786_13211-141G7_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep2_CNhs12684_tpm_rev Tc:K562ToHemin_00hr00minBr2- K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep2_CNhs12684_13145-140I4_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep2_CNhs12684_tpm_fwd Tc:K562ToHemin_00hr00minBr2+ K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep2_CNhs12684_13145-140I4_forward Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep1_CNhs12458_tpm_rev Tc:K562ToHemin_00hr00minBr1- K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep1_CNhs12458_13079-140B1_reverse Regulation 
K562ErythroblasticLeukemiaResponseToHemin00hr00minBiolRep1_CNhs12458_tpm_fwd Tc:K562ToHemin_00hr00minBr1+ K562 erythroblastic leukemia response to hemin, 00hr00min, biol_rep1_CNhs12458_13079-140B1_forward Regulation 
HIPSBiolRep3_CNhs14216_tpm_rev Tc:hIPSBr3- hIPS, biol_rep3_CNhs14216_14382-156B8_reverse Regulation 
HIPSBiolRep3_CNhs14216_tpm_fwd Tc:hIPSBr3+ hIPS, biol_rep3_CNhs14216_14382-156B8_forward Regulation 
HIPSBiolRep2_CNhs14215_tpm_rev Tc:hIPSBr2- hIPS, biol_rep2_CNhs14215_14381-156B7_reverse Regulation 
HIPSBiolRep2_CNhs14215_tpm_fwd Tc:hIPSBr2+ hIPS, biol_rep2_CNhs14215_14381-156B7_forward Regulation 
HIPSBiolRep1_CNhs14214_tpm_rev Tc:hIPSBr1- hIPS, biol_rep1_CNhs14214_14380-156B6_reverse Regulation 
HIPSBiolRep1_CNhs14214_tpm_fwd Tc:hIPSBr1+ hIPS, biol_rep1_CNhs14214_14380-156B6_forward Regulation 
HIPSCCl2BiolRep3_CNhs14219_tpm_rev Tc:hIPS+CCl2Br3- hIPS +CCl2, biol_rep3_CNhs14219_14385-156C2_reverse Regulation 
HIPSCCl2BiolRep3_CNhs14219_tpm_fwd Tc:hIPS+CCl2Br3+ hIPS +CCl2, biol_rep3_CNhs14219_14385-156C2_forward Regulation 
HIPSCCl2BiolRep2_CNhs14218_tpm_rev Tc:hIPS+CCl2Br2- hIPS +CCl2, biol_rep2_CNhs14218_14384-156C1_reverse Regulation 
HIPSCCl2BiolRep2_CNhs14218_tpm_fwd Tc:hIPS+CCl2Br2+ hIPS +CCl2, biol_rep2_CNhs14218_14384-156C1_forward Regulation 
HIPSCCl2BiolRep1_CNhs14217_tpm_rev Tc:hIPS+CCl2Br1- hIPS +CCl2, biol_rep1_CNhs14217_14383-156B9_reverse Regulation 
HIPSCCl2BiolRep1_CNhs14217_tpm_fwd Tc:hIPS+CCl2Br1+ hIPS +CCl2, biol_rep1_CNhs14217_14383-156B9_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep3_CNhs13971_tpm_rev Tc:H1ToHsc_Day09Br3- H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep3_CNhs13971_13531-145G3_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep3_CNhs13971_tpm_fwd Tc:H1ToHsc_Day09Br3+ H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep3_CNhs13971_13531-145G3_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep2_CNhs13970_tpm_rev Tc:H1ToHsc_Day09Br2- H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep2_CNhs13970_13530-145G2_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep2_CNhs13970_tpm_fwd Tc:H1ToHsc_Day09Br2+ H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep2_CNhs13970_13530-145G2_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep1_CNhs13969_tpm_rev Tc:H1ToHsc_Day09Br1- H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep1_CNhs13969_13529-145G1_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay09BiolRep1_CNhs13969_tpm_fwd Tc:H1ToHsc_Day09Br1+ H1 embryonic stem cells differentiation to CD34+ HSC, day09, biol_rep1_CNhs13969_13529-145G1_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep3_CNhs13968_tpm_rev Tc:H1ToHsc_Day03Br3- H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep3_CNhs13968_13528-145F9_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep3_CNhs13968_tpm_fwd Tc:H1ToHsc_Day03Br3+ H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep3_CNhs13968_13528-145F9_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep2_CNhs13966_tpm_rev Tc:H1ToHsc_Day03Br2- H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep2_CNhs13966_13527-145F8_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep2_CNhs13966_tpm_fwd Tc:H1ToHsc_Day03Br2+ H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep2_CNhs13966_13527-145F8_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep1_CNhs13965_tpm_rev Tc:H1ToHsc_Day03Br1- H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep1_CNhs13965_13526-145F7_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay03BiolRep1_CNhs13965_tpm_fwd Tc:H1ToHsc_Day03Br1+ H1 embryonic stem cells differentiation to CD34+ HSC, day03, biol_rep1_CNhs13965_13526-145F7_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep3_CNhs13964_tpm_rev Tc:H1ToHsc_Day00Br3- H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep3_CNhs13964_13525-145F6_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep3_CNhs13964_tpm_fwd Tc:H1ToHsc_Day00Br3+ H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep3_CNhs13964_13525-145F6_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep2_CNhs14068_tpm_rev Tc:H1ToHsc_Day00Br2- H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep2_CNhs14068_13524-145F5_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep2_CNhs14068_tpm_fwd Tc:H1ToHsc_Day00Br2+ H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep2_CNhs14068_13524-145F5_forward Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep1_CNhs14067_tpm_rev Tc:H1ToHsc_Day00Br1- H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep1_CNhs14067_13523-145F4_reverse Regulation 
H1EmbryonicStemCellsDifferentiationToCD34HSCDay00BiolRep1_CNhs14067_tpm_fwd Tc:H1ToHsc_Day00Br1+ H1 embryonic stem cells differentiation to CD34+ HSC, day00, biol_rep1_CNhs14067_13523-145F4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep2_CNhs14536_tpm_rev Tc:ARPE-19Emt_24hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep2_CNhs14536_13680-147E8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep2_CNhs14536_tpm_fwd Tc:ARPE-19Emt_24hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep2_CNhs14536_13680-147E8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep2_CNhs14520_tpm_rev Tc:ARPE-19Emt_06hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep2_CNhs14520_13665-147D2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep2_CNhs14520_tpm_fwd Tc:ARPE-19Emt_06hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep2_CNhs14520_13665-147D2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor3_CNhs14584_tpm_rev MyoblastToMyotubes_Day10D3- Myoblast differentiation to myotubes, day10, control donor3_CNhs14584_13494-145C2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor3_CNhs14584_tpm_fwd MyoblastToMyotubes_Day10D3+ Myoblast differentiation to myotubes, day10, control donor3_CNhs14584_13494-145C2_forward Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor2_CNhs14601_tpm_rev MyoblastToMyotubes_Day06D2- Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor2_CNhs14601_13510-145D9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor2_CNhs14601_tpm_fwd MyoblastToMyotubes_Day06D2+ Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor2_CNhs14601_13510-145D9_forward Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor2_CNhs14568_tpm_rev MyoblastToMyotubes_Day01D2- Myoblast differentiation to myotubes, day01, control donor2_CNhs14568_13479-145A5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor2_CNhs14568_tpm_fwd MyoblastToMyotubes_Day01D2+ Myoblast differentiation to myotubes, day01, control donor2_CNhs14568_13479-145A5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep2_CNhs13631_tpm_rev MscAdipogenicInduction_Day14Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep2_CNhs13631_13278-142F2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep2_CNhs13631_tpm_fwd MscAdipogenicInduction_Day14Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep2_CNhs13631_13278-142F2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep2_CNhs13623_tpm_rev MscAdipogenicInduction_Day04Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep2_CNhs13623_13269-142E2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep2_CNhs13623_tpm_fwd MscAdipogenicInduction_Day04Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep2_CNhs13623_13269-142E2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep1_CNhs13615_tpm_rev MscAdipogenicInduction_Day01Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep1_CNhs13615_13262-142D4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep1_CNhs13615_tpm_fwd MscAdipogenicInduction_Day01Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep1_CNhs13615_13262-142D4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep3_CNhs13614_tpm_rev MscAdipogenicInduction_12hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep3_CNhs13614_13261-142D3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep3_CNhs13614_tpm_fwd MscAdipogenicInduction_12hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep3_CNhs13614_13261-142D3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep2_CNhs13613_tpm_rev MscAdipogenicInduction_12hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep2_CNhs13613_13260-142D2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep2_CNhs13613_tpm_fwd MscAdipogenicInduction_12hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep2_CNhs13613_13260-142D2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep1_CNhs13612_tpm_rev MscAdipogenicInduction_12hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep1_CNhs13612_13259-142D1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction12hr00minBiolRep1_CNhs13612_tpm_fwd MscAdipogenicInduction_12hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 12hr00min, biol_rep1_CNhs13612_13259-142D1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep2_CNhs13610_tpm_rev MscAdipogenicInduction_03hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep2_CNhs13610_13257-142C8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep2_CNhs13610_tpm_fwd MscAdipogenicInduction_03hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep2_CNhs13610_13257-142C8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep2_CNhs13607_tpm_rev MscAdipogenicInduction_02hr30minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep2_CNhs13607_13254-142C5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep2_CNhs13607_tpm_fwd MscAdipogenicInduction_02hr30minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep2_CNhs13607_13254-142C5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep3_CNhs13605_tpm_rev MscAdipogenicInduction_02hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep3_CNhs13605_13252-142C3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep3_CNhs13605_tpm_fwd MscAdipogenicInduction_02hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep3_CNhs13605_13252-142C3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep3_CNhs13599_tpm_rev MscAdipogenicInduction_01hr20minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep3_CNhs13599_13246-142B6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep3_CNhs13599_tpm_fwd MscAdipogenicInduction_01hr20minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep3_CNhs13599_13246-142B6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep2_CNhs13598_tpm_rev MscAdipogenicInduction_01hr20minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep2_CNhs13598_13245-142B5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep2_CNhs13598_tpm_fwd MscAdipogenicInduction_01hr20minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep2_CNhs13598_13245-142B5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep1_CNhs13434_tpm_rev MscAdipogenicInduction_01hr20minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep1_CNhs13434_13244-142B4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr20minBiolRep1_CNhs13434_tpm_fwd MscAdipogenicInduction_01hr20minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr20min, biol_rep1_CNhs13434_13244-142B4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep3_CNhs13427_tpm_rev MscAdipogenicInduction_00hr30minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep3_CNhs13427_13237-142A6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep3_CNhs13427_tpm_fwd MscAdipogenicInduction_00hr30minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep3_CNhs13427_13237-142A6_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor4227_121Ud_24h_CNhs13643_tpm_rev MonocyteMacrophageUdornInfluenza_24hr00minD4- Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor4 (227_121:Ud_24h)_CNhs13643_13314-143A2_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor4227_121Ud_24h_CNhs13643_tpm_fwd MonocyteMacrophageUdornInfluenza_24hr00minD4+ Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor4 (227_121:Ud_24h)_CNhs13643_13314-143A2_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor2150_120Ud_2h_CNhs13647_tpm_rev MonocyteMacrophageUdornInfluenza_02hr00minD2- Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor2 (150_120:Ud_2h)_CNhs13647_13318-143A6_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor2150_120Ud_2h_CNhs13647_tpm_fwd MonocyteMacrophageUdornInfluenza_02hr00minD2+ Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor2 (150_120:Ud_2h)_CNhs13647_13318-143A6_forward Regulation 
MelanocyteDonor3MC3_CNhs13406_tpm_rev MelanocyteD3- Melanocyte, donor3 (MC+3)_CNhs13406_12837-137B2_reverse Regulation 
MelanocyteDonor3MC3_CNhs13406_tpm_fwd MelanocyteD3+ Melanocyte, donor3 (MC+3)_CNhs13406_12837-137B2_forward Regulation 
MelanocyteDonor2MC2_CNhs13156_tpm_rev MelanocyteD2- Melanocyte, donor2 (MC+2)_CNhs13156_12739-135I3_reverse Regulation 
MelanocyteDonor2MC2_CNhs13156_tpm_fwd MelanocyteD2+ Melanocyte, donor2 (MC+2)_CNhs13156_12739-135I3_forward Regulation 
MelanocyteDonor1MC1_CNhs12816_tpm_rev MelanocyteD1- Melanocyte, donor1 (MC+1)_CNhs12816_12641-134G4_reverse Regulation 
MelanocyteDonor1MC1_CNhs12816_tpm_fwd MelanocyteD1+ Melanocyte, donor1 (MC+1)_CNhs12816_12641-134G4_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep1_CNhs13659_tpm_rev Hes3-gfpCardiomyocyticInduction_Day07Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep1_CNhs13659_13334-143C4_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep1_CNhs13659_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day07Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep1_CNhs13659_13334-143C4_forward Regulation 
H9EmbryonicStemCellsBiolRep3H9ES3_CNhs12837_tpm_rev H9EmbryonicStemCellsBr3- H9 Embryonic Stem cells, biol_rep3 (H9ES-3)_CNhs12837_12822-136I5_reverse Regulation 
H9EmbryonicStemCellsBiolRep3H9ES3_CNhs12837_tpm_fwd H9EmbryonicStemCellsBr3+ H9 Embryonic Stem cells, biol_rep3 (H9ES-3)_CNhs12837_12822-136I5_forward Regulation 
H9EmbryonicStemCellsBiolRep2H9ES2_CNhs12824_tpm_rev H9EmbryonicStemCellsBr2- H9 Embryonic Stem cells, biol_rep2 (H9ES-2)_CNhs12824_12724-135G6_reverse Regulation 
H9EmbryonicStemCellsBiolRep2H9ES2_CNhs12824_tpm_fwd H9EmbryonicStemCellsBr2+ H9 Embryonic Stem cells, biol_rep2 (H9ES-2)_CNhs12824_12724-135G6_forward Regulation 
H9EmbryonicStemCellsBiolRep1H9ES1_CNhs11917_tpm_rev H9EmbryonicStemCellsBr1- H9 Embryonic Stem cells, biol_rep1 (H9ES-1)_CNhs11917_12626-134E7_reverse Regulation 
H9EmbryonicStemCellsBiolRep1H9ES1_CNhs11917_tpm_fwd H9EmbryonicStemCellsBr1+ H9 Embryonic Stem cells, biol_rep1 (H9ES-1)_CNhs11917_12626-134E7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep3LK57_CNhs13585_tpm_rev AorticSmsToIL1b_05hrBr3- Aortic smooth muscle cell response to IL1b, 05hr, biol_rep3 (LK57)_CNhs13585_12856-137D3_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep3LK57_CNhs13585_tpm_fwd AorticSmsToIL1b_05hrBr3+ Aortic smooth muscle cell response to IL1b, 05hr, biol_rep3 (LK57)_CNhs13585_12856-137D3_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep3LK51_CNhs13583_tpm_rev AorticSmsToIL1b_03hrBr3- Aortic smooth muscle cell response to IL1b, 03hr, biol_rep3 (LK51)_CNhs13583_12854-137D1_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep3LK51_CNhs13583_tpm_fwd AorticSmsToIL1b_03hrBr3+ Aortic smooth muscle cell response to IL1b, 03hr, biol_rep3 (LK51)_CNhs13583_12854-137D1_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep1LK46_CNhs13354_tpm_rev AorticSmsToIL1b_02hrBr1- Aortic smooth muscle cell response to IL1b, 02hr, biol_rep1 (LK46)_CNhs13354_12657-134I2_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep1LK46_CNhs13354_tpm_fwd AorticSmsToIL1b_02hrBr1+ Aortic smooth muscle cell response to IL1b, 02hr, biol_rep1 (LK46)_CNhs13354_12657-134I2_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep3LK45_CNhs13581_tpm_rev AorticSmsToIL1b_01hrBr3- Aortic smooth muscle cell response to IL1b, 01hr, biol_rep3 (LK45)_CNhs13581_12852-137C8_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep3LK45_CNhs13581_tpm_fwd AorticSmsToIL1b_01hrBr3+ Aortic smooth muscle cell response to IL1b, 01hr, biol_rep3 (LK45)_CNhs13581_12852-137C8_forward Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep3LK24_CNhs13574_tpm_rev AorticSmsToFgf2_04hrBr3- Aortic smooth muscle cell response to FGF2, 04hr, biol_rep3 (LK24)_CNhs13574_12845-137C1_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep3LK24_CNhs13574_tpm_fwd AorticSmsToFgf2_04hrBr3+ Aortic smooth muscle cell response to FGF2, 04hr, biol_rep3 (LK24)_CNhs13574_12845-137C1_forward Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep2LK23_CNhs13365_tpm_rev AorticSmsToFgf2_04hrBr2- Aortic smooth muscle cell response to FGF2, 04hr, biol_rep2 (LK23)_CNhs13365_12747-136A2_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep2LK23_CNhs13365_tpm_fwd AorticSmsToFgf2_04hrBr2+ Aortic smooth muscle cell response to FGF2, 04hr, biol_rep2 (LK23)_CNhs13365_12747-136A2_forward Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep1LK22_CNhs13346_tpm_rev AorticSmsToFgf2_04hrBr1- Aortic smooth muscle cell response to FGF2, 04hr, biol_rep1 (LK22)_CNhs13346_12649-134H3_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF204hrBiolRep1LK22_CNhs13346_tpm_fwd AorticSmsToFgf2_04hrBr1+ Aortic smooth muscle cell response to FGF2, 04hr, biol_rep1 (LK22)_CNhs13346_12649-134H3_forward Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep2LK14_CNhs13362_tpm_rev AorticSmsToFgf2_01hrBr2- Aortic smooth muscle cell response to FGF2, 01hr, biol_rep2 (LK14)_CNhs13362_12744-135I8_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep2LK14_CNhs13362_tpm_fwd AorticSmsToFgf2_01hrBr2+ Aortic smooth muscle cell response to FGF2, 01hr, biol_rep2 (LK14)_CNhs13362_12744-135I8_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep3LK3_CNhs13567_tpm_rev AorticSmsToFgf2_00hr00minBr3- Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep3 (LK3)_CNhs13567_12838-137B3_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep3LK3_CNhs13567_tpm_fwd AorticSmsToFgf2_00hr00minBr3+ Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep3 (LK3)_CNhs13567_12838-137B3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep1_CNhs12564_tpm_rev Mcf7ToEgf1_00hr00minBr1- MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep1_CNhs12564_13031-139E7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep1_CNhs12564_tpm_fwd Mcf7ToEgf1_00hr00minBr1+ MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep1_CNhs12564_13031-139E7_forward Regulation 
WholeBloodRibopureDonor090612Donation3_CNhs11949_tpm_rev WholeBloodD090612Dn3- Whole blood (ribopure), donor090612, donation3_CNhs11949_12184-129A6_reverse Regulation 
WholeBloodRibopureDonor090612Donation3_CNhs11949_tpm_fwd WholeBloodD090612Dn3+ Whole blood (ribopure), donor090612, donation3_CNhs11949_12184-129A6_forward Regulation 
WholeBloodRibopureDonor090612Donation2_CNhs11673_tpm_rev WholeBloodD090612Dn2- Whole blood (ribopure), donor090612, donation2_CNhs11673_12183-129A5_reverse Regulation 
WholeBloodRibopureDonor090612Donation2_CNhs11673_tpm_fwd WholeBloodD090612Dn2+ Whole blood (ribopure), donor090612, donation2_CNhs11673_12183-129A5_forward Regulation 
WholeBloodRibopureDonor090612Donation1_CNhs11672_tpm_rev WholeBloodD090612Dn1- Whole blood (ribopure), donor090612, donation1_CNhs11672_12182-129A4_reverse Regulation 
WholeBloodRibopureDonor090612Donation1_CNhs11672_tpm_fwd WholeBloodD090612Dn1+ Whole blood (ribopure), donor090612, donation1_CNhs11672_12182-129A4_forward Regulation 
WholeBloodRibopureDonor090325Donation2_CNhs11076_tpm_rev WholeBloodD090325Dn2- Whole blood (ribopure), donor090325, donation2_CNhs11076_12177-128I8_reverse Regulation 
WholeBloodRibopureDonor090325Donation2_CNhs11076_tpm_fwd WholeBloodD090325Dn2+ Whole blood (ribopure), donor090325, donation2_CNhs11076_12177-128I8_forward Regulation 
WholeBloodRibopureDonor090325Donation1_CNhs11075_tpm_rev WholeBloodD090325Dn1- Whole blood (ribopure), donor090325, donation1_CNhs11075_12176-128I7_reverse Regulation 
WholeBloodRibopureDonor090325Donation1_CNhs11075_tpm_fwd WholeBloodD090325Dn1+ Whole blood (ribopure), donor090325, donation1_CNhs11075_12176-128I7_forward Regulation 
WholeBloodRibopureDonor090309Donation3_CNhs11948_tpm_rev WholeBloodD090309Dn3- Whole blood (ribopure), donor090309, donation3_CNhs11948_12181-129A3_reverse Regulation 
WholeBloodRibopureDonor090309Donation3_CNhs11948_tpm_fwd WholeBloodD090309Dn3+ Whole blood (ribopure), donor090309, donation3_CNhs11948_12181-129A3_forward Regulation 
WholeBloodRibopureDonor090309Donation2_CNhs11671_tpm_rev WholeBloodD090309Dn2- Whole blood (ribopure), donor090309, donation2_CNhs11671_12180-129A2_reverse Regulation 
WholeBloodRibopureDonor090309Donation2_CNhs11671_tpm_fwd WholeBloodD090309Dn2+ Whole blood (ribopure), donor090309, donation2_CNhs11671_12180-129A2_forward Regulation 
WholeBloodRibopureDonor090309Donation1_CNhs11675_tpm_rev WholeBloodD090309Dn1- Whole blood (ribopure), donor090309, donation1_CNhs11675_12179-129A1_reverse Regulation 
WholeBloodRibopureDonor090309Donation1_CNhs11675_tpm_fwd WholeBloodD090309Dn1+ Whole blood (ribopure), donor090309, donation1_CNhs11675_12179-129A1_forward Regulation 
UrothelialCellsDonor3_CNhs12122_tpm_rev UrothelialCellsD3- Urothelial Cells, donor3_CNhs12122_11681-122H7_reverse Regulation 
UrothelialCellsDonor3_CNhs12122_tpm_fwd UrothelialCellsD3+ Urothelial Cells, donor3_CNhs12122_11681-122H7_forward Regulation 
UrothelialCellsDonor2_CNhs12091_tpm_rev UrothelialCellsD2- Urothelial Cells, donor2_CNhs12091_11600-120H7_reverse Regulation 
UrothelialCellsDonor2_CNhs12091_tpm_fwd UrothelialCellsD2+ Urothelial Cells, donor2_CNhs12091_11600-120H7_forward Regulation 
UrothelialCellsDonor1_CNhs11334_tpm_rev UrothelialCellsD1- Urothelial Cells, donor1_CNhs11334_11520-119H8_reverse Regulation 
UrothelialCellsDonor1_CNhs11334_tpm_fwd UrothelialCellsD1+ Urothelial Cells, donor1_CNhs11334_11520-119H8_forward Regulation 
UrothelialCellsDonor0_CNhs10843_tpm_rev UrothelialCellsD0- Urothelial cells, donor0_CNhs10843_11216-116B1_reverse Regulation 
UrothelialCellsDonor0_CNhs10843_tpm_fwd UrothelialCellsD0+ Urothelial cells, donor0_CNhs10843_11216-116B1_forward Regulation 
TrachealEpithelialCellsDonor3_CNhs12051_tpm_rev TrachealEpithelialCellsD3- Tracheal Epithelial Cells, donor3_CNhs12051_11441-118I1_reverse Regulation 
TrachealEpithelialCellsDonor3_CNhs12051_tpm_fwd TrachealEpithelialCellsD3+ Tracheal Epithelial Cells, donor3_CNhs12051_11441-118I1_forward Regulation 
TrachealEpithelialCellsDonor2_CNhs11993_tpm_rev TrachealEpithelialCellsD2- Tracheal Epithelial Cells, donor2_CNhs11993_11369-118A1_reverse Regulation 
TrachealEpithelialCellsDonor2_CNhs11993_tpm_fwd TrachealEpithelialCellsD2+ Tracheal Epithelial Cells, donor2_CNhs11993_11369-118A1_forward Regulation 
TrachealEpithelialCellsDonor1_CNhs11092_tpm_rev TrachealEpithelialCellsD1- Tracheal Epithelial Cells, donor1_CNhs11092_11292-117A5_reverse Regulation 
TrachealEpithelialCellsDonor1_CNhs11092_tpm_fwd TrachealEpithelialCellsD1+ Tracheal Epithelial Cells, donor1_CNhs11092_11292-117A5_forward Regulation 
TrabecularMeshworkCellsDonor3_CNhs12124_tpm_rev TrabecularMeshworkCellsD3- Trabecular Meshwork Cells, donor3_CNhs12124_11693-123A1_reverse Regulation 
TrabecularMeshworkCellsDonor3_CNhs12124_tpm_fwd TrabecularMeshworkCellsD3+ Trabecular Meshwork Cells, donor3_CNhs12124_11693-123A1_forward Regulation 
TrabecularMeshworkCellsDonor2_CNhs12097_tpm_rev TrabecularMeshworkCellsD2- Trabecular Meshwork Cells, donor2_CNhs12097_11612-122A1_reverse Regulation 
TrabecularMeshworkCellsDonor2_CNhs12097_tpm_fwd TrabecularMeshworkCellsD2+ Trabecular Meshwork Cells, donor2_CNhs12097_11612-122A1_forward Regulation 
TrabecularMeshworkCellsDonor1_CNhs11340_tpm_rev TrabecularMeshworkCellsD1- Trabecular Meshwork Cells, donor1_CNhs11340_11532-120A2_reverse Regulation 
TrabecularMeshworkCellsDonor1_CNhs11340_tpm_fwd TrabecularMeshworkCellsD1+ Trabecular Meshwork Cells, donor1_CNhs11340_11532-120A2_forward Regulation 
TenocyteDonor3_CNhs12641_tpm_rev TenocyteD3- tenocyte, donor3_CNhs12641_11768-123I4_reverse Regulation 
TenocyteDonor3_CNhs12641_tpm_fwd TenocyteD3+ tenocyte, donor3_CNhs12641_11768-123I4_forward Regulation 
TenocyteDonor2_CNhs12640_tpm_rev TenocyteD2- tenocyte, donor2_CNhs12640_11765-123I1_reverse Regulation 
TenocyteDonor2_CNhs12640_tpm_fwd TenocyteD2+ tenocyte, donor2_CNhs12640_11765-123I1_forward Regulation 
TenocyteDonor1_CNhs12639_tpm_rev TenocyteD1- tenocyte, donor1_CNhs12639_11763-123H8_reverse Regulation 
TenocyteDonor1_CNhs12639_tpm_fwd TenocyteD1+ tenocyte, donor1_CNhs12639_11763-123H8_forward Regulation 
SynoviocyteDonor3_CNhs12050_tpm_rev SynoviocyteD3- Synoviocyte, donor3_CNhs12050_11440-118H9_reverse Regulation 
SynoviocyteDonor3_CNhs12050_tpm_fwd SynoviocyteD3+ Synoviocyte, donor3_CNhs12050_11440-118H9_forward Regulation 
SynoviocyteDonor2_CNhs11992_tpm_rev SynoviocyteD2- Synoviocyte, donor2_CNhs11992_11368-117I9_reverse Regulation 
SynoviocyteDonor2_CNhs11992_tpm_fwd SynoviocyteD2+ Synoviocyte, donor2_CNhs11992_11368-117I9_forward Regulation 
SynoviocyteDonor1_CNhs11068_tpm_rev SynoviocyteD1- Synoviocyte, donor1_CNhs11068_11291-117A4_reverse Regulation 
SynoviocyteDonor1_CNhs11068_tpm_fwd SynoviocyteD1+ Synoviocyte, donor1_CNhs11068_11291-117A4_forward Regulation 
SmoothMuscleCellsUterineDonor3_CNhs11927_tpm_rev SmcUterineD3- Smooth Muscle Cells - Uterine, donor3_CNhs11927_11466-119B8_reverse Regulation 
SmoothMuscleCellsUterineDonor3_CNhs11927_tpm_fwd SmcUterineD3+ Smooth Muscle Cells - Uterine, donor3_CNhs11927_11466-119B8_forward Regulation 
SmoothMuscleCellsUterineDonor1_CNhs11921_tpm_rev SmcUterineD1- Smooth Muscle Cells - Uterine, donor1_CNhs11921_11258-116F7_reverse Regulation 
SmoothMuscleCellsUterineDonor1_CNhs11921_tpm_fwd SmcUterineD1+ Smooth Muscle Cells - Uterine, donor1_CNhs11921_11258-116F7_forward Regulation 
SmoothMuscleCellsUmbilicalVeinDonor3_CNhs13076_tpm_rev SmcUmbilicalVeinD3- Smooth Muscle Cells - Umbilical Vein, donor3_CNhs13076_11702-123B1_reverse Regulation 
SmoothMuscleCellsUmbilicalVeinDonor3_CNhs13076_tpm_fwd SmcUmbilicalVeinD3+ Smooth Muscle Cells - Umbilical Vein, donor3_CNhs13076_11702-123B1_forward Regulation 
SmoothMuscleCellsUmbilicalVeinDonor2_CNhs12569_tpm_rev SmcUmbilicalVeinD2- Smooth Muscle Cells - Umbilical Vein, donor2_CNhs12569_11621-122B1_reverse Regulation 
SmoothMuscleCellsUmbilicalVeinDonor2_CNhs12569_tpm_fwd SmcUmbilicalVeinD2+ Smooth Muscle Cells - Umbilical Vein, donor2_CNhs12569_11621-122B1_forward Regulation 
SmoothMuscleCellsUmbilicalVeinDonor1_CNhs12597_tpm_rev SmcUmbilicalVeinD1- Smooth Muscle Cells - Umbilical Vein, donor1_CNhs12597_11541-120B2_reverse Regulation 
SmoothMuscleCellsUmbilicalVeinDonor1_CNhs12597_tpm_fwd SmcUmbilicalVeinD1+ Smooth Muscle Cells - Umbilical Vein, donor1_CNhs12597_11541-120B2_forward Regulation 
SmoothMuscleCellsUmbilicalArteryDonor3_CNhs12049_tpm_rev SmcUmbilicalArteryD3- Smooth Muscle Cells - Umbilical Artery, donor3_CNhs12049_11439-118H8_reverse Regulation 
SmoothMuscleCellsUmbilicalArteryDonor3_CNhs12049_tpm_fwd SmcUmbilicalArteryD3+ Smooth Muscle Cells - Umbilical Artery, donor3_CNhs12049_11439-118H8_forward Regulation 
SmoothMuscleCellsUmbilicalArteryDonor2_CNhs11991_tpm_rev SmcUmbilicalArteryD2- Smooth Muscle Cells - Umbilical Artery, donor2_CNhs11991_11367-117I8_reverse Regulation 
SmoothMuscleCellsUmbilicalArteryDonor2_CNhs11991_tpm_fwd SmcUmbilicalArteryD2+ Smooth Muscle Cells - Umbilical Artery, donor2_CNhs11991_11367-117I8_forward Regulation 
SmoothMuscleCellsUmbilicalArteryDonor1_CNhs11091_tpm_rev SmcUmbilicalArteryD1- Smooth Muscle Cells - Umbilical Artery, donor1_CNhs11091_11290-117A3_reverse Regulation 
SmoothMuscleCellsUmbilicalArteryDonor1_CNhs11091_tpm_fwd SmcUmbilicalArteryD1+ Smooth Muscle Cells - Umbilical Artery, donor1_CNhs11091_11290-117A3_forward Regulation 
SmoothMuscleCellsUmbilicalArteryDonor0_CNhs10839_tpm_rev SmcUmbilicalArteryD0- Smooth Muscle Cells - Umbilical artery, donor0_CNhs10839_11212-116A6_reverse Regulation 
SmoothMuscleCellsUmbilicalArteryDonor0_CNhs10839_tpm_fwd SmcUmbilicalArteryD0+ Smooth Muscle Cells - Umbilical artery, donor0_CNhs10839_11212-116A6_forward Regulation 
SmoothMuscleCellsTrachealDonor3_CNhs12894_tpm_rev SmcTrachealD3- Smooth Muscle Cells - Tracheal, donor3_CNhs12894_11674-122G9_reverse Regulation 
SmoothMuscleCellsTrachealDonor3_CNhs12894_tpm_fwd SmcTrachealD3+ Smooth Muscle Cells - Tracheal, donor3_CNhs12894_11674-122G9_forward Regulation 
SmoothMuscleCellsTrachealDonor2_CNhs12567_tpm_rev SmcTrachealD2- Smooth Muscle Cells - Tracheal, donor2_CNhs12567_11593-120G9_reverse Regulation 
SmoothMuscleCellsTrachealDonor2_CNhs12567_tpm_fwd SmcTrachealD2+ Smooth Muscle Cells - Tracheal, donor2_CNhs12567_11593-120G9_forward Regulation 
SmoothMuscleCellsTrachealDonor1_CNhs11329_tpm_rev SmcTrachealD1- Smooth Muscle Cells - Tracheal, donor1_CNhs11329_11513-119H1_reverse Regulation 
SmoothMuscleCellsTrachealDonor1_CNhs11329_tpm_fwd SmcTrachealD1+ Smooth Muscle Cells - Tracheal, donor1_CNhs11329_11513-119H1_forward Regulation 
SmoothMuscleCellsSubclavianArteryDonor3_CNhs12048_tpm_rev SmcSubclavianArteryD3- Smooth Muscle Cells - Subclavian Artery, donor3_CNhs12048_11438-118H7_reverse Regulation 
SmoothMuscleCellsSubclavianArteryDonor3_CNhs12048_tpm_fwd SmcSubclavianArteryD3+ Smooth Muscle Cells - Subclavian Artery, donor3_CNhs12048_11438-118H7_forward Regulation 
SmoothMuscleCellsSubclavianArteryDonor2_CNhs11990_tpm_rev SmcSubclavianArteryD2- Smooth Muscle Cells - Subclavian Artery, donor2_CNhs11990_11366-117I7_reverse Regulation 
SmoothMuscleCellsSubclavianArteryDonor2_CNhs11990_tpm_fwd SmcSubclavianArteryD2+ Smooth Muscle Cells - Subclavian Artery, donor2_CNhs11990_11366-117I7_forward Regulation 
SmoothMuscleCellsSubclavianArteryDonor1_CNhs11090_tpm_rev SmcSubclavianArteryD1- Smooth Muscle Cells - Subclavian Artery, donor1_CNhs11090_11289-117A2_reverse Regulation 
SmoothMuscleCellsSubclavianArteryDonor1_CNhs11090_tpm_fwd SmcSubclavianArteryD1+ Smooth Muscle Cells - Subclavian Artery, donor1_CNhs11090_11289-117A2_forward Regulation 
SmoothMuscleCellsPulmonaryArteryDonor3_CNhs12047_tpm_rev SmcPulmonaryArteryD3- Smooth Muscle Cells - Pulmonary Artery, donor3_CNhs12047_11437-118H6_reverse Regulation 
SmoothMuscleCellsPulmonaryArteryDonor3_CNhs12047_tpm_fwd SmcPulmonaryArteryD3+ Smooth Muscle Cells - Pulmonary Artery, donor3_CNhs12047_11437-118H6_forward Regulation 
SmoothMuscleCellsPulmonaryArteryDonor2_CNhs11989_tpm_rev SmcPulmonaryArteryD2- Smooth Muscle Cells - Pulmonary Artery, donor2_CNhs11989_11365-117I6_reverse Regulation 
SmoothMuscleCellsPulmonaryArteryDonor2_CNhs11989_tpm_fwd SmcPulmonaryArteryD2+ Smooth Muscle Cells - Pulmonary Artery, donor2_CNhs11989_11365-117I6_forward Regulation 
SmoothMuscleCellsPulmonaryArteryDonor1_CNhs11089_tpm_rev SmcPulmonaryArteryD1- Smooth Muscle Cells - Pulmonary Artery, donor1_CNhs11089_11288-117A1_reverse Regulation 
SmoothMuscleCellsPulmonaryArteryDonor1_CNhs11089_tpm_fwd SmcPulmonaryArteryD1+ Smooth Muscle Cells - Pulmonary Artery, donor1_CNhs11089_11288-117A1_forward Regulation 
SmoothMuscleCellsProstateDonor3_CNhs11910_tpm_rev SmcProstateD3- Smooth Muscle Cells - Prostate, donor3_CNhs11910_11465-119B7_reverse Regulation 
SmoothMuscleCellsProstateDonor3_CNhs11910_tpm_fwd SmcProstateD3+ Smooth Muscle Cells - Prostate, donor3_CNhs11910_11465-119B7_forward Regulation 
SmoothMuscleCellsProstateDonor2_CNhs11976_tpm_rev SmcProstateD2- Smooth Muscle Cells - Prostate, donor2_CNhs11976_11335-117F3_reverse Regulation 
SmoothMuscleCellsProstateDonor2_CNhs11976_tpm_fwd SmcProstateD2+ Smooth Muscle Cells - Prostate, donor2_CNhs11976_11335-117F3_forward Regulation 
SmoothMuscleCellsProstateDonor1_CNhs11920_tpm_rev SmcProstateD1- Smooth Muscle Cells - Prostate, donor1_CNhs11920_11257-116F6_reverse Regulation 
SmoothMuscleCellsProstateDonor1_CNhs11920_tpm_fwd SmcProstateD1+ Smooth Muscle Cells - Prostate, donor1_CNhs11920_11257-116F6_forward Regulation 
SmoothMuscleCellsIntestinalDonor1_CNhs12595_tpm_rev SmcIntestinalD1- Smooth Muscle Cells - Intestinal, donor1_CNhs12595_11509-119G6_reverse Regulation 
SmoothMuscleCellsIntestinalDonor1_CNhs12595_tpm_fwd SmcIntestinalD1+ Smooth Muscle Cells - Intestinal, donor1_CNhs12595_11509-119G6_forward Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor3_CNhs12046_tpm_rev SmcInternalThoracicArteryD3- Smooth Muscle Cells - Internal Thoracic Artery, donor3_CNhs12046_11436-118H5_reverse Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor3_CNhs12046_tpm_fwd SmcInternalThoracicArteryD3+ Smooth Muscle Cells - Internal Thoracic Artery, donor3_CNhs12046_11436-118H5_forward Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor2_CNhs11988_tpm_rev SmcInternalThoracicArteryD2- Smooth Muscle Cells - Internal Thoracic Artery, donor2_CNhs11988_11364-117I5_reverse Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor2_CNhs11988_tpm_fwd SmcInternalThoracicArteryD2+ Smooth Muscle Cells - Internal Thoracic Artery, donor2_CNhs11988_11364-117I5_forward Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor1_CNhs11067_tpm_rev SmcInternalThoracicArteryD1- Smooth Muscle Cells - Internal Thoracic Artery, donor1_CNhs11067_11287-116I9_reverse Regulation 
SmoothMuscleCellsInternalThoracicArteryDonor1_CNhs11067_tpm_fwd SmcInternalThoracicArteryD1+ Smooth Muscle Cells - Internal Thoracic Artery, donor1_CNhs11067_11287-116I9_forward Regulation 
SmoothMuscleCellsEsophagealDonor2_CNhs12727_tpm_rev SmcEsophagealD2- Smooth Muscle Cells - Esophageal, donor2_CNhs12727_11588-120G4_reverse Regulation 
SmoothMuscleCellsEsophagealDonor2_CNhs12727_tpm_fwd SmcEsophagealD2+ Smooth Muscle Cells - Esophageal, donor2_CNhs12727_11588-120G4_forward Regulation 
SmoothMuscleCellsEsophagealDonor1_CNhs11324_tpm_rev SmcEsophagealD1- Smooth Muscle Cells - Esophageal, donor1_CNhs11324_11508-119G5_reverse Regulation 
SmoothMuscleCellsEsophagealDonor1_CNhs11324_tpm_fwd SmcEsophagealD1+ Smooth Muscle Cells - Esophageal, donor1_CNhs11324_11508-119G5_forward Regulation 
SmoothMuscleCellsCoronaryArteryDonor3_CNhs12045_tpm_rev SmcCoronaryArteryD3- Smooth Muscle Cells - Coronary Artery, donor3_CNhs12045_11435-118H4_reverse Regulation 
SmoothMuscleCellsCoronaryArteryDonor3_CNhs12045_tpm_fwd SmcCoronaryArteryD3+ Smooth Muscle Cells - Coronary Artery, donor3_CNhs12045_11435-118H4_forward Regulation 
SmoothMuscleCellsCoronaryArteryDonor2_CNhs11987_tpm_rev SmcCoronaryArteryD2- Smooth Muscle Cells - Coronary Artery, donor2_CNhs11987_11363-117I4_reverse Regulation 
SmoothMuscleCellsCoronaryArteryDonor2_CNhs11987_tpm_fwd SmcCoronaryArteryD2+ Smooth Muscle Cells - Coronary Artery, donor2_CNhs11987_11363-117I4_forward Regulation 
SmoothMuscleCellsCoronaryArteryDonor1_CNhs11088_tpm_rev SmcCoronaryArteryD1- Smooth Muscle Cells - Coronary Artery, donor1_CNhs11088_11286-116I8_reverse Regulation 
SmoothMuscleCellsCoronaryArteryDonor1_CNhs11088_tpm_fwd SmcCoronaryArteryD1+ Smooth Muscle Cells - Coronary Artery, donor1_CNhs11088_11286-116I8_forward Regulation 
SmoothMuscleCellsColonicDonor3_CNhs12007_tpm_rev SmcColonicD3- Smooth Muscle Cells - Colonic, donor3_CNhs12007_11396-118D1_reverse Regulation 
SmoothMuscleCellsColonicDonor3_CNhs12007_tpm_fwd SmcColonicD3+ Smooth Muscle Cells - Colonic, donor3_CNhs12007_11396-118D1_forward Regulation 
SmoothMuscleCellsColonicDonor2_CNhs11963_tpm_rev SmcColonicD2- Smooth Muscle Cells - Colonic, donor2_CNhs11963_11320-117D6_reverse Regulation 
SmoothMuscleCellsColonicDonor2_CNhs11963_tpm_fwd SmcColonicD2+ Smooth Muscle Cells - Colonic, donor2_CNhs11963_11320-117D6_forward Regulation 
SmoothMuscleCellsColonicDonor1_CNhs10868_tpm_rev SmcColonicD1- Smooth Muscle Cells - Colonic, donor1_CNhs10868_11239-116D6_reverse Regulation 
SmoothMuscleCellsColonicDonor1_CNhs10868_tpm_fwd SmcColonicD1+ Smooth Muscle Cells - Colonic, donor1_CNhs10868_11239-116D6_forward Regulation 
SmoothMuscleCellsCarotidDonor3_CNhs12044_tpm_rev SmcCarotidD3- Smooth Muscle Cells - Carotid, donor3_CNhs12044_11434-118H3_reverse Regulation 
SmoothMuscleCellsCarotidDonor3_CNhs12044_tpm_fwd SmcCarotidD3+ Smooth Muscle Cells - Carotid, donor3_CNhs12044_11434-118H3_forward Regulation 
SmoothMuscleCellsCarotidDonor2_CNhs11986_tpm_rev SmcCarotidD2- Smooth Muscle Cells - Carotid, donor2_CNhs11986_11362-117I3_reverse Regulation 
SmoothMuscleCellsCarotidDonor2_CNhs11986_tpm_fwd SmcCarotidD2+ Smooth Muscle Cells - Carotid, donor2_CNhs11986_11362-117I3_forward Regulation 
SmoothMuscleCellsCarotidDonor1_CNhs11087_tpm_rev SmcCarotidD1- Smooth Muscle Cells - Carotid, donor1_CNhs11087_11285-116I7_reverse Regulation 
SmoothMuscleCellsCarotidDonor1_CNhs11087_tpm_fwd SmcCarotidD1+ Smooth Muscle Cells - Carotid, donor1_CNhs11087_11285-116I7_forward Regulation 
SmoothMuscleCellsBronchialDonor2_CNhs12348_tpm_rev SmcBronchialD2- Smooth Muscle Cells - Bronchial, donor2_CNhs12348_11592-120G8_reverse Regulation 
SmoothMuscleCellsBronchialDonor2_CNhs12348_tpm_fwd SmcBronchialD2+ Smooth Muscle Cells - Bronchial, donor2_CNhs12348_11592-120G8_forward Regulation 
SmoothMuscleCellsBronchialDonor1_CNhs11328_tpm_rev SmcBronchialD1- Smooth Muscle Cells - Bronchial, donor1_CNhs11328_11512-119G9_reverse Regulation 
SmoothMuscleCellsBronchialDonor1_CNhs11328_tpm_fwd SmcBronchialD1+ Smooth Muscle Cells - Bronchial, donor1_CNhs11328_11512-119G9_forward Regulation 
SmoothMuscleCellsBrainVascularDonor3_CNhs12004_tpm_rev SmcBrainVascularD3- Smooth Muscle Cells - Brain Vascular, donor3_CNhs12004_11391-118C5_reverse Regulation 
SmoothMuscleCellsBrainVascularDonor3_CNhs12004_tpm_fwd SmcBrainVascularD3+ Smooth Muscle Cells - Brain Vascular, donor3_CNhs12004_11391-118C5_forward Regulation 
SmoothMuscleCellsBrainVascularDonor2_CNhs11900_tpm_rev SmcBrainVascularD2- Smooth Muscle Cells - Brain Vascular, donor2_CNhs11900_11315-117D1_reverse Regulation 
SmoothMuscleCellsBrainVascularDonor2_CNhs11900_tpm_fwd SmcBrainVascularD2+ Smooth Muscle Cells - Brain Vascular, donor2_CNhs11900_11315-117D1_forward Regulation 
SmoothMuscleCellsBrainVascularDonor1_CNhs10863_tpm_rev SmcBrainVascularD1- Smooth Muscle Cells - Brain Vascular, donor1_CNhs10863_11234-116D1_reverse Regulation 
SmoothMuscleCellsBrainVascularDonor1_CNhs10863_tpm_fwd SmcBrainVascularD1+ Smooth Muscle Cells - Brain Vascular, donor1_CNhs10863_11234-116D1_forward Regulation 
SmoothMuscleCellsBrachiocephalicDonor3_CNhs12043_tpm_rev SmcBrachiocephalicD3- Smooth Muscle Cells - Brachiocephalic, donor3_CNhs12043_11433-118H2_reverse Regulation 
SmoothMuscleCellsBrachiocephalicDonor3_CNhs12043_tpm_fwd SmcBrachiocephalicD3+ Smooth Muscle Cells - Brachiocephalic, donor3_CNhs12043_11433-118H2_forward Regulation 
SmoothMuscleCellsBrachiocephalicDonor2_CNhs11985_tpm_rev SmcBrachiocephalicD2- Smooth Muscle Cells - Brachiocephalic, donor2_CNhs11985_11361-117I2_reverse Regulation 
SmoothMuscleCellsBrachiocephalicDonor2_CNhs11985_tpm_fwd SmcBrachiocephalicD2+ Smooth Muscle Cells - Brachiocephalic, donor2_CNhs11985_11361-117I2_forward Regulation 
SmoothMuscleCellsBrachiocephalicDonor1_CNhs11086_tpm_rev SmcBrachiocephalicD1- Smooth Muscle Cells - Brachiocephalic, donor1_CNhs11086_11284-116I6_reverse Regulation 
SmoothMuscleCellsBrachiocephalicDonor1_CNhs11086_tpm_fwd SmcBrachiocephalicD1+ Smooth Muscle Cells - Brachiocephalic, donor1_CNhs11086_11284-116I6_forward Regulation 
SmoothMuscleCellsBladderDonor1_CNhs12893_tpm_rev SmcBladderD1- Smooth Muscle Cells - Bladder, donor1_CNhs12893_11519-119H7_reverse Regulation 
SmoothMuscleCellsBladderDonor1_CNhs12893_tpm_fwd SmcBladderD1+ Smooth Muscle Cells - Bladder, donor1_CNhs12893_11519-119H7_forward Regulation 
SmoothMuscleCellsAorticDonor3_CNhs11309_tpm_rev SmcAorticCytofracD3- Smooth Muscle Cells - Aortic, donor3_CNhs11309_11432-118H1_reverse Regulation 
SmoothMuscleCellsAorticDonor3_CNhs11309_tpm_fwd SmcAorticCytofracD3+ Smooth Muscle Cells - Aortic, donor3_CNhs11309_11432-118H1_forward Regulation 
SmoothMuscleCellsAorticDonor2_CNhs11305_tpm_rev SmcAorticCytofracD2- Smooth Muscle Cells - Aortic, donor2_CNhs11305_11360-117I1_reverse Regulation 
SmoothMuscleCellsAorticDonor2_CNhs11305_tpm_fwd SmcAorticCytofracD2+ Smooth Muscle Cells - Aortic, donor2_CNhs11305_11360-117I1_forward Regulation 
SmoothMuscleCellsAorticDonor1_CNhs11085_tpm_rev SmcAorticCytofracD1- Smooth Muscle Cells - Aortic, donor1_CNhs11085_11283-116I5_reverse Regulation 
SmoothMuscleCellsAorticDonor1_CNhs11085_tpm_fwd SmcAorticCytofracD1+ Smooth Muscle Cells - Aortic, donor1_CNhs11085_11283-116I5_forward Regulation 
SmoothMuscleCellsAorticDonor0_CNhs10838_tpm_rev SmcAorticCytofracD0- Smooth Muscle Cells - Aortic, donor0_CNhs10838_11210-116A4_reverse Regulation 
SmoothMuscleCellsAorticDonor0_CNhs10838_tpm_fwd SmcAorticCytofracD0+ Smooth Muscle Cells - Aortic, donor0_CNhs10838_11210-116A4_forward Regulation 
SmoothMuscleCellsAirwayControlDonor4_CNhs14193_tpm_rev SmcAirwayControlD4- Smooth muscle cells - airway, control, donor4_CNhs14193_11969-126D7_reverse Regulation 
SmoothMuscleCellsAirwayControlDonor4_CNhs14193_tpm_fwd SmcAirwayControlD4+ Smooth muscle cells - airway, control, donor4_CNhs14193_11969-126D7_forward Regulation 
SmoothMuscleCellsAirwayControlDonor3_CNhs14192_tpm_rev SmcAirwayControlD3- Smooth muscle cells - airway, control, donor3_CNhs14192_11968-126D6_reverse Regulation 
SmoothMuscleCellsAirwayControlDonor3_CNhs14192_tpm_fwd SmcAirwayControlD3+ Smooth muscle cells - airway, control, donor3_CNhs14192_11968-126D6_forward Regulation 
SmoothMuscleCellsAirwayControlDonor2_CNhs14191_tpm_rev SmcAirwayControlD2- Smooth muscle cells - airway, control, donor2_CNhs14191_11967-126D5_reverse Regulation 
SmoothMuscleCellsAirwayControlDonor2_CNhs14191_tpm_fwd SmcAirwayControlD2+ Smooth muscle cells - airway, control, donor2_CNhs14191_11967-126D5_forward Regulation 
SmoothMuscleCellsAirwayControlDonor1_CNhs14190_tpm_rev SmcAirwayControlD1- Smooth muscle cells - airway, control, donor1_CNhs14190_11966-126D4_reverse Regulation 
SmoothMuscleCellsAirwayControlDonor1_CNhs14190_tpm_fwd SmcAirwayControlD1+ Smooth muscle cells - airway, control, donor1_CNhs14190_11966-126D4_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor6_CNhs14189_tpm_rev SmcAirwayAsthmaD6- Smooth muscle cells - airway, asthmatic, donor6_CNhs14189_11965-126D3_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor6_CNhs14189_tpm_fwd SmcAirwayAsthmaD6+ Smooth muscle cells - airway, asthmatic, donor6_CNhs14189_11965-126D3_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor5_CNhs14188_tpm_rev SmcAirwayAsthmaD5- Smooth muscle cells - airway, asthmatic, donor5_CNhs14188_11964-126D2_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor5_CNhs14188_tpm_fwd SmcAirwayAsthmaD5+ Smooth muscle cells - airway, asthmatic, donor5_CNhs14188_11964-126D2_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor4_CNhs14187_tpm_rev SmcAirwayAsthmaD4- Smooth muscle cells - airway, asthmatic, donor4_CNhs14187_11963-126D1_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor4_CNhs14187_tpm_fwd SmcAirwayAsthmaD4+ Smooth muscle cells - airway, asthmatic, donor4_CNhs14187_11963-126D1_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor3_CNhs14186_tpm_rev SmcAirwayAsthmaD3- Smooth muscle cells - airway, asthmatic, donor3_CNhs14186_11962-126C9_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor3_CNhs14186_tpm_fwd SmcAirwayAsthmaD3+ Smooth muscle cells - airway, asthmatic, donor3_CNhs14186_11962-126C9_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor2_CNhs14184_tpm_rev SmcAirwayAsthmaD2- Smooth muscle cells - airway, asthmatic, donor2_CNhs14184_11961-126C8_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor2_CNhs14184_tpm_fwd SmcAirwayAsthmaD2+ Smooth muscle cells - airway, asthmatic, donor2_CNhs14184_11961-126C8_forward Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor1_CNhs14183_tpm_rev SmcAirwayAsthmaD1- Smooth muscle cells - airway, asthmatic, donor1_CNhs14183_11960-126C7_reverse Regulation 
SmoothMuscleCellsAirwayAsthmaticDonor1_CNhs14183_tpm_fwd SmcAirwayAsthmaD1+ Smooth muscle cells - airway, asthmatic, donor1_CNhs14183_11960-126C7_forward Regulation 
SmallAirwayEpithelialCellsDonor3_CNhs12016_tpm_rev SmallAirwayEpithelialCellsD3- Small Airway Epithelial Cells, donor3_CNhs12016_11406-118E2_reverse Regulation 
SmallAirwayEpithelialCellsDonor3_CNhs12016_tpm_fwd SmallAirwayEpithelialCellsD3+ Small Airway Epithelial Cells, donor3_CNhs12016_11406-118E2_forward Regulation 
SmallAirwayEpithelialCellsDonor2_CNhs11975_tpm_rev SmallAirwayEpithelialCellsD2- Small Airway Epithelial Cells, donor2_CNhs11975_11334-117F2_reverse Regulation 
SmallAirwayEpithelialCellsDonor2_CNhs11975_tpm_fwd SmallAirwayEpithelialCellsD2+ Small Airway Epithelial Cells, donor2_CNhs11975_11334-117F2_forward Regulation 
SmallAirwayEpithelialCellsDonor1_CNhs10884_tpm_rev SmallAirwayEpithelialCellsD1- Small Airway Epithelial Cells, donor1_CNhs10884_11256-116F5_reverse Regulation 
SmallAirwayEpithelialCellsDonor1_CNhs10884_tpm_fwd SmallAirwayEpithelialCellsD1+ Small Airway Epithelial Cells, donor1_CNhs10884_11256-116F5_forward Regulation 
SkeletalMuscleSatelliteCellsDonor3_CNhs12008_tpm_rev SkeletalMuscleSatelliteCellsD3- Skeletal Muscle Satellite Cells, donor3_CNhs12008_11397-118D2_reverse Regulation 
SkeletalMuscleSatelliteCellsDonor3_CNhs12008_tpm_fwd SkeletalMuscleSatelliteCellsD3+ Skeletal Muscle Satellite Cells, donor3_CNhs12008_11397-118D2_forward Regulation 
SkeletalMuscleSatelliteCellsDonor2_CNhs11964_tpm_rev SkeletalMuscleSatelliteCellsD2- Skeletal Muscle Satellite Cells, donor2_CNhs11964_11321-117D7_reverse Regulation 
SkeletalMuscleSatelliteCellsDonor2_CNhs11964_tpm_fwd SkeletalMuscleSatelliteCellsD2+ Skeletal Muscle Satellite Cells, donor2_CNhs11964_11321-117D7_forward Regulation 
SkeletalMuscleSatelliteCellsDonor1_CNhs10869_tpm_rev SkeletalMuscleSatelliteCellsD1- Skeletal Muscle Satellite Cells, donor1_CNhs10869_11240-116D7_reverse Regulation 
SkeletalMuscleSatelliteCellsDonor1_CNhs10869_tpm_fwd SkeletalMuscleSatelliteCellsD1+ Skeletal Muscle Satellite Cells, donor1_CNhs10869_11240-116D7_forward Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor3_CNhs12041_tpm_rev SkeletalMuscleCellsIntoMyotubesD3- Skeletal muscle cells differentiated into Myotubes - multinucleated, donor3_CNhs12041_11431-118G9_reverse Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor3_CNhs12041_tpm_fwd SkeletalMuscleCellsIntoMyotubesD3+ Skeletal muscle cells differentiated into Myotubes - multinucleated, donor3_CNhs12041_11431-118G9_forward Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor2_CNhs11984_tpm_rev SkeletalMuscleCellsIntoMyotubesD2- Skeletal muscle cells differentiated into Myotubes - multinucleated, donor2_CNhs11984_11359-117H9_reverse Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor2_CNhs11984_tpm_fwd SkeletalMuscleCellsIntoMyotubesD2+ Skeletal muscle cells differentiated into Myotubes - multinucleated, donor2_CNhs11984_11359-117H9_forward Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor1_CNhs11084_tpm_rev SkeletalMuscleCellsIntoMyotubesD1- Skeletal muscle cells differentiated into Myotubes - multinucleated, donor1_CNhs11084_11282-116I4_reverse Regulation 
SkeletalMuscleCellsDifferentiatedIntoMyotubesMultinucleatedDonor1_CNhs11084_tpm_fwd SkeletalMuscleCellsIntoMyotubesD1+ Skeletal muscle cells differentiated into Myotubes - multinucleated, donor1_CNhs11084_11282-116I4_forward Regulation 
SkeletalMuscleCellsDonor6_CNhs12060_tpm_rev SkeletalMuscleCellsD6- Skeletal Muscle Cells, donor6_CNhs12060_11459-119B1_reverse Regulation 
SkeletalMuscleCellsDonor6_CNhs12060_tpm_fwd SkeletalMuscleCellsD6+ Skeletal Muscle Cells, donor6_CNhs12060_11459-119B1_forward Regulation 
SkeletalMuscleCellsDonor5_CNhs12056_tpm_rev SkeletalMuscleCellsD5- Skeletal Muscle Cells, donor5_CNhs12056_11455-119A6_reverse Regulation 
SkeletalMuscleCellsDonor5_CNhs12056_tpm_fwd SkeletalMuscleCellsD5+ Skeletal Muscle Cells, donor5_CNhs12056_11455-119A6_forward Regulation 
SkeletalMuscleCellsDonor4_CNhs12053_tpm_rev SkeletalMuscleCellsD4- Skeletal Muscle Cells, donor4_CNhs12053_11451-119A2_reverse Regulation 
SkeletalMuscleCellsDonor4_CNhs12053_tpm_fwd SkeletalMuscleCellsD4+ Skeletal Muscle Cells, donor4_CNhs12053_11451-119A2_forward Regulation 
SkeletalMuscleCellsDonor3_CNhs12040_tpm_rev SkeletalMuscleCellsD3- Skeletal Muscle Cells, donor3_CNhs12040_11430-118G8_reverse Regulation 
SkeletalMuscleCellsDonor3_CNhs12040_tpm_fwd SkeletalMuscleCellsD3+ Skeletal Muscle Cells, donor3_CNhs12040_11430-118G8_forward Regulation 
SkeletalMuscleCellsDonor2_CNhs11983_tpm_rev SkeletalMuscleCellsD2- Skeletal Muscle Cells, donor2_CNhs11983_11358-117H8_reverse Regulation 
SkeletalMuscleCellsDonor2_CNhs11983_tpm_fwd SkeletalMuscleCellsD2+ Skeletal Muscle Cells, donor2_CNhs11983_11358-117H8_forward Regulation 
SkeletalMuscleCellsDonor1_CNhs11083_tpm_rev SkeletalMuscleCellsD1- Skeletal Muscle Cells, donor1_CNhs11083_11281-116I3_reverse Regulation 
SkeletalMuscleCellsDonor1_CNhs11083_tpm_fwd SkeletalMuscleCellsD1+ Skeletal Muscle Cells, donor1_CNhs11083_11281-116I3_forward Regulation 
SertoliCellsDonor2_CNhs11974_tpm_rev SertoliCellsD2- Sertoli Cells, donor2_CNhs11974_11333-117F1_reverse Regulation 
SertoliCellsDonor2_CNhs11974_tpm_fwd SertoliCellsD2+ Sertoli Cells, donor2_CNhs11974_11333-117F1_forward Regulation 
SertoliCellsDonor1_CNhs10851_tpm_rev SertoliCellsD1- Sertoli Cells, donor1_CNhs10851_11255-116F4_reverse Regulation 
SertoliCellsDonor1_CNhs10851_tpm_fwd SertoliCellsD1+ Sertoli Cells, donor1_CNhs10851_11255-116F4_forward Regulation 
SebocyteDonor3_CNhs11995_tpm_rev SebocyteD3- Sebocyte, donor3_CNhs11995_11378-118B1_reverse Regulation 
SebocyteDonor3_CNhs11995_tpm_fwd SebocyteD3+ Sebocyte, donor3_CNhs11995_11378-118B1_forward Regulation 
SebocyteDonor2_CNhs11951_tpm_rev SebocyteD2- Sebocyte, donor2_CNhs11951_11301-117B5_reverse Regulation 
SebocyteDonor2_CNhs11951_tpm_fwd SebocyteD2+ Sebocyte, donor2_CNhs11951_11301-117B5_forward Regulation 
SebocyteDonor1_CNhs10847_tpm_rev SebocyteD1- Sebocyte, donor1_CNhs10847_11220-116B5_reverse Regulation 
SebocyteDonor1_CNhs10847_tpm_fwd SebocyteD1+ Sebocyte, donor1_CNhs10847_11220-116B5_forward Regulation 
SchwannCellsDonor3_CNhs12621_tpm_rev SchwannCellsD3- Schwann Cells, donor3_CNhs12621_11659-122F3_reverse Regulation 
SchwannCellsDonor3_CNhs12621_tpm_fwd SchwannCellsD3+ Schwann Cells, donor3_CNhs12621_11659-122F3_forward Regulation 
SchwannCellsDonor2_CNhs12345_tpm_rev SchwannCellsD2- Schwann Cells, donor2_CNhs12345_11578-120F3_reverse Regulation 
SchwannCellsDonor2_CNhs12345_tpm_fwd SchwannCellsD2+ Schwann Cells, donor2_CNhs12345_11578-120F3_forward Regulation 
SchwannCellsDonor1_CNhs12073_tpm_rev SchwannCellsD1- Schwann Cells, donor1_CNhs12073_11498-119F4_reverse Regulation 
SchwannCellsDonor1_CNhs12073_tpm_fwd SchwannCellsD1+ Schwann Cells, donor1_CNhs12073_11498-119F4_forward Regulation 
SalivaryAcinarCellsDonor3_CNhs12812_tpm_rev SalivaryAcinarCellsD3- salivary acinar cells, donor3_CNhs12812_11773-123I9_reverse Regulation 
SalivaryAcinarCellsDonor3_CNhs12812_tpm_fwd SalivaryAcinarCellsD3+ salivary acinar cells, donor3_CNhs12812_11773-123I9_forward Regulation 
SalivaryAcinarCellsDonor2_CNhs12811_tpm_rev SalivaryAcinarCellsD2- salivary acinar cells, donor2_CNhs12811_11772-123I8_reverse Regulation 
SalivaryAcinarCellsDonor2_CNhs12811_tpm_fwd SalivaryAcinarCellsD2+ salivary acinar cells, donor2_CNhs12811_11772-123I8_forward Regulation 
SalivaryAcinarCellsDonor1_CNhs12810_tpm_rev SalivaryAcinarCellsD1- salivary acinar cells, donor1_CNhs12810_11771-123I7_reverse Regulation 
SalivaryAcinarCellsDonor1_CNhs12810_tpm_fwd SalivaryAcinarCellsD1+ salivary acinar cells, donor1_CNhs12810_11771-123I7_forward Regulation 
RenalProximalTubularEpithelialCellDonor3_CNhs12120_tpm_rev RptecD3- Renal Proximal Tubular Epithelial Cell, donor3_CNhs12120_11676-122H2_reverse Regulation 
RenalProximalTubularEpithelialCellDonor3_CNhs12120_tpm_fwd RptecD3+ Renal Proximal Tubular Epithelial Cell, donor3_CNhs12120_11676-122H2_forward Regulation 
RenalProximalTubularEpithelialCellDonor2_CNhs12087_tpm_rev RptecD2- Renal Proximal Tubular Epithelial Cell, donor2_CNhs12087_11595-120H2_reverse Regulation 
RenalProximalTubularEpithelialCellDonor2_CNhs12087_tpm_fwd RptecD2+ Renal Proximal Tubular Epithelial Cell, donor2_CNhs12087_11595-120H2_forward Regulation 
RenalProximalTubularEpithelialCellDonor1_CNhs11330_tpm_rev RptecD1- Renal Proximal Tubular Epithelial Cell, donor1_CNhs11330_11515-119H3_reverse Regulation 
RenalProximalTubularEpithelialCellDonor1_CNhs11330_tpm_fwd RptecD1+ Renal Proximal Tubular Epithelial Cell, donor1_CNhs11330_11515-119H3_forward Regulation 
RetinalPigmentEpithelialCellsDonor3_CNhs12733_tpm_rev RpecD3- Retinal Pigment Epithelial Cells, donor3_CNhs12733_11689-122I6_reverse Regulation 
RetinalPigmentEpithelialCellsDonor3_CNhs12733_tpm_fwd RpecD3+ Retinal Pigment Epithelial Cells, donor3_CNhs12733_11689-122I6_forward Regulation 
RetinalPigmentEpithelialCellsDonor2_CNhs12096_tpm_rev RpecD2- Retinal Pigment Epithelial Cells, donor2_CNhs12096_11608-120I6_reverse Regulation 
RetinalPigmentEpithelialCellsDonor2_CNhs12096_tpm_fwd RpecD2+ Retinal Pigment Epithelial Cells, donor2_CNhs12096_11608-120I6_forward Regulation 
RetinalPigmentEpithelialCellsDonor1_CNhs11338_tpm_rev RpecD1- Retinal Pigment Epithelial Cells, donor1_CNhs11338_11528-119I7_reverse Regulation 
RetinalPigmentEpithelialCellsDonor1_CNhs11338_tpm_fwd RpecD1+ Retinal Pigment Epithelial Cells, donor1_CNhs11338_11528-119I7_forward Regulation 
RetinalPigmentEpithelialCellsDonor0_CNhs10842_tpm_rev RpecD0- Retinal Pigment Epithelial Cells, donor0_CNhs10842_11215-116A9_reverse Regulation 
RetinalPigmentEpithelialCellsDonor0_CNhs10842_tpm_fwd RpecD0+ Retinal Pigment Epithelial Cells, donor0_CNhs10842_11215-116A9_forward Regulation 
RenalGlomerularEndothelialCellsDonor4_CNhs13080_tpm_rev RgecD4- Renal Glomerular Endothelial Cells, donor4_CNhs13080_11783-124B1_reverse Regulation 
RenalGlomerularEndothelialCellsDonor4_CNhs13080_tpm_fwd RgecD4+ Renal Glomerular Endothelial Cells, donor4_CNhs13080_11783-124B1_forward Regulation 
RenalGlomerularEndothelialCellsDonor3_CNhs12624_tpm_rev RgecD3- Renal Glomerular Endothelial Cells, donor3_CNhs12624_11675-122H1_reverse Regulation 
RenalGlomerularEndothelialCellsDonor3_CNhs12624_tpm_fwd RgecD3+ Renal Glomerular Endothelial Cells, donor3_CNhs12624_11675-122H1_forward Regulation 
RenalGlomerularEndothelialCellsDonor2_CNhs12086_tpm_rev RgecD2- Renal Glomerular Endothelial Cells, donor2_CNhs12086_11594-120H1_reverse Regulation 
RenalGlomerularEndothelialCellsDonor2_CNhs12086_tpm_fwd RgecD2+ Renal Glomerular Endothelial Cells, donor2_CNhs12086_11594-120H1_forward Regulation 
RenalGlomerularEndothelialCellsDonor1_CNhs12074_tpm_rev RgecD1- Renal Glomerular Endothelial Cells, donor1_CNhs12074_11514-119H2_reverse Regulation 
RenalGlomerularEndothelialCellsDonor1_CNhs12074_tpm_fwd RgecD1+ Renal Glomerular Endothelial Cells, donor1_CNhs12074_11514-119H2_forward Regulation 
RenalMesangialCellsDonor3_CNhs12121_tpm_rev RenalMesangialCellsD3- Renal Mesangial Cells, donor3_CNhs12121_11679-122H5_reverse Regulation 
RenalMesangialCellsDonor3_CNhs12121_tpm_fwd RenalMesangialCellsD3+ Renal Mesangial Cells, donor3_CNhs12121_11679-122H5_forward Regulation 
RenalMesangialCellsDonor2_CNhs12089_tpm_rev RenalMesangialCellsD2- Renal Mesangial Cells, donor2_CNhs12089_11598-120H5_reverse Regulation 
RenalMesangialCellsDonor2_CNhs12089_tpm_fwd RenalMesangialCellsD2+ Renal Mesangial Cells, donor2_CNhs12089_11598-120H5_forward Regulation 
RenalMesangialCellsDonor1_CNhs11333_tpm_rev RenalMesangialCellsD1- Renal Mesangial Cells, donor1_CNhs11333_11518-119H6_reverse Regulation 
RenalMesangialCellsDonor1_CNhs11333_tpm_fwd RenalMesangialCellsD1+ Renal Mesangial Cells, donor1_CNhs11333_11518-119H6_forward Regulation 
RenalEpithelialCellsDonor3_CNhs12732_tpm_rev RenalEpithelialCellsD3- Renal Epithelial Cells, donor3_CNhs12732_11678-122H4_reverse Regulation 
RenalEpithelialCellsDonor3_CNhs12732_tpm_fwd RenalEpithelialCellsD3+ Renal Epithelial Cells, donor3_CNhs12732_11678-122H4_forward Regulation 
RenalEpithelialCellsDonor2_CNhs12088_tpm_rev RenalEpithelialCellsD2- Renal Epithelial Cells, donor2_CNhs12088_11597-120H4_reverse Regulation 
RenalEpithelialCellsDonor2_CNhs12088_tpm_fwd RenalEpithelialCellsD2+ Renal Epithelial Cells, donor2_CNhs12088_11597-120H4_forward Regulation 
RenalEpithelialCellsDonor1_CNhs11332_tpm_rev RenalEpithelialCellsD1- Renal Epithelial Cells, donor1_CNhs11332_11517-119H5_reverse Regulation 
RenalEpithelialCellsDonor1_CNhs11332_tpm_fwd RenalEpithelialCellsD1+ Renal Epithelial Cells, donor1_CNhs11332_11517-119H5_forward Regulation 
RenalCorticalEpithelialCellsDonor2_CNhs12728_tpm_rev RcecD2- Renal Cortical Epithelial Cells, donor2_CNhs12728_11596-120H3_reverse Regulation 
RenalCorticalEpithelialCellsDonor2_CNhs12728_tpm_fwd RcecD2+ Renal Cortical Epithelial Cells, donor2_CNhs12728_11596-120H3_forward Regulation 
RenalCorticalEpithelialCellsDonor1_CNhs11331_tpm_rev RcecD1- Renal Cortical Epithelial Cells, donor1_CNhs11331_11516-119H4_reverse Regulation 
RenalCorticalEpithelialCellsDonor1_CNhs11331_tpm_fwd RcecD1+ Renal Cortical Epithelial Cells, donor1_CNhs11331_11516-119H4_forward Regulation 
ProstateStromalCellsDonor3_CNhs12015_tpm_rev ProstateStromalCellsD3- Prostate Stromal Cells, donor3_CNhs12015_11405-118E1_reverse Regulation 
ProstateStromalCellsDonor3_CNhs12015_tpm_fwd ProstateStromalCellsD3+ Prostate Stromal Cells, donor3_CNhs12015_11405-118E1_forward Regulation 
ProstateStromalCellsDonor2_CNhs11973_tpm_rev ProstateStromalCellsD2- Prostate Stromal Cells, donor2_CNhs11973_11332-117E9_reverse Regulation 
ProstateStromalCellsDonor2_CNhs11973_tpm_fwd ProstateStromalCellsD2+ Prostate Stromal Cells, donor2_CNhs11973_11332-117E9_forward Regulation 
ProstateStromalCellsDonor1_CNhs10883_tpm_rev ProstateStromalCellsD1- Prostate Stromal Cells, donor1_CNhs10883_11254-116F3_reverse Regulation 
ProstateStromalCellsDonor1_CNhs10883_tpm_fwd ProstateStromalCellsD1+ Prostate Stromal Cells, donor1_CNhs10883_11254-116F3_forward Regulation 
ProstateEpithelialCellsDonor3_CNhs12014_tpm_rev ProstateEpithelialCellsD3- Prostate Epithelial Cells, donor3_CNhs12014_11404-118D9_reverse Regulation 
ProstateEpithelialCellsDonor3_CNhs12014_tpm_fwd ProstateEpithelialCellsD3+ Prostate Epithelial Cells, donor3_CNhs12014_11404-118D9_forward Regulation 
ProstateEpithelialCellsDonor2_CNhs11972_tpm_rev ProstateEpithelialCellsD2- Prostate Epithelial Cells, donor2_CNhs11972_11331-117E8_reverse Regulation 
ProstateEpithelialCellsDonor2_CNhs11972_tpm_fwd ProstateEpithelialCellsD2+ Prostate Epithelial Cells, donor2_CNhs11972_11331-117E8_forward Regulation 
ProstateEpithelialCellsPolarizedDonor1_CNhs10882_tpm_rev ProstateEpithelialCellsD1- Prostate Epithelial Cells (polarized), donor1_CNhs10882_11253-116F2_reverse Regulation 
ProstateEpithelialCellsPolarizedDonor1_CNhs10882_tpm_fwd ProstateEpithelialCellsD1+ Prostate Epithelial Cells (polarized), donor1_CNhs10882_11253-116F2_forward Regulation 
PreadipocyteVisceralDonor3_CNhs12039_tpm_rev PreadipocyteVisceralD3- Preadipocyte - visceral, donor3_CNhs12039_11429-118G7_reverse Regulation 
PreadipocyteVisceralDonor3_CNhs12039_tpm_fwd PreadipocyteVisceralD3+ Preadipocyte - visceral, donor3_CNhs12039_11429-118G7_forward Regulation 
PreadipocyteVisceralDonor2_CNhs11982_tpm_rev PreadipocyteVisceralD2- Preadipocyte - visceral, donor2_CNhs11982_11357-117H7_reverse Regulation 
PreadipocyteVisceralDonor2_CNhs11982_tpm_fwd PreadipocyteVisceralD2+ Preadipocyte - visceral, donor2_CNhs11982_11357-117H7_forward Regulation 
PreadipocyteVisceralDonor1_CNhs11082_tpm_rev PreadipocyteVisceralD1- Preadipocyte - visceral, donor1_CNhs11082_11280-116I2_reverse Regulation 
PreadipocyteVisceralDonor1_CNhs11082_tpm_fwd PreadipocyteVisceralD1+ Preadipocyte - visceral, donor1_CNhs11082_11280-116I2_forward Regulation 
PreadipocyteSubcutaneousDonor3_CNhs12038_tpm_rev PreadipocyteSubcutaneousD3- Preadipocyte - subcutaneous, donor3_CNhs12038_11428-118G6_reverse Regulation 
PreadipocyteSubcutaneousDonor3_CNhs12038_tpm_fwd PreadipocyteSubcutaneousD3+ Preadipocyte - subcutaneous, donor3_CNhs12038_11428-118G6_forward Regulation 
PreadipocyteSubcutaneousDonor2_CNhs11981_tpm_rev PreadipocyteSubcutaneousD2- Preadipocyte - subcutaneous, donor2_CNhs11981_11356-117H6_reverse Regulation 
PreadipocyteSubcutaneousDonor2_CNhs11981_tpm_fwd PreadipocyteSubcutaneousD2+ Preadipocyte - subcutaneous, donor2_CNhs11981_11356-117H6_forward Regulation 
PreadipocyteSubcutaneousDonor1_CNhs11081_tpm_rev PreadipocyteSubcutaneousD1- Preadipocyte - subcutaneous, donor1_CNhs11081_11279-116I1_reverse Regulation 
PreadipocyteSubcutaneousDonor1_CNhs11081_tpm_fwd PreadipocyteSubcutaneousD1+ Preadipocyte - subcutaneous, donor1_CNhs11081_11279-116I1_forward Regulation 
PreadipocytePerirenalDonor1_CNhs12065_tpm_rev PreadipocytePerirenalD1- Preadipocyte - perirenal, donor1_CNhs12065_11469-119C2_reverse Regulation 
PreadipocytePerirenalDonor1_CNhs12065_tpm_fwd PreadipocytePerirenalD1+ Preadipocyte - perirenal, donor1_CNhs12065_11469-119C2_forward Regulation 
PreadipocyteOmentalDonor3_CNhs12013_tpm_rev PreadipocyteOmentalD3- Preadipocyte - omental, donor3_CNhs12013_11403-118D8_reverse Regulation 
PreadipocyteOmentalDonor3_CNhs12013_tpm_fwd PreadipocyteOmentalD3+ Preadipocyte - omental, donor3_CNhs12013_11403-118D8_forward Regulation 
PreadipocyteOmentalDonor2_CNhs11902_tpm_rev PreadipocyteOmentalD2- Preadipocyte - omental, donor2_CNhs11902_11329-117E6_reverse Regulation 
PreadipocyteOmentalDonor2_CNhs11902_tpm_fwd PreadipocyteOmentalD2+ Preadipocyte - omental, donor2_CNhs11902_11329-117E6_forward Regulation 
PreadipocyteOmentalDonor1_CNhs11065_tpm_rev PreadipocyteOmentalD1- Preadipocyte - omental, donor1_CNhs11065_11468-119C1_reverse Regulation 
PreadipocyteOmentalDonor1_CNhs11065_tpm_fwd PreadipocyteOmentalD1+ Preadipocyte - omental, donor1_CNhs11065_11468-119C1_forward Regulation 
PreadipocyteBreastDonor2_CNhs11971_tpm_rev PreadipocyteBreastD2- Preadipocyte - breast, donor2_CNhs11971_11328-117E5_reverse Regulation 
PreadipocyteBreastDonor2_CNhs11971_tpm_fwd PreadipocyteBreastD2+ Preadipocyte - breast, donor2_CNhs11971_11328-117E5_forward Regulation 
PreadipocyteBreastDonor1_CNhs11052_tpm_rev PreadipocyteBreastD1- Preadipocyte - breast, donor1_CNhs11052_11467-119B9_reverse Regulation 
PreadipocyteBreastDonor1_CNhs11052_tpm_fwd PreadipocyteBreastD1+ Preadipocyte - breast, donor1_CNhs11052_11467-119B9_forward Regulation 
PlacentalEpithelialCellsDonor3_CNhs12037_tpm_rev PlacentalEpithelialCellsD3- Placental Epithelial Cells, donor3_CNhs12037_11427-118G5_reverse Regulation 
PlacentalEpithelialCellsDonor3_CNhs12037_tpm_fwd PlacentalEpithelialCellsD3+ Placental Epithelial Cells, donor3_CNhs12037_11427-118G5_forward Regulation 
PlacentalEpithelialCellsDonor2_CNhs11386_tpm_rev PlacentalEpithelialCellsD2- Placental Epithelial Cells, donor2_CNhs11386_11355-117H5_reverse Regulation 
PlacentalEpithelialCellsDonor2_CNhs11386_tpm_fwd PlacentalEpithelialCellsD2+ Placental Epithelial Cells, donor2_CNhs11386_11355-117H5_forward Regulation 
PlacentalEpithelialCellsDonor1_CNhs11079_tpm_rev PlacentalEpithelialCellsD1- Placental Epithelial Cells, donor1_CNhs11079_11278-116H9_reverse Regulation 
PlacentalEpithelialCellsDonor1_CNhs11079_tpm_fwd PlacentalEpithelialCellsD1+ Placental Epithelial Cells, donor1_CNhs11079_11278-116H9_forward Regulation 
PeripheralBloodMononuclearCellsDonor3_CNhs12002_tpm_rev PeripheralBloodMononuclearCellsD3- Peripheral Blood Mononuclear Cells, donor3_CNhs12002_11388-118C2_reverse Regulation 
PeripheralBloodMononuclearCellsDonor3_CNhs12002_tpm_fwd PeripheralBloodMononuclearCellsD3+ Peripheral Blood Mononuclear Cells, donor3_CNhs12002_11388-118C2_forward Regulation 
PeripheralBloodMononuclearCellsDonor2_CNhs11958_tpm_rev PeripheralBloodMononuclearCellsD2- Peripheral Blood Mononuclear Cells, donor2_CNhs11958_11312-117C7_reverse Regulation 
PeripheralBloodMononuclearCellsDonor2_CNhs11958_tpm_fwd PeripheralBloodMononuclearCellsD2+ Peripheral Blood Mononuclear Cells, donor2_CNhs11958_11312-117C7_forward Regulation 
PeripheralBloodMononuclearCellsDonor1_CNhs10860_tpm_rev PeripheralBloodMononuclearCellsD1- Peripheral Blood Mononuclear Cells, donor1_CNhs10860_11231-116C7_reverse Regulation 
PeripheralBloodMononuclearCellsDonor1_CNhs10860_tpm_fwd PeripheralBloodMononuclearCellsD1+ Peripheral Blood Mononuclear Cells, donor1_CNhs10860_11231-116C7_forward Regulation 
PerineurialCellsDonor2_CNhs12590_tpm_rev PerineurialCellsD2- Perineurial Cells, donor2_CNhs12590_11579-120F4_reverse Regulation 
PerineurialCellsDonor2_CNhs12590_tpm_fwd PerineurialCellsD2+ Perineurial Cells, donor2_CNhs12590_11579-120F4_forward Regulation 
PerineurialCellsDonor1_CNhs12587_tpm_rev PerineurialCellsD1- Perineurial Cells, donor1_CNhs12587_11499-119F5_reverse Regulation 
PerineurialCellsDonor1_CNhs12587_tpm_fwd PerineurialCellsD1+ Perineurial Cells, donor1_CNhs12587_11499-119F5_forward Regulation 
PericytesDonor3_CNhs12116_tpm_rev PericytesD3- Pericytes, donor3_CNhs12116_11652-122E5_reverse Regulation 
PericytesDonor3_CNhs12116_tpm_fwd PericytesD3+ Pericytes, donor3_CNhs12116_11652-122E5_forward Regulation 
PericytesDonor2_CNhs12079_tpm_rev PericytesD2- Pericytes, donor2_CNhs12079_11571-120E5_reverse Regulation 
PericytesDonor2_CNhs12079_tpm_fwd PericytesD2+ Pericytes, donor2_CNhs12079_11571-120E5_forward Regulation 
PericytesDonor1_CNhs11317_tpm_rev PericytesD1- Pericytes, donor1_CNhs11317_11491-119E6_reverse Regulation 
PericytesDonor1_CNhs11317_tpm_fwd PericytesD1+ Pericytes, donor1_CNhs11317_11491-119E6_forward Regulation 
PancreaticStromalCellsDonor1_CNhs10877_tpm_rev PancreaticStromalCellsD1- Pancreatic stromal cells, donor1_CNhs10877_11249-116E7_reverse Regulation 
PancreaticStromalCellsDonor1_CNhs10877_tpm_fwd PancreaticStromalCellsD1+ Pancreatic stromal cells, donor1_CNhs10877_11249-116E7_forward Regulation 
OsteoblastDifferentiatedDonor3_CNhs12035_tpm_rev OsteoblastDifferentiatedD3- Osteoblast - differentiated, donor3_CNhs12035_11425-118G3_reverse Regulation 
OsteoblastDifferentiatedDonor3_CNhs12035_tpm_fwd OsteoblastDifferentiatedD3+ Osteoblast - differentiated, donor3_CNhs12035_11425-118G3_forward Regulation 
OsteoblastDifferentiatedDonor2_CNhs11980_tpm_rev OsteoblastDifferentiatedD2- Osteoblast - differentiated, donor2_CNhs11980_11353-117H3_reverse Regulation 
OsteoblastDifferentiatedDonor2_CNhs11980_tpm_fwd OsteoblastDifferentiatedD2+ Osteoblast - differentiated, donor2_CNhs11980_11353-117H3_forward Regulation 
OsteoblastDifferentiatedDonor1_CNhs11311_tpm_rev OsteoblastDifferentiatedD1- Osteoblast - differentiated, donor1_CNhs11311_11276-116H7_reverse Regulation 
OsteoblastDifferentiatedDonor1_CNhs11311_tpm_fwd OsteoblastDifferentiatedD1+ Osteoblast - differentiated, donor1_CNhs11311_11276-116H7_forward Regulation 
OsteoblastDonor3_CNhs12036_tpm_rev OsteoblastD3- Osteoblast, donor3_CNhs12036_11426-118G4_reverse Regulation 
OsteoblastDonor3_CNhs12036_tpm_fwd OsteoblastD3+ Osteoblast, donor3_CNhs12036_11426-118G4_forward Regulation 
OsteoblastDonor2_CNhs11385_tpm_rev OsteoblastD2- Osteoblast, donor2_CNhs11385_11354-117H4_reverse Regulation 
OsteoblastDonor2_CNhs11385_tpm_fwd OsteoblastD2+ Osteoblast, donor2_CNhs11385_11354-117H4_forward Regulation 
OsteoblastDonor1_CNhs11078_tpm_rev OsteoblastD1- Osteoblast, donor1_CNhs11078_11277-116H8_reverse Regulation 
OsteoblastDonor1_CNhs11078_tpm_fwd OsteoblastD1+ Osteoblast, donor1_CNhs11078_11277-116H8_forward Regulation 
OligodendrocytePrecursorsDonor1_CNhs12586_tpm_rev OligodendrocytePrecursorsD1- Oligodendrocyte - precursors, donor1_CNhs12586_11496-119F2_reverse Regulation 
OligodendrocytePrecursorsDonor1_CNhs12586_tpm_fwd OligodendrocytePrecursorsD1+ Oligodendrocyte - precursors, donor1_CNhs12586_11496-119F2_forward Regulation 
OlfactoryEpithelialCellsDonor4_CNhs13819_tpm_rev OlfactoryEpithelialCellsD4- Olfactory epithelial cells, donor4_CNhs13819_11936-126A1_reverse Regulation 
OlfactoryEpithelialCellsDonor4_CNhs13819_tpm_fwd OlfactoryEpithelialCellsD4+ Olfactory epithelial cells, donor4_CNhs13819_11936-126A1_forward Regulation 
OlfactoryEpithelialCellsDonor3_CNhs13818_tpm_rev OlfactoryEpithelialCellsD3- Olfactory epithelial cells, donor3_CNhs13818_11935-125I9_reverse Regulation 
OlfactoryEpithelialCellsDonor3_CNhs13818_tpm_fwd OlfactoryEpithelialCellsD3+ Olfactory epithelial cells, donor3_CNhs13818_11935-125I9_forward Regulation 
OlfactoryEpithelialCellsDonor2_CNhs13817_tpm_rev OlfactoryEpithelialCellsD2- Olfactory epithelial cells, donor2_CNhs13817_11934-125I8_reverse Regulation 
OlfactoryEpithelialCellsDonor2_CNhs13817_tpm_fwd OlfactoryEpithelialCellsD2+ Olfactory epithelial cells, donor2_CNhs13817_11934-125I8_forward Regulation 
OlfactoryEpithelialCellsDonor1_CNhs13816_tpm_rev OlfactoryEpithelialCellsD1- Olfactory epithelial cells, donor1_CNhs13816_11933-125I7_reverse Regulation 
OlfactoryEpithelialCellsDonor1_CNhs13816_tpm_fwd OlfactoryEpithelialCellsD1+ Olfactory epithelial cells, donor1_CNhs13816_11933-125I7_forward Regulation 
NucleusPulposusCellDonor3_CNhs12063_tpm_rev NucleusPulposusCellD3- Nucleus Pulposus Cell, donor3_CNhs12063_11462-119B4_reverse Regulation 
NucleusPulposusCellDonor3_CNhs12063_tpm_fwd NucleusPulposusCellD3+ Nucleus Pulposus Cell, donor3_CNhs12063_11462-119B4_forward Regulation 
NucleusPulposusCellDonor2_CNhs12019_tpm_rev NucleusPulposusCellD2- Nucleus Pulposus Cell, donor2_CNhs12019_11409-118E5_reverse Regulation 
NucleusPulposusCellDonor2_CNhs12019_tpm_fwd NucleusPulposusCellD2+ Nucleus Pulposus Cell, donor2_CNhs12019_11409-118E5_forward Regulation 
NucleusPulposusCellDonor1_CNhs10881_tpm_rev NucleusPulposusCellD1- Nucleus Pulposus Cell, donor1_CNhs10881_11252-116F1_reverse Regulation 
NucleusPulposusCellDonor1_CNhs10881_tpm_fwd NucleusPulposusCellD1+ Nucleus Pulposus Cell, donor1_CNhs10881_11252-116F1_forward Regulation 
NeutrophilsDonor3_CNhs11905_tpm_rev NeutrophilsD3- Neutrophils, donor3_CNhs11905_11390-118C4_reverse Regulation 
NeutrophilsDonor3_CNhs11905_tpm_fwd NeutrophilsD3+ Neutrophils, donor3_CNhs11905_11390-118C4_forward Regulation 
NeutrophilsDonor2_CNhs11959_tpm_rev NeutrophilsD2- Neutrophils, donor2_CNhs11959_11314-117C9_reverse Regulation 
NeutrophilsDonor2_CNhs11959_tpm_fwd NeutrophilsD2+ Neutrophils, donor2_CNhs11959_11314-117C9_forward Regulation 
NeutrophilsDonor1_CNhs10862_tpm_rev NeutrophilsD1- Neutrophils, donor1_CNhs10862_11233-116C9_reverse Regulation 
NeutrophilsDonor1_CNhs10862_tpm_fwd NeutrophilsD1+ Neutrophils, donor1_CNhs10862_11233-116C9_forward Regulation 
NeuronsDonor3_CNhs13815_tpm_rev NeuronsD3- Neurons, donor3_CNhs13815_11655-122E8_reverse Regulation 
NeuronsDonor3_CNhs13815_tpm_fwd NeuronsD3+ Neurons, donor3_CNhs13815_11655-122E8_forward Regulation 
NeuronsDonor2_CNhs12726_tpm_rev NeuronsD2- Neurons, donor2_CNhs12726_11574-120E8_reverse Regulation 
NeuronsDonor2_CNhs12726_tpm_fwd NeuronsD2+ Neurons, donor2_CNhs12726_11574-120E8_forward Regulation 
NeuronsDonor1_CNhs12338_tpm_rev NeuronsD1- Neurons, donor1_CNhs12338_11494-119E9_reverse Regulation 
NeuronsDonor1_CNhs12338_tpm_fwd NeuronsD1+ Neurons, donor1_CNhs12338_11494-119E9_forward Regulation 
NeuralStemCellsDonor2_CNhs11384_tpm_rev NeuralStemCellsD2- Neural stem cells, donor2_CNhs11384_11352-117H2_reverse Regulation 
NeuralStemCellsDonor2_CNhs11384_tpm_fwd NeuralStemCellsD2+ Neural stem cells, donor2_CNhs11384_11352-117H2_forward Regulation 
NeuralStemCellsDonor1_CNhs11063_tpm_rev NeuralStemCellsD1- Neural stem cells, donor1_CNhs11063_11275-116H6_reverse Regulation 
NeuralStemCellsDonor1_CNhs11063_tpm_fwd NeuralStemCellsD1+ Neural stem cells, donor1_CNhs11063_11275-116H6_forward Regulation 
NaturalKillerCellsDonor3_CNhs12001_tpm_rev NaturalKillerCellsD3- Natural Killer Cells, donor3_CNhs12001_11387-118C1_reverse Regulation 
NaturalKillerCellsDonor3_CNhs12001_tpm_fwd NaturalKillerCellsD3+ Natural Killer Cells, donor3_CNhs12001_11387-118C1_forward Regulation 
NaturalKillerCellsDonor2_CNhs11957_tpm_rev NaturalKillerCellsD2- Natural Killer Cells, donor2_CNhs11957_11311-117C6_reverse Regulation 
NaturalKillerCellsDonor2_CNhs11957_tpm_fwd NaturalKillerCellsD2+ Natural Killer Cells, donor2_CNhs11957_11311-117C6_forward Regulation 
NaturalKillerCellsDonor1_CNhs10859_tpm_rev NaturalKillerCellsD1- Natural Killer Cells, donor1_CNhs10859_11230-116C6_reverse Regulation 
NaturalKillerCellsDonor1_CNhs10859_tpm_fwd NaturalKillerCellsD1+ Natural Killer Cells, donor1_CNhs10859_11230-116C6_forward Regulation 
NasalEpithelialCellsDonor2_CNhs12574_tpm_rev NasalEpithelialCellsD2- nasal epithelial cells, donor2_CNhs12574_12227-129F4_reverse Regulation 
NasalEpithelialCellsDonor2_CNhs12574_tpm_fwd NasalEpithelialCellsD2+ nasal epithelial cells, donor2_CNhs12574_12227-129F4_forward Regulation 
NasalEpithelialCellsDonor1TechRep1_CNhs12589_tpm_rev NasalEpithelialCellsD1Tr1- nasal epithelial cells, donor1, tech_rep1_CNhs12589_12226-129F3_reverse Regulation 
NasalEpithelialCellsDonor1TechRep1_CNhs12589_tpm_fwd NasalEpithelialCellsD1Tr1+ nasal epithelial cells, donor1, tech_rep1_CNhs12589_12226-129F3_forward Regulation 
MyoblastDonor3_CNhs11908_tpm_rev MyoblastD3- Myoblast, donor3_CNhs11908_11398-118D3_reverse Regulation 
MyoblastDonor3_CNhs11908_tpm_fwd MyoblastD3+ Myoblast, donor3_CNhs11908_11398-118D3_forward Regulation 
MyoblastDonor2_CNhs11965_tpm_rev MyoblastD2- Myoblast, donor2_CNhs11965_11322-117D8_reverse Regulation 
MyoblastDonor2_CNhs11965_tpm_fwd MyoblastD2+ Myoblast, donor2_CNhs11965_11322-117D8_forward Regulation 
MyoblastDonor1_CNhs10870_tpm_rev MyoblastD1- Myoblast, donor1_CNhs10870_11241-116D8_reverse Regulation 
MyoblastDonor1_CNhs10870_tpm_fwd MyoblastD1+ Myoblast, donor1_CNhs10870_11241-116D8_forward Regulation 
MesenchymalStemCellsWhartonsJellyDonor1_CNhs11057_tpm_rev MscWharton'sJellyD1- Mesenchymal Stem Cells - Wharton's Jelly, donor1_CNhs11057_11548-120B9_reverse Regulation 
MesenchymalStemCellsWhartonsJellyDonor1_CNhs11057_tpm_fwd MscWharton'sJellyD1+ Mesenchymal Stem Cells - Wharton's Jelly, donor1_CNhs11057_11548-120B9_forward Regulation 
MesenchymalStemCellsVertebralDonor1_CNhs10846_tpm_rev MscVertebralD1- Mesenchymal Stem Cells - Vertebral, donor1_CNhs10846_11219-116B4_reverse Regulation 
MesenchymalStemCellsVertebralDonor1_CNhs10846_tpm_fwd MscVertebralD1+ Mesenchymal Stem Cells - Vertebral, donor1_CNhs10846_11219-116B4_forward Regulation 
MesenchymalStemCellsUmbilicalDonor3_CNhs12127_tpm_rev MscUmbilicalD3- Mesenchymal Stem Cells - umbilical, donor3_CNhs12127_11700-123A8_reverse Regulation 
MesenchymalStemCellsUmbilicalDonor3_CNhs12127_tpm_fwd MscUmbilicalD3+ Mesenchymal Stem Cells - umbilical, donor3_CNhs12127_11700-123A8_forward Regulation 
MesenchymalStemCellsUmbilicalDonor2_CNhs12102_tpm_rev MscUmbilicalD2- Mesenchymal Stem Cells - umbilical, donor2_CNhs12102_11619-122A8_reverse Regulation 
MesenchymalStemCellsUmbilicalDonor2_CNhs12102_tpm_fwd MscUmbilicalD2+ Mesenchymal Stem Cells - umbilical, donor2_CNhs12102_11619-122A8_forward Regulation 
MesenchymalStemCellsUmbilicalDonor1_CNhs11347_tpm_rev MscUmbilicalD1- Mesenchymal Stem Cells - umbilical, donor1_CNhs11347_11539-120A9_reverse Regulation 
MesenchymalStemCellsUmbilicalDonor1_CNhs11347_tpm_fwd MscUmbilicalD1+ Mesenchymal Stem Cells - umbilical, donor1_CNhs11347_11539-120A9_forward Regulation 
MesenchymalStemCellsUmbilicalDonor0_CNhs12492_tpm_rev MscUmbilicalD0- Mesenchymal stem cells - umbilical, donor0_CNhs12492_11214-116A8_reverse Regulation 
MesenchymalStemCellsUmbilicalDonor0_CNhs12492_tpm_fwd MscUmbilicalD0+ Mesenchymal stem cells - umbilical, donor0_CNhs12492_11214-116A8_forward Regulation 
MesenchymalStemCellsHepaticDonor2_CNhs12730_tpm_rev MscHepaticD2- Mesenchymal Stem Cells - hepatic, donor2_CNhs12730_11618-122A7_reverse Regulation 
MesenchymalStemCellsHepaticDonor2_CNhs12730_tpm_fwd MscHepaticD2+ Mesenchymal Stem Cells - hepatic, donor2_CNhs12730_11618-122A7_forward Regulation 
MesenchymalStemCellsHepaticDonor1_CNhs11346_tpm_rev MscHepaticD1- Mesenchymal Stem Cells - hepatic, donor1_CNhs11346_11538-120A8_reverse Regulation 
MesenchymalStemCellsHepaticDonor1_CNhs11346_tpm_fwd MscHepaticD1+ Mesenchymal Stem Cells - hepatic, donor1_CNhs11346_11538-120A8_forward Regulation 
MesenchymalStemCellsHepaticDonor0_CNhs10845_tpm_rev MscHepaticD0- Mesenchymal stem cells - hepatic, donor0_CNhs10845_11218-116B3_reverse Regulation 
MesenchymalStemCellsHepaticDonor0_CNhs10845_tpm_fwd MscHepaticD0+ Mesenchymal stem cells - hepatic, donor0_CNhs10845_11218-116B3_forward Regulation 
MesenchymalStemCellsBoneMarrowDonor4_CNhs11316_tpm_rev MscBoneMarrowD4- Mesenchymal Stem Cells - bone marrow, donor4_CNhs11316_11464-119B6_reverse Regulation 
MesenchymalStemCellsBoneMarrowDonor4_CNhs11316_tpm_fwd MscBoneMarrowD4+ Mesenchymal Stem Cells - bone marrow, donor4_CNhs11316_11464-119B6_forward Regulation 
MesenchymalStemCellsBoneMarrowDonor3_CNhs12126_tpm_rev MscBoneMarrowD3- Mesenchymal Stem Cells - bone marrow, donor3_CNhs12126_11697-123A5_reverse Regulation 
MesenchymalStemCellsBoneMarrowDonor3_CNhs12126_tpm_fwd MscBoneMarrowD3+ Mesenchymal Stem Cells - bone marrow, donor3_CNhs12126_11697-123A5_forward Regulation 
MesenchymalStemCellsBoneMarrowDonor2_CNhs12100_tpm_rev MscBoneMarrowD2- Mesenchymal Stem Cells - bone marrow, donor2_CNhs12100_11616-122A5_reverse Regulation 
MesenchymalStemCellsBoneMarrowDonor2_CNhs12100_tpm_fwd MscBoneMarrowD2+ Mesenchymal Stem Cells - bone marrow, donor2_CNhs12100_11616-122A5_forward Regulation 
MesenchymalStemCellsBoneMarrowDonor1_CNhs11344_tpm_rev MscBoneMarrowD1- Mesenchymal Stem Cells - bone marrow, donor1_CNhs11344_11536-120A6_reverse Regulation 
MesenchymalStemCellsBoneMarrowDonor1_CNhs11344_tpm_fwd MscBoneMarrowD1+ Mesenchymal Stem Cells - bone marrow, donor1_CNhs11344_11536-120A6_forward Regulation 
MesenchymalStemCellsAmnioticMembraneDonor2_CNhs12104_tpm_rev MscAmnioticMembraneD2- Mesenchymal Stem Cells - amniotic membrane, donor2_CNhs12104_11627-122B7_reverse Regulation 
MesenchymalStemCellsAmnioticMembraneDonor2_CNhs12104_tpm_fwd MscAmnioticMembraneD2+ Mesenchymal Stem Cells - amniotic membrane, donor2_CNhs12104_11627-122B7_forward Regulation 
MesenchymalStemCellsAmnioticMembraneDonor1_CNhs11349_tpm_rev MscAmnioticMembraneD1- Mesenchymal Stem Cells - amniotic membrane, donor1_CNhs11349_11547-120B8_reverse Regulation 
MesenchymalStemCellsAmnioticMembraneDonor1_CNhs11349_tpm_fwd MscAmnioticMembraneD1+ Mesenchymal Stem Cells - amniotic membrane, donor1_CNhs11349_11547-120B8_forward Regulation 
MesenchymalStemCellsAdiposeDonor3_CNhs12922_tpm_rev MscAdiposeD3- Mesenchymal Stem Cells - adipose, donor3_CNhs12922_11698-123A6_reverse Regulation 
MesenchymalStemCellsAdiposeDonor3_CNhs12922_tpm_fwd MscAdiposeD3+ Mesenchymal Stem Cells - adipose, donor3_CNhs12922_11698-123A6_forward Regulation 
MesenchymalStemCellsAdiposeDonor2_CNhs12101_tpm_rev MscAdiposeD2- Mesenchymal Stem Cells - adipose, donor2_CNhs12101_11617-122A6_reverse Regulation 
MesenchymalStemCellsAdiposeDonor2_CNhs12101_tpm_fwd MscAdiposeD2+ Mesenchymal Stem Cells - adipose, donor2_CNhs12101_11617-122A6_forward Regulation 
MesenchymalStemCellsAdiposeDonor1_CNhs11345_tpm_rev MscAdiposeD1- Mesenchymal Stem Cells - adipose, donor1_CNhs11345_11537-120A7_reverse Regulation 
MesenchymalStemCellsAdiposeDonor1_CNhs11345_tpm_fwd MscAdiposeD1+ Mesenchymal Stem Cells - adipose, donor1_CNhs11345_11537-120A7_forward Regulation 
MesenchymalStemCellsAdiposeDonor0_CNhs10844_tpm_rev MscAdiposeD0- Mesenchymal stem cells - adipose, donor0_CNhs10844_11217-116B2_reverse Regulation 
MesenchymalStemCellsAdiposeDonor0_CNhs10844_tpm_fwd MscAdiposeD0+ Mesenchymal stem cells - adipose, donor0_CNhs10844_11217-116B2_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor4_CNhs13096_tpm_rev MpcOvarianCancerRightOvaryD4- mesenchymal precursor cell - ovarian cancer right ovary, donor4_CNhs13096_11837-124H1_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor4_CNhs13096_tpm_fwd MpcOvarianCancerRightOvaryD4+ mesenchymal precursor cell - ovarian cancer right ovary, donor4_CNhs13096_11837-124H1_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor3SOC5702G_CNhs13507_tpm_rev MpcOvarianCancerRightOvaryD3- mesenchymal precursor cell - ovarian cancer right ovary, donor3 (SOC-57-02-G)_CNhs13507_11842-124H6_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor3SOC5702_CNhs12377_tpm_rev MpcOvarianCancerRightOvaryD3- mesenchymal precursor cell - ovarian cancer right ovary, donor3 (SOC-57-02)_CNhs12377_11761-123H6_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor3SOC5702G_CNhs13507_tpm_fwd MpcOvarianCancerRightOvaryD3+ mesenchymal precursor cell - ovarian cancer right ovary, donor3 (SOC-57-02-G)_CNhs13507_11842-124H6_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor3SOC5702_CNhs12377_tpm_fwd MpcOvarianCancerRightOvaryD3+ mesenchymal precursor cell - ovarian cancer right ovary, donor3 (SOC-57-02)_CNhs12377_11761-123H6_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor2_CNhs12375_tpm_rev MpcOvarianCancerRightOvaryD2- mesenchymal precursor cell - ovarian cancer right ovary, donor2_CNhs12375_11759-123H4_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor2_CNhs12375_tpm_fwd MpcOvarianCancerRightOvaryD2+ mesenchymal precursor cell - ovarian cancer right ovary, donor2_CNhs12375_11759-123H4_forward Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor1_CNhs12373_tpm_rev MpcOvarianCancerRightOvaryD1- mesenchymal precursor cell - ovarian cancer right ovary, donor1_CNhs12373_11757-123H2_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerRightOvaryDonor1_CNhs12373_tpm_fwd MpcOvarianCancerRightOvaryD1+ mesenchymal precursor cell - ovarian cancer right ovary, donor1_CNhs12373_11757-123H2_forward Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor4_CNhs13097_tpm_rev MpcOvarianCancerMetastasisD4- mesenchymal precursor cell - ovarian cancer metastasis, donor4_CNhs13097_11838-124H2_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor4_CNhs13097_tpm_fwd MpcOvarianCancerMetastasisD4+ mesenchymal precursor cell - ovarian cancer metastasis, donor4_CNhs13097_11838-124H2_forward Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor3_CNhs12378_tpm_rev MpcOvarianCancerMetastasisD3- mesenchymal precursor cell - ovarian cancer metastasis, donor3_CNhs12378_11762-123H7_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor3_CNhs12378_tpm_fwd MpcOvarianCancerMetastasisD3+ mesenchymal precursor cell - ovarian cancer metastasis, donor3_CNhs12378_11762-123H7_forward Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor2_CNhs13093_tpm_rev MpcOvarianCancerMetastasisD2- mesenchymal precursor cell - ovarian cancer metastasis, donor2_CNhs13093_11835-124G8_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor2_CNhs13093_tpm_fwd MpcOvarianCancerMetastasisD2+ mesenchymal precursor cell - ovarian cancer metastasis, donor2_CNhs13093_11835-124G8_forward Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor1_CNhs12374_tpm_rev MpcOvarianCancerMetastasisD1- mesenchymal precursor cell - ovarian cancer metastasis, donor1_CNhs12374_11758-123H3_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerMetastasisDonor1_CNhs12374_tpm_fwd MpcOvarianCancerMetastasisD1+ mesenchymal precursor cell - ovarian cancer metastasis, donor1_CNhs12374_11758-123H3_forward Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor4_CNhs13094_tpm_rev MpcOvarianCancerLeftOvaryD4- mesenchymal precursor cell - ovarian cancer left ovary, donor4_CNhs13094_11836-124G9_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor4_CNhs13094_tpm_fwd MpcOvarianCancerLeftOvaryD4+ mesenchymal precursor cell - ovarian cancer left ovary, donor4_CNhs13094_11836-124G9_forward Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor3_CNhs12376_tpm_rev MpcOvarianCancerLeftOvaryD3- mesenchymal precursor cell - ovarian cancer left ovary, donor3_CNhs12376_11760-123H5_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor3_CNhs12376_tpm_fwd MpcOvarianCancerLeftOvaryD3+ mesenchymal precursor cell - ovarian cancer left ovary, donor3_CNhs12376_11760-123H5_forward Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor2_CNhs13092_tpm_rev MpcOvarianCancerLeftOvaryD2- mesenchymal precursor cell - ovarian cancer left ovary, donor2_CNhs13092_11833-124G6_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor2_CNhs13092_tpm_fwd MpcOvarianCancerLeftOvaryD2+ mesenchymal precursor cell - ovarian cancer left ovary, donor2_CNhs13092_11833-124G6_forward Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor1_CNhs12372_tpm_rev MpcOvarianCancerLeftOvaryD1- mesenchymal precursor cell - ovarian cancer left ovary, donor1_CNhs12372_11756-123H1_reverse Regulation 
MesenchymalPrecursorCellOvarianCancerLeftOvaryDonor1_CNhs12372_tpm_fwd MpcOvarianCancerLeftOvaryD1+ mesenchymal precursor cell - ovarian cancer left ovary, donor1_CNhs12372_11756-123H1_forward Regulation 
MesenchymalPrecursorCellCardiacDonor4_CNhs12371_tpm_rev MpcCardiacD4- mesenchymal precursor cell - cardiac, donor4_CNhs12371_11755-123G9_reverse Regulation 
MesenchymalPrecursorCellCardiacDonor4_CNhs12371_tpm_fwd MpcCardiacD4+ mesenchymal precursor cell - cardiac, donor4_CNhs12371_11755-123G9_forward Regulation 
MesenchymalPrecursorCellCardiacDonor3_CNhs12370_tpm_rev MpcCardiacD3- mesenchymal precursor cell - cardiac, donor3_CNhs12370_11754-123G8_reverse Regulation 
MesenchymalPrecursorCellCardiacDonor3_CNhs12370_tpm_fwd MpcCardiacD3+ mesenchymal precursor cell - cardiac, donor3_CNhs12370_11754-123G8_forward Regulation 
MesenchymalPrecursorCellCardiacDonor2_CNhs12369_tpm_rev MpcCardiacD2- mesenchymal precursor cell - cardiac, donor2_CNhs12369_11753-123G7_reverse Regulation 
MesenchymalPrecursorCellCardiacDonor2_CNhs12369_tpm_fwd MpcCardiacD2+ mesenchymal precursor cell - cardiac, donor2_CNhs12369_11753-123G7_forward Regulation 
MesenchymalPrecursorCellCardiacDonor1_CNhs12368_tpm_rev MpcCardiacD1- mesenchymal precursor cell - cardiac, donor1_CNhs12368_11752-123G6_reverse Regulation 
MesenchymalPrecursorCellCardiacDonor1_CNhs12368_tpm_fwd MpcCardiacD1+ mesenchymal precursor cell - cardiac, donor1_CNhs12368_11752-123G6_forward Regulation 
MesenchymalPrecursorCellBoneMarrowDonor3_CNhs13098_tpm_rev MpcBoneMarrowD3- mesenchymal precursor cell - bone marrow, donor3_CNhs13098_11840-124H4_reverse Regulation 
MesenchymalPrecursorCellBoneMarrowDonor3_CNhs13098_tpm_fwd MpcBoneMarrowD3+ mesenchymal precursor cell - bone marrow, donor3_CNhs13098_11840-124H4_forward Regulation 
MesenchymalPrecursorCellBoneMarrowDonor2_CNhs12367_tpm_rev MpcBoneMarrowD2- mesenchymal precursor cell - bone marrow, donor2_CNhs12367_11751-123G5_reverse Regulation 
MesenchymalPrecursorCellBoneMarrowDonor2_CNhs12367_tpm_fwd MpcBoneMarrowD2+ mesenchymal precursor cell - bone marrow, donor2_CNhs12367_11751-123G5_forward Regulation 
MesenchymalPrecursorCellBoneMarrowDonor1_CNhs12366_tpm_rev MpcBoneMarrowD1- mesenchymal precursor cell - bone marrow, donor1_CNhs12366_11750-123G4_reverse Regulation 
MesenchymalPrecursorCellBoneMarrowDonor1_CNhs12366_tpm_fwd MpcBoneMarrowD1+ mesenchymal precursor cell - bone marrow, donor1_CNhs12366_11750-123G4_forward Regulation 
MesenchymalPrecursorCellAdiposeDonor3_CNhs12365_tpm_rev MpcAdiposeD3- mesenchymal precursor cell - adipose, donor3_CNhs12365_11749-123G3_reverse Regulation 
MesenchymalPrecursorCellAdiposeDonor3_CNhs12365_tpm_fwd MpcAdiposeD3+ mesenchymal precursor cell - adipose, donor3_CNhs12365_11749-123G3_forward Regulation 
MesenchymalPrecursorCellAdiposeDonor2_CNhs12364_tpm_rev MpcAdiposeD2- mesenchymal precursor cell - adipose, donor2_CNhs12364_11748-123G2_reverse Regulation 
MesenchymalPrecursorCellAdiposeDonor2_CNhs12364_tpm_fwd MpcAdiposeD2+ mesenchymal precursor cell - adipose, donor2_CNhs12364_11748-123G2_forward Regulation 
MesenchymalPrecursorCellAdiposeDonor1_CNhs12363_tpm_rev MpcAdiposeD1- mesenchymal precursor cell - adipose, donor1_CNhs12363_11747-123G1_reverse Regulation 
MesenchymalPrecursorCellAdiposeDonor1_CNhs12363_tpm_fwd MpcAdiposeD1+ mesenchymal precursor cell - adipose, donor1_CNhs12363_11747-123G1_forward Regulation 
MigratoryLangerhansCellsDonor3_CNhs13547_tpm_rev MigratoryLangerhansCellsD3- migratory langerhans cells, donor3_CNhs13547_11903-125F4_reverse Regulation 
MigratoryLangerhansCellsDonor3_CNhs13547_tpm_fwd MigratoryLangerhansCellsD3+ migratory langerhans cells, donor3_CNhs13547_11903-125F4_forward Regulation 
MigratoryLangerhansCellsDonor2_CNhs13536_tpm_rev MigratoryLangerhansCellsD2- migratory langerhans cells, donor2_CNhs13536_11902-125F3_reverse Regulation 
MigratoryLangerhansCellsDonor2_CNhs13536_tpm_fwd MigratoryLangerhansCellsD2+ migratory langerhans cells, donor2_CNhs13536_11902-125F3_forward Regulation 
MigratoryLangerhansCellsDonor1_CNhs13535_tpm_rev MigratoryLangerhansCellsD1- migratory langerhans cells, donor1_CNhs13535_11901-125F2_reverse Regulation 
MigratoryLangerhansCellsDonor1_CNhs13535_tpm_fwd MigratoryLangerhansCellsD1+ migratory langerhans cells, donor1_CNhs13535_11901-125F2_forward Regulation 
MesothelialCellsDonor3_CNhs12012_tpm_rev MesothelialCellsD3- Mesothelial Cells, donor3_CNhs12012_11402-118D7_reverse Regulation 
MesothelialCellsDonor3_CNhs12012_tpm_fwd MesothelialCellsD3+ Mesothelial Cells, donor3_CNhs12012_11402-118D7_forward Regulation 
MesothelialCellsDonor1_CNhs10850_tpm_rev MesothelialCellsD1- Mesothelial Cells, donor1_CNhs10850_11247-116E5_reverse Regulation 
MesothelialCellsDonor1_CNhs10850_tpm_fwd MesothelialCellsD1+ Mesothelial Cells, donor1_CNhs10850_11247-116E5_forward Regulation 
MeningealCellsDonor3_CNhs12731_tpm_rev MeningealCellsD3- Meningeal Cells, donor3_CNhs12731_11654-122E7_reverse Regulation 
MeningealCellsDonor3_CNhs12731_tpm_fwd MeningealCellsD3+ Meningeal Cells, donor3_CNhs12731_11654-122E7_forward Regulation 
MeningealCellsDonor2_CNhs12080_tpm_rev MeningealCellsD2- Meningeal Cells, donor2_CNhs12080_11573-120E7_reverse Regulation 
MeningealCellsDonor2_CNhs12080_tpm_fwd MeningealCellsD2+ Meningeal Cells, donor2_CNhs12080_11573-120E7_forward Regulation 
MeningealCellsDonor1_CNhs11320_tpm_rev MeningealCellsD1- Meningeal Cells, donor1_CNhs11320_11493-119E8_reverse Regulation 
MeningealCellsDonor1_CNhs11320_tpm_fwd MeningealCellsD1+ Meningeal Cells, donor1_CNhs11320_11493-119E8_forward Regulation 
MelanocyteLightDonor3_CNhs12033_tpm_rev MelanocyteLightD3- Melanocyte - light, donor3_CNhs12033_11423-118G1_reverse Regulation 
MelanocyteLightDonor3_CNhs12033_tpm_fwd MelanocyteLightD3+ Melanocyte - light, donor3_CNhs12033_11423-118G1_forward Regulation 
MelanocyteLightDonor2_CNhs11383_tpm_rev MelanocyteLightD2- Melanocyte - light, donor2_CNhs11383_11351-117H1_reverse Regulation 
MelanocyteLightDonor2_CNhs11383_tpm_fwd MelanocyteLightD2+ Melanocyte - light, donor2_CNhs11383_11351-117H1_forward Regulation 
MelanocyteLightDonor1_CNhs11303_tpm_rev MelanocyteLightD1- Melanocyte - light, donor1_CNhs11303_11274-116H5_reverse Regulation 
MelanocyteLightDonor1_CNhs11303_tpm_fwd MelanocyteLightD1+ Melanocyte - light, donor1_CNhs11303_11274-116H5_forward Regulation 
MelanocyteDarkDonor3_CNhs12570_tpm_rev MelanocyteDarkD3- Melanocyte - dark, donor3_CNhs12570_11663-122F7_reverse Regulation 
MelanocyteDarkDonor3_CNhs12570_tpm_fwd MelanocyteDarkD3+ Melanocyte - dark, donor3_CNhs12570_11663-122F7_forward Regulation 
MelanocyteDarkDonor2_CNhs12346_tpm_rev MelanocyteDarkD2- Melanocyte - dark, donor2_CNhs12346_11582-120F7_reverse Regulation 
MelanocyteDarkDonor2_CNhs12346_tpm_fwd MelanocyteDarkD2+ Melanocyte - dark, donor2_CNhs12346_11582-120F7_forward Regulation 
MelanocyteDarkDonor1_CNhs12591_tpm_rev MelanocyteDarkD1- Melanocyte - dark, donor1_CNhs12591_11502-119F8_reverse Regulation 
MelanocyteDarkDonor1_CNhs12591_tpm_fwd MelanocyteDarkD1+ Melanocyte - dark, donor1_CNhs12591_11502-119F8_forward Regulation 
MastCellStimulatedDonor1_CNhs11073_tpm_rev MastCellStimulatedD1- Mast cell - stimulated, donor1_CNhs11073_11487-119E2_reverse Regulation 
MastCellStimulatedDonor1_CNhs11073_tpm_fwd MastCellStimulatedD1+ Mast cell - stimulated, donor1_CNhs11073_11487-119E2_forward Regulation 
MastCellExpandedDonor8_CNhs13926_tpm_rev MastCellExpD8- Mast cell, expanded, donor8_CNhs13926_11941-126A6_reverse Regulation 
MastCellExpandedAndStimulatedDonor8_CNhs13927_tpm_rev MastCellExpD8- Mast cell, expanded and stimulated, donor8_CNhs13927_11942-126A7_reverse Regulation 
MastCellExpandedDonor8_CNhs13926_tpm_fwd MastCellExpD8+ Mast cell, expanded, donor8_CNhs13926_11941-126A6_forward Regulation 
MastCellExpandedAndStimulatedDonor8_CNhs13927_tpm_fwd MastCellExpD8+ Mast cell, expanded and stimulated, donor8_CNhs13927_11942-126A7_forward Regulation 
MastCellExpandedDonor5_CNhs13924_tpm_rev MastCellExpD5- Mast cell, expanded, donor5_CNhs13924_11939-126A4_reverse Regulation 
MastCellExpandedAndStimulatedDonor5_CNhs13925_tpm_rev MastCellExpD5- Mast cell, expanded and stimulated, donor5_CNhs13925_11940-126A5_reverse Regulation 
MastCellExpandedDonor5_CNhs13924_tpm_fwd MastCellExpD5+ Mast cell, expanded, donor5_CNhs13924_11939-126A4_forward Regulation 
MastCellExpandedAndStimulatedDonor5_CNhs13925_tpm_fwd MastCellExpD5+ Mast cell, expanded and stimulated, donor5_CNhs13925_11940-126A5_forward Regulation 
MastCellDonor4_CNhs12592_tpm_rev MastCellD4- Mast cell, donor4_CNhs12592_11567-120E1_reverse Regulation 
MastCellDonor4_CNhs12592_tpm_fwd MastCellD4+ Mast cell, donor4_CNhs12592_11567-120E1_forward Regulation 
MastCellDonor3_CNhs12593_tpm_rev MastCellD3- Mast cell, donor3_CNhs12593_11566-120D9_reverse Regulation 
MastCellDonor3_CNhs12593_tpm_fwd MastCellD3+ Mast cell, donor3_CNhs12593_11566-120D9_forward Regulation 
MastCellDonor2_CNhs12594_tpm_rev MastCellD2- Mast cell, donor2_CNhs12594_11565-120D8_reverse Regulation 
MastCellDonor2_CNhs12594_tpm_fwd MastCellD2+ Mast cell, donor2_CNhs12594_11565-120D8_forward Regulation 
MastCellDonor1_CNhs12566_tpm_rev MastCellD1- Mast cell, donor1_CNhs12566_11563-120D6_reverse Regulation 
MastCellDonor1_CNhs12566_tpm_fwd MastCellD1+ Mast cell, donor1_CNhs12566_11563-120D6_forward Regulation 
MammaryEpithelialCellDonor3_CNhs12032_tpm_rev MammaryEpithelialCellD3- Mammary Epithelial Cell, donor3_CNhs12032_11422-118F9_reverse Regulation 
MammaryEpithelialCellDonor3_CNhs12032_tpm_fwd MammaryEpithelialCellD3+ Mammary Epithelial Cell, donor3_CNhs12032_11422-118F9_forward Regulation 
MammaryEpithelialCellDonor2_CNhs11382_tpm_rev MammaryEpithelialCellD2- Mammary Epithelial Cell, donor2_CNhs11382_11350-117G9_reverse Regulation 
MammaryEpithelialCellDonor2_CNhs11382_tpm_fwd MammaryEpithelialCellD2+ Mammary Epithelial Cell, donor2_CNhs11382_11350-117G9_forward Regulation 
MammaryEpithelialCellDonor1_CNhs11077_tpm_rev MammaryEpithelialCellD1- Mammary Epithelial Cell, donor1_CNhs11077_11273-116H4_reverse Regulation 
MammaryEpithelialCellDonor1_CNhs11077_tpm_fwd MammaryEpithelialCellD1+ Mammary Epithelial Cell, donor1_CNhs11077_11273-116H4_forward Regulation 
MallassezderivedCellsDonor3_CNhs13551_tpm_rev MallassezCellsD3- Mallassez-derived cells, donor3_CNhs13551_11930-125I4_reverse Regulation 
MallassezderivedCellsDonor3_CNhs13551_tpm_fwd MallassezCellsD3+ Mallassez-derived cells, donor3_CNhs13551_11930-125I4_forward Regulation 
MallassezderivedCellsDonor2_CNhs13550_tpm_rev MallassezCellsD2- Mallassez-derived cells, donor2_CNhs13550_11929-125I3_reverse Regulation 
MallassezderivedCellsDonor2_CNhs13550_tpm_fwd MallassezCellsD2+ Mallassez-derived cells, donor2_CNhs13550_11929-125I3_forward Regulation 
MacrophageMonocyteDerivedDonor3_CNhs12003_tpm_rev MacrophageMonocyteD3- Macrophage - monocyte derived, donor3_CNhs12003_11389-118C3_reverse Regulation 
MacrophageMonocyteDerivedDonor3_CNhs12003_tpm_fwd MacrophageMonocyteD3+ Macrophage - monocyte derived, donor3_CNhs12003_11389-118C3_forward Regulation 
MacrophageMonocyteDerivedDonor2_CNhs11899_tpm_rev MacrophageMonocyteD2- Macrophage - monocyte derived, donor2_CNhs11899_11313-117C8_reverse Regulation 
MacrophageMonocyteDerivedDonor2_CNhs11899_tpm_fwd MacrophageMonocyteD2+ Macrophage - monocyte derived, donor2_CNhs11899_11313-117C8_forward Regulation 
MacrophageMonocyteDerivedDonor1_CNhs10861_tpm_rev MacrophageMonocyteD1- Macrophage - monocyte derived, donor1_CNhs10861_11232-116C8_reverse Regulation 
MacrophageMonocyteDerivedDonor1_CNhs10861_tpm_fwd MacrophageMonocyteD1+ Macrophage - monocyte derived, donor1_CNhs10861_11232-116C8_forward Regulation 
LensEpithelialCellsDonor3_CNhs12572_tpm_rev LensEpithelialCellsD3- Lens Epithelial Cells, donor3_CNhs12572_11690-122I7_reverse Regulation 
LensEpithelialCellsDonor3_CNhs12572_tpm_fwd LensEpithelialCellsD3+ Lens Epithelial Cells, donor3_CNhs12572_11690-122I7_forward Regulation 
LensEpithelialCellsDonor2_CNhs12568_tpm_rev LensEpithelialCellsD2- Lens Epithelial Cells, donor2_CNhs12568_11609-120I7_reverse Regulation 
LensEpithelialCellsDonor2_CNhs12568_tpm_fwd LensEpithelialCellsD2+ Lens Epithelial Cells, donor2_CNhs12568_11609-120I7_forward Regulation 
LensEpithelialCellsDonor1_CNhs12342_tpm_rev LensEpithelialCellsD1- Lens Epithelial Cells, donor1_CNhs12342_11529-119I8_reverse Regulation 
LensEpithelialCellsDonor1_CNhs12342_tpm_fwd LensEpithelialCellsD1+ Lens Epithelial Cells, donor1_CNhs12342_11529-119I8_forward Regulation 
KeratocytesDonor3_CNhs12921_tpm_rev KeratocytesD3- Keratocytes, donor3_CNhs12921_11688-122I5_reverse Regulation 
KeratocytesDonor3_CNhs12921_tpm_fwd KeratocytesD3+ Keratocytes, donor3_CNhs12921_11688-122I5_forward Regulation 
KeratocytesDonor2_CNhs12095_tpm_rev KeratocytesD2- Keratocytes, donor2_CNhs12095_11607-120I5_reverse Regulation 
KeratocytesDonor2_CNhs12095_tpm_fwd KeratocytesD2+ Keratocytes, donor2_CNhs12095_11607-120I5_forward Regulation 
KeratocytesDonor1_CNhs11337_tpm_rev KeratocytesD1- Keratocytes, donor1_CNhs11337_11527-119I6_reverse Regulation 
KeratocytesDonor1_CNhs11337_tpm_fwd KeratocytesD1+ Keratocytes, donor1_CNhs11337_11527-119I6_forward Regulation 
KeratinocyteOralDonor1_CNhs10879_tpm_rev KeratinocyteOralD1- Keratinocyte - oral, donor1_CNhs10879_11251-116E9_reverse Regulation 
KeratinocyteOralDonor1_CNhs10879_tpm_fwd KeratinocyteOralD1+ Keratinocyte - oral, donor1_CNhs10879_11251-116E9_forward Regulation 
KeratinocyteEpidermalDonor3_CNhs12031_tpm_rev KeratinocyteEpidermalD3- Keratinocyte - epidermal, donor3_CNhs12031_11421-118F8_reverse Regulation 
KeratinocyteEpidermalDonor3_CNhs12031_tpm_fwd KeratinocyteEpidermalD3+ Keratinocyte - epidermal, donor3_CNhs12031_11421-118F8_forward Regulation 
KeratinocyteEpidermalDonor2_CNhs11381_tpm_rev KeratinocyteEpidermalD2- Keratinocyte - epidermal, donor2_CNhs11381_11349-117G8_reverse Regulation 
KeratinocyteEpidermalDonor2_CNhs11381_tpm_fwd KeratinocyteEpidermalD2+ Keratinocyte - epidermal, donor2_CNhs11381_11349-117G8_forward Regulation 
KeratinocyteEpidermalDonor1_CNhs11064_tpm_rev KeratinocyteEpidermalD1- Keratinocyte - epidermal, donor1_CNhs11064_11272-116H3_reverse Regulation 
KeratinocyteEpidermalDonor1_CNhs11064_tpm_fwd KeratinocyteEpidermalD1+ Keratinocyte - epidermal, donor1_CNhs11064_11272-116H3_forward Regulation 
IrisPigmentEpithelialCellsDonor1_CNhs12596_tpm_rev IrisPigmentEpithelialCellsD1- Iris Pigment Epithelial Cells, donor1_CNhs12596_11530-119I9_reverse Regulation 
IrisPigmentEpithelialCellsDonor1_CNhs12596_tpm_fwd IrisPigmentEpithelialCellsD1+ Iris Pigment Epithelial Cells, donor1_CNhs12596_11530-119I9_forward Regulation 
IntestinalEpithelialCellsPolarizedDonor1_CNhs10875_tpm_rev IntestinalEpithelialCellsD1- Intestinal epithelial cells (polarized), donor1_CNhs10875_11246-116E4_reverse Regulation 
IntestinalEpithelialCellsPolarizedDonor1_CNhs10875_tpm_fwd IntestinalEpithelialCellsD1+ Intestinal epithelial cells (polarized), donor1_CNhs10875_11246-116E4_forward Regulation 
ImmatureLangerhansCellsDonor2_CNhs13480_tpm_rev ImmatureLangerhansCellsD2- immature langerhans cells, donor2_CNhs13480_11905-125F6_reverse Regulation 
ImmatureLangerhansCellsDonor2_CNhs13480_tpm_fwd ImmatureLangerhansCellsD2+ immature langerhans cells, donor2_CNhs13480_11905-125F6_forward Regulation 
ImmatureLangerhansCellsDonor1_CNhs13537_tpm_rev ImmatureLangerhansCellsD1- immature langerhans cells, donor1_CNhs13537_11904-125F5_reverse Regulation 
ImmatureLangerhansCellsDonor1_CNhs13537_tpm_fwd ImmatureLangerhansCellsD1+ immature langerhans cells, donor1_CNhs13537_11904-125F5_forward Regulation 
HepatocyteDonor3_CNhs12626_tpm_rev HepatocyteD3- Hepatocyte, donor3_CNhs12626_11684-122I1_reverse Regulation 
HepatocyteDonor3_CNhs12626_tpm_fwd HepatocyteD3+ Hepatocyte, donor3_CNhs12626_11684-122I1_forward Regulation 
HepatocyteDonor2_CNhs12349_tpm_rev HepatocyteD2- Hepatocyte, donor2_CNhs12349_11603-120I1_reverse Regulation 
HepatocyteDonor2_CNhs12349_tpm_fwd HepatocyteD2+ Hepatocyte, donor2_CNhs12349_11603-120I1_forward Regulation 
HepatocyteDonor1_CNhs12340_tpm_rev HepatocyteD1- Hepatocyte, donor1_CNhs12340_11523-119I2_reverse Regulation 
HepatocyteDonor1_CNhs12340_tpm_fwd HepatocyteD1+ Hepatocyte, donor1_CNhs12340_11523-119I2_forward Regulation 
HepaticStellateCellsLipocyteDonor3_CNhs12627_tpm_rev HepaticStellateCellsD3- Hepatic Stellate Cells (lipocyte), donor3_CNhs12627_11685-122I2_reverse Regulation 
HepaticStellateCellsLipocyteDonor3_CNhs12627_tpm_fwd HepaticStellateCellsD3+ Hepatic Stellate Cells (lipocyte), donor3_CNhs12627_11685-122I2_forward Regulation 
HepaticStellateCellsLipocyteDonor2_CNhs12093_tpm_rev HepaticStellateCellsD2- Hepatic Stellate Cells (lipocyte), donor2_CNhs12093_11604-120I2_reverse Regulation 
HepaticStellateCellsLipocyteDonor2_CNhs12093_tpm_fwd HepaticStellateCellsD2+ Hepatic Stellate Cells (lipocyte), donor2_CNhs12093_11604-120I2_forward Regulation 
HepaticStellateCellsLipocyteDonor1_CNhs11335_tpm_rev HepaticStellateCellsD1- Hepatic Stellate Cells (lipocyte), donor1_CNhs11335_11524-119I3_reverse Regulation 
HepaticStellateCellsLipocyteDonor1_CNhs11335_tpm_fwd HepaticStellateCellsD1+ Hepatic Stellate Cells (lipocyte), donor1_CNhs11335_11524-119I3_forward Regulation 
HepaticSinusoidalEndothelialCellsDonor3_CNhs12625_tpm_rev HepaticSinusoidalEndothelialCellsD3- Hepatic Sinusoidal Endothelial Cells, donor3_CNhs12625_11682-122H8_reverse Regulation 
HepaticSinusoidalEndothelialCellsDonor3_CNhs12625_tpm_fwd HepaticSinusoidalEndothelialCellsD3+ Hepatic Sinusoidal Endothelial Cells, donor3_CNhs12625_11682-122H8_forward Regulation 
HepaticSinusoidalEndothelialCellsDonor2_CNhs12092_tpm_rev HepaticSinusoidalEndothelialCellsD2- Hepatic Sinusoidal Endothelial Cells, donor2_CNhs12092_11601-120H8_reverse Regulation 
HepaticSinusoidalEndothelialCellsDonor2_CNhs12092_tpm_fwd HepaticSinusoidalEndothelialCellsD2+ Hepatic Sinusoidal Endothelial Cells, donor2_CNhs12092_11601-120H8_forward Regulation 
HepaticSinusoidalEndothelialCellsDonor1_CNhs12075_tpm_rev HepaticSinusoidalEndothelialCellsD1- Hepatic Sinusoidal Endothelial Cells, donor1_CNhs12075_11521-119H9_reverse Regulation 
HepaticSinusoidalEndothelialCellsDonor1_CNhs12075_tpm_fwd HepaticSinusoidalEndothelialCellsD1+ Hepatic Sinusoidal Endothelial Cells, donor1_CNhs12075_11521-119H9_forward Regulation 
HairFollicleOuterRootSheathCellsDonor2_CNhs12347_tpm_rev HairFollicleOuterRootSheathCellsD2- Hair Follicle Outer Root Sheath Cells, donor2_CNhs12347_11584-120F9_reverse Regulation 
HairFollicleOuterRootSheathCellsDonor2_CNhs12347_tpm_fwd HairFollicleOuterRootSheathCellsD2+ Hair Follicle Outer Root Sheath Cells, donor2_CNhs12347_11584-120F9_forward Regulation 
HairFollicleOuterRootSheathCellsDonor1_CNhs12339_tpm_rev HairFollicleOuterRootSheathCellsD1- Hair Follicle Outer Root Sheath Cells, donor1_CNhs12339_11504-119G1_reverse Regulation 
HairFollicleOuterRootSheathCellsDonor1_CNhs12339_tpm_fwd HairFollicleOuterRootSheathCellsD1+ Hair Follicle Outer Root Sheath Cells, donor1_CNhs12339_11504-119G1_forward Regulation 
HairFollicleDermalPapillaCellsDonor3_CNhs12030_tpm_rev HairFollicleDermalPapillaCellsD3- Hair Follicle Dermal Papilla Cells, donor3_CNhs12030_11420-118F7_reverse Regulation 
HairFollicleDermalPapillaCellsDonor3_CNhs12030_tpm_fwd HairFollicleDermalPapillaCellsD3+ Hair Follicle Dermal Papilla Cells, donor3_CNhs12030_11420-118F7_forward Regulation 
HairFollicleDermalPapillaCellsDonor2_CNhs11979_tpm_rev HairFollicleDermalPapillaCellsD2- Hair Follicle Dermal Papilla Cells, donor2_CNhs11979_11348-117G7_reverse Regulation 
HairFollicleDermalPapillaCellsDonor2_CNhs11979_tpm_fwd HairFollicleDermalPapillaCellsD2+ Hair Follicle Dermal Papilla Cells, donor2_CNhs11979_11348-117G7_forward Regulation 
HairFollicleDermalPapillaCellsDonor1_CNhs12501_tpm_rev HairFollicleDermalPapillaCellsD1- Hair Follicle Dermal Papilla Cells, donor1_CNhs12501_11271-116H2_reverse Regulation 
HairFollicleDermalPapillaCellsDonor1_CNhs12501_tpm_fwd HairFollicleDermalPapillaCellsD1+ Hair Follicle Dermal Papilla Cells, donor1_CNhs12501_11271-116H2_forward Regulation 
GingivalEpithelialCellsDonor3GEA15_CNhs11903_tpm_rev GingivalEpithelialCellsD3- Gingival epithelial cells, donor3 (GEA15)_CNhs11903_11379-118B2_reverse Regulation 
GingivalEpithelialCellsDonor3GEA15_CNhs11903_tpm_fwd GingivalEpithelialCellsD3+ Gingival epithelial cells, donor3 (GEA15)_CNhs11903_11379-118B2_forward Regulation 
GingivalEpithelialCellsDonor2GEA14_CNhs11896_tpm_rev GingivalEpithelialCellsD2- Gingival epithelial cells, donor2 (GEA14)_CNhs11896_11302-117B6_reverse Regulation 
GingivalEpithelialCellsDonor2GEA14_CNhs11896_tpm_fwd GingivalEpithelialCellsD2+ Gingival epithelial cells, donor2 (GEA14)_CNhs11896_11302-117B6_forward Regulation 
GingivalEpithelialCellsDonor1GEA11_CNhs11061_tpm_rev GingivalEpithelialCellsD1- Gingival epithelial cells, donor1 (GEA11)_CNhs11061_11221-116B6_reverse Regulation 
GingivalEpithelialCellsDonor1GEA11_CNhs11061_tpm_fwd GingivalEpithelialCellsD1+ Gingival epithelial cells, donor1 (GEA11)_CNhs11061_11221-116B6_forward Regulation 
GammaDeltaPositiveTCellsDonor2_CNhs13915_tpm_rev GammaDeltaTcellsD2- gamma delta positive T cells, donor2_CNhs13915_11938-126A3_reverse Regulation 
GammaDeltaPositiveTCellsDonor2_CNhs13915_tpm_fwd GammaDeltaTcellsD2+ gamma delta positive T cells, donor2_CNhs13915_11938-126A3_forward Regulation 
GammaDeltaPositiveTCellsDonor1_CNhs13914_tpm_rev GammaDeltaTcellsD1- gamma delta positive T cells, donor1_CNhs13914_11937-126A2_reverse Regulation 
GammaDeltaPositiveTCellsDonor1_CNhs13914_tpm_fwd GammaDeltaTcellsD1+ gamma delta positive T cells, donor1_CNhs13914_11937-126A2_forward Regulation 
FibroblastVillousMesenchymalDonor3_CNhs12920_tpm_rev FibroVillousMesenchymalD3- Fibroblast - Villous Mesenchymal, donor3_CNhs12920_11696-123A4_reverse Regulation 
FibroblastVillousMesenchymalDonor3_CNhs12920_tpm_fwd FibroVillousMesenchymalD3+ Fibroblast - Villous Mesenchymal, donor3_CNhs12920_11696-123A4_forward Regulation 
FibroblastVillousMesenchymalDonor2_CNhs12099_tpm_rev FibroVillousMesenchymalD2- Fibroblast - Villous Mesenchymal, donor2_CNhs12099_11615-122A4_reverse Regulation 
FibroblastVillousMesenchymalDonor2_CNhs12099_tpm_fwd FibroVillousMesenchymalD2+ Fibroblast - Villous Mesenchymal, donor2_CNhs12099_11615-122A4_forward Regulation 
FibroblastVillousMesenchymalDonor1_CNhs11343_tpm_rev FibroVillousMesenchymalD1- Fibroblast - Villous Mesenchymal, donor1_CNhs11343_11535-120A5_reverse Regulation 
FibroblastVillousMesenchymalDonor1_CNhs11343_tpm_fwd FibroVillousMesenchymalD1+ Fibroblast - Villous Mesenchymal, donor1_CNhs11343_11535-120A5_forward Regulation 
FibroblastSkinWalkerWarburgDonor1_CNhs11352_tpm_rev FibroSkinWalkerWarburgD1- Fibroblast - skin walker warburg, donor1_CNhs11352_11554-120C6_reverse Regulation 
FibroblastSkinWalkerWarburgDonor1_CNhs11352_tpm_fwd FibroSkinWalkerWarburgD1+ Fibroblast - skin walker warburg, donor1_CNhs11352_11554-120C6_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor3_CNhs11912_tpm_rev FibroSkinSpinalMuscularAtrophyNucfracD3- Fibroblast - skin spinal muscular atrophy, donor3_CNhs11912_11559-120D2_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor3_CNhs11912_tpm_fwd FibroSkinSpinalMuscularAtrophyNucfracD3+ Fibroblast - skin spinal muscular atrophy, donor3_CNhs11912_11559-120D2_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor2_CNhs11911_tpm_rev FibroSkinSpinalMuscularAtrophyNucfracD2- Fibroblast - skin spinal muscular atrophy, donor2_CNhs11911_11558-120D1_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor2_CNhs11911_tpm_fwd FibroSkinSpinalMuscularAtrophyNucfracD2+ Fibroblast - skin spinal muscular atrophy, donor2_CNhs11911_11558-120D1_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor1_CNhs11074_tpm_rev FibroSkinSpinalMuscularAtrophyNucfracD1- Fibroblast - skin spinal muscular atrophy, donor1_CNhs11074_11555-120C7_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor1_CNhs11074_tpm_fwd FibroSkinSpinalMuscularAtrophyNucfracD1+ Fibroblast - skin spinal muscular atrophy, donor1_CNhs11074_11555-120C7_forward Regulation 
FibroblastSkinNormalDonor2_CNhs11914_tpm_rev FibroSkinNormalNucfracD2- Fibroblast - skin normal, donor2_CNhs11914_11561-120D4_reverse Regulation 
FibroblastSkinNormalDonor2_CNhs11914_tpm_fwd FibroSkinNormalNucfracD2+ Fibroblast - skin normal, donor2_CNhs11914_11561-120D4_forward Regulation 
FibroblastSkinNormalDonor1_CNhs11351_tpm_rev FibroSkinNormalNucfracD1- Fibroblast - skin normal, donor1_CNhs11351_11553-120C5_reverse Regulation 
FibroblastSkinNormalDonor1_CNhs11351_tpm_fwd FibroSkinNormalNucfracD1+ Fibroblast - skin normal, donor1_CNhs11351_11553-120C5_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor3_CNhs11913_tpm_rev FibroSkinDystrophiaMyotonicaNucfracD3- Fibroblast - skin dystrophia myotonica, donor3_CNhs11913_11560-120D3_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor3_CNhs11913_tpm_fwd FibroSkinDystrophiaMyotonicaNucfracD3+ Fibroblast - skin dystrophia myotonica, donor3_CNhs11913_11560-120D3_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor2_CNhs11354_tpm_rev FibroSkinDystrophiaMyotonicaNucfracD2- Fibroblast - skin dystrophia myotonica, donor2_CNhs11354_11557-120C9_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor2_CNhs11354_tpm_fwd FibroSkinDystrophiaMyotonicaNucfracD2+ Fibroblast - skin dystrophia myotonica, donor2_CNhs11354_11557-120C9_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor1_CNhs11353_tpm_rev FibroSkinDystrophiaMyotonicaNucfracD1- Fibroblast - skin dystrophia myotonica, donor1_CNhs11353_11556-120C8_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor1_CNhs11353_tpm_fwd FibroSkinDystrophiaMyotonicaNucfracD1+ Fibroblast - skin dystrophia myotonica, donor1_CNhs11353_11556-120C8_forward Regulation 
FibroblastPulmonaryArteryDonor1_CNhs10878_tpm_rev FibroPulmonaryArteryD1- Fibroblast - Pulmonary Artery, donor1_CNhs10878_11250-116E8_reverse Regulation 
FibroblastPulmonaryArteryDonor1_CNhs10878_tpm_fwd FibroPulmonaryArteryD1+ Fibroblast - Pulmonary Artery, donor1_CNhs10878_11250-116E8_forward Regulation 
FibroblastPeriodontalLigamentDonor6PLH3_CNhs11996_tpm_rev FibroPeriodontalLigamentD6- Fibroblast - Periodontal Ligament, donor6 (PLH3)_CNhs11996_11380-118B3_reverse Regulation 
FibroblastPeriodontalLigamentDonor6PLH3_CNhs11996_tpm_fwd FibroPeriodontalLigamentD6+ Fibroblast - Periodontal Ligament, donor6 (PLH3)_CNhs11996_11380-118B3_forward Regulation 
FibroblastPeriodontalLigamentDonor5PL30_CNhs11953_tpm_rev FibroPeriodontalLigamentD5- Fibroblast - Periodontal Ligament, donor5 (PL30)_CNhs11953_11304-117B8_reverse Regulation 
FibroblastPeriodontalLigamentDonor5PL30_CNhs11953_tpm_fwd FibroPeriodontalLigamentD5+ Fibroblast - Periodontal Ligament, donor5 (PL30)_CNhs11953_11304-117B8_forward Regulation 
FibroblastPeriodontalLigamentDonor4PL29_CNhs12493_tpm_rev FibroPeriodontalLigamentD4- Fibroblast - Periodontal Ligament, donor4 (PL29)_CNhs12493_11223-116B8_reverse Regulation 
FibroblastPeriodontalLigamentDonor4PL29_CNhs12493_tpm_fwd FibroPeriodontalLigamentD4+ Fibroblast - Periodontal Ligament, donor4 (PL29)_CNhs12493_11223-116B8_forward Regulation 
FibroblastPeriodontalLigamentDonor3_CNhs11907_tpm_rev FibroPeriodontalLigamentD3- Fibroblast - Periodontal Ligament, donor3_CNhs11907_11395-118C9_reverse Regulation 
FibroblastPeriodontalLigamentDonor3_CNhs11907_tpm_fwd FibroPeriodontalLigamentD3+ Fibroblast - Periodontal Ligament, donor3_CNhs11907_11395-118C9_forward Regulation 
FibroblastPeriodontalLigamentDonor2_CNhs11962_tpm_rev FibroPeriodontalLigamentD2- Fibroblast - Periodontal Ligament, donor2_CNhs11962_11319-117D5_reverse Regulation 
FibroblastPeriodontalLigamentDonor2_CNhs11962_tpm_fwd FibroPeriodontalLigamentD2+ Fibroblast - Periodontal Ligament, donor2_CNhs11962_11319-117D5_forward Regulation 
FibroblastPeriodontalLigamentDonor1_CNhs10867_tpm_rev FibroPeriodontalLigamentD1- Fibroblast - Periodontal Ligament, donor1_CNhs10867_11238-116D5_reverse Regulation 
FibroblastPeriodontalLigamentDonor1_CNhs10867_tpm_fwd FibroPeriodontalLigamentD1+ Fibroblast - Periodontal Ligament, donor1_CNhs10867_11238-116D5_forward Regulation 
FibroblastMammaryDonor3_CNhs12128_tpm_rev FibroMammaryD3- Fibroblast - Mammary, donor3_CNhs12128_11701-123A9_reverse Regulation 
FibroblastMammaryDonor3_CNhs12128_tpm_fwd FibroMammaryD3+ Fibroblast - Mammary, donor3_CNhs12128_11701-123A9_forward Regulation 
FibroblastMammaryDonor2_CNhs12103_tpm_rev FibroMammaryD2- Fibroblast - Mammary, donor2_CNhs12103_11620-122A9_reverse Regulation 
FibroblastMammaryDonor2_CNhs12103_tpm_fwd FibroMammaryD2+ Fibroblast - Mammary, donor2_CNhs12103_11620-122A9_forward Regulation 
FibroblastMammaryDonor1_CNhs11348_tpm_rev FibroMammaryD1- Fibroblast - Mammary, donor1_CNhs11348_11540-120B1_reverse Regulation 
FibroblastMammaryDonor1_CNhs11348_tpm_fwd FibroMammaryD1+ Fibroblast - Mammary, donor1_CNhs11348_11540-120B1_forward Regulation 
FibroblastLymphaticDonor3_CNhs12118_tpm_rev FibroLymphaticD3- Fibroblast - Lymphatic, donor3_CNhs12118_11667-122G2_reverse Regulation 
FibroblastLymphaticDonor3_CNhs12118_tpm_fwd FibroLymphaticD3+ Fibroblast - Lymphatic, donor3_CNhs12118_11667-122G2_forward Regulation 
FibroblastLymphaticDonor2_CNhs12082_tpm_rev FibroLymphaticD2- Fibroblast - Lymphatic, donor2_CNhs12082_11586-120G2_reverse Regulation 
FibroblastLymphaticDonor2_CNhs12082_tpm_fwd FibroLymphaticD2+ Fibroblast - Lymphatic, donor2_CNhs12082_11586-120G2_forward Regulation 
FibroblastLymphaticDonor1_CNhs11322_tpm_rev FibroLymphaticD1- Fibroblast - Lymphatic, donor1_CNhs11322_11506-119G3_reverse Regulation 
FibroblastLymphaticDonor1_CNhs11322_tpm_fwd FibroLymphaticD1+ Fibroblast - Lymphatic, donor1_CNhs11322_11506-119G3_forward Regulation 
FibroblastLungDonor3_CNhs12029_tpm_rev FibroLungD3- Fibroblast - Lung, donor3_CNhs12029_11419-118F6_reverse Regulation 
FibroblastLungDonor3_CNhs12029_tpm_fwd FibroLungD3+ Fibroblast - Lung, donor3_CNhs12029_11419-118F6_forward Regulation 
FibroblastLungDonor2_CNhs11380_tpm_rev FibroLungD2- Fibroblast - Lung, donor2_CNhs11380_11347-117G6_reverse Regulation 
FibroblastLungDonor2_CNhs11380_tpm_fwd FibroLungD2+ Fibroblast - Lung, donor2_CNhs11380_11347-117G6_forward Regulation 
FibroblastLungDonor1_CNhs12500_tpm_rev FibroLungD1- Fibroblast - Lung, donor1_CNhs12500_11270-116H1_reverse Regulation 
FibroblastLungDonor1_CNhs12500_tpm_fwd FibroLungD1+ Fibroblast - Lung, donor1_CNhs12500_11270-116H1_forward Regulation 
FibroblastGingivalDonor9Control_CNhs14134_tpm_rev FibroGingivalD9- Fibroblast - Gingival, donor9 (control)_CNhs14134_11927-125I1_reverse Regulation 
FibroblastGingivalDonor9Control_CNhs14134_tpm_fwd FibroGingivalD9+ Fibroblast - Gingival, donor9 (control)_CNhs14134_11927-125I1_forward Regulation 
FibroblastGingivalDonor8Control_CNhs14133_tpm_rev FibroGingivalD8- Fibroblast - Gingival, donor8 (control)_CNhs14133_11926-125H9_reverse Regulation 
FibroblastGingivalDonor8ChronicPeriodontitis_CNhs14132_tpm_rev FibroGingivalD8- Fibroblast - Gingival, donor8 (chronic periodontitis)_CNhs14132_11925-125H8_reverse Regulation 
FibroblastGingivalDonor8ChronicPeriodontitis_CNhs14132_tpm_fwd FibroGingivalD8+ Fibroblast - Gingival, donor8 (chronic periodontitis)_CNhs14132_11925-125H8_forward Regulation 
FibroblastGingivalDonor8Control_CNhs14133_tpm_fwd FibroGingivalD8+ Fibroblast - Gingival, donor8 (control)_CNhs14133_11926-125H9_forward Regulation 
FibroblastGingivalDonor7AggressivePeriodontitis_CNhs14130_tpm_rev FibroGingivalD7- Fibroblast - Gingival, donor7 (aggressive periodontitis)_CNhs14130_11923-125H6_reverse Regulation 
FibroblastGingivalDonor7Control_CNhs14131_tpm_rev FibroGingivalD7- Fibroblast - Gingival, donor7 (control)_CNhs14131_11924-125H7_reverse Regulation 
FibroblastGingivalDonor7AggressivePeriodontitis_CNhs14130_tpm_fwd FibroGingivalD7+ Fibroblast - Gingival, donor7 (aggressive periodontitis)_CNhs14130_11923-125H6_forward Regulation 
FibroblastGingivalDonor7Control_CNhs14131_tpm_fwd FibroGingivalD7+ Fibroblast - Gingival, donor7 (control)_CNhs14131_11924-125H7_forward Regulation 
FibroblastGingivalDonor6Control_CNhs14129_tpm_rev FibroGingivalD6- Fibroblast - Gingival, donor6 (control)_CNhs14129_11922-125H5_reverse Regulation 
FibroblastGingivalDonor6AggressivePeriodontitis_CNhs14128_tpm_rev FibroGingivalD6- Fibroblast - Gingival, donor6 (aggressive periodontitis)_CNhs14128_11921-125H4_reverse Regulation 
FibroblastGingivalDonor6Control_CNhs14129_tpm_fwd FibroGingivalD6+ Fibroblast - Gingival, donor6 (control)_CNhs14129_11922-125H5_forward Regulation 
FibroblastGingivalDonor6AggressivePeriodontitis_CNhs14128_tpm_fwd FibroGingivalD6+ Fibroblast - Gingival, donor6 (aggressive periodontitis)_CNhs14128_11921-125H4_forward Regulation 
FibroblastGingivalDonor5GFH3_CNhs11952_tpm_rev FibroGingivalD5- Fibroblast - Gingival, donor5 (GFH3)_CNhs11952_11303-117B7_reverse Regulation 
FibroblastGingivalDonor5GFH3_CNhs11952_tpm_fwd FibroGingivalD5+ Fibroblast - Gingival, donor5 (GFH3)_CNhs11952_11303-117B7_forward Regulation 
FibroblastGingivalDonor4GFH2_CNhs10848_tpm_rev FibroGingivalD4- Fibroblast - Gingival, donor4 (GFH2)_CNhs10848_11222-116B7_reverse Regulation 
FibroblastGingivalDonor4GFH2_CNhs10848_tpm_fwd FibroGingivalD4+ Fibroblast - Gingival, donor4 (GFH2)_CNhs10848_11222-116B7_forward Regulation 
FibroblastGingivalDonor3_CNhs12006_tpm_rev FibroGingivalD3- Fibroblast - Gingival, donor3_CNhs12006_11394-118C8_reverse Regulation 
FibroblastGingivalDonor3_CNhs12006_tpm_fwd FibroGingivalD3+ Fibroblast - Gingival, donor3_CNhs12006_11394-118C8_forward Regulation 
FibroblastGingivalDonor2_CNhs11961_tpm_rev FibroGingivalD2- Fibroblast - Gingival, donor2_CNhs11961_11318-117D4_reverse Regulation 
FibroblastGingivalDonor2_CNhs11961_tpm_fwd FibroGingivalD2+ Fibroblast - Gingival, donor2_CNhs11961_11318-117D4_forward Regulation 
FibroblastGingivalDonor10Periodontitis_CNhs14135_tpm_rev FibroGingivalD10 (p- Fibroblast - Gingival, donor10 (periodontitis)_CNhs14135_11928-125I2_reverse Regulation 
FibroblastGingivalDonor10Periodontitis_CNhs14135_tpm_fwd FibroGingivalD10 (p+ Fibroblast - Gingival, donor10 (periodontitis)_CNhs14135_11928-125I2_forward Regulation 
FibroblastGingivalDonor1_CNhs10866_tpm_rev FibroGingivalD1- Fibroblast - Gingival, donor1_CNhs10866_11237-116D4_reverse Regulation 
FibroblastGingivalDonor1_CNhs10866_tpm_fwd FibroGingivalD1+ Fibroblast - Gingival, donor1_CNhs10866_11237-116D4_forward Regulation 
FibroblastDermalDonor6_CNhs12059_tpm_rev FibroDermalD6- Fibroblast - Dermal, donor6_CNhs12059_11458-119A9_reverse Regulation 
FibroblastDermalDonor6_CNhs12059_tpm_fwd FibroDermalD6+ Fibroblast - Dermal, donor6_CNhs12059_11458-119A9_forward Regulation 
FibroblastDermalDonor5_CNhs12055_tpm_rev FibroDermalD5- Fibroblast - Dermal, donor5_CNhs12055_11454-119A5_reverse Regulation 
FibroblastDermalDonor5_CNhs12055_tpm_fwd FibroDermalD5+ Fibroblast - Dermal, donor5_CNhs12055_11454-119A5_forward Regulation 
FibroblastDermalDonor4_CNhs12052_tpm_rev FibroDermalD4- Fibroblast - Dermal, donor4_CNhs12052_11450-119A1_reverse Regulation 
FibroblastDermalDonor4_CNhs12052_tpm_fwd FibroDermalD4+ Fibroblast - Dermal, donor4_CNhs12052_11450-119A1_forward Regulation 
FibroblastDermalDonor3_CNhs12028_tpm_rev FibroDermalD3- Fibroblast - Dermal, donor3_CNhs12028_11418-118F5_reverse Regulation 
FibroblastDermalDonor3_CNhs12028_tpm_fwd FibroDermalD3+ Fibroblast - Dermal, donor3_CNhs12028_11418-118F5_forward Regulation 
FibroblastDermalDonor2_CNhs11379_tpm_rev FibroDermalD2- Fibroblast - Dermal, donor2_CNhs11379_11346-117G5_reverse Regulation 
FibroblastDermalDonor2_CNhs11379_tpm_fwd FibroDermalD2+ Fibroblast - Dermal, donor2_CNhs11379_11346-117G5_forward Regulation 
FibroblastDermalDonor1_CNhs12499_tpm_rev FibroDermalD1- Fibroblast - Dermal, donor1_CNhs12499_11269-116G9_reverse Regulation 
FibroblastDermalDonor1_CNhs12499_tpm_fwd FibroDermalD1+ Fibroblast - Dermal, donor1_CNhs12499_11269-116G9_forward Regulation 
FibroblastConjunctivalDonor3_CNhs12734_tpm_rev FibroConjunctivalD3- Fibroblast - Conjunctival, donor3_CNhs12734_11692-122I9_reverse Regulation 
FibroblastConjunctivalDonor3_CNhs12734_tpm_fwd FibroConjunctivalD3+ Fibroblast - Conjunctival, donor3_CNhs12734_11692-122I9_forward Regulation 
FibroblastConjunctivalDonor1_CNhs11339_tpm_rev FibroConjunctivalD1- Fibroblast - Conjunctival, donor1_CNhs11339_11531-120A1_reverse Regulation 
FibroblastConjunctivalDonor1_CNhs11339_tpm_fwd FibroConjunctivalD1+ Fibroblast - Conjunctival, donor1_CNhs11339_11531-120A1_forward Regulation 
FibroblastChoroidPlexusDonor3_CNhs12620_tpm_rev FibroChoroidPlexusD3- Fibroblast - Choroid Plexus, donor3_CNhs12620_11653-122E6_reverse Regulation 
FibroblastChoroidPlexusDonor3_CNhs12620_tpm_fwd FibroChoroidPlexusD3+ Fibroblast - Choroid Plexus, donor3_CNhs12620_11653-122E6_forward Regulation 
FibroblastChoroidPlexusDonor2_CNhs12344_tpm_rev FibroChoroidPlexusD2- Fibroblast - Choroid Plexus, donor2_CNhs12344_11572-120E6_reverse Regulation 
FibroblastChoroidPlexusDonor2_CNhs12344_tpm_fwd FibroChoroidPlexusD2+ Fibroblast - Choroid Plexus, donor2_CNhs12344_11572-120E6_forward Regulation 
FibroblastChoroidPlexusDonor1_CNhs11319_tpm_rev FibroChoroidPlexusD1- Fibroblast - Choroid Plexus, donor1_CNhs11319_11492-119E7_reverse Regulation 
FibroblastChoroidPlexusDonor1_CNhs11319_tpm_fwd FibroChoroidPlexusD1+ Fibroblast - Choroid Plexus, donor1_CNhs11319_11492-119E7_forward Regulation 
FibroblastCardiacDonor6_CNhs12061_tpm_rev FibroCardiacD6- Fibroblast - Cardiac, donor6_CNhs12061_11460-119B2_reverse Regulation 
FibroblastCardiacDonor6_CNhs12061_tpm_fwd FibroCardiacD6+ Fibroblast - Cardiac, donor6_CNhs12061_11460-119B2_forward Regulation 
FibroblastCardiacDonor5_CNhs12057_tpm_rev FibroCardiacD5- Fibroblast - Cardiac, donor5_CNhs12057_11456-119A7_reverse Regulation 
FibroblastCardiacDonor5_CNhs12057_tpm_fwd FibroCardiacD5+ Fibroblast - Cardiac, donor5_CNhs12057_11456-119A7_forward Regulation 
FibroblastCardiacDonor4_CNhs11909_tpm_rev FibroCardiacD4- Fibroblast - Cardiac, donor4_CNhs11909_11452-119A3_reverse Regulation 
FibroblastCardiacDonor4_CNhs11909_tpm_fwd FibroCardiacD4+ Fibroblast - Cardiac, donor4_CNhs11909_11452-119A3_forward Regulation 
FibroblastCardiacDonor3_CNhs12027_tpm_rev FibroCardiacD3- Fibroblast - Cardiac, donor3_CNhs12027_11417-118F4_reverse Regulation 
FibroblastCardiacDonor3_CNhs12027_tpm_fwd FibroCardiacD3+ Fibroblast - Cardiac, donor3_CNhs12027_11417-118F4_forward Regulation 
FibroblastCardiacDonor2_CNhs11378_tpm_rev FibroCardiacD2- Fibroblast - Cardiac, donor2_CNhs11378_11345-117G4_reverse Regulation 
FibroblastCardiacDonor2_CNhs11378_tpm_fwd FibroCardiacD2+ Fibroblast - Cardiac, donor2_CNhs11378_11345-117G4_forward Regulation 
FibroblastCardiacDonor1_CNhs12498_tpm_rev FibroCardiacD1- Fibroblast - Cardiac, donor1_CNhs12498_11268-116G8_reverse Regulation 
FibroblastCardiacDonor1_CNhs12498_tpm_fwd FibroCardiacD1+ Fibroblast - Cardiac, donor1_CNhs12498_11268-116G8_forward Regulation 
FibroblastAorticAdventitialDonor3_CNhs12011_tpm_rev FibroAorticAdventitialD3- Fibroblast - Aortic Adventitial, donor3_CNhs12011_11401-118D6_reverse Regulation 
FibroblastAorticAdventitialDonor3_CNhs12011_tpm_fwd FibroAorticAdventitialD3+ Fibroblast - Aortic Adventitial, donor3_CNhs12011_11401-118D6_forward Regulation 
FibroblastAorticAdventitialDonor2_CNhs11968_tpm_rev FibroAorticAdventitialD2- Fibroblast - Aortic Adventitial, donor2_CNhs11968_11326-117E3_reverse Regulation 
FibroblastAorticAdventitialDonor2_CNhs11968_tpm_fwd FibroAorticAdventitialD2+ Fibroblast - Aortic Adventitial, donor2_CNhs11968_11326-117E3_forward Regulation 
FibroblastAorticAdventitialDonor1_CNhs10874_tpm_rev FibroAorticAdventitialD1- Fibroblast - Aortic Adventitial, donor1_CNhs10874_11245-116E3_reverse Regulation 
FibroblastAorticAdventitialDonor1_CNhs10874_tpm_fwd FibroAorticAdventitialD1+ Fibroblast - Aortic Adventitial, donor1_CNhs10874_11245-116E3_forward Regulation 
EsophagealEpithelialCellsDonor3_CNhs12622_tpm_rev EsophagealEpithelialCellsD3- Esophageal Epithelial Cells, donor3_CNhs12622_11668-122G3_reverse Regulation 
EsophagealEpithelialCellsDonor3_CNhs12622_tpm_fwd EsophagealEpithelialCellsD3+ Esophageal Epithelial Cells, donor3_CNhs12622_11668-122G3_forward Regulation 
EsophagealEpithelialCellsDonor2_CNhs12083_tpm_rev EsophagealEpithelialCellsD2- Esophageal Epithelial Cells, donor2_CNhs12083_11587-120G3_reverse Regulation 
EsophagealEpithelialCellsDonor2_CNhs12083_tpm_fwd EsophagealEpithelialCellsD2+ Esophageal Epithelial Cells, donor2_CNhs12083_11587-120G3_forward Regulation 
EsophagealEpithelialCellsDonor1_CNhs11323_tpm_rev EsophagealEpithelialCellsD1- Esophageal Epithelial Cells, donor1_CNhs11323_11507-119G4_reverse Regulation 
EsophagealEpithelialCellsDonor1_CNhs11323_tpm_fwd EsophagealEpithelialCellsD1+ Esophageal Epithelial Cells, donor1_CNhs11323_11507-119G4_forward Regulation 
EndothelialCellsVeinDonor3_CNhs12026_tpm_rev EndothelialCellsVeinD3- Endothelial Cells - Vein, donor3_CNhs12026_11416-118F3_reverse Regulation 
EndothelialCellsVeinDonor3_CNhs12026_tpm_fwd EndothelialCellsVeinD3+ Endothelial Cells - Vein, donor3_CNhs12026_11416-118F3_forward Regulation 
EndothelialCellsVeinDonor2_CNhs11377_tpm_rev EndothelialCellsVeinD2- Endothelial Cells - Vein, donor2_CNhs11377_11344-117G3_reverse Regulation 
EndothelialCellsVeinDonor2_CNhs11377_tpm_fwd EndothelialCellsVeinD2+ Endothelial Cells - Vein, donor2_CNhs11377_11344-117G3_forward Regulation 
EndothelialCellsVeinDonor1_CNhs12497_tpm_rev EndothelialCellsVeinD1- Endothelial Cells - Vein, donor1_CNhs12497_11267-116G7_reverse Regulation 
EndothelialCellsVeinDonor1_CNhs12497_tpm_fwd EndothelialCellsVeinD1+ Endothelial Cells - Vein, donor1_CNhs12497_11267-116G7_forward Regulation 
EndothelialCellsUmbilicalVeinDonor3_CNhs12010_tpm_rev EndothelialCellsUmbilicalVeinD3- Endothelial Cells - Umbilical vein, donor3_CNhs12010_11400-118D5_reverse Regulation 
EndothelialCellsUmbilicalVeinDonor3_CNhs12010_tpm_fwd EndothelialCellsUmbilicalVeinD3+ Endothelial Cells - Umbilical vein, donor3_CNhs12010_11400-118D5_forward Regulation 
EndothelialCellsUmbilicalVeinDonor2_CNhs11967_tpm_rev EndothelialCellsUmbilicalVeinD2- Endothelial Cells - Umbilical vein, donor2_CNhs11967_11324-117E1_reverse Regulation 
EndothelialCellsUmbilicalVeinDonor2_CNhs11967_tpm_fwd EndothelialCellsUmbilicalVeinD2+ Endothelial Cells - Umbilical vein, donor2_CNhs11967_11324-117E1_forward Regulation 
EndothelialCellsUmbilicalVeinDonor1_CNhs10872_tpm_rev EndothelialCellsUmbilicalVeinD1- Endothelial Cells - Umbilical vein, donor1_CNhs10872_11243-116E1_reverse Regulation 
EndothelialCellsUmbilicalVeinDonor1_CNhs10872_tpm_fwd EndothelialCellsUmbilicalVeinD1+ Endothelial Cells - Umbilical vein, donor1_CNhs10872_11243-116E1_forward Regulation 
EndothelialCellsThoracicDonor2_CNhs11978_tpm_rev EndothelialCellsThoracicD2- Endothelial Cells - Thoracic, donor2_CNhs11978_11343-117G2_reverse Regulation 
EndothelialCellsThoracicDonor2_CNhs11978_tpm_fwd EndothelialCellsThoracicD2+ Endothelial Cells - Thoracic, donor2_CNhs11978_11343-117G2_forward Regulation 
EndothelialCellsThoracicDonor1_CNhs11926_tpm_rev EndothelialCellsThoracicD1- Endothelial Cells - Thoracic, donor1_CNhs11926_11266-116G6_reverse Regulation 
EndothelialCellsThoracicDonor1_CNhs11926_tpm_fwd EndothelialCellsThoracicD1+ Endothelial Cells - Thoracic, donor1_CNhs11926_11266-116G6_forward Regulation 
EndothelialCellsMicrovascularDonor3_CNhs12024_tpm_rev EndothelialCellsMicrovascularD3- Endothelial Cells - Microvascular, donor3_CNhs12024_11414-118F1_reverse Regulation 
EndothelialCellsMicrovascularDonor3_CNhs12024_tpm_fwd EndothelialCellsMicrovascularD3+ Endothelial Cells - Microvascular, donor3_CNhs12024_11414-118F1_forward Regulation 
EndothelialCellsMicrovascularDonor2_CNhs11376_tpm_rev EndothelialCellsMicrovascularD2- Endothelial Cells - Microvascular, donor2_CNhs11376_11342-117G1_reverse Regulation 
EndothelialCellsMicrovascularDonor2_CNhs11376_tpm_fwd EndothelialCellsMicrovascularD2+ Endothelial Cells - Microvascular, donor2_CNhs11376_11342-117G1_forward Regulation 
EndothelialCellsMicrovascularDonor1_CNhs11925_tpm_rev EndothelialCellsMicrovascularD1- Endothelial Cells - Microvascular, donor1_CNhs11925_11265-116G5_reverse Regulation 
EndothelialCellsMicrovascularDonor1_CNhs11925_tpm_fwd EndothelialCellsMicrovascularD1+ Endothelial Cells - Microvascular, donor1_CNhs11925_11265-116G5_forward Regulation 
EndothelialCellsLymphaticDonor3_CNhs11906_tpm_rev EndothelialCellsLymphaticD3- Endothelial Cells - Lymphatic, donor3_CNhs11906_11393-118C7_reverse Regulation 
EndothelialCellsLymphaticDonor3_CNhs11906_tpm_fwd EndothelialCellsLymphaticD3+ Endothelial Cells - Lymphatic, donor3_CNhs11906_11393-118C7_forward Regulation 
EndothelialCellsLymphaticDonor2_CNhs11901_tpm_rev EndothelialCellsLymphaticD2- Endothelial Cells - Lymphatic, donor2_CNhs11901_11317-117D3_reverse Regulation 
EndothelialCellsLymphaticDonor2_CNhs11901_tpm_fwd EndothelialCellsLymphaticD2+ Endothelial Cells - Lymphatic, donor2_CNhs11901_11317-117D3_forward Regulation 
EndothelialCellsLymphaticDonor1_CNhs10865_tpm_rev EndothelialCellsLymphaticD1- Endothelial Cells - Lymphatic, donor1_CNhs10865_11236-116D3_reverse Regulation 
EndothelialCellsLymphaticDonor1_CNhs10865_tpm_fwd EndothelialCellsLymphaticD1+ Endothelial Cells - Lymphatic, donor1_CNhs10865_11236-116D3_forward Regulation 
EndothelialCellsArteryDonor3_CNhs12023_tpm_rev EndothelialCellsArteryD3- Endothelial Cells - Artery, donor3_CNhs12023_11413-118E9_reverse Regulation 
EndothelialCellsArteryDonor3_CNhs12023_tpm_fwd EndothelialCellsArteryD3+ Endothelial Cells - Artery, donor3_CNhs12023_11413-118E9_forward Regulation 
EndothelialCellsArteryDonor2_CNhs11977_tpm_rev EndothelialCellsArteryD2- Endothelial Cells - Artery, donor2_CNhs11977_11341-117F9_reverse Regulation 
EndothelialCellsArteryDonor2_CNhs11977_tpm_fwd EndothelialCellsArteryD2+ Endothelial Cells - Artery, donor2_CNhs11977_11341-117F9_forward Regulation 
EndothelialCellsArteryDonor1_CNhs12496_tpm_rev EndothelialCellsArteryD1- Endothelial Cells - Artery, donor1_CNhs12496_11264-116G4_reverse Regulation 
EndothelialCellsArteryDonor1_CNhs12496_tpm_fwd EndothelialCellsArteryD1+ Endothelial Cells - Artery, donor1_CNhs12496_11264-116G4_forward Regulation 
EndothelialCellsAorticDonor3_CNhs12022_tpm_rev EndothelialCellsAorticD3- Endothelial Cells - Aortic, donor3_CNhs12022_11412-118E8_reverse Regulation 
EndothelialCellsAorticDonor3_CNhs12022_tpm_fwd EndothelialCellsAorticD3+ Endothelial Cells - Aortic, donor3_CNhs12022_11412-118E8_forward Regulation 
EndothelialCellsAorticDonor2_CNhs11375_tpm_rev EndothelialCellsAorticD2- Endothelial Cells - Aortic, donor2_CNhs11375_11340-117F8_reverse Regulation 
EndothelialCellsAorticDonor2_CNhs11375_tpm_fwd EndothelialCellsAorticD2+ Endothelial Cells - Aortic, donor2_CNhs11375_11340-117F8_forward Regulation 
EndothelialCellsAorticDonor1_CNhs12495_tpm_rev EndothelialCellsAorticD1- Endothelial Cells - Aortic, donor1_CNhs12495_11263-116G3_reverse Regulation 
EndothelialCellsAorticDonor1_CNhs12495_tpm_fwd EndothelialCellsAorticD1+ Endothelial Cells - Aortic, donor1_CNhs12495_11263-116G3_forward Regulation 
EndothelialCellsAorticDonor0_CNhs10837_tpm_rev EndothelialCellsAorticD0- Endothelial Cells - Aortic, donor0_CNhs10837_11207-116A1_reverse Regulation 
EndothelialCellsAorticDonor0_CNhs10837_tpm_fwd EndothelialCellsAorticD0+ Endothelial Cells - Aortic, donor0_CNhs10837_11207-116A1_forward Regulation 
DendriticCellsPlasmacytoidDonor1_CNhs10857_tpm_rev DendriticCellsPlasmacytoidD1- Dendritic Cells - plasmacytoid, donor1_CNhs10857_11228-116C4_reverse Regulation 
DendriticCellsPlasmacytoidDonor1_CNhs10857_tpm_fwd DendriticCellsPlasmacytoidD1+ Dendritic Cells - plasmacytoid, donor1_CNhs10857_11228-116C4_forward Regulation 
DendriticCellsMonocyteImmatureDerivedDonor3_CNhs12000_tpm_rev DendriticCellsMonocyteImmatureD3- Dendritic Cells - monocyte immature derived, donor3_CNhs12000_11384-118B7_reverse Regulation 
DendriticCellsMonocyteImmatureDerivedDonor3_CNhs12000_tpm_fwd DendriticCellsMonocyteImmatureD3+ Dendritic Cells - monocyte immature derived, donor3_CNhs12000_11384-118B7_forward Regulation 
DendriticCellsMonocyteImmatureDerivedDonor1TechRep2_CNhs11062_tpm_rev DendriticCellsMonocyteImmatureD1Tr2- Dendritic Cells - monocyte immature derived, donor1, tech_rep2_CNhs11062_11227-116C3_reverse Regulation 
DendriticCellsMonocyteImmatureDerivedDonor1TechRep2_CNhs11062_tpm_fwd DendriticCellsMonocyteImmatureD1Tr2+ Dendritic Cells - monocyte immature derived, donor1, tech_rep2_CNhs11062_11227-116C3_forward Regulation 
DendriticCellsMonocyteImmatureDerivedDonor1TechRep1_CNhs10855_tpm_rev DendriticCellsMonocyteImmatureD1Tr1- Dendritic Cells - monocyte immature derived, donor1, tech_rep1_CNhs10855_11227-116C3_reverse Regulation 
DendriticCellsMonocyteImmatureDerivedDonor1TechRep1_CNhs10855_tpm_fwd DendriticCellsMonocyteImmatureD1Tr1+ Dendritic Cells - monocyte immature derived, donor1, tech_rep1_CNhs10855_11227-116C3_forward Regulation 
CornealEpithelialCellsDonor3_CNhs12123_tpm_rev CornealEpithelialCellsD3- Corneal Epithelial Cells, donor3_CNhs12123_11687-122I4_reverse Regulation 
CornealEpithelialCellsDonor3_CNhs12123_tpm_fwd CornealEpithelialCellsD3+ Corneal Epithelial Cells, donor3_CNhs12123_11687-122I4_forward Regulation 
CornealEpithelialCellsDonor2_CNhs12094_tpm_rev CornealEpithelialCellsD2- Corneal Epithelial Cells, donor2_CNhs12094_11606-120I4_reverse Regulation 
CornealEpithelialCellsDonor2_CNhs12094_tpm_fwd CornealEpithelialCellsD2+ Corneal Epithelial Cells, donor2_CNhs12094_11606-120I4_forward Regulation 
CornealEpithelialCellsDonor1_CNhs11336_tpm_rev CornealEpithelialCellsD1- Corneal Epithelial Cells, donor1_CNhs11336_11526-119I5_reverse Regulation 
CornealEpithelialCellsDonor1_CNhs11336_tpm_fwd CornealEpithelialCellsD1+ Corneal Epithelial Cells, donor1_CNhs11336_11526-119I5_forward Regulation 
CiliaryEpithelialCellsDonor3_CNhs12009_tpm_rev CiliaryEpithelialCellsD3- Ciliary Epithelial Cells, donor3_CNhs12009_11399-118D4_reverse Regulation 
CiliaryEpithelialCellsDonor3_CNhs12009_tpm_fwd CiliaryEpithelialCellsD3+ Ciliary Epithelial Cells, donor3_CNhs12009_11399-118D4_forward Regulation 
CiliaryEpithelialCellsDonor2_CNhs11966_tpm_rev CiliaryEpithelialCellsD2- Ciliary Epithelial Cells, donor2_CNhs11966_11323-117D9_reverse Regulation 
CiliaryEpithelialCellsDonor2_CNhs11966_tpm_fwd CiliaryEpithelialCellsD2+ Ciliary Epithelial Cells, donor2_CNhs11966_11323-117D9_forward Regulation 
CiliaryEpithelialCellsDonor1_CNhs10871_tpm_rev CiliaryEpithelialCellsD1- Ciliary Epithelial Cells, donor1_CNhs10871_11242-116D9_reverse Regulation 
CiliaryEpithelialCellsDonor1_CNhs10871_tpm_fwd CiliaryEpithelialCellsD1+ Ciliary Epithelial Cells, donor1_CNhs10871_11242-116D9_forward Regulation 
ChorionicMembraneCellsDonor3_CNhs12380_tpm_rev ChorionicMembraneCellsD3- chorionic membrane cells, donor3_CNhs12380_12240-129G8_reverse Regulation 
ChorionicMembraneCellsDonor3_CNhs12380_tpm_fwd ChorionicMembraneCellsD3+ chorionic membrane cells, donor3_CNhs12380_12240-129G8_forward Regulation 
ChorionicMembraneCellsDonor2_CNhs12506_tpm_rev ChorionicMembraneCellsD2- chorionic membrane cells, donor2_CNhs12506_12239-129G7_reverse Regulation 
ChorionicMembraneCellsDonor2_CNhs12506_tpm_fwd ChorionicMembraneCellsD2+ chorionic membrane cells, donor2_CNhs12506_12239-129G7_forward Regulation 
ChorionicMembraneCellsDonor1_CNhs12504_tpm_rev ChorionicMembraneCellsD1- chorionic membrane cells, donor1_CNhs12504_12238-129G6_reverse Regulation 
ChorionicMembraneCellsDonor1_CNhs12504_tpm_fwd ChorionicMembraneCellsD1+ chorionic membrane cells, donor1_CNhs12504_12238-129G6_forward Regulation 
ChondrocyteReDiffDonor3_CNhs12021_tpm_rev ChondrocyteReDiffD3- Chondrocyte - re diff, donor3_CNhs12021_11411-118E7_reverse Regulation 
ChondrocyteReDiffDonor3_CNhs12021_tpm_fwd ChondrocyteReDiffD3+ Chondrocyte - re diff, donor3_CNhs12021_11411-118E7_forward Regulation 
ChondrocyteReDiffDonor2_CNhs11373_tpm_rev ChondrocyteReDiffD2- Chondrocyte - re diff, donor2_CNhs11373_11339-117F7_reverse Regulation 
ChondrocyteReDiffDonor2_CNhs11373_tpm_fwd ChondrocyteReDiffD2+ Chondrocyte - re diff, donor2_CNhs11373_11339-117F7_forward Regulation 
ChondrocyteDeDiffDonor3_CNhs12020_tpm_rev ChondrocyteDeDiffD3- Chondrocyte - de diff, donor3_CNhs12020_11410-118E6_reverse Regulation 
ChondrocyteDeDiffDonor3_CNhs12020_tpm_fwd ChondrocyteDeDiffD3+ Chondrocyte - de diff, donor3_CNhs12020_11410-118E6_forward Regulation 
ChondrocyteDeDiffDonor2_CNhs11372_tpm_rev ChondrocyteDeDiffD2- Chondrocyte - de diff, donor2_CNhs11372_11338-117F6_reverse Regulation 
ChondrocyteDeDiffDonor2_CNhs11372_tpm_fwd ChondrocyteDeDiffD2+ Chondrocyte - de diff, donor2_CNhs11372_11338-117F6_forward Regulation 
ChondrocyteDeDiffDonor1_CNhs11923_tpm_rev ChondrocyteDeDiffD1- Chondrocyte - de diff, donor1_CNhs11923_11261-116G1_reverse Regulation 
ChondrocyteDeDiffDonor1_CNhs11923_tpm_fwd ChondrocyteDeDiffD1+ Chondrocyte - de diff, donor1_CNhs11923_11261-116G1_forward Regulation 
CD8TCellsDonor3_CNhs11999_tpm_rev Cd8+TCellsD3- CD8+ T Cells, donor3_CNhs11999_11383-118B6_reverse Regulation 
CD8TCellsDonor3_CNhs11999_tpm_fwd Cd8+TCellsD3+ CD8+ T Cells, donor3_CNhs11999_11383-118B6_forward Regulation 
CD8TCellsDonor2_CNhs11956_tpm_rev Cd8+TCellsD2- CD8+ T Cells, donor2_CNhs11956_11307-117C2_reverse Regulation 
CD8TCellsDonor2_CNhs11956_tpm_fwd Cd8+TCellsD2+ CD8+ T Cells, donor2_CNhs11956_11307-117C2_forward Regulation 
CD8TCellsDonor1_CNhs10854_tpm_rev Cd8+TCellsD1- CD8+ T Cells, donor1_CNhs10854_11226-116C2_reverse Regulation 
CD8TCellsDonor1_CNhs10854_tpm_fwd Cd8+TCellsD1+ CD8+ T Cells, donor1_CNhs10854_11226-116C2_forward Regulation 
CD4TCellsDonor3_CNhs11998_tpm_rev Cd4+TCellsD3- CD4+ T Cells, donor3_CNhs11998_11382-118B5_reverse Regulation 
CD4TCellsDonor3_CNhs11998_tpm_fwd Cd4+TCellsD3+ CD4+ T Cells, donor3_CNhs11998_11382-118B5_forward Regulation 
CD4TCellsDonor2_CNhs11955_tpm_rev Cd4+TCellsD2- CD4+ T Cells, donor2_CNhs11955_11306-117C1_reverse Regulation 
CD4TCellsDonor2_CNhs11955_tpm_fwd Cd4+TCellsD2+ CD4+ T Cells, donor2_CNhs11955_11306-117C1_forward Regulation 
CD4TCellsDonor1_CNhs10853_tpm_rev Cd4+TCellsD1- CD4+ T Cells, donor1_CNhs10853_11225-116C1_reverse Regulation 
CD4TCellsDonor1_CNhs10853_tpm_fwd Cd4+TCellsD1+ CD4+ T Cells, donor1_CNhs10853_11225-116C1_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor3_CNhs13921_tpm_rev Cd4+cd25-cd45ra-ExpdD3- CD4+CD25-CD45RA- memory conventional T cells expanded, donor3_CNhs13921_11918-125H1_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor3_CNhs13921_tpm_fwd Cd4+cd25-cd45ra-ExpdD3+ CD4+CD25-CD45RA- memory conventional T cells expanded, donor3_CNhs13921_11918-125H1_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor2_CNhs13920_tpm_rev Cd4+cd25-cd45ra-ExpdD2- CD4+CD25-CD45RA- memory conventional T cells expanded, donor2_CNhs13920_11914-125G6_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor2_CNhs13920_tpm_fwd Cd4+cd25-cd45ra-ExpdD2+ CD4+CD25-CD45RA- memory conventional T cells expanded, donor2_CNhs13920_11914-125G6_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor1_CNhs13215_tpm_rev Cd4+cd25-cd45ra-ExpdD1- CD4+CD25-CD45RA- memory conventional T cells expanded, donor1_CNhs13215_11792-124C1_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsExpandedDonor1_CNhs13215_tpm_fwd Cd4+cd25-cd45ra-ExpdD1+ CD4+CD25-CD45RA- memory conventional T cells expanded, donor1_CNhs13215_11792-124C1_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor3_CNhs13539_tpm_rev Cd4+cd25-cd45ra-D3- CD4+CD25-CD45RA- memory conventional T cells, donor3_CNhs13539_11909-125G1_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor3_CNhs13539_tpm_fwd Cd4+cd25-cd45ra-D3+ CD4+CD25-CD45RA- memory conventional T cells, donor3_CNhs13539_11909-125G1_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor3_CNhs13814_tpm_rev Cd4+cd25-cd45ra+ExpdD3- CD4+CD25-CD45RA+ naive conventional T cells expanded, donor3_CNhs13814_11917-125G9_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor3_CNhs13814_tpm_fwd Cd4+cd25-cd45ra+ExpdD3+ CD4+CD25-CD45RA+ naive conventional T cells expanded, donor3_CNhs13814_11917-125G9_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor2_CNhs13813_tpm_rev Cd4+cd25-cd45ra+ExpdD2- CD4+CD25-CD45RA+ naive conventional T cells expanded, donor2_CNhs13813_11913-125G5_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor2_CNhs13813_tpm_fwd Cd4+cd25-cd45ra+ExpdD2+ CD4+CD25-CD45RA+ naive conventional T cells expanded, donor2_CNhs13813_11913-125G5_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor1_CNhs13202_tpm_rev Cd4+cd25-cd45ra+ExpdD1- CD4+CD25-CD45RA+ naive conventional T cells expanded, donor1_CNhs13202_11791-124B9_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsExpandedDonor1_CNhs13202_tpm_fwd Cd4+cd25-cd45ra+ExpdD1+ CD4+CD25-CD45RA+ naive conventional T cells expanded, donor1_CNhs13202_11791-124B9_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor3_CNhs13512_tpm_rev Cd4+cd25-cd45ra+D3- CD4+CD25-CD45RA+ naive conventional T cells, donor3_CNhs13512_11906-125F7_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor3_CNhs13512_tpm_fwd Cd4+cd25-cd45ra+D3+ CD4+CD25-CD45RA+ naive conventional T cells, donor3_CNhs13512_11906-125F7_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor2_CNhs13205_tpm_rev Cd4+cd25-cd45ra+D2- CD4+CD25-CD45RA+ naive conventional T cells, donor2_CNhs13205_11795-124C4_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor2_CNhs13205_tpm_fwd Cd4+cd25-cd45ra+D2+ CD4+CD25-CD45RA+ naive conventional T cells, donor2_CNhs13205_11795-124C4_forward Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor1_CNhs13223_tpm_rev Cd4+cd25-cd45ra+D1- CD4+CD25-CD45RA+ naive conventional T cells, donor1_CNhs13223_11784-124B2_reverse Regulation 
CD4CD25CD45RANaiveConventionalTCellsDonor1_CNhs13223_tpm_fwd Cd4+cd25-cd45ra+D1+ CD4+CD25-CD45RA+ naive conventional T cells, donor1_CNhs13223_11784-124B2_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor3_CNhs13812_tpm_rev Cd4+cd25+cd45ra-ExpdD3- CD4+CD25+CD45RA- memory regulatory T cells expanded, donor3_CNhs13812_11920-125H3_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor3_CNhs13812_tpm_fwd Cd4+cd25+cd45ra-ExpdD3+ CD4+CD25+CD45RA- memory regulatory T cells expanded, donor3_CNhs13812_11920-125H3_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor2_CNhs13811_tpm_rev Cd4+cd25+cd45ra-ExpdD2- CD4+CD25+CD45RA- memory regulatory T cells expanded, donor2_CNhs13811_11916-125G8_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor2_CNhs13811_tpm_fwd Cd4+cd25+cd45ra-ExpdD2+ CD4+CD25+CD45RA- memory regulatory T cells expanded, donor2_CNhs13811_11916-125G8_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor1_CNhs13204_tpm_rev Cd4+cd25+cd45ra-ExpdD1- CD4+CD25+CD45RA- memory regulatory T cells expanded, donor1_CNhs13204_11794-124C3_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsExpandedDonor1_CNhs13204_tpm_fwd Cd4+cd25+cd45ra-ExpdD1+ CD4+CD25+CD45RA- memory regulatory T cells expanded, donor1_CNhs13204_11794-124C3_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor3_CNhs13538_tpm_rev Cd4+cd25+cd45ra-D3- CD4+CD25+CD45RA- memory regulatory T cells, donor3_CNhs13538_11908-125F9_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor3_CNhs13538_tpm_fwd Cd4+cd25+cd45ra-D3+ CD4+CD25+CD45RA- memory regulatory T cells, donor3_CNhs13538_11908-125F9_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor2_CNhs13206_tpm_rev Cd4+cd25+cd45ra-D2- CD4+CD25+CD45RA- memory regulatory T cells, donor2_CNhs13206_11797-124C6_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor2_CNhs13206_tpm_fwd Cd4+cd25+cd45ra-D2+ CD4+CD25+CD45RA- memory regulatory T cells, donor2_CNhs13206_11797-124C6_forward Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor1_CNhs13195_tpm_rev Cd4+cd25+cd45ra-D1- CD4+CD25+CD45RA- memory regulatory T cells, donor1_CNhs13195_11782-124A9_reverse Regulation 
CD4CD25CD45RAMemoryRegulatoryTCellsDonor1_CNhs13195_tpm_fwd Cd4+cd25+cd45ra-D1+ CD4+CD25+CD45RA- memory regulatory T cells, donor1_CNhs13195_11782-124A9_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor3_CNhs13919_tpm_rev Cd4+cd25+cd45ra+ExpdD3- CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor3_CNhs13919_11919-125H2_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor3_CNhs13919_tpm_fwd Cd4+cd25+cd45ra+ExpdD3+ CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor3_CNhs13919_11919-125H2_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor2_CNhs13918_tpm_rev Cd4+cd25+cd45ra+ExpdD2- CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor2_CNhs13918_11915-125G7_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor2_CNhs13918_tpm_fwd Cd4+cd25+cd45ra+ExpdD2+ CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor2_CNhs13918_11915-125G7_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor1_CNhs13203_tpm_rev Cd4+cd25+cd45ra+ExpdD1- CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor1_CNhs13203_11793-124C2_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsExpandedDonor1_CNhs13203_tpm_fwd Cd4+cd25+cd45ra+ExpdD1+ CD4+CD25+CD45RA+ naive regulatory T cells expanded, donor1_CNhs13203_11793-124C2_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor3_CNhs13513_tpm_rev Cd4+cd25+cd45ra+D3- CD4+CD25+CD45RA+ naive regulatory T cells, donor3_CNhs13513_11907-125F8_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor3_CNhs13513_tpm_fwd Cd4+cd25+cd45ra+D3+ CD4+CD25+CD45RA+ naive regulatory T cells, donor3_CNhs13513_11907-125F8_forward Regulation 
CD34CellsDifferentiatedToErythrocyteLineageBiol_Rep2_CNhs13553_tpm_rev Cd34ErythrocyteBr2- CD34 cells differentiated to erythrocyte lineage, biol_ rep2_CNhs13553_11932-125I6_reverse Regulation 
CD34CellsDifferentiatedToErythrocyteLineageBiol_Rep2_CNhs13553_tpm_fwd Cd34ErythrocyteBr2+ CD34 cells differentiated to erythrocyte lineage, biol_ rep2_CNhs13553_11932-125I6_forward Regulation 
CD34CellsDifferentiatedToErythrocyteLineageBiol_Rep1_CNhs13552_tpm_rev Cd34ErythrocyteBr1- CD34 cells differentiated to erythrocyte lineage, biol_ rep1_CNhs13552_11931-125I5_reverse Regulation 
CD34CellsDifferentiatedToErythrocyteLineageBiol_Rep1_CNhs13552_tpm_fwd Cd34ErythrocyteBr1+ CD34 cells differentiated to erythrocyte lineage, biol_ rep1_CNhs13552_11931-125I5_forward Regulation 
CD34StemCellsAdultBoneMarrowDerivedDonor1TechRep1_CNhs12588_tpm_rev Cd34+StemCellsAdultBoneMarrowD1Tr1- CD34+ stem cells - adult bone marrow derived, donor1, tech_rep1_CNhs12588_12225-129F2_reverse Regulation 
CD34StemCellsAdultBoneMarrowDerivedDonor1TechRep1_CNhs12588_tpm_fwd Cd34+StemCellsAdultBoneMarrowD1Tr1+ CD34+ stem cells - adult bone marrow derived, donor1, tech_rep1_CNhs12588_12225-129F2_forward Regulation 
CD19BCellsDonor3_CNhs12354_tpm_rev Cd19+BCellsD3- CD19+ B Cells, donor3_CNhs12354_11705-123B4_reverse Regulation 
CD19BCellsDonor3_CNhs12354_tpm_fwd Cd19+BCellsD3+ CD19+ B Cells, donor3_CNhs12354_11705-123B4_forward Regulation 
CD19BCellsDonor2_CNhs12352_tpm_rev Cd19+BCellsD2- CD19+ B Cells, donor2_CNhs12352_11624-122B4_reverse Regulation 
CD19BCellsDonor2_CNhs12352_tpm_fwd Cd19+BCellsD2+ CD19+ B Cells, donor2_CNhs12352_11624-122B4_forward Regulation 
CD19BCellsDonor1_CNhs12343_tpm_rev Cd19+BCellsD1- CD19+ B Cells, donor1_CNhs12343_11544-120B5_reverse Regulation 
CD19BCellsDonor1_CNhs12343_tpm_fwd Cd19+BCellsD1+ CD19+ B Cells, donor1_CNhs12343_11544-120B5_forward Regulation 
CD14CD16MonocytesDonor3_CNhs13548_tpm_rev Cd14-cd16+MonocytesD3- CD14-CD16+ Monocytes, donor3_CNhs13548_11911-125G3_reverse Regulation 
CD14CD16MonocytesDonor3_CNhs13548_tpm_fwd Cd14-cd16+MonocytesD3+ CD14-CD16+ Monocytes, donor3_CNhs13548_11911-125G3_forward Regulation 
CD14CD16MonocytesDonor2_CNhs13207_tpm_rev Cd14-cd16+MonocytesD2- CD14-CD16+ Monocytes, donor2_CNhs13207_11800-124C9_reverse Regulation 
CD14CD16MonocytesDonor2_CNhs13207_tpm_fwd Cd14-cd16+MonocytesD2+ CD14-CD16+ Monocytes, donor2_CNhs13207_11800-124C9_forward Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor3_CNhs13544_tpm_rev Cd14+MoW/TrehaloseDimycolateD3- CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor3_CNhs13544_11882-125D1_reverse Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor3_CNhs13544_tpm_fwd Cd14+MoW/TrehaloseDimycolateD3+ CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor3_CNhs13544_11882-125D1_forward Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor2_CNhs13483_tpm_rev Cd14+MoW/TrehaloseDimycolateD2- CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor2_CNhs13483_11872-125B9_reverse Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor2_CNhs13483_tpm_fwd Cd14+MoW/TrehaloseDimycolateD2+ CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor2_CNhs13483_11872-125B9_forward Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor1_CNhs13467_tpm_rev Cd14+MoW/TrehaloseDimycolateD1- CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor1_CNhs13467_11862-125A8_reverse Regulation 
CD14MonocytesTreatedWithTrehaloseDimycolateTDMDonor1_CNhs13467_tpm_fwd Cd14+MoW/TrehaloseDimycolateD1+ CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor1_CNhs13467_11862-125A8_forward Regulation 
CD14MonocytesTreatedWithSalmonellaDonor3_CNhs13493_tpm_rev Cd14+MoW/SalmonellaD3- CD14+ monocytes - treated with Salmonella, donor3_CNhs13493_11886-125D5_reverse Regulation 
CD14MonocytesTreatedWithSalmonellaDonor3_CNhs13493_tpm_fwd Cd14+MoW/SalmonellaD3+ CD14+ monocytes - treated with Salmonella, donor3_CNhs13493_11886-125D5_forward Regulation 
CD14MonocytesTreatedWithSalmonellaDonor2_CNhs13485_tpm_rev Cd14+MoW/SalmonellaD2- CD14+ monocytes - treated with Salmonella, donor2_CNhs13485_11876-125C4_reverse Regulation 
CD14MonocytesTreatedWithSalmonellaDonor2_CNhs13485_tpm_fwd Cd14+MoW/SalmonellaD2+ CD14+ monocytes - treated with Salmonella, donor2_CNhs13485_11876-125C4_forward Regulation 
CD14MonocytesTreatedWithSalmonellaDonor1_CNhs13471_tpm_rev Cd14+MoW/SalmonellaD1- CD14+ monocytes - treated with Salmonella, donor1_CNhs13471_11866-125B3_reverse Regulation 
CD14MonocytesTreatedWithSalmonellaDonor1_CNhs13471_tpm_fwd Cd14+MoW/SalmonellaD1+ CD14+ monocytes - treated with Salmonella, donor1_CNhs13471_11866-125B3_forward Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor3_CNhs13545_tpm_rev Cd14+MoW/LipopolysaccharideD3- CD14+ monocytes - treated with lipopolysaccharide, donor3_CNhs13545_11885-125D4_reverse Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor3_CNhs13545_tpm_fwd Cd14+MoW/LipopolysaccharideD3+ CD14+ monocytes - treated with lipopolysaccharide, donor3_CNhs13545_11885-125D4_forward Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor2_CNhs13533_tpm_rev Cd14+MoW/LipopolysaccharideD2- CD14+ monocytes - treated with lipopolysaccharide, donor2_CNhs13533_11875-125C3_reverse Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor2_CNhs13533_tpm_fwd Cd14+MoW/LipopolysaccharideD2+ CD14+ monocytes - treated with lipopolysaccharide, donor2_CNhs13533_11875-125C3_forward Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor1_CNhs13470_tpm_rev Cd14+MoW/LipopolysaccharideD1- CD14+ monocytes - treated with lipopolysaccharide, donor1_CNhs13470_11865-125B2_reverse Regulation 
CD14MonocytesTreatedWithLipopolysaccharideDonor1_CNhs13470_tpm_fwd Cd14+MoW/LipopolysaccharideD1+ CD14+ monocytes - treated with lipopolysaccharide, donor1_CNhs13470_11865-125B2_forward Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor3_CNhs13490_tpm_rev Cd14+MoW/Ifn+N-hexaneD3- CD14+ monocytes - treated with IFN + N-hexane, donor3_CNhs13490_11881-125C9_reverse Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor3_CNhs13490_tpm_fwd Cd14+MoW/Ifn+N-hexaneD3+ CD14+ monocytes - treated with IFN + N-hexane, donor3_CNhs13490_11881-125C9_forward Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor2_CNhs13476_tpm_rev Cd14+MoW/Ifn+N-hexaneD2- CD14+ monocytes - treated with IFN + N-hexane, donor2_CNhs13476_11871-125B8_reverse Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor2_CNhs13476_tpm_fwd Cd14+MoW/Ifn+N-hexaneD2+ CD14+ monocytes - treated with IFN + N-hexane, donor2_CNhs13476_11871-125B8_forward Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor1_CNhs13466_tpm_rev Cd14+MoW/Ifn+N-hexaneD1- CD14+ monocytes - treated with IFN + N-hexane, donor1_CNhs13466_11861-125A7_reverse Regulation 
CD14MonocytesTreatedWithIFNNhexaneDonor1_CNhs13466_tpm_fwd Cd14+MoW/Ifn+N-hexaneD1+ CD14+ monocytes - treated with IFN + N-hexane, donor1_CNhs13466_11861-125A7_forward Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor3_CNhs13492_tpm_rev Cd14+MoW/GroupAStreptococciD3- CD14+ monocytes - treated with Group A streptococci, donor3_CNhs13492_11884-125D3_reverse Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor3_CNhs13492_tpm_fwd Cd14+MoW/GroupAStreptococciD3+ CD14+ monocytes - treated with Group A streptococci, donor3_CNhs13492_11884-125D3_forward Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor2_CNhs13532_tpm_rev Cd14+MoW/GroupAStreptococciD2- CD14+ monocytes - treated with Group A streptococci, donor2_CNhs13532_11874-125C2_reverse Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor2_CNhs13532_tpm_fwd Cd14+MoW/GroupAStreptococciD2+ CD14+ monocytes - treated with Group A streptococci, donor2_CNhs13532_11874-125C2_forward Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor1_CNhs13469_tpm_rev Cd14+MoW/GroupAStreptococciD1- CD14+ monocytes - treated with Group A streptococci, donor1_CNhs13469_11864-125B1_reverse Regulation 
CD14MonocytesTreatedWithGroupAStreptococciDonor1_CNhs13469_tpm_fwd Cd14+MoW/GroupAStreptococciD1+ CD14+ monocytes - treated with Group A streptococci, donor1_CNhs13469_11864-125B1_forward Regulation 
CD14MonocytesTreatedWithCryptococcusDonor3_CNhs13546_tpm_rev Cd14+MoW/CryptococcusD3- CD14+ monocytes - treated with Cryptococcus, donor3_CNhs13546_11887-125D6_reverse Regulation 
CD14MonocytesTreatedWithCryptococcusDonor3_CNhs13546_tpm_fwd Cd14+MoW/CryptococcusD3+ CD14+ monocytes - treated with Cryptococcus, donor3_CNhs13546_11887-125D6_forward Regulation 
CD14MonocytesTreatedWithCryptococcusDonor2_CNhs13487_tpm_rev Cd14+MoW/CryptococcusD2- CD14+ monocytes - treated with Cryptococcus, donor2_CNhs13487_11877-125C5_reverse Regulation 
CD14MonocytesTreatedWithCryptococcusDonor2_CNhs13487_tpm_fwd Cd14+MoW/CryptococcusD2+ CD14+ monocytes - treated with Cryptococcus, donor2_CNhs13487_11877-125C5_forward Regulation 
CD14MonocytesTreatedWithCryptococcusDonor1_CNhs13472_tpm_rev Cd14+MoW/CryptococcusD1- CD14+ monocytes - treated with Cryptococcus, donor1_CNhs13472_11867-125B4_reverse Regulation 
CD14MonocytesTreatedWithCryptococcusDonor1_CNhs13472_tpm_fwd Cd14+MoW/CryptococcusD1+ CD14+ monocytes - treated with Cryptococcus, donor1_CNhs13472_11867-125B4_forward Regulation 
CD14MonocytesTreatedWithCandidaDonor3_CNhs13494_tpm_rev Cd14+MoW/CandidaD3- CD14+ monocytes - treated with Candida, donor3_CNhs13494_11888-125D7_reverse Regulation 
CD14MonocytesTreatedWithCandidaDonor3_CNhs13494_tpm_fwd Cd14+MoW/CandidaD3+ CD14+ monocytes - treated with Candida, donor3_CNhs13494_11888-125D7_forward Regulation 
CD14MonocytesTreatedWithCandidaDonor2_CNhs13488_tpm_rev Cd14+MoW/CandidaD2- CD14+ monocytes - treated with Candida, donor2_CNhs13488_11878-125C6_reverse Regulation 
CD14MonocytesTreatedWithCandidaDonor2_CNhs13488_tpm_fwd Cd14+MoW/CandidaD2+ CD14+ monocytes - treated with Candida, donor2_CNhs13488_11878-125C6_forward Regulation 
CD14MonocytesTreatedWithCandidaDonor1_CNhs13473_tpm_rev Cd14+MoW/CandidaD1- CD14+ monocytes - treated with Candida, donor1_CNhs13473_11868-125B5_reverse Regulation 
CD14MonocytesTreatedWithCandidaDonor1_CNhs13473_tpm_fwd Cd14+MoW/CandidaD1+ CD14+ monocytes - treated with Candida, donor1_CNhs13473_11868-125B5_forward Regulation 
CD14MonocytesTreatedWithBCGDonor3_CNhs13543_tpm_rev Cd14+MoW/BcgD3- CD14+ monocytes - treated with BCG, donor3_CNhs13543_11880-125C8_reverse Regulation 
CD14MonocytesTreatedWithBCGDonor3_CNhs13543_tpm_fwd Cd14+MoW/BcgD3+ CD14+ monocytes - treated with BCG, donor3_CNhs13543_11880-125C8_forward Regulation 
CD14MonocytesTreatedWithBCGDonor2_CNhs13475_tpm_rev Cd14+MoW/BcgD2- CD14+ monocytes - treated with BCG, donor2_CNhs13475_11870-125B7_reverse Regulation 
CD14MonocytesTreatedWithBCGDonor2_CNhs13475_tpm_fwd Cd14+MoW/BcgD2+ CD14+ monocytes - treated with BCG, donor2_CNhs13475_11870-125B7_forward Regulation 
CD14MonocytesTreatedWithBCGDonor1_CNhs13465_tpm_rev Cd14+MoW/BcgD1- CD14+ monocytes - treated with BCG, donor1_CNhs13465_11860-125A6_reverse Regulation 
CD14MonocytesTreatedWithBCGDonor1_CNhs13465_tpm_fwd Cd14+MoW/BcgD1+ CD14+ monocytes - treated with BCG, donor1_CNhs13465_11860-125A6_forward Regulation 
CD14MonocytesTreatedWithBglucanDonor3_CNhs13495_tpm_rev Cd14+MoW/B-glucanD3- CD14+ monocytes - treated with B-glucan, donor3_CNhs13495_11889-125D8_reverse Regulation 
CD14MonocytesTreatedWithBglucanDonor3_CNhs13495_tpm_fwd Cd14+MoW/B-glucanD3+ CD14+ monocytes - treated with B-glucan, donor3_CNhs13495_11889-125D8_forward Regulation 
CD14MonocytesTreatedWithBglucanDonor2_CNhs13489_tpm_rev Cd14+MoW/B-glucanD2- CD14+ monocytes - treated with B-glucan, donor2_CNhs13489_11879-125C7_reverse Regulation 
CD14MonocytesTreatedWithBglucanDonor2_CNhs13489_tpm_fwd Cd14+MoW/B-glucanD2+ CD14+ monocytes - treated with B-glucan, donor2_CNhs13489_11879-125C7_forward Regulation 
CD14MonocytesTreatedWithBglucanDonor1_CNhs13474_tpm_rev Cd14+MoW/B-glucanD1- CD14+ monocytes - treated with B-glucan, donor1_CNhs13474_11869-125B6_reverse Regulation 
CD14MonocytesTreatedWithBglucanDonor1_CNhs13474_tpm_fwd Cd14+MoW/B-glucanD1+ CD14+ monocytes - treated with B-glucan, donor1_CNhs13474_11869-125B6_forward Regulation 
CD14MonocytesMockTreatedDonor3_CNhs13491_tpm_rev Cd14+MoMockTreatedD3- CD14+ monocytes - mock treated, donor3_CNhs13491_11883-125D2_reverse Regulation 
CD14MonocytesMockTreatedDonor3_CNhs13491_tpm_fwd Cd14+MoMockTreatedD3+ CD14+ monocytes - mock treated, donor3_CNhs13491_11883-125D2_forward Regulation 
CD14MonocytesMockTreatedDonor2_CNhs13484_tpm_rev Cd14+MoMockTreatedD2- CD14+ monocytes - mock treated, donor2_CNhs13484_11873-125C1_reverse Regulation 
CD14MonocytesMockTreatedDonor2_CNhs13484_tpm_fwd Cd14+MoMockTreatedD2+ CD14+ monocytes - mock treated, donor2_CNhs13484_11873-125C1_forward Regulation 
CD14MonocytesMockTreatedDonor1_CNhs13468_tpm_rev Cd14+MoMockTreatedD1- CD14+ monocytes - mock treated, donor1_CNhs13468_11863-125A9_reverse Regulation 
CD14MonocytesMockTreatedDonor1_CNhs13468_tpm_fwd Cd14+MoMockTreatedD1+ CD14+ monocytes - mock treated, donor1_CNhs13468_11863-125A9_forward Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor3_CNhs11904_tpm_rev Cd14+MoEndothelialProgenitorCellsD3- CD14+ monocyte derived endothelial progenitor cells, donor3_CNhs11904_11386-118B9_reverse Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor3_CNhs11904_tpm_fwd Cd14+MoEndothelialProgenitorCellsD3+ CD14+ monocyte derived endothelial progenitor cells, donor3_CNhs11904_11386-118B9_forward Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor2_CNhs11897_tpm_rev Cd14+MoEndothelialProgenitorCellsD2- CD14+ monocyte derived endothelial progenitor cells, donor2_CNhs11897_11310-117C5_reverse Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor2_CNhs11897_tpm_fwd Cd14+MoEndothelialProgenitorCellsD2+ CD14+ monocyte derived endothelial progenitor cells, donor2_CNhs11897_11310-117C5_forward Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor1_CNhs10858_tpm_rev Cd14+MoEndothelialProgenitorCellsD1- CD14+ monocyte derived endothelial progenitor cells, donor1_CNhs10858_11229-116C5_reverse Regulation 
CD14MonocyteDerivedEndothelialProgenitorCellsDonor1_CNhs10858_tpm_fwd Cd14+MoEndothelialProgenitorCellsD1+ CD14+ monocyte derived endothelial progenitor cells, donor1_CNhs10858_11229-116C5_forward Regulation 
CD14MonocytesDonor3_CNhs11997_tpm_rev Cd14+MoD3- CD14+ Monocytes, donor3_CNhs11997_11381-118B4_reverse Regulation 
CD14MonocytesDonor3_CNhs11997_tpm_fwd Cd14+MoD3+ CD14+ Monocytes, donor3_CNhs11997_11381-118B4_forward Regulation 
CD14MonocytesDonor2_CNhs11954_tpm_rev Cd14+MoD2- CD14+ Monocytes, donor2_CNhs11954_11305-117B9_reverse Regulation 
CD14MonocytesDonor2_CNhs11954_tpm_fwd Cd14+MoD2+ CD14+ Monocytes, donor2_CNhs11954_11305-117B9_forward Regulation 
CD14MonocytesDonor1_CNhs10852_tpm_rev Cd14+MoD1- CD14+ Monocytes, donor1_CNhs10852_11224-116B9_reverse Regulation 
CD14MonocytesDonor1_CNhs10852_tpm_fwd Cd14+MoD1+ CD14+ Monocytes, donor1_CNhs10852_11224-116B9_forward Regulation 
CD14CD16MonocytesDonor3_CNhs13540_tpm_rev Cd14+cd16-MonocytesD3- CD14+CD16- Monocytes, donor3_CNhs13540_11910-125G2_reverse Regulation 
CD14CD16MonocytesDonor3_CNhs13540_tpm_fwd Cd14+cd16-MonocytesD3+ CD14+CD16- Monocytes, donor3_CNhs13540_11910-125G2_forward Regulation 
CD14CD16MonocytesDonor2_CNhs13216_tpm_rev Cd14+cd16-MonocytesD2- CD14+CD16- Monocytes, donor2_CNhs13216_11799-124C8_reverse Regulation 
CD14CD16MonocytesDonor2_CNhs13216_tpm_fwd Cd14+cd16-MonocytesD2+ CD14+CD16- Monocytes, donor2_CNhs13216_11799-124C8_forward Regulation 
CD14CD16MonocytesDonor1_CNhs13224_tpm_rev Cd14+cd16-MonocytesD1- CD14+CD16- Monocytes, donor1_CNhs13224_11788-124B6_reverse Regulation 
CD14CD16MonocytesDonor1_CNhs13224_tpm_fwd Cd14+cd16-MonocytesD1+ CD14+CD16- Monocytes, donor1_CNhs13224_11788-124B6_forward Regulation 
CD14CD16MonocytesDonor3_CNhs13549_tpm_rev Cd14+cd16+MonocytesD3- CD14+CD16+ Monocytes, donor3_CNhs13549_11912-125G4_reverse Regulation 
CD14CD16MonocytesDonor3_CNhs13549_tpm_fwd Cd14+cd16+MonocytesD3+ CD14+CD16+ Monocytes, donor3_CNhs13549_11912-125G4_forward Regulation 
CD14CD16MonocytesDonor2_CNhs13208_tpm_rev Cd14+cd16+MonocytesD2- CD14+CD16+ Monocytes, donor2_CNhs13208_11801-124D1_reverse Regulation 
CD14CD16MonocytesDonor2_CNhs13208_tpm_fwd Cd14+cd16+MonocytesD2+ CD14+CD16+ Monocytes, donor2_CNhs13208_11801-124D1_forward Regulation 
CD14CD16MonocytesDonor1_CNhs13541_tpm_rev Cd14+cd16+MonocytesD1- CD14+CD16+ Monocytes, donor1_CNhs13541_11789-124B7_reverse Regulation 
CD14CD16MonocytesDonor1_CNhs13541_tpm_fwd Cd14+cd16+MonocytesD1+ CD14+CD16+ Monocytes, donor1_CNhs13541_11789-124B7_forward Regulation 
MultipotentCordBloodUnrestrictedSomaticStemCellsDonor2_CNhs12105_tpm_rev CbStemCellsD2- Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor2_CNhs12105_11629-122B9_reverse Regulation 
MultipotentCordBloodUnrestrictedSomaticStemCellsDonor2_CNhs12105_tpm_fwd CbStemCellsD2+ Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor2_CNhs12105_11629-122B9_forward Regulation 
MultipotentCordBloodUnrestrictedSomaticStemCellsDonor1_CNhs11350_tpm_rev CbStemCellsD1- Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor1_CNhs11350_11549-120C1_reverse Regulation 
MultipotentCordBloodUnrestrictedSomaticStemCellsDonor1_CNhs11350_tpm_fwd CbStemCellsD1+ Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor1_CNhs11350_11549-120C1_forward Regulation 
CardiacMyocyteDonor3_CNhs12571_tpm_rev CardiacMyocyteD3- Cardiac Myocyte, donor3_CNhs12571_11686-122I3_reverse Regulation 
CardiacMyocyteDonor3_CNhs12571_tpm_fwd CardiacMyocyteD3+ Cardiac Myocyte, donor3_CNhs12571_11686-122I3_forward Regulation 
CardiacMyocyteDonor2_CNhs12350_tpm_rev CardiacMyocyteD2- Cardiac Myocyte, donor2_CNhs12350_11605-120I3_reverse Regulation 
CardiacMyocyteDonor2_CNhs12350_tpm_fwd CardiacMyocyteD2+ Cardiac Myocyte, donor2_CNhs12350_11605-120I3_forward Regulation 
CardiacMyocyteDonor1_CNhs12341_tpm_rev CardiacMyocyteD1- Cardiac Myocyte, donor1_CNhs12341_11525-119I4_reverse Regulation 
CardiacMyocyteDonor1_CNhs12341_tpm_fwd CardiacMyocyteD1+ Cardiac Myocyte, donor1_CNhs12341_11525-119I4_forward Regulation 
BronchialEpithelialCellDonor7_CNhs12642_tpm_rev BronchialEpithelialCellD7- Bronchial Epithelial Cell, donor7_CNhs12642_11769-123I5_reverse Regulation 
BronchialEpithelialCellDonor7_CNhs12642_tpm_fwd BronchialEpithelialCellD7+ Bronchial Epithelial Cell, donor7_CNhs12642_11769-123I5_forward Regulation 
BronchialEpithelialCellDonor6_CNhs12062_tpm_rev BronchialEpithelialCellD6- Bronchial Epithelial Cell, donor6_CNhs12062_11461-119B3_reverse Regulation 
BronchialEpithelialCellDonor6_CNhs12062_tpm_fwd BronchialEpithelialCellD6+ Bronchial Epithelial Cell, donor6_CNhs12062_11461-119B3_forward Regulation 
BronchialEpithelialCellDonor5_CNhs12058_tpm_rev BronchialEpithelialCellD5- Bronchial Epithelial Cell, donor5_CNhs12058_11457-119A8_reverse Regulation 
BronchialEpithelialCellDonor5_CNhs12058_tpm_fwd BronchialEpithelialCellD5+ Bronchial Epithelial Cell, donor5_CNhs12058_11457-119A8_forward Regulation 
BronchialEpithelialCellDonor4_CNhs12054_tpm_rev BronchialEpithelialCellD4- Bronchial Epithelial Cell, donor4_CNhs12054_11453-119A4_reverse Regulation 
BronchialEpithelialCellDonor4_CNhs12054_tpm_fwd BronchialEpithelialCellD4+ Bronchial Epithelial Cell, donor4_CNhs12054_11453-119A4_forward Regulation 
BronchialEpithelialCellDonor3_CNhs12623_tpm_rev BronchialEpithelialCellD3- Bronchial Epithelial Cell, donor3_CNhs12623_11672-122G7_reverse Regulation 
BronchialEpithelialCellDonor3_CNhs12623_tpm_fwd BronchialEpithelialCellD3+ Bronchial Epithelial Cell, donor3_CNhs12623_11672-122G7_forward Regulation 
BronchialEpithelialCellDonor2_CNhs12085_tpm_rev BronchialEpithelialCellD2- Bronchial Epithelial Cell, donor2_CNhs12085_11591-120G7_reverse Regulation 
BronchialEpithelialCellDonor2_CNhs12085_tpm_fwd BronchialEpithelialCellD2+ Bronchial Epithelial Cell, donor2_CNhs12085_11591-120G7_forward Regulation 
BronchialEpithelialCellDonor1_CNhs11327_tpm_rev BronchialEpithelialCellD1- Bronchial Epithelial Cell, donor1_CNhs11327_11511-119G8_reverse Regulation 
BronchialEpithelialCellDonor1_CNhs11327_tpm_fwd BronchialEpithelialCellD1+ Bronchial Epithelial Cell, donor1_CNhs11327_11511-119G8_forward Regulation 
BasophilsDonor3_CNhs12575_tpm_rev BasophilsD3- Basophils, donor3_CNhs12575_12243-129H2_reverse Regulation 
BasophilsDonor3_CNhs12575_tpm_fwd BasophilsD3+ Basophils, donor3_CNhs12575_12243-129H2_forward Regulation 
AstrocyteCerebralCortexDonor3_CNhs12005_tpm_rev AstrocyteCerebralCortexD3- Astrocyte - cerebral cortex, donor3_CNhs12005_11392-118C6_reverse Regulation 
AstrocyteCerebralCortexDonor3_CNhs12005_tpm_fwd AstrocyteCerebralCortexD3+ Astrocyte - cerebral cortex, donor3_CNhs12005_11392-118C6_forward Regulation 
AstrocyteCerebralCortexDonor2_CNhs11960_tpm_rev AstrocyteCerebralCortexD2- Astrocyte - cerebral cortex, donor2_CNhs11960_11316-117D2_reverse Regulation 
AstrocyteCerebralCortexDonor2_CNhs11960_tpm_fwd AstrocyteCerebralCortexD2+ Astrocyte - cerebral cortex, donor2_CNhs11960_11316-117D2_forward Regulation 
AstrocyteCerebralCortexDonor1_CNhs10864_tpm_rev AstrocyteCerebralCortexD1- Astrocyte - cerebral cortex, donor1_CNhs10864_11235-116D2_reverse Regulation 
AstrocyteCerebralCortexDonor1_CNhs10864_tpm_fwd AstrocyteCerebralCortexD1+ Astrocyte - cerebral cortex, donor1_CNhs10864_11235-116D2_forward Regulation 
AstrocyteCerebellumDonor3_CNhs12117_tpm_rev AstrocyteCerebellumD3- Astrocyte - cerebellum, donor3_CNhs12117_11661-122F5_reverse Regulation 
AstrocyteCerebellumDonor3_CNhs12117_tpm_fwd AstrocyteCerebellumD3+ Astrocyte - cerebellum, donor3_CNhs12117_11661-122F5_forward Regulation 
AstrocyteCerebellumDonor2_CNhs12081_tpm_rev AstrocyteCerebellumD2- Astrocyte - cerebellum, donor2_CNhs12081_11580-120F5_reverse Regulation 
AstrocyteCerebellumDonor2_CNhs12081_tpm_fwd AstrocyteCerebellumD2+ Astrocyte - cerebellum, donor2_CNhs12081_11580-120F5_forward Regulation 
AstrocyteCerebellumDonor1_CNhs11321_tpm_rev AstrocyteCerebellumD1- Astrocyte - cerebellum, donor1_CNhs11321_11500-119F6_reverse Regulation 
AstrocyteCerebellumDonor1_CNhs11321_tpm_fwd AstrocyteCerebellumD1+ Astrocyte - cerebellum, donor1_CNhs11321_11500-119F6_forward Regulation 
AnulusPulposusCellDonor2_CNhs12064_tpm_rev AnulusPulposusCellD2- Anulus Pulposus Cell, donor2_CNhs12064_11463-119B5_reverse Regulation 
AnulusPulposusCellDonor2_CNhs12064_tpm_fwd AnulusPulposusCellD2+ Anulus Pulposus Cell, donor2_CNhs12064_11463-119B5_forward Regulation 
AnulusPulposusCellDonor1_CNhs10876_tpm_rev AnulusPulposusCellD1- Anulus Pulposus Cell, donor1_CNhs10876_11248-116E6_reverse Regulation 
AnulusPulposusCellDonor1_CNhs10876_tpm_fwd AnulusPulposusCellD1+ Anulus Pulposus Cell, donor1_CNhs10876_11248-116E6_forward Regulation 
AmnioticMembraneCellsDonor3_CNhs12379_tpm_rev AmnioticMembraneCellsD3- amniotic membrane cells, donor3_CNhs12379_12237-129G5_reverse Regulation 
AmnioticMembraneCellsDonor3_CNhs12379_tpm_fwd AmnioticMembraneCellsD3+ amniotic membrane cells, donor3_CNhs12379_12237-129G5_forward Regulation 
AmnioticMembraneCellsDonor2_CNhs12503_tpm_rev AmnioticMembraneCellsD2- amniotic membrane cells, donor2_CNhs12503_12236-129G4_reverse Regulation 
AmnioticMembraneCellsDonor2_CNhs12503_tpm_fwd AmnioticMembraneCellsD2+ amniotic membrane cells, donor2_CNhs12503_12236-129G4_forward Regulation 
AmnioticMembraneCellsDonor1_CNhs12502_tpm_rev AmnioticMembraneCellsD1- amniotic membrane cells, donor1_CNhs12502_12235-129G3_reverse Regulation 
AmnioticMembraneCellsDonor1_CNhs12502_tpm_fwd AmnioticMembraneCellsD1+ amniotic membrane cells, donor1_CNhs12502_12235-129G3_forward Regulation 
AmnioticEpithelialCellsDonor3_CNhs12125_tpm_rev AmnioticEpithelialCellsD3- Amniotic Epithelial Cells, donor3_CNhs12125_11694-123A2_reverse Regulation 
AmnioticEpithelialCellsDonor3_CNhs12125_tpm_fwd AmnioticEpithelialCellsD3+ Amniotic Epithelial Cells, donor3_CNhs12125_11694-123A2_forward Regulation 
AmnioticEpithelialCellsDonor2_CNhs12098_tpm_rev AmnioticEpithelialCellsD2- Amniotic Epithelial Cells, donor2_CNhs12098_11613-122A2_reverse Regulation 
AmnioticEpithelialCellsDonor2_CNhs12098_tpm_fwd AmnioticEpithelialCellsD2+ Amniotic Epithelial Cells, donor2_CNhs12098_11613-122A2_forward Regulation 
AmnioticEpithelialCellsDonor1_CNhs11341_tpm_rev AmnioticEpithelialCellsD1- Amniotic Epithelial Cells, donor1_CNhs11341_11533-120A3_reverse Regulation 
AmnioticEpithelialCellsDonor1_CNhs11341_tpm_fwd AmnioticEpithelialCellsD1+ Amniotic Epithelial Cells, donor1_CNhs11341_11533-120A3_forward Regulation 
AlveolarEpithelialCellsDonor3_CNhs12119_tpm_rev AlveolarEpithelialCellsD3- Alveolar Epithelial Cells, donor3_CNhs12119_11671-122G6_reverse Regulation 
AlveolarEpithelialCellsDonor3_CNhs12119_tpm_fwd AlveolarEpithelialCellsD3+ Alveolar Epithelial Cells, donor3_CNhs12119_11671-122G6_forward Regulation 
AlveolarEpithelialCellsDonor2_CNhs12084_tpm_rev AlveolarEpithelialCellsD2- Alveolar Epithelial Cells, donor2_CNhs12084_11590-120G6_reverse Regulation 
AlveolarEpithelialCellsDonor2_CNhs12084_tpm_fwd AlveolarEpithelialCellsD2+ Alveolar Epithelial Cells, donor2_CNhs12084_11590-120G6_forward Regulation 
AlveolarEpithelialCellsDonor1_CNhs11325_tpm_rev AlveolarEpithelialCellsD1- Alveolar Epithelial Cells, donor1_CNhs11325_11510-119G7_reverse Regulation 
AlveolarEpithelialCellsDonor1_CNhs11325_tpm_fwd AlveolarEpithelialCellsD1+ Alveolar Epithelial Cells, donor1_CNhs11325_11510-119G7_forward Regulation 
AdipocyteSubcutaneousDonor3_CNhs12017_tpm_rev AdipocyteSubcutaneousD3- Adipocyte - subcutaneous, donor3_CNhs12017_11408-118E4_reverse Regulation 
AdipocyteSubcutaneousDonor3_CNhs12017_tpm_fwd AdipocyteSubcutaneousD3+ Adipocyte - subcutaneous, donor3_CNhs12017_11408-118E4_forward Regulation 
AdipocyteSubcutaneousDonor2_CNhs11371_tpm_rev AdipocyteSubcutaneousD2- Adipocyte - subcutaneous, donor2_CNhs11371_11336-117F4_reverse Regulation 
AdipocyteSubcutaneousDonor2_CNhs11371_tpm_fwd AdipocyteSubcutaneousD2+ Adipocyte - subcutaneous, donor2_CNhs11371_11336-117F4_forward Regulation 
AdipocyteSubcutaneousDonor1_CNhs12494_tpm_rev AdipocyteSubcutaneousD1- Adipocyte - subcutaneous, donor1_CNhs12494_11259-116F8_reverse Regulation 
AdipocyteSubcutaneousDonor1_CNhs12494_tpm_fwd AdipocyteSubcutaneousD1+ Adipocyte - subcutaneous, donor1_CNhs12494_11259-116F8_forward Regulation 
AdipocytePerirenalDonor1_CNhs12069_tpm_rev AdipocytePerirenalD1- Adipocyte - perirenal, donor1_CNhs12069_11476-119C9_reverse Regulation 
AdipocytePerirenalDonor1_CNhs12069_tpm_fwd AdipocytePerirenalD1+ Adipocyte - perirenal, donor1_CNhs12069_11476-119C9_forward Regulation 
AdipocyteOmentalDonor3_CNhs12068_tpm_rev AdipocyteOmentalD3- Adipocyte - omental, donor3_CNhs12068_11475-119C8_reverse Regulation 
AdipocyteOmentalDonor3_CNhs12068_tpm_fwd AdipocyteOmentalD3+ Adipocyte - omental, donor3_CNhs12068_11475-119C8_forward Regulation 
AdipocyteOmentalDonor2_CNhs12067_tpm_rev AdipocyteOmentalD2- Adipocyte - omental, donor2_CNhs12067_11474-119C7_reverse Regulation 
AdipocyteOmentalDonor2_CNhs12067_tpm_fwd AdipocyteOmentalD2+ Adipocyte - omental, donor2_CNhs12067_11474-119C7_forward Regulation 
AdipocyteOmentalDonor1_CNhs11054_tpm_rev AdipocyteOmentalD1- Adipocyte - omental, donor1_CNhs11054_11473-119C6_reverse Regulation 
AdipocyteOmentalDonor1_CNhs11054_tpm_fwd AdipocyteOmentalD1+ Adipocyte - omental, donor1_CNhs11054_11473-119C6_forward Regulation 
AdipocyteBreastDonor2_CNhs11969_tpm_rev AdipocyteBreastD2- Adipocyte - breast, donor2_CNhs11969_11327-117E4_reverse Regulation 
AdipocyteBreastDonor2_CNhs11969_tpm_fwd AdipocyteBreastD2+ Adipocyte - breast, donor2_CNhs11969_11327-117E4_forward Regulation 
AdipocyteBreastDonor1_CNhs11051_tpm_rev AdipocyteBreastD1- Adipocyte - breast, donor1_CNhs11051_11376-118A8_reverse Regulation 
AdipocyteBreastDonor1_CNhs11051_tpm_fwd AdipocyteBreastD1+ Adipocyte - breast, donor1_CNhs11051_11376-118A8_forward Regulation 
PromyelocytesmyelocytesPMCDonor3_CNhs12529_tpm_rev Promyelocytes/myelocytesPmcD3- promyelocytes/myelocytes PMC, donor3_CNhs12529_12140-128E7_reverse Regulation 
PromyelocytesmyelocytesPMCDonor3_CNhs12529_tpm_fwd Promyelocytes/myelocytesPmcD3+ promyelocytes/myelocytes PMC, donor3_CNhs12529_12140-128E7_forward Regulation 
PromyelocytesmyelocytesPMCDonor2_CNhs12525_tpm_rev Promyelocytes/myelocytesPmcD2- promyelocytes/myelocytes PMC, donor2_CNhs12525_12136-128E3_reverse Regulation 
PromyelocytesmyelocytesPMCDonor2_CNhs12525_tpm_fwd Promyelocytes/myelocytesPmcD2+ promyelocytes/myelocytes PMC, donor2_CNhs12525_12136-128E3_forward Regulation 
PromyelocytesmyelocytesPMCDonor1_CNhs12520_tpm_rev Promyelocytes/myelocytesPmcD1- promyelocytes/myelocytes PMC, donor1_CNhs12520_12132-128D8_reverse Regulation 
PromyelocytesmyelocytesPMCDonor1_CNhs12520_tpm_fwd Promyelocytes/myelocytesPmcD1+ promyelocytes/myelocytes PMC, donor1_CNhs12520_12132-128D8_forward Regulation 
NeutrophilPMNDonor3_CNhs12530_tpm_rev NeutrophilPmnD3- neutrophil PMN, donor3_CNhs12530_12141-128E8_reverse Regulation 
NeutrophilPMNDonor3_CNhs12530_tpm_fwd NeutrophilPmnD3+ neutrophil PMN, donor3_CNhs12530_12141-128E8_forward Regulation 
NeutrophilPMNDonor2_CNhs12526_tpm_rev NeutrophilPmnD2- neutrophil PMN, donor2_CNhs12526_12137-128E4_reverse Regulation 
NeutrophilPMNDonor2_CNhs12526_tpm_fwd NeutrophilPmnD2+ neutrophil PMN, donor2_CNhs12526_12137-128E4_forward Regulation 
NeutrophilPMNDonor1_CNhs12522_tpm_rev NeutrophilPmnD1- neutrophil PMN, donor1_CNhs12522_12133-128D9_reverse Regulation 
NeutrophilPMNDonor1_CNhs12522_tpm_fwd NeutrophilPmnD1+ neutrophil PMN, donor1_CNhs12522_12133-128D9_forward Regulation 
NasalEpithelialCellsDonor1TechRep2_CNhs12554_tpm_rev NasalEpithelialCellsD1Tr2- nasal epithelial cells, donor1, tech_rep2_CNhs12554_12226-129F3_reverse Regulation 
NasalEpithelialCellsDonor1TechRep2_CNhs12554_tpm_fwd NasalEpithelialCellsD1Tr2+ nasal epithelial cells, donor1, tech_rep2_CNhs12554_12226-129F3_forward Regulation 
MesothelialCellsDonor2_CNhs12197_tpm_rev MesothelialCellsD2- Mesothelial Cells, donor2_CNhs12197_12156-128G5_reverse Regulation 
MesothelialCellsDonor2_CNhs12197_tpm_fwd MesothelialCellsD2+ Mesothelial Cells, donor2_CNhs12197_12156-128G5_forward Regulation 
MatureAdipocyteDonor4_CNhs12562_tpm_rev MatureAdipocyteD4- mature adipocyte, donor4_CNhs12562_12234-129G2_reverse Regulation 
MatureAdipocyteDonor4_CNhs12562_tpm_fwd MatureAdipocyteD4+ mature adipocyte, donor4_CNhs12562_12234-129G2_forward Regulation 
MatureAdipocyteDonor3_CNhs12560_tpm_rev MatureAdipocyteD3- mature adipocyte, donor3_CNhs12560_12233-129G1_reverse Regulation 
MatureAdipocyteDonor3_CNhs12560_tpm_fwd MatureAdipocyteD3+ mature adipocyte, donor3_CNhs12560_12233-129G1_forward Regulation 
MatureAdipocyteDonor2_CNhs12559_tpm_rev MatureAdipocyteD2- mature adipocyte, donor2_CNhs12559_12232-129F9_reverse Regulation 
MatureAdipocyteDonor2_CNhs12559_tpm_fwd MatureAdipocyteD2+ mature adipocyte, donor2_CNhs12559_12232-129F9_forward Regulation 
MatureAdipocyteDonor1_CNhs12558_tpm_rev MatureAdipocyteD1- mature adipocyte, donor1_CNhs12558_12231-129F8_reverse Regulation 
MatureAdipocyteDonor1_CNhs12558_tpm_fwd MatureAdipocyteD1+ mature adipocyte, donor1_CNhs12558_12231-129F8_forward Regulation 
MallassezderivedCellsDonor1MZH3_CNhs12538_tpm_rev MallassezCellsD1- Mallassez-derived cells, donor1 (MZH3)_CNhs12538_12142-128E9_reverse Regulation 
MallassezderivedCellsDonor1MZH3_CNhs12538_tpm_fwd MallassezCellsD1+ Mallassez-derived cells, donor1 (MZH3)_CNhs12538_12142-128E9_forward Regulation 
GranulocyteMacrophageProgenitorDonor3_CNhs12528_tpm_rev GranulocyteMacrophageProgenitorD3- granulocyte macrophage progenitor, donor3_CNhs12528_12139-128E6_reverse Regulation 
GranulocyteMacrophageProgenitorDonor3_CNhs12528_tpm_fwd GranulocyteMacrophageProgenitorD3+ granulocyte macrophage progenitor, donor3_CNhs12528_12139-128E6_forward Regulation 
GranulocyteMacrophageProgenitorDonor2_CNhs12524_tpm_rev GranulocyteMacrophageProgenitorD2- granulocyte macrophage progenitor, donor2_CNhs12524_12135-128E2_reverse Regulation 
GranulocyteMacrophageProgenitorDonor2_CNhs12524_tpm_fwd GranulocyteMacrophageProgenitorD2+ granulocyte macrophage progenitor, donor2_CNhs12524_12135-128E2_forward Regulation 
GranulocyteMacrophageProgenitorDonor1_CNhs12519_tpm_rev GranulocyteMacrophageProgenitorD1- granulocyte macrophage progenitor, donor1_CNhs12519_12131-128D7_reverse Regulation 
GranulocyteMacrophageProgenitorDonor1_CNhs12519_tpm_fwd GranulocyteMacrophageProgenitorD1+ granulocyte macrophage progenitor, donor1_CNhs12519_12131-128D7_forward Regulation 
EosinophilsDonor3_CNhs12549_tpm_rev EosinophilsD3- Eosinophils, donor3_CNhs12549_12246-129H5_reverse Regulation 
EosinophilsDonor3_CNhs12549_tpm_fwd EosinophilsD3+ Eosinophils, donor3_CNhs12549_12246-129H5_forward Regulation 
EosinophilsDonor2_CNhs12548_tpm_rev EosinophilsD2- Eosinophils, donor2_CNhs12548_12245-129H4_reverse Regulation 
EosinophilsDonor2_CNhs12548_tpm_fwd EosinophilsD2+ Eosinophils, donor2_CNhs12548_12245-129H4_forward Regulation 
EosinophilsDonor1_CNhs12547_tpm_rev EosinophilsD1- Eosinophils, donor1_CNhs12547_12244-129H3_reverse Regulation 
EosinophilsDonor1_CNhs12547_tpm_fwd EosinophilsD1+ Eosinophils, donor1_CNhs12547_12244-129H3_forward Regulation 
DendriticCellsPlasmacytoidDonor3_CNhs12200_tpm_rev DendriticCellsPlasmacytoidD3- Dendritic Cells - plasmacytoid, donor3_CNhs12200_11385-118B8_reverse Regulation 
DendriticCellsPlasmacytoidDonor3_CNhs12200_tpm_fwd DendriticCellsPlasmacytoidD3+ Dendritic Cells - plasmacytoid, donor3_CNhs12200_11385-118B8_forward Regulation 
DendriticCellsPlasmacytoidDonor2_CNhs12196_tpm_rev DendriticCellsPlasmacytoidD2- Dendritic Cells - plasmacytoid, donor2_CNhs12196_11309-117C4_reverse Regulation 
DendriticCellsPlasmacytoidDonor2_CNhs12196_tpm_fwd DendriticCellsPlasmacytoidD2+ Dendritic Cells - plasmacytoid, donor2_CNhs12196_11309-117C4_forward Regulation 
DendriticCellsMonocyteImmatureDerivedDonor2_CNhs12195_tpm_rev DendriticCellsMonocyteImmatureD2- Dendritic Cells - monocyte immature derived, donor2_CNhs12195_11308-117C3_reverse Regulation 
DendriticCellsMonocyteImmatureDerivedDonor2_CNhs12195_tpm_fwd DendriticCellsMonocyteImmatureD2+ Dendritic Cells - monocyte immature derived, donor2_CNhs12195_11308-117C3_forward Regulation 
CommonMyeloidProgenitorCMPDonor2_CNhs12523_tpm_rev CommonMyeloidProgenitorCmpD2- common myeloid progenitor CMP, donor2_CNhs12523_12134-128E1_reverse Regulation 
CommonMyeloidProgenitorCMPDonor2_CNhs12523_tpm_fwd CommonMyeloidProgenitorCmpD2+ common myeloid progenitor CMP, donor2_CNhs12523_12134-128E1_forward Regulation 
CommonMyeloidProgenitorCMPDonor1_CNhs12518_tpm_rev CommonMyeloidProgenitorCmpD1- common myeloid progenitor CMP, donor1_CNhs12518_12130-128D6_reverse Regulation 
CommonMyeloidProgenitorCMPDonor1_CNhs12518_tpm_fwd CommonMyeloidProgenitorCmpD1+ common myeloid progenitor CMP, donor1_CNhs12518_12130-128D6_forward Regulation 
CD8TCellsPluriselectDonor090612Donation3_CNhs12187_tpm_rev Cd8+TCellsPluriD090612Dn3- CD8+ T Cells (pluriselect), donor090612, donation3_CNhs12187_12211-129D6_reverse Regulation 
CD8TCellsPluriselectDonor090612Donation3_CNhs12187_tpm_fwd Cd8+TCellsPluriD090612Dn3+ CD8+ T Cells (pluriselect), donor090612, donation3_CNhs12187_12211-129D6_forward Regulation 
CD8TCellsPluriselectDonor090612Donation2_CNhs12184_tpm_rev Cd8+TCellsPluriD090612Dn2- CD8+ T Cells (pluriselect), donor090612, donation2_CNhs12184_12206-129D1_reverse Regulation 
CD8TCellsPluriselectDonor090612Donation2_CNhs12184_tpm_fwd Cd8+TCellsPluriD090612Dn2+ CD8+ T Cells (pluriselect), donor090612, donation2_CNhs12184_12206-129D1_forward Regulation 
CD8TCellsPluriselectDonor090612Donation1_CNhs12182_tpm_rev Cd8+TCellsPluriD090612Dn1- CD8+ T Cells (pluriselect), donor090612, donation1_CNhs12182_12201-129C5_reverse Regulation 
CD8TCellsPluriselectDonor090612Donation1_CNhs12182_tpm_fwd Cd8+TCellsPluriD090612Dn1+ CD8+ T Cells (pluriselect), donor090612, donation1_CNhs12182_12201-129C5_forward Regulation 
CD8TCellsPluriselectDonor090325Donation2_CNhs12199_tpm_rev Cd8+TCellsPluriD090325Dn2- CD8+ T Cells (pluriselect), donor090325, donation2_CNhs12199_12171-128I2_reverse Regulation 
CD8TCellsPluriselectDonor090325Donation2_CNhs12199_tpm_fwd Cd8+TCellsPluriD090325Dn2+ CD8+ T Cells (pluriselect), donor090325, donation2_CNhs12199_12171-128I2_forward Regulation 
CD8TCellsPluriselectDonor090325Donation1_CNhs12201_tpm_rev Cd8+TCellsPluriD090325Dn1- CD8+ T Cells (pluriselect), donor090325, donation1_CNhs12201_12148-128F6_reverse Regulation 
CD8TCellsPluriselectDonor090325Donation1_CNhs12201_tpm_fwd Cd8+TCellsPluriD090325Dn1+ CD8+ T Cells (pluriselect), donor090325, donation1_CNhs12201_12148-128F6_forward Regulation 
CD8TCellsPluriselectDonor090309Donation3_CNhs12180_tpm_rev Cd8+TCellsPluriD090309Dn3- CD8+ T Cells (pluriselect), donor090309, donation3_CNhs12180_12196-129B9_reverse Regulation 
CD8TCellsPluriselectDonor090309Donation3_CNhs12180_tpm_fwd Cd8+TCellsPluriD090309Dn3+ CD8+ T Cells (pluriselect), donor090309, donation3_CNhs12180_12196-129B9_forward Regulation 
CD8TCellsPluriselectDonor090309Donation2_CNhs12178_tpm_rev Cd8+TCellsPluriD090309Dn2- CD8+ T Cells (pluriselect), donor090309, donation2_CNhs12178_12191-129B4_reverse Regulation 
CD8TCellsPluriselectDonor090309Donation2_CNhs12178_tpm_fwd Cd8+TCellsPluriD090309Dn2+ CD8+ T Cells (pluriselect), donor090309, donation2_CNhs12178_12191-129B4_forward Regulation 
CD8TCellsPluriselectDonor090309Donation1_CNhs12176_tpm_rev Cd8+TCellsPluriD090309Dn1- CD8+ T Cells (pluriselect), donor090309, donation1_CNhs12176_12186-129A8_reverse Regulation 
CD8TCellsPluriselectDonor090309Donation1_CNhs12176_tpm_fwd Cd8+TCellsPluriD090309Dn1+ CD8+ T Cells (pluriselect), donor090309, donation1_CNhs12176_12186-129A8_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor2_CNhs13237_tpm_rev Cd4+cd25-cd45ra-D2- CD4+CD25-CD45RA- memory conventional T cells, donor2_CNhs13237_11798-124C7_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor2_CNhs13237_tpm_fwd Cd4+cd25-cd45ra-D2+ CD4+CD25-CD45RA- memory conventional T cells, donor2_CNhs13237_11798-124C7_forward Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor1_CNhs13239_tpm_rev Cd4+cd25-cd45ra-D1- CD4+CD25-CD45RA- memory conventional T cells, donor1_CNhs13239_11786-124B4_reverse Regulation 
CD4CD25CD45RAMemoryConventionalTCellsDonor1_CNhs13239_tpm_fwd Cd4+cd25-cd45ra-D1+ CD4+CD25-CD45RA- memory conventional T cells, donor1_CNhs13239_11786-124B4_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor2_CNhs13235_tpm_rev Cd4+cd25+cd45ra+D2- CD4+CD25+CD45RA+ naive regulatory T cells, donor2_CNhs13235_11796-124C5_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor2_CNhs13235_tpm_fwd Cd4+cd25+cd45ra+D2+ CD4+CD25+CD45RA+ naive regulatory T cells, donor2_CNhs13235_11796-124C5_forward Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor1_CNhs13238_tpm_rev Cd4+cd25+cd45ra+D1- CD4+CD25+CD45RA+ naive regulatory T cells, donor1_CNhs13238_11780-124A7_reverse Regulation 
CD4CD25CD45RANaiveRegulatoryTCellsDonor1_CNhs13238_tpm_fwd Cd4+cd25+cd45ra+D1+ CD4+CD25+CD45RA+ naive regulatory T cells, donor1_CNhs13238_11780-124A7_forward Regulation 
CD34StemCellsAdultBoneMarrowDerivedDonor1TechRep2_CNhs12553_tpm_rev Cd34+StemCellsAdultBoneMarrowD1Tr2- CD34+ stem cells - adult bone marrow derived, donor1, tech_rep2_CNhs12553_12225-129F2_reverse Regulation 
CD34StemCellsAdultBoneMarrowDerivedDonor1TechRep2_CNhs12553_tpm_fwd Cd34+StemCellsAdultBoneMarrowD1Tr2+ CD34+ stem cells - adult bone marrow derived, donor1, tech_rep2_CNhs12553_12225-129F2_forward Regulation 
CD34ProgenitorsDonor2_CNhs12205_tpm_rev Cd34+ProgenitorsD2- CD34+ Progenitors, donor2_CNhs12205_11625-122B5_reverse Regulation 
CD34ProgenitorsDonor2_CNhs12205_tpm_fwd Cd34+ProgenitorsD2+ CD34+ Progenitors, donor2_CNhs12205_11625-122B5_forward Regulation 
CD34ProgenitorsDonor1_CNhs13227_tpm_rev Cd34+ProgenitorsD1- CD34+ Progenitors, donor1_CNhs13227_11545-120B6_reverse Regulation 
CD34ProgenitorsDonor1_CNhs13227_tpm_fwd Cd34+ProgenitorsD1+ CD34+ Progenitors, donor1_CNhs13227_11545-120B6_forward Regulation 
CD19BCellsPluriselectDonor090612Donation3_CNhs12188_tpm_rev Cd19+BCellsPluriD090612Dn3- CD19+ B Cells (pluriselect), donor090612, donation3_CNhs12188_12214-129D9_reverse Regulation 
CD19BCellsPluriselectDonor090612Donation3_CNhs12188_tpm_fwd Cd19+BCellsPluriD090612Dn3+ CD19+ B Cells (pluriselect), donor090612, donation3_CNhs12188_12214-129D9_forward Regulation 
CD19BCellsPluriselectDonor090612Donation2_CNhs12185_tpm_rev Cd19+BCellsPluriD090612Dn2- CD19+ B Cells (pluriselect), donor090612, donation2_CNhs12185_12209-129D4_reverse Regulation 
CD19BCellsPluriselectDonor090612Donation2_CNhs12185_tpm_fwd Cd19+BCellsPluriD090612Dn2+ CD19+ B Cells (pluriselect), donor090612, donation2_CNhs12185_12209-129D4_forward Regulation 
CD19BCellsPluriselectDonor090612Donation1_CNhs12183_tpm_rev Cd19+BCellsPluriD090612Dn1- CD19+ B Cells (pluriselect), donor090612, donation1_CNhs12183_12204-129C8_reverse Regulation 
CD19BCellsPluriselectDonor090612Donation1_CNhs12183_tpm_fwd Cd19+BCellsPluriD090612Dn1+ CD19+ B Cells (pluriselect), donor090612, donation1_CNhs12183_12204-129C8_forward Regulation 
CD19BCellsPluriselectDonor090325Donation2_CNhs12175_tpm_rev Cd19+BCellsPluriD090325Dn2- CD19+ B Cells (pluriselect), donor090325, donation2_CNhs12175_12174-128I5_reverse Regulation 
CD19BCellsPluriselectDonor090325Donation2_CNhs12175_tpm_fwd Cd19+BCellsPluriD090325Dn2+ CD19+ B Cells (pluriselect), donor090325, donation2_CNhs12175_12174-128I5_forward Regulation 
CD19BCellsPluriselectDonor090325Donation1_CNhs12531_tpm_rev Cd19+BCellsPluriD090325Dn1- CD19+ B Cells (pluriselect), donor090325, donation1_CNhs12531_12151-128F9_reverse Regulation 
CD19BCellsPluriselectDonor090325Donation1_CNhs12531_tpm_fwd Cd19+BCellsPluriD090325Dn1+ CD19+ B Cells (pluriselect), donor090325, donation1_CNhs12531_12151-128F9_forward Regulation 
CD19BCellsPluriselectDonor090309Donation3_CNhs12181_tpm_rev Cd19+BCellsPluriD090309Dn3- CD19+ B Cells (pluriselect), donor090309, donation3_CNhs12181_12199-129C3_reverse Regulation 
CD19BCellsPluriselectDonor090309Donation3_CNhs12181_tpm_fwd Cd19+BCellsPluriD090309Dn3+ CD19+ B Cells (pluriselect), donor090309, donation3_CNhs12181_12199-129C3_forward Regulation 
CD19BCellsPluriselectDonor090309Donation2_CNhs12179_tpm_rev Cd19+BCellsPluriD090309Dn2- CD19+ B Cells (pluriselect), donor090309, donation2_CNhs12179_12194-129B7_reverse Regulation 
CD19BCellsPluriselectDonor090309Donation2_CNhs12179_tpm_fwd Cd19+BCellsPluriD090309Dn2+ CD19+ B Cells (pluriselect), donor090309, donation2_CNhs12179_12194-129B7_forward Regulation 
CD19BCellsPluriselectDonor090309Donation1_CNhs12177_tpm_rev Cd19+BCellsPluriD090309Dn1- CD19+ B Cells (pluriselect), donor090309, donation1_CNhs12177_12189-129B2_reverse Regulation 
CD19BCellsPluriselectDonor090309Donation1_CNhs12177_tpm_fwd Cd19+BCellsPluriD090309Dn1+ CD19+ B Cells (pluriselect), donor090309, donation1_CNhs12177_12189-129B2_forward Regulation 
CD14CD16MonocytesDonor1_CNhs13229_tpm_rev Cd14-cd16+MonocytesD1- CD14-CD16+ Monocytes, donor1_CNhs13229_11790-124B8_reverse Regulation 
CD14CD16MonocytesDonor1_CNhs13229_tpm_fwd Cd14-cd16+MonocytesD1+ CD14-CD16+ Monocytes, donor1_CNhs13229_11790-124B8_forward Regulation 
CD133StemCellsCordBloodDerivedPool1_CNhs12545_tpm_rev Cd133+StemCellsCordBloodPl1- CD133+ stem cells - cord blood derived, pool1_CNhs12545_12223-129E9_reverse Regulation 
CD133StemCellsCordBloodDerivedPool1_CNhs12545_tpm_fwd Cd133+StemCellsCordBloodPl1+ CD133+ stem cells - cord blood derived, pool1_CNhs12545_12223-129E9_forward Regulation 
CD133StemCellsAdultBoneMarrowDerivedPool1_CNhs12552_tpm_rev Cd133+StemCellsAdultBoneMarrowPl1- CD133+ stem cells - adult bone marrow derived, pool1_CNhs12552_12224-129F1_reverse Regulation 
CD133StemCellsAdultBoneMarrowDerivedPool1_CNhs12552_tpm_fwd Cd133+StemCellsAdultBoneMarrowPl1+ CD133+ stem cells - adult bone marrow derived, pool1_CNhs12552_12224-129F1_forward Regulation 
BasophilsDonor2_CNhs12563_tpm_rev BasophilsD2- Basophils, donor2_CNhs12563_12242-129H1_reverse Regulation 
BasophilsDonor2_CNhs12563_tpm_fwd BasophilsD2+ Basophils, donor2_CNhs12563_12242-129H1_forward Regulation 
BasophilsDonor1_CNhs12546_tpm_rev BasophilsD1- Basophils, donor1_CNhs12546_12241-129G9_reverse Regulation 
BasophilsDonor1_CNhs12546_tpm_fwd BasophilsD1+ Basophils, donor1_CNhs12546_12241-129G9_forward Regulation 
SmoothMuscleCellsAorticDonor0NuclearFraction_CNhs12402_tpm_rev SmcAorticCytofracD0- Smooth Muscle Cells - Aortic, donor0 (nuclear fraction)_CNhs12402_14314-155D3_reverse Regulation 
SmoothMuscleCellsAorticDonor0CytoplasmicFraction_CNhs12401_tpm_rev SmcAorticCytofracD0- Smooth Muscle Cells - Aortic, donor0 (cytoplasmic fraction)_CNhs12401_14313-155D2_reverse Regulation 
SmoothMuscleCellsAorticDonor0NuclearFraction_CNhs12402_tpm_fwd SmcAorticCytofracD0+ Smooth Muscle Cells - Aortic, donor0 (nuclear fraction)_CNhs12402_14314-155D3_forward Regulation 
SmoothMuscleCellsAorticDonor0CytoplasmicFraction_CNhs12401_tpm_fwd SmcAorticCytofracD0+ Smooth Muscle Cells - Aortic, donor0 (cytoplasmic fraction)_CNhs12401_14313-155D2_forward Regulation 
SmallAirwayEpithelialCellsDonor3CytoplasmicFraction_CNhs14563_tpm_rev SmallAirwayEpithelialCellsD3- Small Airway Epithelial Cells donor3 (cytoplasmic fraction)_CNhs14563_14316-155D5_reverse Regulation 
SmallAirwayEpithelialCellsDonor3NuclearFraction_CNhs12583_tpm_rev SmallAirwayEpithelialCellsD3- Small Airway Epithelial Cells, donor3 (nuclear fraction)_CNhs12583_14317-155D6_reverse Regulation 
SmallAirwayEpithelialCellsDonor3CytoplasmicFraction_CNhs14563_tpm_fwd SmallAirwayEpithelialCellsD3+ Small Airway Epithelial Cells donor3 (cytoplasmic fraction)_CNhs14563_14316-155D5_forward Regulation 
SmallAirwayEpithelialCellsDonor3NuclearFraction_CNhs12583_tpm_fwd SmallAirwayEpithelialCellsD3+ Small Airway Epithelial Cells, donor3 (nuclear fraction)_CNhs12583_14317-155D6_forward Regulation 
SmallAirwayEpithelialCellsDonor2NuclearFraction_CNhs14565_tpm_rev SmallAirwayEpithelialCellsD2- Small Airway Epithelial Cells donor2 (nuclear fraction)_CNhs14565_14335-155F6_reverse Regulation 
SmallAirwayEpithelialCellsDonor2CytoplasmicFraction_CNhs14564_tpm_rev SmallAirwayEpithelialCellsD2- Small Airway Epithelial Cells donor2 (cytoplasmic fraction)_CNhs14564_14334-155F5_reverse Regulation 
SmallAirwayEpithelialCellsDonor2NuclearFraction_CNhs14565_tpm_fwd SmallAirwayEpithelialCellsD2+ Small Airway Epithelial Cells donor2 (nuclear fraction)_CNhs14565_14335-155F6_forward Regulation 
SmallAirwayEpithelialCellsDonor2CytoplasmicFraction_CNhs14564_tpm_fwd SmallAirwayEpithelialCellsD2+ Small Airway Epithelial Cells donor2 (cytoplasmic fraction)_CNhs14564_14334-155F5_forward Regulation 
PreadipocyteBreastDonor2CytoplasmicFraction_CNhs14562_tpm_rev PreadipocyteBreastD2- Preadipocyte - breast donor2 (cytoplasmic fraction)_CNhs14562_14319-155D8_reverse Regulation 
PreadipocyteBreastDonor2NuclearFraction_CNhs12584_tpm_rev PreadipocyteBreastD2- Preadipocyte - breast, donor2 (nuclear fraction)_CNhs12584_14320-155D9_reverse Regulation 
PreadipocyteBreastDonor2CytoplasmicFraction_CNhs14562_tpm_fwd PreadipocyteBreastD2+ Preadipocyte - breast donor2 (cytoplasmic fraction)_CNhs14562_14319-155D8_forward Regulation 
PreadipocyteBreastDonor2NuclearFraction_CNhs12584_tpm_fwd PreadipocyteBreastD2+ Preadipocyte - breast, donor2 (nuclear fraction)_CNhs12584_14320-155D9_forward Regulation 
FibroblastSkinNormalDonor2CytoplasmicFraction_CNhs14561_tpm_rev FibrosSkinD2- Fibroblast - skin, normal donor2 (cytoplasmic fraction)_CNhs14561_14301-155B8_reverse Regulation 
FibroblastSkinNormalDonor2CytoplasmicFraction_CNhs14561_tpm_fwd FibrosSkinD2+ Fibroblast - skin, normal donor2 (cytoplasmic fraction)_CNhs14561_14301-155B8_forward Regulation 
FibroblastSkinNormalDonor1CytoplasmicFraction_CNhs14560_tpm_rev FibrosSkinD1- Fibroblast - skin, normal donor1 (cytoplasmic fraction)_CNhs14560_14322-155E2_reverse Regulation 
FibroblastSkinNormalDonor1CytoplasmicFraction_CNhs14560_tpm_fwd FibrosSkinD1+ Fibroblast - skin, normal donor1 (cytoplasmic fraction)_CNhs14560_14322-155E2_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor3NuclearFraction_CNhs12398_tpm_rev FibroSkinSpinalMuscularAtrophyNucfracD3- Fibroblast - skin spinal muscular atrophy, donor3 (nuclear fraction)_CNhs12398_14305-155C3_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor3NuclearFraction_CNhs12398_tpm_fwd FibroSkinSpinalMuscularAtrophyNucfracD3+ Fibroblast - skin spinal muscular atrophy, donor3 (nuclear fraction)_CNhs12398_14305-155C3_forward Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor1NuclearFraction_CNhs12404_tpm_rev FibroSkinSpinalMuscularAtrophyNucfracD1- Fibroblast - skin spinal muscular atrophy, donor1 (nuclear fraction)_CNhs12404_14326-155E6_reverse Regulation 
FibroblastSkinSpinalMuscularAtrophyDonor1NuclearFraction_CNhs12404_tpm_fwd FibroSkinSpinalMuscularAtrophyNucfracD1+ Fibroblast - skin spinal muscular atrophy, donor1 (nuclear fraction)_CNhs12404_14326-155E6_forward Regulation 
FibroblastSkinNormalDonor2NuclearFraction_CNhs12582_tpm_rev FibroSkinNormalNucfracD2- Fibroblast - skin normal, donor2 (nuclear fraction)_CNhs12582_14302-155B9_reverse Regulation 
FibroblastSkinNormalDonor2NuclearFraction_CNhs12582_tpm_fwd FibroSkinNormalNucfracD2+ Fibroblast - skin normal, donor2 (nuclear fraction)_CNhs12582_14302-155B9_forward Regulation 
FibroblastSkinNormalDonor1NuclearFraction_CNhs12403_tpm_rev FibroSkinNormalNucfracD1- Fibroblast - skin normal, donor1 (nuclear fraction)_CNhs12403_14323-155E3_reverse Regulation 
FibroblastSkinNormalDonor1NuclearFraction_CNhs12403_tpm_fwd FibroSkinNormalNucfracD1+ Fibroblast - skin normal, donor1 (nuclear fraction)_CNhs12403_14323-155E3_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor3NuclearFraction_CNhs12399_tpm_rev FibroSkinDystrophiaMyotonicaNucfracD3- Fibroblast - skin dystrophia myotonica, donor3 (nuclear fraction)_CNhs12399_14308-155C6_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor3NuclearFraction_CNhs12399_tpm_fwd FibroSkinDystrophiaMyotonicaNucfracD3+ Fibroblast - skin dystrophia myotonica, donor3 (nuclear fraction)_CNhs12399_14308-155C6_forward Regulation 
FibroblastSkinDystrophiaMyotonicaDonor1NuclearFraction_CNhs12405_tpm_rev FibroSkinDystrophiaMyotonicaNucfracD1- Fibroblast - skin dystrophia myotonica, donor1 (nuclear fraction)_CNhs12405_14329-155E9_reverse Regulation 
FibroblastSkinDystrophiaMyotonicaDonor1NuclearFraction_CNhs12405_tpm_fwd FibroSkinDystrophiaMyotonicaNucfracD1+ Fibroblast - skin dystrophia myotonica, donor1 (nuclear fraction)_CNhs12405_14329-155E9_forward Regulation 
FibroblastAorticAdventitialDonor3NuclearFraction_CNhs12400_tpm_rev FibroAorticAdventitialD3- Fibroblast - Aortic Adventitial, donor3 (nuclear fraction)_CNhs12400_14311-155C9_reverse Regulation 
FibroblastAorticAdventitialDonor3CytoplasmicFraction_CNhs14559_tpm_rev FibroAorticAdventitialD3- Fibroblast - Aortic Adventitial donor3 (cytoplasmic fraction)_CNhs14559_14310-155C8_reverse Regulation 
FibroblastAorticAdventitialDonor3NuclearFraction_CNhs12400_tpm_fwd FibroAorticAdventitialD3+ Fibroblast - Aortic Adventitial, donor3 (nuclear fraction)_CNhs12400_14311-155C9_forward Regulation 
FibroblastAorticAdventitialDonor3CytoplasmicFraction_CNhs14559_tpm_fwd FibroAorticAdventitialD3+ Fibroblast - Aortic Adventitial donor3 (cytoplasmic fraction)_CNhs14559_14310-155C8_forward Regulation 
FibroblastAorticAdventitialDonor2NuclearFraction_CNhs12581_tpm_rev FibroAorticAdventitialD2- Fibroblast - Aortic Adventitial, donor2 (nuclear fraction)_CNhs12581_14332-155F3_reverse Regulation 
FibroblastAorticAdventitialDonor2CytoplasmicFraction_CNhs14558_tpm_rev FibroAorticAdventitialD2- Fibroblast - Aortic Adventitial donor2 (cytoplasmic fraction)_CNhs14558_14331-155F2_reverse Regulation 
FibroblastAorticAdventitialDonor2NuclearFraction_CNhs12581_tpm_fwd FibroAorticAdventitialD2+ Fibroblast - Aortic Adventitial, donor2 (nuclear fraction)_CNhs12581_14332-155F3_forward Regulation 
FibroblastAorticAdventitialDonor2CytoplasmicFraction_CNhs14558_tpm_fwd FibroAorticAdventitialD2+ Fibroblast - Aortic Adventitial donor2 (cytoplasmic fraction)_CNhs14558_14331-155F2_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1CytoplasmicFraction_CNhs14556_tpm_rev Cl:THP-1cyto- acute myeloid leukemia (FAB M5) cell line:THP-1 (cytoplasmic fraction)_CNhs14556_14298-155B5_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1CytoplasmicFraction_CNhs14556_tpm_fwd Cl:THP-1cyto+ acute myeloid leukemia (FAB M5) cell line:THP-1 (cytoplasmic fraction)_CNhs14556_14298-155B5_forward Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep3_CNhs13499_tpm_rev Hep2W/StreptococciJrs4Br3- Hep-2 cells treated with Streptococci strain JRS4, biol_rep3_CNhs13499_11896-125E6_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep3_CNhs13499_tpm_fwd Hep2W/StreptococciJrs4Br3+ Hep-2 cells treated with Streptococci strain JRS4, biol_rep3_CNhs13499_11896-125E6_forward Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep2_CNhs13498_tpm_rev Hep2W/StreptococciJrs4Br2- Hep-2 cells treated with Streptococci strain JRS4, biol_rep2_CNhs13498_11895-125E5_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep2_CNhs13498_tpm_fwd Hep2W/StreptococciJrs4Br2+ Hep-2 cells treated with Streptococci strain JRS4, biol_rep2_CNhs13498_11895-125E5_forward Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep1_CNhs13478_tpm_rev Hep2W/StreptococciJrs4Br1- Hep-2 cells treated with Streptococci strain JRS4, biol_rep1_CNhs13478_11894-125E4_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrainJRS4BiolRep1_CNhs13478_tpm_fwd Hep2W/StreptococciJrs4Br1+ Hep-2 cells treated with Streptococci strain JRS4, biol_rep1_CNhs13478_11894-125E4_forward Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep3_CNhs13497_tpm_rev Hep2W/Streptococci5448Br3- Hep-2 cells treated with Streptococci strain 5448, biol_rep3_CNhs13497_11892-125E2_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep3_CNhs13497_tpm_fwd Hep2W/Streptococci5448Br3+ Hep-2 cells treated with Streptococci strain 5448, biol_rep3_CNhs13497_11892-125E2_forward Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep2_CNhs13496_tpm_rev Hep2W/Streptococci5448Br2- Hep-2 cells treated with Streptococci strain 5448, biol_rep2_CNhs13496_11891-125E1_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep2_CNhs13496_tpm_fwd Hep2W/Streptococci5448Br2+ Hep-2 cells treated with Streptococci strain 5448, biol_rep2_CNhs13496_11891-125E1_forward Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep1_CNhs13477_tpm_rev Hep2W/Streptococci5448Br1- Hep-2 cells treated with Streptococci strain 5448, biol_rep1_CNhs13477_11890-125D9_reverse Regulation 
Hep2CellsTreatedWithStreptococciStrain5448BiolRep1_CNhs13477_tpm_fwd Hep2W/Streptococci5448Br1+ Hep-2 cells treated with Streptococci strain 5448, biol_rep1_CNhs13477_11890-125D9_forward Regulation 
Hep2CellsMockTreatedBiolRep3_CNhs13501_tpm_rev Hep2MockTreatedBr3- Hep-2 cells mock treated, biol_rep3_CNhs13501_11900-125F1_reverse Regulation 
Hep2CellsMockTreatedBiolRep3_CNhs13501_tpm_fwd Hep2MockTreatedBr3+ Hep-2 cells mock treated, biol_rep3_CNhs13501_11900-125F1_forward Regulation 
Hep2CellsMockTreatedBiolRep2_CNhs13500_tpm_rev Hep2MockTreatedBr2- Hep-2 cells mock treated, biol_rep2_CNhs13500_11899-125E9_reverse Regulation 
Hep2CellsMockTreatedBiolRep2_CNhs13500_tpm_fwd Hep2MockTreatedBr2+ Hep-2 cells mock treated, biol_rep2_CNhs13500_11899-125E9_forward Regulation 
Hep2CellsMockTreatedBiolRep1_CNhs13479_tpm_rev Hep2MockTreatedBr1- Hep-2 cells mock treated, biol_rep1_CNhs13479_11898-125E8_reverse Regulation 
Hep2CellsMockTreatedBiolRep1_CNhs13479_tpm_fwd Hep2MockTreatedBr1+ Hep-2 cells mock treated, biol_rep1_CNhs13479_11898-125E8_forward Regulation 
RetinoblastomaCellLineY79_CNhs11267_tpm_rev Cl:Y79- retinoblastoma cell line:Y79_CNhs11267_10475-106I7_reverse Regulation 
RetinoblastomaCellLineY79_CNhs11267_tpm_fwd Cl:Y79+ retinoblastoma cell line:Y79_CNhs11267_10475-106I7_forward Regulation 
XerodermaPigentosumBCellLineXPL17_CNhs11813_tpm_rev Cl:XPL17- xeroderma pigentosum b cell line:XPL 17_CNhs11813_10563-108A5_reverse Regulation 
XerodermaPigentosumBCellLineXPL17_CNhs11813_tpm_fwd Cl:XPL17+ xeroderma pigentosum b cell line:XPL 17_CNhs11813_10563-108A5_forward Regulation 
HereditarySpherocyticAnemiaCellLineWIL2NS_CNhs11891_tpm_rev Cl:WIL2-NS- hereditary spherocytic anemia cell line:WIL2-NS_CNhs11891_10808-111A7_reverse Regulation 
HereditarySpherocyticAnemiaCellLineWIL2NS_CNhs11891_tpm_fwd Cl:WIL2-NS+ hereditary spherocytic anemia cell line:WIL2-NS_CNhs11891_10808-111A7_forward Regulation 
SmallCellLungCarcinomaCellLineWAhT_CNhs11812_tpm_rev Cl:WA-hT- small cell lung carcinoma cell line:WA-hT_CNhs11812_10562-108A4_reverse Regulation 
SmallCellLungCarcinomaCellLineWAhT_CNhs11812_tpm_fwd Cl:WA-hT+ small cell lung carcinoma cell line:WA-hT_CNhs11812_10562-108A4_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineU937DE4_CNhs13058_tpm_rev Cl:U-937DE-4- acute myeloid leukemia (FAB M5) cell line:U-937 DE-4_CNhs13058_10834-111D6_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineU937DE4_CNhs13058_tpm_fwd Cl:U-937DE-4+ acute myeloid leukemia (FAB M5) cell line:U-937 DE-4_CNhs13058_10834-111D6_forward Regulation 
ThymicCarcinomaCellLineTy82_CNhs14139_tpm_rev Cl:Ty-82- thymic carcinoma cell line:Ty-82_CNhs14139_10803-111A2_reverse Regulation 
ThymicCarcinomaCellLineTy82_CNhs14139_tpm_fwd Cl:Ty-82+ thymic carcinoma cell line:Ty-82_CNhs14139_10803-111A2_forward Regulation 
RenalCellCarcinomaCellLineTUHR10TKB_CNhs11257_tpm_rev Cl:TUHR10TKB- renal cell carcinoma cell line:TUHR10TKB_CNhs11257_10471-106I3_reverse Regulation 
RenalCellCarcinomaCellLineTUHR10TKB_CNhs11257_tpm_fwd Cl:TUHR10TKB+ renal cell carcinoma cell line:TUHR10TKB_CNhs11257_10471-106I3_forward Regulation 
RectalCancerCellLineTT1TKB_CNhs11255_tpm_rev Cl:TT1TKB- rectal cancer cell line:TT1TKB_CNhs11255_10469-106I1_reverse Regulation 
RectalCancerCellLineTT1TKB_CNhs11255_tpm_fwd Cl:TT1TKB+ rectal cancer cell line:TT1TKB_CNhs11255_10469-106I1_forward Regulation 
AstrocytomaCellLineTM31_CNhs10742_tpm_rev Cl:TM-31- astrocytoma cell line:TM-31_CNhs10742_10425-106D2_reverse Regulation 
AstrocytomaCellLineTM31_CNhs10742_tpm_fwd Cl:TM-31+ astrocytoma cell line:TM-31_CNhs10742_10425-106D2_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Thawed_CNhs10724_tpm_rev Cl:THP-1thawed- acute myeloid leukemia (FAB M5) cell line:THP-1 (thawed)_CNhs10724_10405-106A9_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Thawed_CNhs10724_tpm_fwd Cl:THP-1thawed+ acute myeloid leukemia (FAB M5) cell line:THP-1 (thawed)_CNhs10724_10405-106A9_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Revived_CNhs10723_tpm_rev Cl:THP-1revived- acute myeloid leukemia (FAB M5) cell line:THP-1 (revived)_CNhs10723_10400-106A4_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Revived_CNhs10723_tpm_fwd Cl:THP-1revived+ acute myeloid leukemia (FAB M5) cell line:THP-1 (revived)_CNhs10723_10400-106A4_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Fresh_CNhs10722_tpm_rev Cl:THP-1fresh- acute myeloid leukemia (FAB M5) cell line:THP-1 (fresh)_CNhs10722_10399-106A3_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineTHP1Fresh_CNhs10722_tpm_fwd Cl:THP-1fresh+ acute myeloid leukemia (FAB M5) cell line:THP-1 (fresh)_CNhs10722_10399-106A3_forward Regulation 
GallBladderCarcinomaCellLineTGBC2TKB_CNhs10733_tpm_rev Cl:TGBC2TKB- gall bladder carcinoma cell line:TGBC2TKB_CNhs10733_10415-106C1_reverse Regulation 
GallBladderCarcinomaCellLineTGBC2TKB_CNhs10733_tpm_fwd Cl:TGBC2TKB+ gall bladder carcinoma cell line:TGBC2TKB_CNhs10733_10415-106C1_forward Regulation 
PapillotubularAdenocarcinomaCellLineTGBC18TKB_CNhs10734_tpm_rev Cl:TGBC18TKB- papillotubular adenocarcinoma cell line:TGBC18TKB_CNhs10734_10417-106C3_reverse Regulation 
PapillotubularAdenocarcinomaCellLineTGBC18TKB_CNhs10734_tpm_fwd Cl:TGBC18TKB+ papillotubular adenocarcinoma cell line:TGBC18TKB_CNhs10734_10417-106C3_forward Regulation 
GallBladderCarcinomaCellLineTGBC14TKB_CNhs11256_tpm_rev Cl:TGBC14TKB- gall bladder carcinoma cell line:TGBC14TKB_CNhs11256_10470-106I2_reverse Regulation 
GallBladderCarcinomaCellLineTGBC14TKB_CNhs11256_tpm_fwd Cl:TGBC14TKB+ gall bladder carcinoma cell line:TGBC14TKB_CNhs11256_10470-106I2_forward Regulation 
BileDuctCarcinomaCellLineTFK1_CNhs11265_tpm_rev Cl:TFK-1- bile duct carcinoma cell line:TFK-1_CNhs11265_10496-107C1_reverse Regulation 
BileDuctCarcinomaCellLineTFK1_CNhs11265_tpm_fwd Cl:TFK-1+ bile duct carcinoma cell line:TFK-1_CNhs11265_10496-107C1_forward Regulation 
ClearCellCarcinomaCellLineTEN_CNhs11930_tpm_rev Cl:TEN- clear cell carcinoma cell line:TEN_CNhs11930_10636-108I6_reverse Regulation 
ClearCellCarcinomaCellLineTEN_CNhs11930_tpm_fwd Cl:TEN+ clear cell carcinoma cell line:TEN_CNhs11930_10636-108I6_forward Regulation 
BasalCellCarcinomaCellLineTE354_T_CNhs11932_tpm_rev Cl:TE354_T- basal cell carcinoma cell line:TE 354_T_CNhs11932_10702-109G9_reverse Regulation 
BasalCellCarcinomaCellLineTE354_T_CNhs11932_tpm_fwd Cl:TE354_T+ basal cell carcinoma cell line:TE 354_T_CNhs11932_10702-109G9_forward Regulation 
ThyroidCarcinomaCellLineTCO1_CNhs11872_tpm_rev Cl:TCO-1- thyroid carcinoma cell line:TCO-1_CNhs11872_10783-110G9_reverse Regulation 
ThyroidCarcinomaCellLineTCO1_CNhs11872_tpm_fwd Cl:TCO-1+ thyroid carcinoma cell line:TCO-1_CNhs11872_10783-110G9_forward Regulation 
ArgyrophilSmallCellCarcinomaCellLineTCYIK_CNhs11725_tpm_rev Cl:TC-YIK- argyrophil small cell carcinoma cell line:TC-YIK_CNhs11725_10589-108D4_reverse Regulation 
ArgyrophilSmallCellCarcinomaCellLineTCYIK_CNhs11725_tpm_fwd Cl:TC-YIK+ argyrophil small cell carcinoma cell line:TC-YIK_CNhs11725_10589-108D4_forward Regulation 
NeuroectodermalTumorCellLineTASK1_CNhs11866_tpm_rev Cl:TASK1- neuroectodermal tumor cell line:TASK1_CNhs11866_10774-110F9_reverse Regulation 
NeuroectodermalTumorCellLineTASK1_CNhs11866_tpm_fwd Cl:TASK1+ neuroectodermal tumor cell line:TASK1_CNhs11866_10774-110F9_forward Regulation 
GlioblastomaCellLineT98G_CNhs11272_tpm_rev Cl:T98G- glioblastoma cell line:T98G_CNhs11272_10485-107A8_reverse Regulation 
GlioblastomaCellLineT98G_CNhs11272_tpm_fwd Cl:T98G+ glioblastoma cell line:T98G_CNhs11272_10485-107A8_forward Regulation 
SquamousCellCarcinomaCellLineT3M5_CNhs11739_tpm_rev Cl:T3M-5- squamous cell carcinoma cell line:T3M-5_CNhs11739_10616-108G4_reverse Regulation 
SquamousCellCarcinomaCellLineT3M5_CNhs11739_tpm_fwd Cl:T3M-5+ squamous cell carcinoma cell line:T3M-5_CNhs11739_10616-108G4_forward Regulation 
ChoriocarcinomaCellLineT3M3_CNhs11820_tpm_rev Cl:T3M-3- choriocarcinoma cell line:T3M-3_CNhs11820_10618-108G6_reverse Regulation 
ChoriocarcinomaCellLineT3M3_CNhs11820_tpm_fwd Cl:T3M-3+ choriocarcinoma cell line:T3M-3_CNhs11820_10618-108G6_forward Regulation 
LiposarcomaCellLineSW872_CNhs11851_tpm_rev Cl:SW872- liposarcoma cell line:SW 872_CNhs11851_10726-110A6_reverse Regulation 
LiposarcomaCellLineSW872_CNhs11851_tpm_fwd Cl:SW872+ liposarcoma cell line:SW 872_CNhs11851_10726-110A6_forward Regulation 
AlveolarCellCarcinomaCellLineSW1573_CNhs11838_tpm_rev Cl:SW1573- alveolar cell carcinoma cell line:SW 1573_CNhs11838_10708-109H6_reverse Regulation 
AlveolarCellCarcinomaCellLineSW1573_CNhs11838_tpm_fwd Cl:SW1573+ alveolar cell carcinoma cell line:SW 1573_CNhs11838_10708-109H6_forward Regulation 
ChondrosarcomaCellLineSW1353_CNhs11833_tpm_rev Cl:SW1353- chondrosarcoma cell line:SW 1353_CNhs11833_10700-109G7_reverse Regulation 
ChondrosarcomaCellLineSW1353_CNhs11833_tpm_fwd Cl:SW1353+ chondrosarcoma cell line:SW 1353_CNhs11833_10700-109G7_forward Regulation 
AdrenalCortexAdenocarcinomaCellLineSW13_CNhs11893_tpm_rev Cl:SW-13- adrenal cortex adenocarcinoma cell line:SW-13_CNhs11893_10810-111A9_reverse Regulation 
AdrenalCortexAdenocarcinomaCellLineSW13_CNhs11893_tpm_fwd Cl:SW-13+ adrenal cortex adenocarcinoma cell line:SW-13_CNhs11893_10810-111A9_forward Regulation 
TubularAdenocarcinomaCellLineSUIT2_CNhs11883_tpm_rev Cl:SUIT-2- tubular adenocarcinoma cell line:SUIT-2_CNhs11883_10797-110I5_reverse Regulation 
TubularAdenocarcinomaCellLineSUIT2_CNhs11883_tpm_fwd Cl:SUIT-2+ tubular adenocarcinoma cell line:SUIT-2_CNhs11883_10797-110I5_forward Regulation 
BoneMarrowStromalCellLineStromaNKtert_CNhs11931_tpm_rev Cl:StromaNKtert- bone marrow stromal cell line:StromaNKtert_CNhs11931_10686-109F2_reverse Regulation 
BoneMarrowStromalCellLineStromaNKtert_CNhs11931_tpm_fwd Cl:StromaNKtert+ bone marrow stromal cell line:StromaNKtert_CNhs11931_10686-109F2_forward Regulation 
LensEpithelialCellLineSRA0104_CNhs11750_tpm_rev Cl:SRA01/04- lens epithelial cell line:SRA 01/04_CNhs11750_10647-109A8_reverse Regulation 
LensEpithelialCellLineSRA0104_CNhs11750_tpm_fwd Cl:SRA01/04+ lens epithelial cell line:SRA 01/04_CNhs11750_10647-109A8_forward Regulation 
PleomorphicHepatocellularCarcinomaCellLineSNU387_CNhs11933_tpm_rev Cl:SNU-387- pleomorphic hepatocellular carcinoma cell line:SNU-387_CNhs11933_10706-109H4_reverse Regulation 
PleomorphicHepatocellularCarcinomaCellLineSNU387_CNhs11933_tpm_fwd Cl:SNU-387+ pleomorphic hepatocellular carcinoma cell line:SNU-387_CNhs11933_10706-109H4_forward Regulation 
SplenicLymphomaWithVillousLymphocytesCellLineSLVL_CNhs10741_tpm_rev Cl:SLVL- splenic lymphoma with villous lymphocytes cell line:SLVL_CNhs10741_10424-106D1_reverse Regulation 
SplenicLymphomaWithVillousLymphocytesCellLineSLVL_CNhs10741_tpm_fwd Cl:SLVL+ splenic lymphoma with villous lymphocytes cell line:SLVL_CNhs10741_10424-106D1_forward Regulation 
ChronicLymphocyticLeukemiaTCLLCellLineSKW3_CNhs11714_tpm_rev Cl:SKW-3- chronic lymphocytic leukemia (T-CLL) cell line:SKW-3_CNhs11714_10416-106C2_reverse Regulation 
ChronicLymphocyticLeukemiaTCLLCellLineSKW3_CNhs11714_tpm_fwd Cl:SKW-3+ chronic lymphocytic leukemia (T-CLL) cell line:SKW-3_CNhs11714_10416-106C2_forward Regulation 
MyelodysplasticSyndromeCellLineSKM1_CNhs11934_tpm_rev Cl:SKM-1- myelodysplastic syndrome cell line:SKM-1_CNhs11934_10772-110F7_reverse Regulation 
MyelodysplasticSyndromeCellLineSKM1_CNhs11934_tpm_fwd Cl:SKM-1+ myelodysplastic syndrome cell line:SKM-1_CNhs11934_10772-110F7_forward Regulation 
LargeCellNonkeratinizingSquamousCarcinomaCellLineSKGIISF_CNhs11825_tpm_rev Cl:SKG-II-SF- large cell non-keratinizing squamous carcinoma cell line:SKG-II-SF_CNhs11825_10692-109F8_reverse Regulation 
LargeCellNonkeratinizingSquamousCarcinomaCellLineSKGIISF_CNhs11825_tpm_fwd Cl:SKG-II-SF+ large cell non-keratinizing squamous carcinoma cell line:SKG-II-SF_CNhs11825_10692-109F8_forward Regulation 
CarcinoidCellLineSKPNDW_CNhs11846_tpm_rev Cl:SK-PN-DW- carcinoid cell line:SK-PN-DW_CNhs11846_10719-109I8_reverse Regulation 
CarcinoidCellLineSKPNDW_CNhs11846_tpm_fwd Cl:SK-PN-DW+ carcinoid cell line:SK-PN-DW_CNhs11846_10719-109I8_forward Regulation 
SerousAdenocarcinomaCellLineSKOV3RAfterCocultureWithSOC5702GBiolRep1_CNhs13508_tpm_rev Cl:SK-OV-3-RwithSOC-57-02-GBr1- serous adenocarcinoma cell line:SK-OV-3-R after co-culture with SOC-57-02-G, biol_rep1_CNhs13508_11843-124H7_reverse Regulation 
SerousAdenocarcinomaCellLineSKOV3RAfterCocultureWithSOC5702GBiolRep1_CNhs13508_tpm_fwd Cl:SK-OV-3-RwithSOC-57-02-GBr1+ serous adenocarcinoma cell line:SK-OV-3-R after co-culture with SOC-57-02-G, biol_rep1_CNhs13508_11843-124H7_forward Regulation 
SerousAdenocarcinomaCellLineSKOV3RBiolRep1_CNhs13099_tpm_rev Cl:SK-OV-3-RBr1- serous adenocarcinoma cell line:SK-OV-3-R, biol_rep1_CNhs13099_11841-124H5_reverse Regulation 
SerousAdenocarcinomaCellLineSKOV3RBiolRep1_CNhs13099_tpm_fwd Cl:SK-OV-3-RBr1+ serous adenocarcinoma cell line:SK-OV-3-R, biol_rep1_CNhs13099_11841-124H5_forward Regulation 
NeuroepitheliomaCellLineSKNMC_CNhs11853_tpm_rev Cl:SK-N-MC- neuroepithelioma cell line:SK-N-MC_CNhs11853_10728-110A8_reverse Regulation 
NeuroepitheliomaCellLineSKNMC_CNhs11853_tpm_fwd Cl:SK-N-MC+ neuroepithelioma cell line:SK-N-MC_CNhs11853_10728-110A8_forward Regulation 
ChoriocarcinomaCellLineSCH_CNhs11875_tpm_rev Cl:SCH- choriocarcinoma cell line:SCH_CNhs11875_10785-110H2_reverse Regulation 
ChoriocarcinomaCellLineSCH_CNhs11875_tpm_fwd Cl:SCH+ choriocarcinoma cell line:SCH_CNhs11875_10785-110H2_forward Regulation 
OralSquamousCellCarcinomaCellLineSAS_CNhs11810_tpm_rev Cl:SAS- oral squamous cell carcinoma cell line:SAS_CNhs11810_10544-107H4_reverse Regulation 
OralSquamousCellCarcinomaCellLineSAS_CNhs11810_tpm_fwd Cl:SAS+ oral squamous cell carcinoma cell line:SAS_CNhs11810_10544-107H4_forward Regulation 
AnaplasticSquamousCellCarcinomaCellLineRPMI2650_CNhs11889_tpm_rev Cl:RPMI2650- anaplastic squamous cell carcinoma cell line:RPMI 2650_CNhs11889_10805-111A4_reverse Regulation 
AnaplasticSquamousCellCarcinomaCellLineRPMI2650_CNhs11889_tpm_fwd Cl:RPMI2650+ anaplastic squamous cell carcinoma cell line:RPMI 2650_CNhs11889_10805-111A4_forward Regulation 
BCellLineRPMI1788_CNhs10744_tpm_rev Cl:RPMI1788- b cell line:RPMI1788_CNhs10744_10427-106D4_reverse Regulation 
BCellLineRPMI1788_CNhs10744_tpm_fwd Cl:RPMI1788+ b cell line:RPMI1788_CNhs10744_10427-106D4_forward Regulation 
RhabdomyosarcomaCellLineRMSYM_CNhs11269_tpm_rev Cl:RMS-YM- rhabdomyosarcoma cell line:RMS-YM_CNhs11269_10477-106I9_reverse Regulation 
RhabdomyosarcomaCellLineRMSYM_CNhs11269_tpm_fwd Cl:RMS-YM+ rhabdomyosarcoma cell line:RMS-YM_CNhs11269_10477-106I9_forward Regulation 
SquamousCellLungCarcinomaCellLineRERFLCAI_CNhs14240_tpm_rev Cl:RERF-LC-AI- squamous cell lung carcinoma cell line:RERF-LC-AI_CNhs14240_10501-107C6_reverse Regulation 
SquamousCellLungCarcinomaCellLineRERFLCAI_CNhs14240_tpm_fwd Cl:RERF-LC-AI+ squamous cell lung carcinoma cell line:RERF-LC-AI_CNhs14240_10501-107C6_forward Regulation 
BurkittsLymphomaCellLineRAJI_CNhs11268_tpm_rev Cl:RAJI- Burkitt's lymphoma cell line:RAJI_CNhs11268_10476-106I8_reverse Regulation 
BurkittsLymphomaCellLineRAJI_CNhs11268_tpm_fwd Cl:RAJI+ Burkitt's lymphoma cell line:RAJI_CNhs11268_10476-106I8_forward Regulation 
SomatostatinomaCellLineQGP1_CNhs11869_tpm_rev Cl:QGP-1- somatostatinoma cell line:QGP-1_CNhs11869_10781-110G7_reverse Regulation 
SomatostatinomaCellLineQGP1_CNhs11869_tpm_fwd Cl:QGP-1+ somatostatinoma cell line:QGP-1_CNhs11869_10781-110G7_forward Regulation 
MyelomaCellLinePCM6_CNhs11258_tpm_rev Cl:PCM6- myeloma cell line:PCM6_CNhs11258_10474-106I6_reverse Regulation 
MyelomaCellLinePCM6_CNhs11258_tpm_fwd Cl:PCM6+ myeloma cell line:PCM6_CNhs11258_10474-106I6_forward Regulation 
ProstateCancerCellLinePC3_CNhs11243_tpm_rev Cl:PC-3- prostate cancer cell line:PC-3_CNhs11243_10439-106E7_reverse Regulation 
ProstateCancerCellLinePC3_CNhs11243_tpm_fwd Cl:PC-3+ prostate cancer cell line:PC-3_CNhs11243_10439-106E7_forward Regulation 
LungAdenocarcinomaCellLinePC14_CNhs10726_tpm_rev Cl:PC-14- lung adenocarcinoma cell line:PC-14_CNhs10726_10408-106B3_reverse Regulation 
LungAdenocarcinomaCellLinePC14_CNhs10726_tpm_fwd Cl:PC-14+ lung adenocarcinoma cell line:PC-14_CNhs10726_10408-106B3_forward Regulation 
TeratocarcinomaCellLinePA1_CNhs11890_tpm_rev Cl:PA-1- teratocarcinoma cell line:PA-1_CNhs11890_10807-111A6_reverse Regulation 
TeratocarcinomaCellLinePA1_CNhs11890_tpm_fwd Cl:PA-1+ teratocarcinoma cell line:PA-1_CNhs11890_10807-111A6_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineP31FUJ_CNhs13051_tpm_rev Cl:P31/FUJ- acute myeloid leukemia (FAB M5) cell line:P31/FUJ_CNhs13051_10770-110F5_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineP31FUJ_CNhs13051_tpm_fwd Cl:P31/FUJ+ acute myeloid leukemia (FAB M5) cell line:P31/FUJ_CNhs13051_10770-110F5_forward Regulation 
NonTNonBAcuteLymphoblasticLeukemiaALLCellLineP30OHK_CNhs10747_tpm_rev Cl:P30/OHK- non T non B acute lymphoblastic leukemia (ALL) cell line:P30/OHK_CNhs10747_10430-106D7_reverse Regulation 
NonTNonBAcuteLymphoblasticLeukemiaALLCellLineP30OHK_CNhs10747_tpm_fwd Cl:P30/OHK+ non T non B acute lymphoblastic leukemia (ALL) cell line:P30/OHK_CNhs10747_10430-106D7_forward Regulation 
RenalCellCarcinomaCellLineOSRC2_CNhs10729_tpm_rev Cl:OS-RC-2- renal cell carcinoma cell line:OS-RC-2_CNhs10729_10411-106B6_reverse Regulation 
RenalCellCarcinomaCellLineOSRC2_CNhs10729_tpm_fwd Cl:OS-RC-2+ renal cell carcinoma cell line:OS-RC-2_CNhs10729_10411-106B6_forward Regulation 
MedulloblastomaCellLineONS76_CNhs11861_tpm_rev Cl:ONS-76- medulloblastoma cell line:ONS-76_CNhs11861_10759-110E3_reverse Regulation 
MedulloblastomaCellLineONS76_CNhs11861_tpm_fwd Cl:ONS-76+ medulloblastoma cell line:ONS-76_CNhs11861_10759-110E3_forward Regulation 
MesotheliomaCellLineONE58_CNhs13075_tpm_rev Cl:ONE58- mesothelioma cell line:ONE58_CNhs13075_10858-111G3_reverse Regulation 
MesotheliomaCellLineONE58_CNhs13075_tpm_fwd Cl:ONE58+ mesothelioma cell line:ONE58_CNhs13075_10858-111G3_forward Regulation 
EndometrialStromalSarcomaCellLineOMC9_CNhs11249_tpm_rev Cl:OMC-9- endometrial stromal sarcoma cell line:OMC-9_CNhs11249_10448-106F7_reverse Regulation 
EndometrialStromalSarcomaCellLineOMC9_CNhs11249_tpm_fwd Cl:OMC-9+ endometrial stromal sarcoma cell line:OMC-9_CNhs11249_10448-106F7_forward Regulation 
EndometrialCarcinomaCellLineOMC2_CNhs11266_tpm_rev Cl:OMC-2- endometrial carcinoma cell line:OMC-2_CNhs11266_10497-107C2_reverse Regulation 
EndometrialCarcinomaCellLineOMC2_CNhs11266_tpm_fwd Cl:OMC-2+ endometrial carcinoma cell line:OMC-2_CNhs11266_10497-107C2_forward Regulation 
SignetRingCarcinomaCellLineNUGC4_CNhs11270_tpm_rev Cl:NUGC-4- signet ring carcinoma cell line:NUGC-4_CNhs11270_10483-107A6_reverse Regulation 
SignetRingCarcinomaCellLineNUGC4_CNhs11270_tpm_fwd Cl:NUGC-4+ signet ring carcinoma cell line:NUGC-4_CNhs11270_10483-107A6_forward Regulation 
PancreaticCarcinomaCellLineNORP1_CNhs11832_tpm_rev Cl:NOR-P1- pancreatic carcinoma cell line:NOR-P1_CNhs11832_10698-109G5_reverse Regulation 
PancreaticCarcinomaCellLineNORP1_CNhs11832_tpm_fwd Cl:NOR-P1+ pancreatic carcinoma cell line:NOR-P1_CNhs11832_10698-109G5_forward Regulation 
AcuteMyeloidLeukemiaFABM5CellLineNOMO1_CNhs13050_tpm_rev Cl:NOMO-1- acute myeloid leukemia (FAB M5) cell line:NOMO-1_CNhs13050_10764-110E8_reverse Regulation 
AcuteMyeloidLeukemiaFABM5CellLineNOMO1_CNhs13050_tpm_fwd Cl:NOMO-1+ acute myeloid leukemia (FAB M5) cell line:NOMO-1_CNhs13050_10764-110E8_forward Regulation 
MesotheliomaCellLineNo36_CNhs13074_tpm_rev Cl:No36- mesothelioma cell line:No36_CNhs13074_10857-111G2_reverse Regulation 
MesotheliomaCellLineNo36_CNhs13074_tpm_fwd Cl:No36+ mesothelioma cell line:No36_CNhs13074_10857-111G2_forward Regulation 
MyxofibrosarcomaCellLineNMFH1_CNhs11821_tpm_rev Cl:NMFH-1- myxofibrosarcoma cell line:NMFH-1_CNhs11821_10684-109E9_reverse Regulation 
MyxofibrosarcomaCellLineNMFH1_CNhs11821_tpm_fwd Cl:NMFH-1+ myxofibrosarcoma cell line:NMFH-1_CNhs11821_10684-109E9_forward Regulation 
AcuteMyeloidLeukemiaFABM2CellLineNKM1_CNhs11864_tpm_rev Cl:NKM-1- acute myeloid leukemia (FAB M2) cell line:NKM-1_CNhs11864_10765-110E9_reverse Regulation 
AcuteMyeloidLeukemiaFABM2CellLineNKM1_CNhs11864_tpm_fwd Cl:NKM-1+ acute myeloid leukemia (FAB M2) cell line:NKM-1_CNhs11864_10765-110E9_forward Regulation 
NeuroblastomaCellLineNH12_CNhs11811_tpm_rev Cl:NH-12- neuroblastoma cell line:NH-12_CNhs11811_10555-107I6_reverse Regulation 
NeuroblastomaCellLineNH12_CNhs11811_tpm_fwd Cl:NH-12+ neuroblastoma cell line:NH-12_CNhs11811_10555-107I6_forward Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC8_CNhs11726_tpm_rev Cl:NEC8- testicular germ cell embryonal carcinoma cell line:NEC8_CNhs11726_10590-108D5_reverse Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC8_CNhs11726_tpm_fwd Cl:NEC8+ testicular germ cell embryonal carcinoma cell line:NEC8_CNhs11726_10590-108D5_forward Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC15_CNhs12362_tpm_rev Cl:NEC15- testicular germ cell embryonal carcinoma cell line:NEC15_CNhs12362_10593-108D8_reverse Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC15_CNhs12362_tpm_fwd Cl:NEC15+ testicular germ cell embryonal carcinoma cell line:NEC15_CNhs12362_10593-108D8_forward Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC14_CNhs12351_tpm_rev Cl:NEC14- testicular germ cell embryonal carcinoma cell line:NEC14_CNhs12351_10591-108D6_reverse Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineNEC14_CNhs12351_tpm_fwd Cl:NEC14+ testicular germ cell embryonal carcinoma cell line:NEC14_CNhs12351_10591-108D6_forward Regulation 
TeratocarcinomaCellLineNCRG1_CNhs11884_tpm_rev Cl:NCR-G1- teratocarcinoma cell line:NCR-G1_CNhs11884_10798-110I6_reverse Regulation 
TeratocarcinomaCellLineNCRG1_CNhs11884_tpm_fwd Cl:NCR-G1+ teratocarcinoma cell line:NCR-G1_CNhs11884_10798-110I6_forward Regulation 
SmallCellLungCarcinomaCellLineNCIH82_CNhs12809_tpm_rev Cl:NCI-H82- small cell lung carcinoma cell line:NCI-H82_CNhs12809_10842-111E5_reverse Regulation 
SmallCellLungCarcinomaCellLineNCIH82_CNhs12809_tpm_fwd Cl:NCI-H82+ small cell lung carcinoma cell line:NCI-H82_CNhs12809_10842-111E5_forward Regulation 
CarcinoidCellLineNCIH727_CNhs14244_tpm_rev Cl:NCI-H727- carcinoid cell line:NCI-H727_CNhs14244_10735-110B6_reverse Regulation 
CarcinoidCellLineNCIH727_CNhs14244_tpm_fwd Cl:NCI-H727+ carcinoid cell line:NCI-H727_CNhs14244_10735-110B6_forward Regulation 
BronchioalveolarCarcinomaCellLineNCIH650_CNhs14138_tpm_rev Cl:NCI-H650- bronchioalveolar carcinoma cell line:NCI-H650_CNhs14138_10715-109I4_reverse Regulation 
BronchioalveolarCarcinomaCellLineNCIH650_CNhs14138_tpm_fwd Cl:NCI-H650+ bronchioalveolar carcinoma cell line:NCI-H650_CNhs14138_10715-109I4_forward Regulation 
LargeCellLungCarcinomaCellLineNCIH460_CNhs12806_tpm_rev Cl:NCI-H460- large cell lung carcinoma cell line:NCI-H460_CNhs12806_10839-111E2_reverse Regulation 
LargeCellLungCarcinomaCellLineNCIH460_CNhs12806_tpm_fwd Cl:NCI-H460+ large cell lung carcinoma cell line:NCI-H460_CNhs12806_10839-111E2_forward Regulation 
LungAdenocarcinomaPapillaryCellLineNCIH441_CNhs14245_tpm_rev Cl:NCI-H441- lung adenocarcinoma, papillary cell line:NCI-H441_CNhs14245_10742-110C4_reverse Regulation 
LungAdenocarcinomaPapillaryCellLineNCIH441_CNhs14245_tpm_fwd Cl:NCI-H441+ lung adenocarcinoma, papillary cell line:NCI-H441_CNhs14245_10742-110C4_forward Regulation 
BronchioalveolarCarcinomaCellLineNCIH358_CNhs11840_tpm_rev Cl:NCI-H358- bronchioalveolar carcinoma cell line:NCI-H358_CNhs11840_10709-109H7_reverse Regulation 
BronchioalveolarCarcinomaCellLineNCIH358_CNhs11840_tpm_fwd Cl:NCI-H358+ bronchioalveolar carcinoma cell line:NCI-H358_CNhs11840_10709-109H7_forward Regulation 
MesotheliomaCellLineNCIH28_CNhs13061_tpm_rev Cl:NCI-H28- mesothelioma cell line:NCI-H28_CNhs13061_10845-111E8_reverse Regulation 
MesotheliomaCellLineNCIH28_CNhs13061_tpm_fwd Cl:NCI-H28+ mesothelioma cell line:NCI-H28_CNhs13061_10845-111E8_forward Regulation 
MesotheliomaCellLineNCIH2452_CNhs13064_tpm_rev Cl:NCI-H2452- mesothelioma cell line:NCI-H2452_CNhs13064_10848-111F2_reverse Regulation 
MesotheliomaCellLineNCIH2452_CNhs13064_tpm_fwd Cl:NCI-H2452+ mesothelioma cell line:NCI-H2452_CNhs13064_10848-111F2_forward Regulation 
MesotheliomaCellLineNCIH226_CNhs13062_tpm_rev Cl:NCI-H226- mesothelioma cell line:NCI-H226_CNhs13062_10846-111E9_reverse Regulation 
MesotheliomaCellLineNCIH226_CNhs13062_tpm_fwd Cl:NCI-H226+ mesothelioma cell line:NCI-H226_CNhs13062_10846-111E9_forward Regulation 
MesotheliomaCellLineNCIH2052_CNhs13063_tpm_rev Cl:NCI-H2052- mesothelioma cell line:NCI-H2052_CNhs13063_10847-111F1_reverse Regulation 
MesotheliomaCellLineNCIH2052_CNhs13063_tpm_fwd Cl:NCI-H2052+ mesothelioma cell line:NCI-H2052_CNhs13063_10847-111F1_forward Regulation 
CarcinoidCellLineNCIH1770_CNhs11834_tpm_rev Cl:NCI-H1770- carcinoid cell line:NCI-H1770_CNhs11834_10703-109H1_reverse Regulation 
CarcinoidCellLineNCIH1770_CNhs11834_tpm_fwd Cl:NCI-H1770+ carcinoid cell line:NCI-H1770_CNhs11834_10703-109H1_forward Regulation 
TeratocarcinomaCellLineNCCITA3_CNhs11878_tpm_rev Cl:NCC-IT-A3- teratocarcinoma cell line:NCC-IT-A3_CNhs11878_10790-110H7_reverse Regulation 
TeratocarcinomaCellLineNCCITA3_CNhs11878_tpm_fwd Cl:NCC-IT-A3+ teratocarcinoma cell line:NCC-IT-A3_CNhs11878_10790-110H7_forward Regulation 
NeuroblastomaCellLineNBsusSR_CNhs11818_tpm_rev Cl:NBsusSR- neuroblastoma cell line:NBsusSR_CNhs11818_10607-108F4_reverse Regulation 
NeuroblastomaCellLineNBsusSR_CNhs11818_tpm_fwd Cl:NBsusSR+ neuroblastoma cell line:NBsusSR_CNhs11818_10607-108F4_forward Regulation 
NeuroblastomaCellLineNB1_CNhs11284_tpm_rev Cl:NB-1- neuroblastoma cell line:NB-1_CNhs11284_10539-107G8_reverse Regulation 
NeuroblastomaCellLineNB1_CNhs11284_tpm_fwd Cl:NB-1+ neuroblastoma cell line:NB-1_CNhs11284_10539-107G8_forward Regulation 
AcuteLymphoblasticLeukemiaBALLCellLineNALM6_CNhs11282_tpm_rev Cl:NALM-6- acute lymphoblastic leukemia (B-ALL) cell line:NALM-6_CNhs11282_10534-107G3_reverse Regulation 
AcuteLymphoblasticLeukemiaBALLCellLineNALM6_CNhs11282_tpm_fwd Cl:NALM-6+ acute lymphoblastic leukemia (B-ALL) cell line:NALM-6_CNhs11282_10534-107G3_forward Regulation 
BiphenotypicBMyelomonocyticLeukemiaCellLineMV411_CNhs11845_tpm_rev Cl:MV-4-11- biphenotypic B myelomonocytic leukemia cell line:MV-4-11_CNhs11845_10718-109I7_reverse Regulation 
BiphenotypicBMyelomonocyticLeukemiaCellLineMV411_CNhs11845_tpm_fwd Cl:MV-4-11+ biphenotypic B myelomonocytic leukemia cell line:MV-4-11_CNhs11845_10718-109I7_forward Regulation 
MerkelCellCarcinomaCellLineMS1_CNhs12839_tpm_rev Cl:MS-1- merkel cell carcinoma cell line:MS-1_CNhs12839_10844-111E7_reverse Regulation 
MerkelCellCarcinomaCellLineMS1_CNhs12839_tpm_fwd Cl:MS-1+ merkel cell carcinoma cell line:MS-1_CNhs12839_10844-111E7_forward Regulation 
HairyCellLeukemiaCellLineMo_CNhs11843_tpm_rev Cl:Mo- hairy cell leukemia cell line:Mo_CNhs11843_10712-109I1_reverse Regulation 
HairyCellLeukemiaCellLineMo_CNhs11843_tpm_fwd Cl:Mo+ hairy cell leukemia cell line:Mo_CNhs11843_10712-109I1_forward Regulation 
LymphomaMalignantHairyBcellCellLineMLMA_CNhs11935_tpm_rev Cl:MLMA- lymphoma, malignant, hairy B-cell cell line:MLMA_CNhs11935_10775-110G1_reverse Regulation 
LymphomaMalignantHairyBcellCellLineMLMA_CNhs11935_tpm_fwd Cl:MLMA+ lymphoma, malignant, hairy B-cell cell line:MLMA_CNhs11935_10775-110G1_forward Regulation 
AcuteMyeloidLeukemiaFABM7CellLineMKPL1_CNhs11888_tpm_rev Cl:MKPL-1- acute myeloid leukemia (FAB M7) cell line:MKPL-1_CNhs11888_10802-111A1_reverse Regulation 
AcuteMyeloidLeukemiaFABM7CellLineMKPL1_CNhs11888_tpm_fwd Cl:MKPL-1+ acute myeloid leukemia (FAB M7) cell line:MKPL-1_CNhs11888_10802-111A1_forward Regulation 
GastricAdenocarcinomaCellLineMKN45_CNhs11819_tpm_rev Cl:MKN45- gastric adenocarcinoma cell line:MKN45_CNhs11819_10612-108F9_reverse Regulation 
GastricAdenocarcinomaCellLineMKN45_CNhs11819_tpm_fwd Cl:MKN45+ gastric adenocarcinoma cell line:MKN45_CNhs11819_10612-108F9_forward Regulation 
GastricAdenocarcinomaCellLineMKN1_CNhs11737_tpm_rev Cl:MKN1- gastric adenocarcinoma cell line:MKN1_CNhs11737_10614-108G2_reverse Regulation 
GastricAdenocarcinomaCellLineMKN1_CNhs11737_tpm_fwd Cl:MKN1+ gastric adenocarcinoma cell line:MKN1_CNhs11737_10614-108G2_forward Regulation 
MerkelCellCarcinomaCellLineMKL1_CNhs12838_tpm_rev Cl:MKL-1- merkel cell carcinoma cell line:MKL-1_CNhs12838_10843-111E6_reverse Regulation 
MerkelCellCarcinomaCellLineMKL1_CNhs12838_tpm_fwd Cl:MKL-1+ merkel cell carcinoma cell line:MKL-1_CNhs12838_10843-111E6_forward Regulation 
DuctalCellCarcinomaCellLineMIAPaca2_CNhs11259_tpm_rev Cl:MIAPaca2- ductal cell carcinoma cell line:MIA Paca2_CNhs11259_10488-107B2_reverse Regulation 
DuctalCellCarcinomaCellLineMIAPaca2_CNhs11259_tpm_fwd Cl:MIAPaca2+ ductal cell carcinoma cell line:MIA Paca2_CNhs11259_10488-107B2_forward Regulation 
MyxofibrosarcomaCellLineMFHino_CNhs11729_tpm_rev Cl:MFH-ino- myxofibrosarcoma cell line:MFH-ino_CNhs11729_10600-108E6_reverse Regulation 
MyxofibrosarcomaCellLineMFHino_CNhs11729_tpm_fwd Cl:MFH-ino+ myxofibrosarcoma cell line:MFH-ino_CNhs11729_10600-108E6_forward Regulation 
MesotheliomaCellLineMero95_CNhs13073_tpm_rev Cl:Mero-95- mesothelioma cell line:Mero-95_CNhs13073_10856-111G1_reverse Regulation 
MesotheliomaCellLineMero95_CNhs13073_tpm_fwd Cl:Mero-95+ mesothelioma cell line:Mero-95_CNhs13073_10856-111G1_forward Regulation 
MesotheliomaCellLineMero84_CNhs13072_tpm_rev Cl:Mero-84- mesothelioma cell line:Mero-84_CNhs13072_10855-111F9_reverse Regulation 
MesotheliomaCellLineMero84_CNhs13072_tpm_fwd Cl:Mero-84+ mesothelioma cell line:Mero-84_CNhs13072_10855-111F9_forward Regulation 
MesotheliomaCellLineMero83_CNhs13070_tpm_rev Cl:Mero-83- mesothelioma cell line:Mero-83_CNhs13070_10854-111F8_reverse Regulation 
MesotheliomaCellLineMero83_CNhs13070_tpm_fwd Cl:Mero-83+ mesothelioma cell line:Mero-83_CNhs13070_10854-111F8_forward Regulation 
MesotheliomaCellLineMero82_CNhs13069_tpm_rev Cl:Mero-82- mesothelioma cell line:Mero-82_CNhs13069_10853-111F7_reverse Regulation 
MesotheliomaCellLineMero82_CNhs13069_tpm_fwd Cl:Mero-82+ mesothelioma cell line:Mero-82_CNhs13069_10853-111F7_forward Regulation 
MesotheliomaCellLineMero48a_CNhs13068_tpm_rev Cl:Mero-48a- mesothelioma cell line:Mero-48a_CNhs13068_10852-111F6_reverse Regulation 
MesotheliomaCellLineMero48a_CNhs13068_tpm_fwd Cl:Mero-48a+ mesothelioma cell line:Mero-48a_CNhs13068_10852-111F6_forward Regulation 
MesotheliomaCellLineMero41_CNhs13067_tpm_rev Cl:Mero-41- mesothelioma cell line:Mero-41_CNhs13067_10851-111F5_reverse Regulation 
MesotheliomaCellLineMero41_CNhs13067_tpm_fwd Cl:Mero-41+ mesothelioma cell line:Mero-41_CNhs13067_10851-111F5_forward Regulation 
MesotheliomaCellLineMero25_CNhs13066_tpm_rev Cl:Mero-25- mesothelioma cell line:Mero-25_CNhs13066_10850-111F4_reverse Regulation 
MesotheliomaCellLineMero25_CNhs13066_tpm_fwd Cl:Mero-25+ mesothelioma cell line:Mero-25_CNhs13066_10850-111F4_forward Regulation 
MesotheliomaCellLineMero14TechRep1_CNhs13065_tpm_rev Cl:Mero-14Tr1- mesothelioma cell line:Mero-14, tech_rep1_CNhs13065_10849-111F3_reverse Regulation 
MesotheliomaCellLineMero14TechRep1_CNhs13065_tpm_fwd Cl:Mero-14Tr1+ mesothelioma cell line:Mero-14, tech_rep1_CNhs13065_10849-111F3_forward Regulation 
ChronicMyelogenousLeukemiaCMLCellLineMEGA2_CNhs11865_tpm_rev Cl:MEG-A2- chronic myelogenous leukemia (CML) cell line:MEG-A2_CNhs11865_10766-110F1_reverse Regulation 
ChronicMyelogenousLeukemiaCMLCellLineMEGA2_CNhs11865_tpm_fwd Cl:MEG-A2+ chronic myelogenous leukemia (CML) cell line:MEG-A2_CNhs11865_10766-110F1_forward Regulation 
LeukemiaChronicMegakaryoblasticCellLineMEG01_CNhs11859_tpm_rev Cl:MEG-01- leukemia, chronic megakaryoblastic cell line:MEG-01_CNhs11859_10752-110D5_reverse Regulation 
LeukemiaChronicMegakaryoblasticCellLineMEG01_CNhs11859_tpm_fwd Cl:MEG-01+ leukemia, chronic megakaryoblastic cell line:MEG-01_CNhs11859_10752-110D5_forward Regulation 
CervicalCancerCellLineME180_CNhs11289_tpm_rev Cl:ME-180- cervical cancer cell line:ME-180_CNhs11289_10553-107I4_reverse Regulation 
CervicalCancerCellLineME180_CNhs11289_tpm_fwd Cl:ME-180+ cervical cancer cell line:ME-180_CNhs11289_10553-107I4_forward Regulation 
BreastCarcinomaCellLineMDAMB453_CNhs10736_tpm_rev Cl:MDA-MB-453- breast carcinoma cell line:MDA-MB-453_CNhs10736_10419-106C5_reverse Regulation 
BreastCarcinomaCellLineMDAMB453_CNhs10736_tpm_fwd Cl:MDA-MB-453+ breast carcinoma cell line:MDA-MB-453_CNhs10736_10419-106C5_forward Regulation 
BreastCarcinomaCellLineMCF7_CNhs11943_tpm_rev Cl:MCF7- breast carcinoma cell line:MCF7_CNhs11943_10482-107A5_reverse Regulation 
BreastCarcinomaCellLineMCF7_CNhs11943_tpm_fwd Cl:MCF7+ breast carcinoma cell line:MCF7_CNhs11943_10482-107A5_forward Regulation 
MucinousCystadenocarcinomaCellLineMCAS_CNhs11873_tpm_rev Cl:MCAS- mucinous cystadenocarcinoma cell line:MCAS_CNhs11873_10784-110H1_reverse Regulation 
MucinousCystadenocarcinomaCellLineMCAS_CNhs11873_tpm_fwd Cl:MCAS+ mucinous cystadenocarcinoma cell line:MCAS_CNhs11873_10784-110H1_forward Regulation 
AcuteMyeloidLeukemiaFABM7CellLineMMOK_CNhs13049_tpm_rev Cl:M-MOK- acute myeloid leukemia (FAB M7) cell line:M-MOK_CNhs13049_10699-109G6_reverse Regulation 
AcuteMyeloidLeukemiaFABM7CellLineMMOK_CNhs13049_tpm_fwd Cl:M-MOK+ acute myeloid leukemia (FAB M7) cell line:M-MOK_CNhs13049_10699-109G6_forward Regulation 
GiantCellCarcinomaCellLineLu99B_CNhs10751_tpm_rev Cl:Lu99B- giant cell carcinoma cell line:Lu99B_CNhs10751_10433-106E1_reverse Regulation 
GiantCellCarcinomaCellLineLu99B_CNhs10751_tpm_fwd Cl:Lu99B+ giant cell carcinoma cell line:Lu99B_CNhs10751_10433-106E1_forward Regulation 
GiantCellCarcinomaCellLineLU65_CNhs11274_tpm_rev Cl:LU65- giant cell carcinoma cell line:LU65_CNhs11274_10487-107B1_reverse Regulation 
GiantCellCarcinomaCellLineLU65_CNhs11274_tpm_fwd Cl:LU65+ giant cell carcinoma cell line:LU65_CNhs11274_10487-107B1_forward Regulation 
SmallCellLungCarcinomaCellLineLK2_CNhs11285_tpm_rev Cl:LK-2- small cell lung carcinoma cell line:LK-2_CNhs11285_10541-107H1_reverse Regulation 
SmallCellLungCarcinomaCellLineLK2_CNhs11285_tpm_fwd Cl:LK-2+ small cell lung carcinoma cell line:LK-2_CNhs11285_10541-107H1_forward Regulation 
HepaticMesenchymalTumorCellLineLI90_CNhs11868_tpm_rev Cl:LI90- hepatic mesenchymal tumor cell line:LI90_CNhs11868_10778-110G4_reverse Regulation 
HepaticMesenchymalTumorCellLineLI90_CNhs11868_tpm_fwd Cl:LI90+ hepatic mesenchymal tumor cell line:LI90_CNhs11868_10778-110G4_forward Regulation 
HepatomaCellLineLi7_CNhs11271_tpm_rev Cl:Li-7- hepatoma cell line:Li-7_CNhs11271_10484-107A7_reverse Regulation 
HepatomaCellLineLi7_CNhs11271_tpm_fwd Cl:Li-7+ hepatoma cell line:Li-7_CNhs11271_10484-107A7_forward Regulation 
SquamousCellLungCarcinomaCellLineLC1F_CNhs14238_tpm_rev Cl:LC-1F- squamous cell lung carcinoma cell line:LC-1F_CNhs14238_10457-106G7_reverse Regulation 
SquamousCellLungCarcinomaCellLineLC1F_CNhs14238_tpm_fwd Cl:LC-1F+ squamous cell lung carcinoma cell line:LC-1F_CNhs14238_10457-106G7_forward Regulation 
RhabdomyosarcomaCellLineKYM1_CNhs11877_tpm_rev Cl:KYM-1- rhabdomyosarcoma cell line:KYM-1_CNhs11877_10787-110H4_reverse Regulation 
RhabdomyosarcomaCellLineKYM1_CNhs11877_tpm_fwd Cl:KYM-1+ rhabdomyosarcoma cell line:KYM-1_CNhs11877_10787-110H4_forward Regulation 
ChronicMyelogenousLeukemiaCellLineKU812_CNhs10727_tpm_rev Cl:KU812- chronic myelogenous leukemia cell line:KU812_CNhs10727_10409-106B4_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineKU812_CNhs10727_tpm_fwd Cl:KU812+ chronic myelogenous leukemia cell line:KU812_CNhs10727_10409-106B4_forward Regulation 
PeripheralNeuroectodermalTumorCellLineKUSN_CNhs11830_tpm_rev Cl:KU-SN- peripheral neuroectodermal tumor cell line:KU-SN_CNhs11830_10697-109G4_reverse Regulation 
PeripheralNeuroectodermalTumorCellLineKUSN_CNhs11830_tpm_fwd Cl:KU-SN+ peripheral neuroectodermal tumor cell line:KU-SN_CNhs11830_10697-109G4_forward Regulation 
BronchialSquamousCellCarcinomaCellLineKNS62_CNhs11862_tpm_rev Cl:KNS-62- bronchial squamous cell carcinoma cell line:KNS-62_CNhs11862_10760-110E4_reverse Regulation 
BronchialSquamousCellCarcinomaCellLineKNS62_CNhs11862_tpm_fwd Cl:KNS-62+ bronchial squamous cell carcinoma cell line:KNS-62_CNhs11862_10760-110E4_forward Regulation 
LiposarcomaCellLineKMLS1_CNhs11870_tpm_rev Cl:KMLS-1- liposarcoma cell line:KMLS-1_CNhs11870_10782-110G8_reverse Regulation 
LiposarcomaCellLineKMLS1_CNhs11870_tpm_fwd Cl:KMLS-1+ liposarcoma cell line:KMLS-1_CNhs11870_10782-110G8_forward Regulation 
DuctalCellCarcinomaCellLineKLM1_CNhs11100_tpm_rev Cl:KLM-1- ductal cell carcinoma cell line:KLM-1_CNhs11100_10438-106E6_reverse Regulation 
DuctalCellCarcinomaCellLineKLM1_CNhs11100_tpm_fwd Cl:KLM-1+ ductal cell carcinoma cell line:KLM-1_CNhs11100_10438-106E6_forward Regulation 
AnaplasticLargeCellLymphomaCellLineKiJK_CNhs11881_tpm_rev Cl:Ki-JK- anaplastic large cell lymphoma cell line:Ki-JK_CNhs11881_10795-110I3_reverse Regulation 
AnaplasticLargeCellLymphomaCellLineKiJK_CNhs11881_tpm_fwd Cl:Ki-JK+ anaplastic large cell lymphoma cell line:Ki-JK_CNhs11881_10795-110I3_forward Regulation 
NKTCellLeukemiaCellLineKHYG1_CNhs11867_tpm_rev Cl:KHYG-1- NK T cell leukemia cell line:KHYG-1_CNhs11867_10777-110G3_reverse Regulation 
NKTCellLeukemiaCellLineKHYG1_CNhs11867_tpm_fwd Cl:KHYG-1+ NK T cell leukemia cell line:KHYG-1_CNhs11867_10777-110G3_forward Regulation 
ThyroidCarcinomaCellLineKHM5M_CNhs14140_tpm_rev Cl:KHM-5M- thyroid carcinoma cell line:KHM-5M_CNhs14140_10776-110G2_reverse Regulation 
ThyroidCarcinomaCellLineKHM5M_CNhs14140_tpm_fwd Cl:KHM-5M+ thyroid carcinoma cell line:KHM-5M_CNhs14140_10776-110G2_forward Regulation 
GranulosaCellTumorCellLineKGN_CNhs11740_tpm_rev Cl:KGN- granulosa cell tumor cell line:KGN_CNhs11740_10624-108H3_reverse Regulation 
GranulosaCellTumorCellLineKGN_CNhs11740_tpm_fwd Cl:KGN+ granulosa cell tumor cell line:KGN_CNhs11740_10624-108H3_forward Regulation 
AcuteMyeloidLeukemiaFABM0CellLineKG1_CNhs13053_tpm_rev Cl:KG-1- acute myeloid leukemia (FAB M0) cell line:KG-1_CNhs13053_10827-111C8_reverse Regulation 
AcuteMyeloidLeukemiaFABM0CellLineKG1_CNhs13053_tpm_fwd Cl:KG-1+ acute myeloid leukemia (FAB M0) cell line:KG-1_CNhs13053_10827-111C8_forward Regulation 
ChronicMyeloblasticLeukemiaCMLCellLineKCL22_CNhs11886_tpm_rev Cl:KCL-22- chronic myeloblastic leukemia (CML) cell line:KCL-22_CNhs11886_10801-110I9_reverse Regulation 
ChronicMyeloblasticLeukemiaCMLCellLineKCL22_CNhs11886_tpm_fwd Cl:KCL-22+ chronic myeloblastic leukemia (CML) cell line:KCL-22_CNhs11886_10801-110I9_forward Regulation 
SignetRingCarcinomaCellLineKatoIII_CNhs10753_tpm_rev Cl:KatoIII- signet ring carcinoma cell line:Kato III_CNhs10753_10436-106E4_reverse Regulation 
SignetRingCarcinomaCellLineKatoIII_CNhs10753_tpm_fwd Cl:KatoIII+ signet ring carcinoma cell line:Kato III_CNhs10753_10436-106E4_forward Regulation 
AcuteMyeloidLeukemiaFABM2CellLineKasumi6_CNhs13052_tpm_rev Cl:Kasumi-6- acute myeloid leukemia (FAB M2) cell line:Kasumi-6_CNhs13052_10792-110H9_reverse Regulation 
AcuteMyeloidLeukemiaFABM2CellLineKasumi6_CNhs13052_tpm_fwd Cl:Kasumi-6+ acute myeloid leukemia (FAB M2) cell line:Kasumi-6_CNhs13052_10792-110H9_forward Regulation 
AcuteMyeloidLeukemiaFABM2CellLineKasumi1_CNhs13502_tpm_rev Cl:Kasumi-1- acute myeloid leukemia (FAB M2) cell line:Kasumi-1_CNhs13502_10788-110H5_reverse Regulation 
AcuteMyeloidLeukemiaFABM2CellLineKasumi1_CNhs13502_tpm_fwd Cl:Kasumi-1+ acute myeloid leukemia (FAB M2) cell line:Kasumi-1_CNhs13502_10788-110H5_forward Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep3_CNhs12336_tpm_rev Cl:K562Br3- chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep3_CNhs12336_10826-111C7_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep3_CNhs12336_tpm_fwd Cl:K562Br3+ chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep3_CNhs12336_10826-111C7_forward Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep2_CNhs12335_tpm_rev Cl:K562Br2- chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep2_CNhs12335_10825-111C6_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep2_CNhs12335_tpm_fwd Cl:K562Br2+ chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep2_CNhs12335_10825-111C6_forward Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep1_CNhs12334_tpm_rev Cl:K562Br1- chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep1_CNhs12334_10824-111C5_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineK562ENCODEBiolRep1_CNhs12334_tpm_fwd Cl:K562Br1+ chronic myelogenous leukemia cell line:K562 ENCODE, biol_rep1_CNhs12334_10824-111C5_forward Regulation 
ChronicMyelogenousLeukemiaCellLineK562_CNhs11250_tpm_rev Cl:K562- chronic myelogenous leukemia cell line:K562_CNhs11250_10454-106G4_reverse Regulation 
ChronicMyelogenousLeukemiaCellLineK562_CNhs11250_tpm_fwd Cl:K562+ chronic myelogenous leukemia cell line:K562_CNhs11250_10454-106G4_forward Regulation 
AcuteLymphoblasticLeukemiaTALLCellLineJurkat_CNhs11253_tpm_rev Cl:Jurkat- acute lymphoblastic leukemia (T-ALL) cell line:Jurkat_CNhs11253_10464-106H5_reverse Regulation 
AcuteLymphoblasticLeukemiaTALLCellLineJurkat_CNhs11253_tpm_fwd Cl:Jurkat+ acute lymphoblastic leukemia (T-ALL) cell line:Jurkat_CNhs11253_10464-106H5_forward Regulation 
TransitionalcellCarcinomaCellLineJMSU1_CNhs11261_tpm_rev Cl:JMSU1- transitional-cell carcinoma cell line:JMSU1_CNhs11261_10492-107B6_reverse Regulation 
TransitionalcellCarcinomaCellLineJMSU1_CNhs11261_tpm_fwd Cl:JMSU1+ transitional-cell carcinoma cell line:JMSU1_CNhs11261_10492-107B6_forward Regulation 
SquamousCellCarcinomaCellLineJHUSnk1_CNhs11749_tpm_rev Cl:JHUS-nk1- squamous cell carcinoma cell line:JHUS-nk1_CNhs11749_10646-109A7_reverse Regulation 
SquamousCellCarcinomaCellLineJHUSnk1_CNhs11749_tpm_fwd Cl:JHUS-nk1+ squamous cell carcinoma cell line:JHUS-nk1_CNhs11749_10646-109A7_forward Regulation 
EndometrioidAdenocarcinomaCellLineJHUEM1_CNhs11748_tpm_rev Cl:JHUEM-1- endometrioid adenocarcinoma cell line:JHUEM-1_CNhs11748_10643-109A4_reverse Regulation 
EndometrioidAdenocarcinomaCellLineJHUEM1_CNhs11748_tpm_fwd Cl:JHUEM-1+ endometrioid adenocarcinoma cell line:JHUEM-1_CNhs11748_10643-109A4_forward Regulation 
CarcinosarcomaCellLineJHUCS1_CNhs11747_tpm_rev Cl:JHUCS-1- carcinosarcoma cell line:JHUCS-1_CNhs11747_10642-109A3_reverse Regulation 
CarcinosarcomaCellLineJHUCS1_CNhs11747_tpm_fwd Cl:JHUCS-1+ carcinosarcoma cell line:JHUCS-1_CNhs11747_10642-109A3_forward Regulation 
SerousAdenocarcinomaCellLineJHOS2_CNhs11746_tpm_rev Cl:JHOS-2- serous adenocarcinoma cell line:JHOS-2_CNhs11746_10639-108I9_reverse Regulation 
SerousAdenocarcinomaCellLineJHOS2_CNhs11746_tpm_fwd Cl:JHOS-2+ serous adenocarcinoma cell line:JHOS-2_CNhs11746_10639-108I9_forward Regulation 
MucinousAdenocarcinomaCellLineJHOM1_CNhs11752_tpm_rev Cl:JHOM-1- mucinous adenocarcinoma cell line:JHOM-1_CNhs11752_10648-109A9_reverse Regulation 
MucinousAdenocarcinomaCellLineJHOM1_CNhs11752_tpm_fwd Cl:JHOM-1+ mucinous adenocarcinoma cell line:JHOM-1_CNhs11752_10648-109A9_forward Regulation 
ClearCellCarcinomaCellLineJHOC5_CNhs11745_tpm_rev Cl:JHOC-5- clear cell carcinoma cell line:JHOC-5_CNhs11745_10638-108I8_reverse Regulation 
ClearCellCarcinomaCellLineJHOC5_CNhs11745_tpm_fwd Cl:JHOC-5+ clear cell carcinoma cell line:JHOC-5_CNhs11745_10638-108I8_forward Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineITOII_CNhs11876_tpm_rev Cl:ITO-II- testicular germ cell embryonal carcinoma cell line:ITO-II_CNhs11876_10786-110H3_reverse Regulation 
TesticularGermCellEmbryonalCarcinomaCellLineITOII_CNhs11876_tpm_fwd Cl:ITO-II+ testicular germ cell embryonal carcinoma cell line:ITO-II_CNhs11876_10786-110H3_forward Regulation 
AdenocarcinomaCellLineIM95m_CNhs11882_tpm_rev Cl:IM95m- adenocarcinoma cell line:IM95m_CNhs11882_10796-110I4_reverse Regulation 
AdenocarcinomaCellLineIM95m_CNhs11882_tpm_fwd Cl:IM95m+ adenocarcinoma cell line:IM95m_CNhs11882_10796-110I4_forward Regulation 
LargeCellLungCarcinomaCellLineIALM_CNhs11277_tpm_rev Cl:IA-LM- large cell lung carcinoma cell line:IA-LM_CNhs11277_10509-107D5_reverse Regulation 
LargeCellLungCarcinomaCellLineIALM_CNhs11277_tpm_fwd Cl:IA-LM+ large cell lung carcinoma cell line:IA-LM_CNhs11277_10509-107D5_forward Regulation 
AcuteMyeloidLeukemiaFABM1CellLineHYT1_CNhs13054_tpm_rev Cl:HYT-1- acute myeloid leukemia (FAB M1) cell line:HYT-1_CNhs13054_10828-111C9_reverse Regulation 
AcuteMyeloidLeukemiaFABM1CellLineHYT1_CNhs13054_tpm_fwd Cl:HYT-1+ acute myeloid leukemia (FAB M1) cell line:HYT-1_CNhs13054_10828-111C9_forward Regulation 
MycosisFungoidesTCellLymphomaCellLineHuT102TIB162_CNhs11858_tpm_rev Cl:HuT102TIB-162- mycosis fungoides, T cell lymphoma cell line:HuT 102 TIB-162_CNhs11858_10744-110C6_reverse Regulation 
MycosisFungoidesTCellLymphomaCellLineHuT102TIB162_CNhs11858_tpm_fwd Cl:HuT102TIB-162+ mycosis fungoides, T cell lymphoma cell line:HuT 102 TIB-162_CNhs11858_10744-110C6_forward Regulation 
HepatoblastomaCellLineHuH6_CNhs11742_tpm_rev Cl:HuH-6- hepatoblastoma cell line:HuH-6_CNhs11742_10633-108I3_reverse Regulation 
HepatoblastomaCellLineHuH6_CNhs11742_tpm_fwd Cl:HuH-6+ hepatoblastoma cell line:HuH-6_CNhs11742_10633-108I3_forward Regulation 
CholangiocellularCarcinomaCellLineHuH28_CNhs11283_tpm_rev Cl:HuH-28- cholangiocellular carcinoma cell line:HuH-28_CNhs11283_10536-107G5_reverse Regulation 
CholangiocellularCarcinomaCellLineHuH28_CNhs11283_tpm_fwd Cl:HuH-28+ cholangiocellular carcinoma cell line:HuH-28_CNhs11283_10536-107G5_forward Regulation 
BileDuctCarcinomaCellLineHuCCT1_CNhs10750_tpm_rev Cl:HuCCT1- bile duct carcinoma cell line:HuCCT1_CNhs10750_10432-106D9_reverse Regulation 
BileDuctCarcinomaCellLineHuCCT1_CNhs10750_tpm_fwd Cl:HuCCT1+ bile duct carcinoma cell line:HuCCT1_CNhs10750_10432-106D9_forward Regulation 
MesenchymalStemCellLineHu5E18_CNhs11718_tpm_rev Cl:Hu5/E18- mesenchymal stem cell line:Hu5/E18_CNhs11718_10568-108B1_reverse Regulation 
MesenchymalStemCellLineHu5E18_CNhs11718_tpm_fwd Cl:Hu5/E18+ mesenchymal stem cell line:Hu5/E18_CNhs11718_10568-108B1_forward Regulation 
SacrococcigealTeratomaCellLineHTST_CNhs11829_tpm_rev Cl:HTST- sacrococcigeal teratoma cell line:HTST_CNhs11829_10695-109G2_reverse Regulation 
SacrococcigealTeratomaCellLineHTST_CNhs11829_tpm_fwd Cl:HTST+ sacrococcigeal teratoma cell line:HTST_CNhs11829_10695-109G2_forward Regulation 
SerousCystadenocarcinomaCellLineHTOA_CNhs11827_tpm_rev Cl:HTOA- serous cystadenocarcinoma cell line:HTOA_CNhs11827_10693-109F9_reverse Regulation 
SerousCystadenocarcinomaCellLineHTOA_CNhs11827_tpm_fwd Cl:HTOA+ serous cystadenocarcinoma cell line:HTOA_CNhs11827_10693-109F9_forward Regulation 
MixedMullerianTumorCellLineHTMMT_CNhs11944_tpm_rev Cl:HTMMT- mixed mullerian tumor cell line:HTMMT_CNhs11944_10689-109F5_reverse Regulation 
MixedMullerianTumorCellLineHTMMT_CNhs11944_tpm_fwd Cl:HTMMT+ mixed mullerian tumor cell line:HTMMT_CNhs11944_10689-109F5_forward Regulation 
FibrosarcomaCellLineHT1080_CNhs11860_tpm_rev Cl:HT-1080- fibrosarcoma cell line:HT-1080_CNhs11860_10758-110E2_reverse Regulation 
FibrosarcomaCellLineHT1080_CNhs11860_tpm_fwd Cl:HT-1080+ fibrosarcoma cell line:HT-1080_CNhs11860_10758-110E2_forward Regulation 
MaxillarySinusTumorCellLineHSQ89_CNhs10732_tpm_rev Cl:HSQ-89- maxillary sinus tumor cell line:HSQ-89_CNhs10732_10414-106B9_reverse Regulation 
MaxillarySinusTumorCellLineHSQ89_CNhs10732_tpm_fwd Cl:HSQ-89+ maxillary sinus tumor cell line:HSQ-89_CNhs10732_10414-106B9_forward Regulation 
KrukenbergTumorCellLineHSKTC_CNhs11822_tpm_rev Cl:HSKTC- Krukenberg tumor cell line:HSKTC_CNhs11822_10687-109F3_reverse Regulation 
KrukenbergTumorCellLineHSKTC_CNhs11822_tpm_fwd Cl:HSKTC+ Krukenberg tumor cell line:HSKTC_CNhs11822_10687-109F3_forward Regulation 
OralSquamousCellCarcinomaCellLineHSC3_CNhs11717_tpm_rev Cl:HSC-3- oral squamous cell carcinoma cell line:HSC-3_CNhs11717_10545-107H5_reverse Regulation 
OralSquamousCellCarcinomaCellLineHSC3_CNhs11717_tpm_fwd Cl:HSC-3+ oral squamous cell carcinoma cell line:HSC-3_CNhs11717_10545-107H5_forward Regulation 
PagetoidSarcomaCellLineHs925_T_CNhs11856_tpm_rev Cl:Hs925_T- pagetoid sarcoma cell line:Hs 925_T_CNhs11856_10732-110B3_reverse Regulation 
PagetoidSarcomaCellLineHs925_T_CNhs11856_tpm_fwd Cl:Hs925_T+ pagetoid sarcoma cell line:Hs 925_T_CNhs11856_10732-110B3_forward Regulation 
EwingsSarcomaCellLineHs863_T_CNhs11836_tpm_rev Cl:Hs863_T- Ewing's sarcoma cell line:Hs 863_T_CNhs11836_10705-109H3_reverse Regulation 
EwingsSarcomaCellLineHs863_T_CNhs11836_tpm_fwd Cl:Hs863_T+ Ewing's sarcoma cell line:Hs 863_T_CNhs11836_10705-109H3_forward Regulation 
TransitionalCellCarcinomaCellLineHs769_T_CNhs11837_tpm_rev Cl:Hs769_T- transitional cell carcinoma cell line:Hs 769_T_CNhs11837_10707-109H5_reverse Regulation 
TransitionalCellCarcinomaCellLineHs769_T_CNhs11837_tpm_fwd Cl:Hs769_T+ transitional cell carcinoma cell line:Hs 769_T_CNhs11837_10707-109H5_forward Regulation 
OsteoclastomaCellLineHs706_T_CNhs11835_tpm_rev Cl:Hs706_T- osteoclastoma cell line:Hs 706_T_CNhs11835_10704-109H2_reverse Regulation 
OsteoclastomaCellLineHs706_T_CNhs11835_tpm_fwd Cl:Hs706_T+ osteoclastoma cell line:Hs 706_T_CNhs11835_10704-109H2_forward Regulation 
NeurofibromaCellLineHs53_T_CNhs11854_tpm_rev Cl:Hs53_T- neurofibroma cell line:Hs 53_T_CNhs11854_10729-110A9_reverse Regulation 
NeurofibromaCellLineHs53_T_CNhs11854_tpm_fwd Cl:Hs53_T+ neurofibroma cell line:Hs 53_T_CNhs11854_10729-110A9_forward Regulation 
SpindleCellSarcomaCellLineHs132_T_CNhs11857_tpm_rev Cl:Hs132_T- spindle cell sarcoma cell line:Hs 132_T_CNhs11857_10737-110B8_reverse Regulation 
SpindleCellSarcomaCellLineHs132_T_CNhs11857_tpm_fwd Cl:Hs132_T+ spindle cell sarcoma cell line:Hs 132_T_CNhs11857_10737-110B8_forward Regulation 
SynovialSarcomaCellLineHSSYII_CNhs11244_tpm_rev Cl:HS-SY-II- synovial sarcoma cell line:HS-SY-II_CNhs11244_10441-106E9_reverse Regulation 
SynovialSarcomaCellLineHSSYII_CNhs11244_tpm_fwd Cl:HS-SY-II+ synovial sarcoma cell line:HS-SY-II_CNhs11244_10441-106E9_forward Regulation 
SchwannomaCellLineHSPSSTechRep2_CNhs11245_tpm_rev Cl:HS-PSSTr2- schwannoma cell line:HS-PSS, tech_rep2_CNhs11245_10442-106F1_reverse Regulation 
SchwannomaCellLineHSPSSTechRep2_CNhs11245_tpm_fwd Cl:HS-PSSTr2+ schwannoma cell line:HS-PSS, tech_rep2_CNhs11245_10442-106F1_forward Regulation 
SchwannomaCellLineHSPSS_CNhs11183_tpm_rev Cl:HS-PSS- schwannoma cell line:HS-PSS_CNhs11183_10442-106F1_reverse Regulation 
SchwannomaCellLineHSPSS_CNhs11183_tpm_fwd Cl:HS-PSS+ schwannoma cell line:HS-PSS_CNhs11183_10442-106F1_forward Regulation 
OsteosarcomaCellLineHSOs1_CNhs11290_tpm_rev Cl:HS-Os-1- osteosarcoma cell line:HS-Os-1_CNhs11290_10558-107I9_reverse Regulation 
OsteosarcomaCellLineHSOs1_CNhs11290_tpm_fwd Cl:HS-Os-1+ osteosarcoma cell line:HS-Os-1_CNhs11290_10558-107I9_forward Regulation 
EpithelioidSarcomaCellLineHSES2R_CNhs14239_tpm_rev Cl:HS-ES-2R- epithelioid sarcoma cell line:HS-ES-2R_CNhs14239_10495-107B9_reverse Regulation 
EpithelioidSarcomaCellLineHSES2R_CNhs14239_tpm_fwd Cl:HS-ES-2R+ epithelioid sarcoma cell line:HS-ES-2R_CNhs14239_10495-107B9_forward Regulation 
EpithelioidSarcomaCellLineHSES1_CNhs11247_tpm_rev Cl:HS-ES-1- epithelioid sarcoma cell line:HS-ES-1_CNhs11247_10443-106F2_reverse Regulation 
EpithelioidSarcomaCellLineHSES1_CNhs11247_tpm_fwd Cl:HS-ES-1+ epithelioid sarcoma cell line:HS-ES-1_CNhs11247_10443-106F2_forward Regulation 
AcuteLymphoblasticLeukemiaTALLCellLineHPBALL_CNhs10746_tpm_rev Cl:HPB-ALL- acute lymphoblastic leukemia (T-ALL) cell line:HPB-ALL_CNhs10746_10429-106D6_reverse Regulation 
AcuteLymphoblasticLeukemiaTALLCellLineHPBALL_CNhs10746_tpm_fwd Cl:HPB-ALL+ acute lymphoblastic leukemia (T-ALL) cell line:HPB-ALL_CNhs10746_10429-106D6_forward Regulation 
GlassyCellCarcinomaCellLineHOKUG_CNhs11824_tpm_rev Cl:HOKUG- glassy cell carcinoma cell line:HOKUG_CNhs11824_10688-109F4_reverse Regulation 
GlassyCellCarcinomaCellLineHOKUG_CNhs11824_tpm_fwd Cl:HOKUG+ glassy cell carcinoma cell line:HOKUG_CNhs11824_10688-109F4_forward Regulation 
OralSquamousCellCarcinomaCellLineHO1u1_CNhs11287_tpm_rev Cl:HO-1-u-1- oral squamous cell carcinoma cell line:HO-1-u-1_CNhs11287_10550-107I1_reverse Regulation 
OralSquamousCellCarcinomaCellLineHO1u1_CNhs11287_tpm_fwd Cl:HO-1-u-1+ oral squamous cell carcinoma cell line:HO-1-u-1_CNhs11287_10550-107I1_forward Regulation 
AcuteMyeloidLeukemiaFABM4CellLineHNT34_CNhs13504_tpm_rev Cl:HNT-34- acute myeloid leukemia (FAB M4) cell line:HNT-34_CNhs13504_10831-111D3_reverse Regulation 
AcuteMyeloidLeukemiaFABM4CellLineHNT34_CNhs13504_tpm_fwd Cl:HNT-34+ acute myeloid leukemia (FAB M4) cell line:HNT-34_CNhs13504_10831-111D3_forward Regulation 
AcuteMyeloidLeukemiaFABM3CellLineHL60_CNhs13055_tpm_rev Cl:HL60- acute myeloid leukemia (FAB M3) cell line:HL60_CNhs13055_10829-111D1_reverse Regulation 
AcuteMyeloidLeukemiaFABM3CellLineHL60_CNhs13055_tpm_fwd Cl:HL60+ acute myeloid leukemia (FAB M3) cell line:HL60_CNhs13055_10829-111D1_forward Regulation 
MeningiomaCellLineHKBMM_CNhs11945_tpm_rev Cl:HKBMM- meningioma cell line:HKBMM_CNhs11945_10691-109F7_reverse Regulation 
MeningiomaCellLineHKBMM_CNhs11945_tpm_fwd Cl:HKBMM+ meningioma cell line:HKBMM_CNhs11945_10691-109F7_forward Regulation 
KeratoacanthomaCellLineHKA1_CNhs11880_tpm_rev Cl:HKA-1- keratoacanthoma cell line:HKA-1_CNhs11880_10791-110H8_reverse Regulation 
KeratoacanthomaCellLineHKA1_CNhs11880_tpm_fwd Cl:HKA-1+ keratoacanthoma cell line:HKA-1_CNhs11880_10791-110H8_forward Regulation 
TridermalTeratomaCellLineHGRT_CNhs11828_tpm_rev Cl:HGRT- tridermal teratoma cell line:HGRT_CNhs11828_10694-109G1_reverse Regulation 
TridermalTeratomaCellLineHGRT_CNhs11828_tpm_fwd Cl:HGRT+ tridermal teratoma cell line:HGRT_CNhs11828_10694-109G1_forward Regulation 
WilmsTumorCellLineHFWT_CNhs11728_tpm_rev Cl:HFWT- Wilms' tumor cell line:HFWT_CNhs11728_10597-108E3_reverse Regulation 
WilmsTumorCellLineHFWT_CNhs11728_tpm_fwd Cl:HFWT+ Wilms' tumor cell line:HFWT_CNhs11728_10597-108E3_forward Regulation 
NormalEmbryonicPalatalMesenchymalCellLineHEPM_CNhs11894_tpm_rev Cl:HEPM- normal embryonic palatal mesenchymal cell line:HEPM_CNhs11894_10813-111B3_reverse Regulation 
NormalEmbryonicPalatalMesenchymalCellLineHEPM_CNhs11894_tpm_fwd Cl:HEPM+ normal embryonic palatal mesenchymal cell line:HEPM_CNhs11894_10813-111B3_forward Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep3_CNhs12330_tpm_rev Cl:HepG2Br3- hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep3_CNhs12330_10820-111C1_reverse Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep3_CNhs12330_tpm_fwd Cl:HepG2Br3+ hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep3_CNhs12330_10820-111C1_forward Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep2_CNhs12329_tpm_rev Cl:HepG2Br2- hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep2_CNhs12329_10819-111B9_reverse Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep2_CNhs12329_tpm_fwd Cl:HepG2Br2+ hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep2_CNhs12329_10819-111B9_forward Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep1_CNhs12328_tpm_rev Cl:HepG2Br1- hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep1_CNhs12328_10818-111B8_reverse Regulation 
HepatocellularCarcinomaCellLineHepG2ENCODEBiolRep1_CNhs12328_tpm_fwd Cl:HepG2Br1+ hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep1_CNhs12328_10818-111B8_forward Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep3_CNhs12327_tpm_rev Cl:HelaS3Br3- epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep3_CNhs12327_10817-111B7_reverse Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep3_CNhs12327_tpm_fwd Cl:HelaS3Br3+ epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep3_CNhs12327_10817-111B7_forward Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep2_CNhs12326_tpm_rev Cl:HelaS3Br2- epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep2_CNhs12326_10816-111B6_reverse Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep2_CNhs12326_tpm_fwd Cl:HelaS3Br2+ epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep2_CNhs12326_10816-111B6_forward Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep1_CNhs12325_tpm_rev Cl:HelaS3Br1- epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep1_CNhs12325_10815-111B5_reverse Regulation 
EpitheloidCarcinomaCellLineHelaS3ENCODEBiolRep1_CNhs12325_tpm_fwd Cl:HelaS3Br1+ epitheloid carcinoma cell line: HelaS3 ENCODE, biol_rep1_CNhs12325_10815-111B5_forward Regulation 
EmbryonicKidneyCellLineHEK293SLAMUntreated_CNhs11046_tpm_rev Cl:HEK293/SLAMuntreated- embryonic kidney cell line: HEK293/SLAM untreated_CNhs11046_10450-106F9_reverse Regulation 
EmbryonicKidneyCellLineHEK293SLAMUntreated_CNhs11046_tpm_fwd Cl:HEK293/SLAMuntreated+ embryonic kidney cell line: HEK293/SLAM untreated_CNhs11046_10450-106F9_forward Regulation 
EmbryonicKidneyCellLineHEK293SLAMInfection24hr_CNhs11047_tpm_rev Cl:HEK293/SLAMinfection,24hr- embryonic kidney cell line: HEK293/SLAM infection, 24hr_CNhs11047_10451-106G1_reverse Regulation 
EmbryonicKidneyCellLineHEK293SLAMInfection24hr_CNhs11047_tpm_fwd Cl:HEK293/SLAMinfection,24hr+ embryonic kidney cell line: HEK293/SLAM infection, 24hr_CNhs11047_10451-106G1_forward Regulation 
HodgkinsLymphomaCellLineHDMar2_CNhs11715_tpm_rev Cl:HD-Mar2- Hodgkin's lymphoma cell line:HD-Mar2_CNhs11715_10435-106E3_reverse Regulation 
HodgkinsLymphomaCellLineHDMar2_CNhs11715_tpm_fwd Cl:HD-Mar2+ Hodgkin's lymphoma cell line:HD-Mar2_CNhs11715_10435-106E3_forward Regulation 
SmallCellCervicalCancerCellLineHCSC1_CNhs11885_tpm_rev Cl:HCSC-1- small cell cervical cancer cell line:HCSC-1_CNhs11885_10800-110I8_reverse Regulation 
SmallCellCervicalCancerCellLineHCSC1_CNhs11885_tpm_fwd Cl:HCSC-1+ small cell cervical cancer cell line:HCSC-1_CNhs11885_10800-110I8_forward Regulation 
AcantholyticSquamousCarcinomaCellLineHCC1806_CNhs11844_tpm_rev Cl:HCC1806- acantholytic squamous carcinoma cell line:HCC1806_CNhs11844_10717-109I6_reverse Regulation 
AcantholyticSquamousCarcinomaCellLineHCC1806_CNhs11844_tpm_fwd Cl:HCC1806+ acantholytic squamous carcinoma cell line:HCC1806_CNhs11844_10717-109I6_forward Regulation 
ExtraskeletalMyxoidChondrosarcomaCellLineHEMCSS_CNhs10728_tpm_rev Cl:H-EMC-SS- extraskeletal myxoid chondrosarcoma cell line:H-EMC-SS_CNhs10728_10410-106B5_reverse Regulation 
ExtraskeletalMyxoidChondrosarcomaCellLineHEMCSS_CNhs10728_tpm_fwd Cl:H-EMC-SS+ extraskeletal myxoid chondrosarcoma cell line:H-EMC-SS_CNhs10728_10410-106B5_forward Regulation 
GastricCancerCellLineGSS_CNhs14241_tpm_rev Cl:GSS- gastric cancer cell line:GSS_CNhs14241_10560-108A2_reverse Regulation 
GastricCancerCellLineGSS_CNhs14241_tpm_fwd Cl:GSS+ gastric cancer cell line:GSS_CNhs14241_10560-108A2_forward Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep3_CNhs12333_tpm_rev Cl:GM12878Br3- B lymphoblastoid cell line: GM12878 ENCODE, biol_rep3_CNhs12333_10823-111C4_reverse Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep3_CNhs12333_tpm_fwd Cl:GM12878Br3+ B lymphoblastoid cell line: GM12878 ENCODE, biol_rep3_CNhs12333_10823-111C4_forward Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep2_CNhs12332_tpm_rev Cl:GM12878Br2- B lymphoblastoid cell line: GM12878 ENCODE, biol_rep2_CNhs12332_10822-111C3_reverse Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep2_CNhs12332_tpm_fwd Cl:GM12878Br2+ B lymphoblastoid cell line: GM12878 ENCODE, biol_rep2_CNhs12332_10822-111C3_forward Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep1_CNhs12331_tpm_rev Cl:GM12878Br1- B lymphoblastoid cell line: GM12878 ENCODE, biol_rep1_CNhs12331_10821-111C2_reverse Regulation 
BLymphoblastoidCellLineGM12878ENCODEBiolRep1_CNhs12331_tpm_fwd Cl:GM12878Br1+ B lymphoblastoid cell line: GM12878 ENCODE, biol_rep1_CNhs12331_10821-111C2_forward Regulation 
GliomaCellLineGI1_CNhs10731_tpm_rev Cl:GI-1- glioma cell line:GI-1_CNhs10731_10413-106B8_reverse Regulation 
GliomaCellLineGI1_CNhs10731_tpm_fwd Cl:GI-1+ glioma cell line:GI-1_CNhs10731_10413-106B8_forward Regulation 
FibrousHistiocytomaCellLineGCTTIB223_CNhs11842_tpm_rev Cl:GCTTIB-223- fibrous histiocytoma cell line:GCT TIB-223_CNhs11842_10711-109H9_reverse Regulation 
FibrousHistiocytomaCellLineGCTTIB223_CNhs11842_tpm_fwd Cl:GCTTIB-223+ fibrous histiocytoma cell line:GCT TIB-223_CNhs11842_10711-109H9_forward Regulation 
LeiomyoblastomaCellLineG402_CNhs11848_tpm_rev Cl:G-402- leiomyoblastoma cell line:G-402_CNhs11848_10721-110A1_reverse Regulation 
LeiomyoblastomaCellLineG402_CNhs11848_tpm_fwd Cl:G-402+ leiomyoblastoma cell line:G-402_CNhs11848_10721-110A1_forward Regulation 
WilmsTumorCellLineG401_CNhs11892_tpm_rev Cl:G-401- Wilms' tumor cell line:G-401_CNhs11892_10809-111A8_reverse Regulation 
WilmsTumorCellLineG401_CNhs11892_tpm_fwd Cl:G-401+ Wilms' tumor cell line:G-401_CNhs11892_10809-111A8_forward Regulation 
MelanomaCellLineG361_CNhs11254_tpm_rev Cl:G-361- melanoma cell line:G-361_CNhs11254_10465-106H6_reverse Regulation 
MelanomaCellLineG361_CNhs11254_tpm_fwd Cl:G-361+ melanoma cell line:G-361_CNhs11254_10465-106H6_forward Regulation 
NeuroectodermalTumorCellLineFURPNT2_CNhs11753_tpm_rev Cl:FU-RPNT-2- neuroectodermal tumor cell line:FU-RPNT-2_CNhs11753_10663-109C6_reverse Regulation 
NeuroectodermalTumorCellLineFURPNT2_CNhs11753_tpm_fwd Cl:FU-RPNT-2+ neuroectodermal tumor cell line:FU-RPNT-2_CNhs11753_10663-109C6_forward Regulation 
NeuroectodermalTumorCellLineFURPNT1_CNhs11744_tpm_rev Cl:FU-RPNT-1- neuroectodermal tumor cell line:FU-RPNT-1_CNhs11744_10637-108I7_reverse Regulation 
NeuroectodermalTumorCellLineFURPNT1_CNhs11744_tpm_fwd Cl:FU-RPNT-1+ neuroectodermal tumor cell line:FU-RPNT-1_CNhs11744_10637-108I7_forward Regulation 
AcuteMyeloidLeukemiaFABM4CellLineFKH1_CNhs13503_tpm_rev Cl:FKH-1- acute myeloid leukemia (FAB M4) cell line:FKH-1_CNhs13503_10830-111D2_reverse Regulation 
AcuteMyeloidLeukemiaFABM4CellLineFKH1_CNhs13503_tpm_fwd Cl:FKH-1+ acute myeloid leukemia (FAB M4) cell line:FKH-1_CNhs13503_10830-111D2_forward Regulation 
NormalIntestinalEpithelialCellLineFHs74Int_CNhs11950_tpm_rev Cl:FHs74Int- normal intestinal epithelial cell line:FHs 74 Int_CNhs11950_10812-111B2_reverse Regulation 
NormalIntestinalEpithelialCellLineFHs74Int_CNhs11950_tpm_fwd Cl:FHs74Int+ normal intestinal epithelial cell line:FHs 74 Int_CNhs11950_10812-111B2_forward Regulation 
AcuteMyeloidLeukemiaFABM6CellLineF36P_CNhs13505_tpm_rev Cl:F-36P- acute myeloid leukemia (FAB M6) cell line:F-36P_CNhs13505_10837-111D9_reverse Regulation 
AcuteMyeloidLeukemiaFABM6CellLineF36P_CNhs13505_tpm_fwd Cl:F-36P+ acute myeloid leukemia (FAB M6) cell line:F-36P_CNhs13505_10837-111D9_forward Regulation 
AcuteMyeloidLeukemiaFABM6CellLineF36E_CNhs13060_tpm_rev Cl:F-36E- acute myeloid leukemia (FAB M6) cell line:F-36E_CNhs13060_10836-111D8_reverse Regulation 
AcuteMyeloidLeukemiaFABM6CellLineF36E_CNhs13060_tpm_fwd Cl:F-36E+ acute myeloid leukemia (FAB M6) cell line:F-36E_CNhs13060_10836-111D8_forward Regulation 
AcuteMyeloidLeukemiaFABM4eoCellLineEoL3_CNhs13057_tpm_rev Cl:EoL-3- acute myeloid leukemia (FAB M4eo) cell line:EoL-3_CNhs13057_10833-111D5_reverse Regulation 
AcuteMyeloidLeukemiaFABM4eoCellLineEoL3_CNhs13057_tpm_fwd Cl:EoL-3+ acute myeloid leukemia (FAB M4eo) cell line:EoL-3_CNhs13057_10833-111D5_forward Regulation 
AcuteMyeloidLeukemiaFABM4eoCellLineEoL1_CNhs13056_tpm_rev Cl:EoL-1- acute myeloid leukemia (FAB M4eo) cell line:EoL-1_CNhs13056_10832-111D4_reverse Regulation 
AcuteMyeloidLeukemiaFABM4eoCellLineEoL1_CNhs13056_tpm_fwd Cl:EoL-1+ acute myeloid leukemia (FAB M4eo) cell line:EoL-1_CNhs13056_10832-111D4_forward Regulation 
AcuteMyeloidLeukemiaFABM6CellLineEEB_CNhs13059_tpm_rev Cl:EEB- acute myeloid leukemia (FAB M6) cell line:EEB_CNhs13059_10835-111D7_reverse Regulation 
AcuteMyeloidLeukemiaFABM6CellLineEEB_CNhs13059_tpm_fwd Cl:EEB+ acute myeloid leukemia (FAB M6) cell line:EEB_CNhs13059_10835-111D7_forward Regulation 
SmallcellGastrointestinalCarcinomaCellLineECC4_CNhs11734_tpm_rev Cl:ECC4- small-cell gastrointestinal carcinoma cell line:ECC4_CNhs11734_10609-108F6_reverse Regulation 
SmallcellGastrointestinalCarcinomaCellLineECC4_CNhs11734_tpm_fwd Cl:ECC4+ small-cell gastrointestinal carcinoma cell line:ECC4_CNhs11734_10609-108F6_forward Regulation 
GastrointestinalCarcinomaCellLineECC12_CNhs11738_tpm_rev Cl:ECC12- gastrointestinal carcinoma cell line:ECC12_CNhs11738_10615-108G3_reverse Regulation 
GastrointestinalCarcinomaCellLineECC12_CNhs11738_tpm_fwd Cl:ECC12+ gastrointestinal carcinoma cell line:ECC12_CNhs11738_10615-108G3_forward Regulation 
SmallCellGastrointestinalCarcinomaCellLineECC10_CNhs11736_tpm_rev Cl:ECC10- small cell gastrointestinal carcinoma cell line:ECC10_CNhs11736_10610-108F7_reverse Regulation 
SmallCellGastrointestinalCarcinomaCellLineECC10_CNhs11736_tpm_fwd Cl:ECC10+ small cell gastrointestinal carcinoma cell line:ECC10_CNhs11736_10610-108F7_forward Regulation 
SquamousCellCarcinomaCellLineECGI10_CNhs11252_tpm_rev Cl:EC-GI-10- squamous cell carcinoma cell line:EC-GI-10_CNhs11252_10463-106H4_reverse Regulation 
SquamousCellCarcinomaCellLineECGI10_CNhs11252_tpm_fwd Cl:EC-GI-10+ squamous cell carcinoma cell line:EC-GI-10_CNhs11252_10463-106H4_forward Regulation 
SquamousCellLungCarcinomaCellLineEBC1_CNhs11273_tpm_rev Cl:EBC-1- squamous cell lung carcinoma cell line:EBC-1_CNhs11273_10486-107A9_reverse Regulation 
SquamousCellLungCarcinomaCellLineEBC1_CNhs11273_tpm_fwd Cl:EBC-1+ squamous cell lung carcinoma cell line:EBC-1_CNhs11273_10486-107A9_forward Regulation 
ProstateCancerCellLineDU145_CNhs11260_tpm_rev Cl:DU145- prostate cancer cell line:DU145_CNhs11260_10490-107B4_reverse Regulation 
ProstateCancerCellLineDU145_CNhs11260_tpm_fwd Cl:DU145+ prostate cancer cell line:DU145_CNhs11260_10490-107B4_forward Regulation 
LymphangiectasiaCellLineDS1_CNhs11852_tpm_rev Cl:DS-1- lymphangiectasia cell line:DS-1_CNhs11852_10727-110A7_reverse Regulation 
LymphangiectasiaCellLineDS1_CNhs11852_tpm_fwd Cl:DS-1+ lymphangiectasia cell line:DS-1_CNhs11852_10727-110A7_forward Regulation 
SmallCellLungCarcinomaCellLineDMS144_CNhs12808_tpm_rev Cl:DMS144- small cell lung carcinoma cell line:DMS 144_CNhs12808_10841-111E4_reverse Regulation 
SmallCellLungCarcinomaCellLineDMS144_CNhs12808_tpm_fwd Cl:DMS144+ small cell lung carcinoma cell line:DMS 144_CNhs12808_10841-111E4_forward Regulation 
MalignantTrichilemmalCystCellLineDJM1_CNhs10730_tpm_rev Cl:DJM-1- malignant trichilemmal cyst cell line:DJM-1_CNhs10730_10412-106B7_reverse Regulation 
MalignantTrichilemmalCystCellLineDJM1_CNhs10730_tpm_fwd Cl:DJM-1+ malignant trichilemmal cyst cell line:DJM-1_CNhs10730_10412-106B7_forward Regulation 
PharyngealCarcinomaCellLineDetroit562_CNhs11849_tpm_rev Cl:Detroit562- pharyngeal carcinoma cell line:Detroit 562_CNhs11849_10723-110A3_reverse Regulation 
PharyngealCarcinomaCellLineDetroit562_CNhs11849_tpm_fwd Cl:Detroit562+ pharyngeal carcinoma cell line:Detroit 562_CNhs11849_10723-110A3_forward Regulation 
BurkittsLymphomaCellLineDAUDI_CNhs10739_tpm_rev Cl:DAUDI- Burkitt's lymphoma cell line:DAUDI_CNhs10739_10422-106C8_reverse Regulation 
BurkittsLymphomaCellLineDAUDI_CNhs10739_tpm_fwd Cl:DAUDI+ Burkitt's lymphoma cell line:DAUDI_CNhs10739_10422-106C8_forward Regulation 
CervicalCancerCellLineD98AH2_CNhs11288_tpm_rev Cl:D98-AH2- cervical cancer cell line:D98-AH2_CNhs11288_10552-107I3_reverse Regulation 
CervicalCancerCellLineD98AH2_CNhs11288_tpm_fwd Cl:D98-AH2+ cervical cancer cell line:D98-AH2_CNhs11288_10552-107I3_forward Regulation 
MedulloblastomaCellLineD283Med_CNhs12805_tpm_rev Cl:D283Med- medulloblastoma cell line:D283 Med_CNhs12805_10838-111E1_reverse Regulation 
MedulloblastomaCellLineD283Med_CNhs12805_tpm_fwd Cl:D283Med+ medulloblastoma cell line:D283 Med_CNhs12805_10838-111E1_forward Regulation 
DiffuseLargeBcellLymphomaCellLineCTB1_CNhs11741_tpm_rev Cl:CTB-1- diffuse large B-cell lymphoma cell line:CTB-1_CNhs11741_10631-108I1_reverse Regulation 
DiffuseLargeBcellLymphomaCellLineCTB1_CNhs11741_tpm_fwd Cl:CTB-1+ diffuse large B-cell lymphoma cell line:CTB-1_CNhs11741_10631-108I1_forward Regulation 
MelanomaCellLineCOLO679_CNhs11281_tpm_rev Cl:COLO679- melanoma cell line:COLO 679_CNhs11281_10514-107E1_reverse Regulation 
MelanomaCellLineCOLO679_CNhs11281_tpm_fwd Cl:COLO679+ melanoma cell line:COLO 679_CNhs11281_10514-107E1_forward Regulation 
ColonCarcinomaCellLineCOLO320_CNhs10737_tpm_rev Cl:COLO-320- colon carcinoma cell line:COLO-320_CNhs10737_10420-106C6_reverse Regulation 
ColonCarcinomaCellLineCOLO320_CNhs10737_tpm_fwd Cl:COLO-320+ colon carcinoma cell line:COLO-320_CNhs10737_10420-106C6_forward Regulation 
CordBloodDerivedCellLineCOBLaUntreated_CNhs11045_tpm_rev Cl:COBL-auntreated- cord blood derived cell line:COBL-a untreated_CNhs11045_10449-106F8_reverse Regulation 
CordBloodDerivedCellLineCOBLaUntreated_CNhs11045_tpm_fwd Cl:COBL-auntreated+ cord blood derived cell line:COBL-a untreated_CNhs11045_10449-106F8_forward Regulation 
CordBloodDerivedCellLineCOBLa24hInfection_CNhs11050_tpm_rev Cl:COBL-a24hinfection- cord blood derived cell line:COBL-a 24h infection_CNhs11050_10453-106G3_reverse Regulation 
CordBloodDerivedCellLineCOBLa24hInfection_CNhs11050_tpm_fwd Cl:COBL-a24hinfection+ cord blood derived cell line:COBL-a 24h infection_CNhs11050_10453-106G3_forward Regulation 
CordBloodDerivedCellLineCOBLa24hInfectionC_CNhs11049_tpm_rev Cl:COBL-a24hinfection(-C)- cord blood derived cell line:COBL-a 24h infection(-C)_CNhs11049_10452-106G2_reverse Regulation 
CordBloodDerivedCellLineCOBLa24hInfectionC_CNhs11049_tpm_fwd Cl:COBL-a24hinfection(-C)+ cord blood derived cell line:COBL-a 24h infection(-C)_CNhs11049_10452-106G2_forward Regulation 
NeuroblastomaCellLineCHP134_CNhs11276_tpm_rev Cl:CHP-134- neuroblastoma cell line:CHP-134_CNhs11276_10508-107D4_reverse Regulation 
NeuroblastomaCellLineCHP134_CNhs11276_tpm_fwd Cl:CHP-134+ neuroblastoma cell line:CHP-134_CNhs11276_10508-107D4_forward Regulation 
BronchogenicCarcinomaCellLineChaGoK1_CNhs11841_tpm_rev Cl:ChaGo-K-1- bronchogenic carcinoma cell line:ChaGo-K-1_CNhs11841_10710-109H8_reverse Regulation 
BronchogenicCarcinomaCellLineChaGoK1_CNhs11841_tpm_fwd Cl:ChaGo-K-1+ bronchogenic carcinoma cell line:ChaGo-K-1_CNhs11841_10710-109H8_forward Regulation 
EpidermoidCarcinomaCellLineCaSki_CNhs10748_tpm_rev Cl:CaSki- epidermoid carcinoma cell line:Ca Ski_CNhs10748_10431-106D8_reverse Regulation 
EpidermoidCarcinomaCellLineCaSki_CNhs10748_tpm_fwd Cl:CaSki+ epidermoid carcinoma cell line:Ca Ski_CNhs10748_10431-106D8_forward Regulation 
ColonCarcinomaCellLineCACO2_CNhs11280_tpm_rev Cl:CACO-2- colon carcinoma cell line:CACO-2_CNhs11280_10513-107D9_reverse Regulation 
ColonCarcinomaCellLineCACO2_CNhs11280_tpm_fwd Cl:CACO-2+ colon carcinoma cell line:CACO-2_CNhs11280_10513-107D9_forward Regulation 
OralSquamousCellCarcinomaCellLineCa922_CNhs10752_tpm_rev Cl:Ca9-22- oral squamous cell carcinoma cell line:Ca9-22_CNhs10752_10434-106E2_reverse Regulation 
OralSquamousCellCarcinomaCellLineCa922_CNhs10752_tpm_fwd Cl:Ca9-22+ oral squamous cell carcinoma cell line:Ca9-22_CNhs10752_10434-106E2_forward Regulation 
ChoriocarcinomaCellLineBeWo_CNhs10740_tpm_rev Cl:BeWo- choriocarcinoma cell line:BeWo_CNhs10740_10423-106C9_reverse Regulation 
ChoriocarcinomaCellLineBeWo_CNhs10740_tpm_fwd Cl:BeWo+ choriocarcinoma cell line:BeWo_CNhs10740_10423-106C9_forward Regulation 
AcuteLymphoblasticLeukemiaBALLCellLineBALL1_CNhs11251_tpm_rev Cl:BALL-1- acute lymphoblastic leukemia (B-ALL) cell line:BALL-1_CNhs11251_10455-106G5_reverse Regulation 
AcuteLymphoblasticLeukemiaBALLCellLineBALL1_CNhs11251_tpm_fwd Cl:BALL-1+ acute lymphoblastic leukemia (B-ALL) cell line:BALL-1_CNhs11251_10455-106G5_forward Regulation 
GastricCancerCellLineAZ521_CNhs11286_tpm_rev Cl:AZ521- gastric cancer cell line:AZ521_CNhs11286_10549-107H9_reverse Regulation 
GastricCancerCellLineAZ521_CNhs11286_tpm_fwd Cl:AZ521+ gastric cancer cell line:AZ521_CNhs11286_10549-107H9_forward Regulation 
AdultTcellLeukemiaCellLineATN1_CNhs10738_tpm_rev Cl:ATN-1- adult T-cell leukemia cell line:ATN-1_CNhs10738_10421-106C7_reverse Regulation 
AdultTcellLeukemiaCellLineATN1_CNhs10738_tpm_fwd Cl:ATN-1+ adult T-cell leukemia cell line:ATN-1_CNhs10738_10421-106C7_forward Regulation 
PlasmaCellLeukemiaCellLineARH77_CNhs12807_tpm_rev Cl:ARH-77- plasma cell leukemia cell line:ARH-77_CNhs12807_10840-111E3_reverse Regulation 
PlasmaCellLeukemiaCellLineARH77_CNhs12807_tpm_fwd Cl:ARH-77+ plasma cell leukemia cell line:ARH-77_CNhs12807_10840-111E3_forward Regulation 
MesotheliomaCellLineACCMESO4_CNhs11264_tpm_rev Cl:ACC-MESO-4- mesothelioma cell line:ACC-MESO-4_CNhs11264_10494-107B8_reverse Regulation 
MesotheliomaCellLineACCMESO4_CNhs11264_tpm_fwd Cl:ACC-MESO-4+ mesothelioma cell line:ACC-MESO-4_CNhs11264_10494-107B8_forward Regulation 
MesotheliomaCellLineACCMESO1_CNhs11263_tpm_rev Cl:ACC-MESO-1- mesothelioma cell line:ACC-MESO-1_CNhs11263_10493-107B7_reverse Regulation 
MesotheliomaCellLineACCMESO1_CNhs11263_tpm_fwd Cl:ACC-MESO-1+ mesothelioma cell line:ACC-MESO-1_CNhs11263_10493-107B7_forward Regulation 
LungAdenocarcinomaCellLineA549_CNhs11275_tpm_rev Cl:A549- lung adenocarcinoma cell line:A549_CNhs11275_10499-107C4_reverse Regulation 
LungAdenocarcinomaCellLineA549_CNhs11275_tpm_fwd Cl:A549+ lung adenocarcinoma cell line:A549_CNhs11275_10499-107C4_forward Regulation 
EpidermoidCarcinomaCellLineA431_CNhs10743_tpm_rev Cl:A431- epidermoid carcinoma cell line:A431_CNhs10743_10426-106D3_reverse Regulation 
EpidermoidCarcinomaCellLineA431_CNhs10743_tpm_fwd Cl:A431+ epidermoid carcinoma cell line:A431_CNhs10743_10426-106D3_forward Regulation 
GlioblastomaCellLineA172TechRep2_CNhs11248_tpm_rev Cl:A172Tr2- glioblastoma cell line:A172, tech_rep2_CNhs11248_10444-106F3_reverse Regulation 
GlioblastomaCellLineA172TechRep2_CNhs11248_tpm_fwd Cl:A172Tr2+ glioblastoma cell line:A172, tech_rep2_CNhs11248_10444-106F3_forward Regulation 
GlioblastomaCellLineA172_CNhs11185_tpm_rev Cl:A172- glioblastoma cell line:A172_CNhs11185_10444-106F3_reverse Regulation 
GlioblastomaCellLineA172_CNhs11185_tpm_fwd Cl:A172+ glioblastoma cell line:A172_CNhs11185_10444-106F3_forward Regulation 
PapillaryAdenocarcinomaCellLine8505C_CNhs11716_tpm_rev Cl:8505C- papillary adenocarcinoma cell line:8505C_CNhs11716_10437-106E5_reverse Regulation 
PapillaryAdenocarcinomaCellLine8505C_CNhs11716_tpm_fwd Cl:8505C+ papillary adenocarcinoma cell line:8505C_CNhs11716_10437-106E5_forward Regulation 
AnaplasticCarcinomaCellLine8305C_CNhs10745_tpm_rev Cl:8305C- anaplastic carcinoma cell line:8305C_CNhs10745_10428-106D5_reverse Regulation 
AnaplasticCarcinomaCellLine8305C_CNhs10745_tpm_fwd Cl:8305C+ anaplastic carcinoma cell line:8305C_CNhs10745_10428-106D5_forward Regulation 
TransitionalcellCarcinomaCellLine5637_CNhs10735_tpm_rev Cl:5637- transitional-cell carcinoma cell line:5637_CNhs10735_10418-106C4_reverse Regulation 
TransitionalcellCarcinomaCellLine5637_CNhs10735_tpm_fwd Cl:5637+ transitional-cell carcinoma cell line:5637_CNhs10735_10418-106C4_forward Regulation 
EmbryonicPancreasCellLine2C6_CNhs11814_tpm_rev Cl:2C6- embryonic pancreas cell line:2C6_CNhs11814_10603-108E9_reverse Regulation 
EmbryonicPancreasCellLine2C6_CNhs11814_tpm_fwd Cl:2C6+ embryonic pancreas cell line:2C6_CNhs11814_10603-108E9_forward Regulation 
EmbryonicPancreasCellLine1C3IKEI_CNhs11733_tpm_rev Cl:1C3IKEI- embryonic pancreas cell line:1C3IKEI_CNhs11733_10606-108F3_reverse Regulation 
EmbryonicPancreasCellLine1C3IKEI_CNhs11733_tpm_fwd Cl:1C3IKEI+ embryonic pancreas cell line:1C3IKEI_CNhs11733_10606-108F3_forward Regulation 
EmbryonicPancreasCellLine1C3D3_CNhs11732_tpm_rev Cl:1C3D3- embryonic pancreas cell line:1C3D3_CNhs11732_10605-108F2_reverse Regulation 
EmbryonicPancreasCellLine1C3D3_CNhs11732_tpm_fwd Cl:1C3D3+ embryonic pancreas cell line:1C3D3_CNhs11732_10605-108F2_forward Regulation 
EmbryonicPancreasCellLine1B2C6_CNhs11731_tpm_rev Cl:1B2C6- embryonic pancreas cell line:1B2C6_CNhs11731_10604-108F1_reverse Regulation 
EmbryonicPancreasCellLine1B2C6_CNhs11731_tpm_fwd Cl:1B2C6+ embryonic pancreas cell line:1B2C6_CNhs11731_10604-108F1_forward Regulation 
LeiomyomaCellLine15425_CNhs11724_tpm_rev Cl:15425- leiomyoma cell line:15425_CNhs11724_10571-108B4_reverse Regulation 
LeiomyomaCellLine15425_CNhs11724_tpm_fwd Cl:15425+ leiomyoma cell line:15425_CNhs11724_10571-108B4_forward Regulation 
LeiomyomaCellLine15242A_CNhs11723_tpm_rev Cl:15242A- leiomyoma cell line:15242A_CNhs11723_10570-108B3_reverse Regulation 
LeiomyomaCellLine15242A_CNhs11723_tpm_fwd Cl:15242A+ leiomyoma cell line:15242A_CNhs11723_10570-108B3_forward Regulation 
OsteosarcomaCellLine143BTKneoR_CNhs11279_tpm_rev Cl:143B/TK^(-)neo^(R)- osteosarcoma cell line:143B/TK^(-)neo^(R)_CNhs11279_10510-107D6_reverse Regulation 
OsteosarcomaCellLine143BTKneoR_CNhs11279_tpm_fwd Cl:143B/TK^(-)neo^(R)+ osteosarcoma cell line:143B/TK^(-)neo^(R)_CNhs11279_10510-107D6_forward Regulation 
LeiomyomaCellLine10964C_CNhs11722_tpm_rev Cl:10964C- leiomyoma cell line:10964C_CNhs11722_10569-108B2_reverse Regulation 
LeiomyomaCellLine10964C_CNhs11722_tpm_fwd Cl:10964C+ leiomyoma cell line:10964C_CNhs11722_10569-108B2_forward Regulation 
NonsmallCellLungCancerCellLineNCIH1385_CNhs12193_tpm_rev Cl:NCI-H1385- non-small cell lung cancer cell line:NCI-H1385_CNhs12193_10730-110B1_reverse Regulation 
NonsmallCellLungCancerCellLineNCIH1385_CNhs12193_tpm_fwd Cl:NCI-H1385+ non-small cell lung cancer cell line:NCI-H1385_CNhs12193_10730-110B1_forward Regulation 
MesotheliomaCellLineMero14TechRep2_CNhs14376_tpm_rev Cl:Mero-14Tr2- mesothelioma cell line:Mero-14, tech_rep2_CNhs14376_10849-111F3_reverse Regulation 
MesotheliomaCellLineMero14TechRep2_CNhs14376_tpm_fwd Cl:Mero-14Tr2+ mesothelioma cell line:Mero-14, tech_rep2_CNhs14376_10849-111F3_forward Regulation 
AcuteMyeloidLeukemiaFABM0CellLineKasumi3_CNhs13241_tpm_rev Cl:Kasumi-3- acute myeloid leukemia (FAB M0) cell line:Kasumi-3_CNhs13241_10789-110H6_reverse Regulation 
AcuteMyeloidLeukemiaFABM0CellLineKasumi3_CNhs13241_tpm_fwd Cl:Kasumi-3+ acute myeloid leukemia (FAB M0) cell line:Kasumi-3_CNhs13241_10789-110H6_forward Regulation 
LeiomyosarcomaCellLineHs5_T_CNhs12192_tpm_rev Cl:Hs5_T- leiomyosarcoma cell line:Hs 5_T_CNhs12192_10722-110A2_reverse Regulation 
LeiomyosarcomaCellLineHs5_T_CNhs12192_tpm_fwd Cl:Hs5_T+ leiomyosarcoma cell line:Hs 5_T_CNhs12192_10722-110A2_forward Regulation 
MesodermalTumorCellLineHIRSBM_CNhs12191_tpm_rev Cl:HIRS-BM- mesodermal tumor cell line:HIRS-BM_CNhs12191_10696-109G3_reverse Regulation 
MesodermalTumorCellLineHIRSBM_CNhs12191_tpm_fwd Cl:HIRS-BM+ mesodermal tumor cell line:HIRS-BM_CNhs12191_10696-109G3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep3A3T17_CNhs12892_tpm_rev Saos-2W/AscorbicAcidBgp_Day28Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep3 (A3 T17)_CNhs12892_12875-137F4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep3A3T17_CNhs12892_tpm_fwd Saos-2W/AscorbicAcidBgp_Day28Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep3 (A3 T17)_CNhs12892_12875-137F4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep2A2T17_CNhs12876_tpm_rev Saos-2W/AscorbicAcidBgp_Day28Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep2 (A2 T17)_CNhs12876_12777-136D5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep2A2T17_CNhs12876_tpm_fwd Saos-2W/AscorbicAcidBgp_Day28Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep2 (A2 T17)_CNhs12876_12777-136D5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep1A1T17_CNhs11919_tpm_rev Saos-2W/AscorbicAcidBgp_Day28Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep1 (A1 T17)_CNhs11919_12679-135B6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay28BiolRep1A1T17_CNhs11919_tpm_fwd Saos-2W/AscorbicAcidBgp_Day28Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day28, biol_rep1 (A1 T17)_CNhs11919_12679-135B6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep3A3T16_CNhs12891_tpm_rev Saos-2W/AscorbicAcidBgp_Day21Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep3 (A3 T16)_CNhs12891_12874-137F3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep3A3T16_CNhs12891_tpm_fwd Saos-2W/AscorbicAcidBgp_Day21Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep3 (A3 T16)_CNhs12891_12874-137F3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep2A2T16_CNhs12875_tpm_rev Saos-2W/AscorbicAcidBgp_Day21Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep2 (A2 T16)_CNhs12875_12776-136D4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep2A2T16_CNhs12875_tpm_fwd Saos-2W/AscorbicAcidBgp_Day21Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep2 (A2 T16)_CNhs12875_12776-136D4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep1A1T16_CNhs12397_tpm_rev Saos-2W/AscorbicAcidBgp_Day21Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep1 (A1 T16)_CNhs12397_12678-135B5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay21BiolRep1A1T16_CNhs12397_tpm_fwd Saos-2W/AscorbicAcidBgp_Day21Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day21, biol_rep1 (A1 T16)_CNhs12397_12678-135B5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep3A3T15_CNhs12890_tpm_rev Saos-2W/AscorbicAcidBgp_Day14Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep3 (A3 T15)_CNhs12890_12873-137F2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep3A3T15_CNhs12890_tpm_fwd Saos-2W/AscorbicAcidBgp_Day14Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep3 (A3 T15)_CNhs12890_12873-137F2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep2A2T15_CNhs12953_tpm_rev Saos-2W/AscorbicAcidBgp_Day14Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep2 (A2 T15)_CNhs12953_12775-136D3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep2A2T15_CNhs12953_tpm_fwd Saos-2W/AscorbicAcidBgp_Day14Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep2 (A2 T15)_CNhs12953_12775-136D3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep1A1T15_CNhs12396_tpm_rev Saos-2W/AscorbicAcidBgp_Day14Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep1 (A1 T15)_CNhs12396_12677-135B4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay14BiolRep1A1T15_CNhs12396_tpm_fwd Saos-2W/AscorbicAcidBgp_Day14Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day14, biol_rep1 (A1 T15)_CNhs12396_12677-135B4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep3A3T14_CNhs12888_tpm_rev Saos-2W/AscorbicAcidBgp_Day07Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep3 (A3 T14)_CNhs12888_12872-137F1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep3A3T14_CNhs12888_tpm_fwd Saos-2W/AscorbicAcidBgp_Day07Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep3 (A3 T14)_CNhs12888_12872-137F1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep2A2T14_CNhs12874_tpm_rev Saos-2W/AscorbicAcidBgp_Day07Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep2 (A2 T14)_CNhs12874_12774-136D2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep2A2T14_CNhs12874_tpm_fwd Saos-2W/AscorbicAcidBgp_Day07Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep2 (A2 T14)_CNhs12874_12774-136D2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep1A1T14_CNhs12395_tpm_rev Saos-2W/AscorbicAcidBgp_Day07Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep1 (A1 T14)_CNhs12395_12676-135B3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay07BiolRep1A1T14_CNhs12395_tpm_fwd Saos-2W/AscorbicAcidBgp_Day07Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day07, biol_rep1 (A1 T14)_CNhs12395_12676-135B3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep3A3T13_CNhs12887_tpm_rev Saos-2W/AscorbicAcidBgp_Day04Br3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep3 (A3 T13)_CNhs12887_12871-137E9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep3A3T13_CNhs12887_tpm_fwd Saos-2W/AscorbicAcidBgp_Day04Br3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep3 (A3 T13)_CNhs12887_12871-137E9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep2A2T13_CNhs12873_tpm_rev Saos-2W/AscorbicAcidBgp_Day04Br2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep2 (A2 T13)_CNhs12873_12773-136D1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep2A2T13_CNhs12873_tpm_fwd Saos-2W/AscorbicAcidBgp_Day04Br2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep2 (A2 T13)_CNhs12873_12773-136D1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep1A1T13_CNhs12394_tpm_rev Saos-2W/AscorbicAcidBgp_Day04Br1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep1 (A1 T13)_CNhs12394_12675-135B2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcificationDay04BiolRep1A1T13_CNhs12394_tpm_fwd Saos-2W/AscorbicAcidBgp_Day04Br1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep1 (A1 T13)_CNhs12394_12675-135B2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep3A3T12_CNhs12886_tpm_rev Saos-2W/AscorbicAcidBgp_24hrBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep3 (A3 T12)_CNhs12886_12870-137E8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep3A3T12_CNhs12886_tpm_fwd Saos-2W/AscorbicAcidBgp_24hrBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep3 (A3 T12)_CNhs12886_12870-137E8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep2A2T12_CNhs12872_tpm_rev Saos-2W/AscorbicAcidBgp_24hrBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep2 (A2 T12)_CNhs12872_12772-136C9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep2A2T12_CNhs12872_tpm_fwd Saos-2W/AscorbicAcidBgp_24hrBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep2 (A2 T12)_CNhs12872_12772-136C9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep1A1T12_CNhs12393_tpm_rev Saos-2W/AscorbicAcidBgp_24hrBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep1 (A1 T12)_CNhs12393_12674-135B1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification24hrBiolRep1A1T12_CNhs12393_tpm_fwd Saos-2W/AscorbicAcidBgp_24hrBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 24hr, biol_rep1 (A1 T12)_CNhs12393_12674-135B1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep3A3T11_CNhs12885_tpm_rev Saos-2W/AscorbicAcidBgp_08hrBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep3 (A3 T11)_CNhs12885_12869-137E7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep3A3T11_CNhs12885_tpm_fwd Saos-2W/AscorbicAcidBgp_08hrBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep3 (A3 T11)_CNhs12885_12869-137E7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep2A2T11_CNhs12871_tpm_rev Saos-2W/AscorbicAcidBgp_08hrBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep2 (A2 T11)_CNhs12871_12771-136C8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep2A2T11_CNhs12871_tpm_fwd Saos-2W/AscorbicAcidBgp_08hrBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep2 (A2 T11)_CNhs12871_12771-136C8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep1A1T11_CNhs12392_tpm_rev Saos-2W/AscorbicAcidBgp_08hrBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep1 (A1 T11)_CNhs12392_12673-135A9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification08hrBiolRep1A1T11_CNhs12392_tpm_fwd Saos-2W/AscorbicAcidBgp_08hrBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 08hr, biol_rep1 (A1 T11)_CNhs12392_12673-135A9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep3A3T10_CNhs12884_tpm_rev Saos-2W/AscorbicAcidBgp_04hrBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep3 (A3 T10)_CNhs12884_12868-137E6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep3A3T10_CNhs12884_tpm_fwd Saos-2W/AscorbicAcidBgp_04hrBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep3 (A3 T10)_CNhs12884_12868-137E6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep2A2T10_CNhs12870_tpm_rev Saos-2W/AscorbicAcidBgp_04hrBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep2 (A2 T10)_CNhs12870_12770-136C7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep2A2T10_CNhs12870_tpm_fwd Saos-2W/AscorbicAcidBgp_04hrBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep2 (A2 T10)_CNhs12870_12770-136C7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep1A1T10_CNhs12391_tpm_rev Saos-2W/AscorbicAcidBgp_04hrBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep1 (A1 T10)_CNhs12391_12672-135A8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification04hrBiolRep1A1T10_CNhs12391_tpm_fwd Saos-2W/AscorbicAcidBgp_04hrBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 04hr, biol_rep1 (A1 T10)_CNhs12391_12672-135A8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep3A3T9_CNhs12883_tpm_rev Saos-2W/AscorbicAcidBgp_03hrBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep3 (A3 T9)_CNhs12883_12867-137E5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep3A3T9_CNhs12883_tpm_fwd Saos-2W/AscorbicAcidBgp_03hrBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep3 (A3 T9)_CNhs12883_12867-137E5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep2A2T9_CNhs12869_tpm_rev Saos-2W/AscorbicAcidBgp_03hrBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep2 (A2 T9)_CNhs12869_12769-136C6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep2A2T9_CNhs12869_tpm_fwd Saos-2W/AscorbicAcidBgp_03hrBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep2 (A2 T9)_CNhs12869_12769-136C6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep1A1T9_CNhs12390_tpm_rev Saos-2W/AscorbicAcidBgp_03hrBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep1 (A1 T9)_CNhs12390_12671-135A7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification03hrBiolRep1A1T9_CNhs12390_tpm_fwd Saos-2W/AscorbicAcidBgp_03hrBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 03hr, biol_rep1 (A1 T9)_CNhs12390_12671-135A7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep3A3T8_CNhs12882_tpm_rev Saos-2W/AscorbicAcidBgp_02hr30minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep3 (A3 T8)_CNhs12882_12866-137E4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep3A3T8_CNhs12882_tpm_fwd Saos-2W/AscorbicAcidBgp_02hr30minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep3 (A3 T8)_CNhs12882_12866-137E4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep2A2T8_CNhs12868_tpm_rev Saos-2W/AscorbicAcidBgp_02hr30minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep2 (A2 T8)_CNhs12868_12768-136C5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep2A2T8_CNhs12868_tpm_fwd Saos-2W/AscorbicAcidBgp_02hr30minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep2 (A2 T8)_CNhs12868_12768-136C5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep1A1T8_CNhs12389_tpm_rev Saos-2W/AscorbicAcidBgp_02hr30minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep1 (A1 T8)_CNhs12389_12670-135A6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr30minBiolRep1A1T8_CNhs12389_tpm_fwd Saos-2W/AscorbicAcidBgp_02hr30minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr30min, biol_rep1 (A1 T8)_CNhs12389_12670-135A6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep3A3T7_CNhs12881_tpm_rev Saos-2W/AscorbicAcidBgp_02hr00minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep3 (A3 T7)_CNhs12881_12865-137E3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep3A3T7_CNhs12881_tpm_fwd Saos-2W/AscorbicAcidBgp_02hr00minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep3 (A3 T7)_CNhs12881_12865-137E3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep2A2T7_CNhs12867_tpm_rev Saos-2W/AscorbicAcidBgp_02hr00minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep2 (A2 T7)_CNhs12867_12767-136C4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep2A2T7_CNhs12867_tpm_fwd Saos-2W/AscorbicAcidBgp_02hr00minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep2 (A2 T7)_CNhs12867_12767-136C4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep1A1T7_CNhs12388_tpm_rev Saos-2W/AscorbicAcidBgp_02hr00minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep1 (A1 T7)_CNhs12388_12669-135A5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification02hr00minBiolRep1A1T7_CNhs12388_tpm_fwd Saos-2W/AscorbicAcidBgp_02hr00minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 02hr00min, biol_rep1 (A1 T7)_CNhs12388_12669-135A5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep3A3T6_CNhs12880_tpm_rev Saos-2W/AscorbicAcidBgp_01hr40minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep3 (A3 T6)_CNhs12880_12864-137E2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep3A3T6_CNhs12880_tpm_fwd Saos-2W/AscorbicAcidBgp_01hr40minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep3 (A3 T6)_CNhs12880_12864-137E2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep2A2T6_CNhs12866_tpm_rev Saos-2W/AscorbicAcidBgp_01hr40minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep2 (A2 T6)_CNhs12866_12766-136C3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep2A2T6_CNhs12866_tpm_fwd Saos-2W/AscorbicAcidBgp_01hr40minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep2 (A2 T6)_CNhs12866_12766-136C3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep1A1T6_CNhs12387_tpm_rev Saos-2W/AscorbicAcidBgp_01hr40minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep1 (A1 T6)_CNhs12387_12668-135A4_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr40minBiolRep1A1T6_CNhs12387_tpm_fwd Saos-2W/AscorbicAcidBgp_01hr40minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr40min, biol_rep1 (A1 T6)_CNhs12387_12668-135A4_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep3A3T5_CNhs12879_tpm_rev Saos-2W/AscorbicAcidBgp_01hr20minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep3 (A3 T5)_CNhs12879_12863-137E1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep3A3T5_CNhs12879_tpm_fwd Saos-2W/AscorbicAcidBgp_01hr20minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep3 (A3 T5)_CNhs12879_12863-137E1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep2A2T5_CNhs12864_tpm_rev Saos-2W/AscorbicAcidBgp_01hr20minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep2 (A2 T5)_CNhs12864_12765-136C2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep2A2T5_CNhs12864_tpm_fwd Saos-2W/AscorbicAcidBgp_01hr20minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep2 (A2 T5)_CNhs12864_12765-136C2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep1A1T5_CNhs12386_tpm_rev Saos-2W/AscorbicAcidBgp_01hr20minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep1 (A1 T5)_CNhs12386_12667-135A3_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr20minBiolRep1A1T5_CNhs12386_tpm_fwd Saos-2W/AscorbicAcidBgp_01hr20minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr20min, biol_rep1 (A1 T5)_CNhs12386_12667-135A3_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep3A3T4_CNhs12955_tpm_rev Saos-2W/AscorbicAcidBgp_01hr00minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep3 (A3 T4)_CNhs12955_12862-137D9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep3A3T4_CNhs12955_tpm_fwd Saos-2W/AscorbicAcidBgp_01hr00minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep3 (A3 T4)_CNhs12955_12862-137D9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep2A2T4_CNhs12863_tpm_rev Saos-2W/AscorbicAcidBgp_01hr00minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep2 (A2 T4)_CNhs12863_12764-136C1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep2A2T4_CNhs12863_tpm_fwd Saos-2W/AscorbicAcidBgp_01hr00minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep2 (A2 T4)_CNhs12863_12764-136C1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep1A1T4_CNhs12384_tpm_rev Saos-2W/AscorbicAcidBgp_01hr00minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep1 (A1 T4)_CNhs12384_12666-135A2_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification01hr00minBiolRep1A1T4_CNhs12384_tpm_fwd Saos-2W/AscorbicAcidBgp_01hr00minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 01hr00min, biol_rep1 (A1 T4)_CNhs12384_12666-135A2_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep3A3T3_CNhs12878_tpm_rev Saos-2W/AscorbicAcidBgp_00hr45minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep3 (A3 T3)_CNhs12878_12861-137D8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep3A3T3_CNhs12878_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr45minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep3 (A3 T3)_CNhs12878_12861-137D8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep2A2T3_CNhs12862_tpm_rev Saos-2W/AscorbicAcidBgp_00hr45minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep2 (A2 T3)_CNhs12862_12763-136B9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep2A2T3_CNhs12862_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr45minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep2 (A2 T3)_CNhs12862_12763-136B9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep1A1T3_CNhs12383_tpm_rev Saos-2W/AscorbicAcidBgp_00hr45minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep1 (A1 T3)_CNhs12383_12665-135A1_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr45minBiolRep1A1T3_CNhs12383_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr45minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr45min, biol_rep1 (A1 T3)_CNhs12383_12665-135A1_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep3A3T2_CNhs12954_tpm_rev Saos-2W/AscorbicAcidBgp_00hr30minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep3 (A3 T2)_CNhs12954_12860-137D7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep3A3T2_CNhs12954_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr30minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep3 (A3 T2)_CNhs12954_12860-137D7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep2A2T2_CNhs12861_tpm_rev Saos-2W/AscorbicAcidBgp_00hr30minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep2 (A2 T2)_CNhs12861_12762-136B8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep2A2T2_CNhs12861_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr30minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep2 (A2 T2)_CNhs12861_12762-136B8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep1A1T2_CNhs12382_tpm_rev Saos-2W/AscorbicAcidBgp_00hr30minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep1 (A1 T2)_CNhs12382_12664-134I9_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr30minBiolRep1A1T2_CNhs12382_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr30minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr30min, biol_rep1 (A1 T2)_CNhs12382_12664-134I9_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep3A3T1_CNhs12877_tpm_rev Saos-2W/AscorbicAcidBgp_00hr15minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep3 (A3 T1)_CNhs12877_12859-137D6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep3A3T1_CNhs12877_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr15minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep3 (A3 T1)_CNhs12877_12859-137D6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep2A2T1_CNhs12860_tpm_rev Saos-2W/AscorbicAcidBgp_00hr15minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep2 (A2 T1)_CNhs12860_12761-136B7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep2A2T1_CNhs12860_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr15minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep2 (A2 T1)_CNhs12860_12761-136B7_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep1A1T1_CNhs12381_tpm_rev Saos-2W/AscorbicAcidBgp_00hr15minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep1 (A1 T1)_CNhs12381_12663-134I8_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr15minBiolRep1A1T1_CNhs12381_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr15minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr15min, biol_rep1 (A1 T1)_CNhs12381_12663-134I8_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep3A3T0_CNhs12952_tpm_rev Saos-2W/AscorbicAcidBgp_00hr00minBr3- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep3 (A3 T0)_CNhs12952_12858-137D5_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep3A3T0_CNhs12952_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr00minBr3+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep3 (A3 T0)_CNhs12952_12858-137D5_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep2A2T0_CNhs12859_tpm_rev Saos-2W/AscorbicAcidBgp_00hr00minBr2- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep2 (A2 T0)_CNhs12859_12760-136B6_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep2A2T0_CNhs12859_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr00minBr2+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep2 (A2 T0)_CNhs12859_12760-136B6_forward Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep1A1T0_CNhs11918_tpm_rev Saos-2W/AscorbicAcidBgp_00hr00minBr1- Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep1 (A1 T0)_CNhs11918_12662-134I7_reverse Regulation 
Saos2OsteosarcomaTreatedWithAscorbicAcidAndBGPToInduceCalcification00hr00minBiolRep1A1T0_CNhs11918_tpm_fwd Saos-2W/AscorbicAcidBgp_00hr00minBr1+ Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, 00hr00min, biol_rep1 (A1 T0)_CNhs11918_12662-134I7_forward Regulation 
COBLaRinderpestInfection48hrBiolRep3_CNhs14434_tpm_rev Tc:COBL-aRinderpest_48hrBr3- COBL-a rinderpest infection, 48hr, biol_rep3_CNhs14434_13567-146B3_reverse Regulation 
COBLaRinderpestInfection48hrBiolRep3_CNhs14434_tpm_fwd Tc:COBL-aRinderpest_48hrBr3+ COBL-a rinderpest infection, 48hr, biol_rep3_CNhs14434_13567-146B3_forward Regulation 
COBLaRinderpestInfection48hrBiolRep2_CNhs14432_tpm_rev Tc:COBL-aRinderpest_48hrBr2- COBL-a rinderpest infection, 48hr, biol_rep2_CNhs14432_13566-146B2_reverse Regulation 
COBLaRinderpestInfection48hrBiolRep2_CNhs14432_tpm_fwd Tc:COBL-aRinderpest_48hrBr2+ COBL-a rinderpest infection, 48hr, biol_rep2_CNhs14432_13566-146B2_forward Regulation 
COBLaRinderpestInfection48hrBiolRep1_CNhs14431_tpm_rev Tc:COBL-aRinderpest_48hrBr1- COBL-a rinderpest infection, 48hr, biol_rep1_CNhs14431_13565-146B1_reverse Regulation 
COBLaRinderpestInfection48hrBiolRep1_CNhs14431_tpm_fwd Tc:COBL-aRinderpest_48hrBr1+ COBL-a rinderpest infection, 48hr, biol_rep1_CNhs14431_13565-146B1_forward Regulation 
COBLaRinderpestInfection24hrBiolRep3_CNhs14430_tpm_rev Tc:COBL-aRinderpest_24hrBr3- COBL-a rinderpest infection, 24hr, biol_rep3_CNhs14430_13564-146A9_reverse Regulation 
COBLaRinderpestInfection24hrBiolRep3_CNhs14430_tpm_fwd Tc:COBL-aRinderpest_24hrBr3+ COBL-a rinderpest infection, 24hr, biol_rep3_CNhs14430_13564-146A9_forward Regulation 
COBLaRinderpestInfection24hrBiolRep2_CNhs14429_tpm_rev Tc:COBL-aRinderpest_24hrBr2- COBL-a rinderpest infection, 24hr, biol_rep2_CNhs14429_13563-146A8_reverse Regulation 
COBLaRinderpestInfection24hrBiolRep2_CNhs14429_tpm_fwd Tc:COBL-aRinderpest_24hrBr2+ COBL-a rinderpest infection, 24hr, biol_rep2_CNhs14429_13563-146A8_forward Regulation 
COBLaRinderpestInfection24hrBiolRep1_CNhs14428_tpm_rev Tc:COBL-aRinderpest_24hrBr1- COBL-a rinderpest infection, 24hr, biol_rep1_CNhs14428_13562-146A7_reverse Regulation 
COBLaRinderpestInfection24hrBiolRep1_CNhs14428_tpm_fwd Tc:COBL-aRinderpest_24hrBr1+ COBL-a rinderpest infection, 24hr, biol_rep1_CNhs14428_13562-146A7_forward Regulation 
COBLaRinderpestInfection12hrBiolRep3_CNhs14427_tpm_rev Tc:COBL-aRinderpest_12hrBr3- COBL-a rinderpest infection, 12hr, biol_rep3_CNhs14427_13561-146A6_reverse Regulation 
COBLaRinderpestInfection12hrBiolRep3_CNhs14427_tpm_fwd Tc:COBL-aRinderpest_12hrBr3+ COBL-a rinderpest infection, 12hr, biol_rep3_CNhs14427_13561-146A6_forward Regulation 
COBLaRinderpestInfection12hrBiolRep2_CNhs14426_tpm_rev Tc:COBL-aRinderpest_12hrBr2- COBL-a rinderpest infection, 12hr, biol_rep2_CNhs14426_13560-146A5_reverse Regulation 
COBLaRinderpestInfection12hrBiolRep2_CNhs14426_tpm_fwd Tc:COBL-aRinderpest_12hrBr2+ COBL-a rinderpest infection, 12hr, biol_rep2_CNhs14426_13560-146A5_forward Regulation 
COBLaRinderpestInfection12hrBiolRep1_CNhs14425_tpm_rev Tc:COBL-aRinderpest_12hrBr1- COBL-a rinderpest infection, 12hr, biol_rep1_CNhs14425_13559-146A4_reverse Regulation 
COBLaRinderpestInfection12hrBiolRep1_CNhs14425_tpm_fwd Tc:COBL-aRinderpest_12hrBr1+ COBL-a rinderpest infection, 12hr, biol_rep1_CNhs14425_13559-146A4_forward Regulation 
COBLaRinderpestInfection06hrBiolRep3_CNhs14424_tpm_rev Tc:COBL-aRinderpest_06hrBr3- COBL-a rinderpest infection, 06hr, biol_rep3_CNhs14424_13558-146A3_reverse Regulation 
COBLaRinderpestInfection06hrBiolRep3_CNhs14424_tpm_fwd Tc:COBL-aRinderpest_06hrBr3+ COBL-a rinderpest infection, 06hr, biol_rep3_CNhs14424_13558-146A3_forward Regulation 
COBLaRinderpestInfection06hrBiolRep2_CNhs14423_tpm_rev Tc:COBL-aRinderpest_06hrBr2- COBL-a rinderpest infection, 06hr, biol_rep2_CNhs14423_13557-146A2_reverse Regulation 
COBLaRinderpestInfection06hrBiolRep2_CNhs14423_tpm_fwd Tc:COBL-aRinderpest_06hrBr2+ COBL-a rinderpest infection, 06hr, biol_rep2_CNhs14423_13557-146A2_forward Regulation 
COBLaRinderpestInfection06hrBiolRep1_CNhs14422_tpm_rev Tc:COBL-aRinderpest_06hrBr1- COBL-a rinderpest infection, 06hr, biol_rep1_CNhs14422_13556-146A1_reverse Regulation 
COBLaRinderpestInfection06hrBiolRep1_CNhs14422_tpm_fwd Tc:COBL-aRinderpest_06hrBr1+ COBL-a rinderpest infection, 06hr, biol_rep1_CNhs14422_13556-146A1_forward Regulation 
COBLaRinderpestInfection00hrBiolRep3_CNhs14421_tpm_rev Tc:COBL-aRinderpest_00hrBr3- COBL-a rinderpest infection, 00hr, biol_rep3_CNhs14421_13555-145I9_reverse Regulation 
COBLaRinderpestInfection00hrBiolRep3_CNhs14421_tpm_fwd Tc:COBL-aRinderpest_00hrBr3+ COBL-a rinderpest infection, 00hr, biol_rep3_CNhs14421_13555-145I9_forward Regulation 
COBLaRinderpestInfection00hrBiolRep2_CNhs14420_tpm_rev Tc:COBL-aRinderpest_00hrBr2- COBL-a rinderpest infection, 00hr, biol_rep2_CNhs14420_13554-145I8_reverse Regulation 
COBLaRinderpestInfection00hrBiolRep2_CNhs14420_tpm_fwd Tc:COBL-aRinderpest_00hrBr2+ COBL-a rinderpest infection, 00hr, biol_rep2_CNhs14420_13554-145I8_forward Regulation 
COBLaRinderpestInfection00hrBiolRep1_CNhs14419_tpm_rev Tc:COBL-aRinderpest_00hrBr1- COBL-a rinderpest infection, 00hr, biol_rep1_CNhs14419_13553-145I7_reverse Regulation 
COBLaRinderpestInfection00hrBiolRep1_CNhs14419_tpm_fwd Tc:COBL-aRinderpest_00hrBr1+ COBL-a rinderpest infection, 00hr, biol_rep1_CNhs14419_13553-145I7_forward Regulation 
COBLaRinderpestCInfection48hrBiolRep3_CNhs14446_tpm_rev Tc:COBL-aRinderpest(-C)_48hrBr3- COBL-a rinderpest(-C) infection, 48hr, biol_rep3_CNhs14446_13579-146C6_reverse Regulation 
COBLaRinderpestCInfection48hrBiolRep3_CNhs14446_tpm_fwd Tc:COBL-aRinderpest(-C)_48hrBr3+ COBL-a rinderpest(-C) infection, 48hr, biol_rep3_CNhs14446_13579-146C6_forward Regulation 
COBLaRinderpestCInfection48hrBiolRep2_CNhs14445_tpm_rev Tc:COBL-aRinderpest(-C)_48hrBr2- COBL-a rinderpest(-C) infection, 48hr, biol_rep2_CNhs14445_13578-146C5_reverse Regulation 
COBLaRinderpestCInfection48hrBiolRep2_CNhs14445_tpm_fwd Tc:COBL-aRinderpest(-C)_48hrBr2+ COBL-a rinderpest(-C) infection, 48hr, biol_rep2_CNhs14445_13578-146C5_forward Regulation 
COBLaRinderpestCInfection48hrBiolRep1_CNhs14444_tpm_rev Tc:COBL-aRinderpest(-C)_48hrBr1- COBL-a rinderpest(-C) infection, 48hr, biol_rep1_CNhs14444_13577-146C4_reverse Regulation 
COBLaRinderpestCInfection48hrBiolRep1_CNhs14444_tpm_fwd Tc:COBL-aRinderpest(-C)_48hrBr1+ COBL-a rinderpest(-C) infection, 48hr, biol_rep1_CNhs14444_13577-146C4_forward Regulation 
COBLaRinderpestCInfection24hrBiolRep3_CNhs14443_tpm_rev Tc:COBL-aRinderpest(-C)_24hrBr3- COBL-a rinderpest(-C) infection, 24hr, biol_rep3_CNhs14443_13576-146C3_reverse Regulation 
COBLaRinderpestCInfection24hrBiolRep3_CNhs14443_tpm_fwd Tc:COBL-aRinderpest(-C)_24hrBr3+ COBL-a rinderpest(-C) infection, 24hr, biol_rep3_CNhs14443_13576-146C3_forward Regulation 
COBLaRinderpestCInfection24hrBiolRep2_CNhs14442_tpm_rev Tc:COBL-aRinderpest(-C)_24hrBr2- COBL-a rinderpest(-C) infection, 24hr, biol_rep2_CNhs14442_13575-146C2_reverse Regulation 
COBLaRinderpestCInfection24hrBiolRep2_CNhs14442_tpm_fwd Tc:COBL-aRinderpest(-C)_24hrBr2+ COBL-a rinderpest(-C) infection, 24hr, biol_rep2_CNhs14442_13575-146C2_forward Regulation 
COBLaRinderpestCInfection24hrBiolRep1_CNhs14441_tpm_rev Tc:COBL-aRinderpest(-C)_24hrBr1- COBL-a rinderpest(-C) infection, 24hr, biol_rep1_CNhs14441_13574-146C1_reverse Regulation 
COBLaRinderpestCInfection24hrBiolRep1_CNhs14441_tpm_fwd Tc:COBL-aRinderpest(-C)_24hrBr1+ COBL-a rinderpest(-C) infection, 24hr, biol_rep1_CNhs14441_13574-146C1_forward Regulation 
COBLaRinderpestCInfection12hrBiolRep3_CNhs14440_tpm_rev Tc:COBL-aRinderpest(-C)_12hrBr3- COBL-a rinderpest(-C) infection, 12hr, biol_rep3_CNhs14440_13573-146B9_reverse Regulation 
COBLaRinderpestCInfection12hrBiolRep3_CNhs14440_tpm_fwd Tc:COBL-aRinderpest(-C)_12hrBr3+ COBL-a rinderpest(-C) infection, 12hr, biol_rep3_CNhs14440_13573-146B9_forward Regulation 
COBLaRinderpestCInfection12hrBiolRep2_CNhs14439_tpm_rev Tc:COBL-aRinderpest(-C)_12hrBr2- COBL-a rinderpest(-C) infection, 12hr, biol_rep2_CNhs14439_13572-146B8_reverse Regulation 
COBLaRinderpestCInfection12hrBiolRep2_CNhs14439_tpm_fwd Tc:COBL-aRinderpest(-C)_12hrBr2+ COBL-a rinderpest(-C) infection, 12hr, biol_rep2_CNhs14439_13572-146B8_forward Regulation 
COBLaRinderpestCInfection12hrBiolRep1_CNhs14438_tpm_rev Tc:COBL-aRinderpest(-C)_12hrBr1- COBL-a rinderpest(-C) infection, 12hr, biol_rep1_CNhs14438_13571-146B7_reverse Regulation 
COBLaRinderpestCInfection12hrBiolRep1_CNhs14438_tpm_fwd Tc:COBL-aRinderpest(-C)_12hrBr1+ COBL-a rinderpest(-C) infection, 12hr, biol_rep1_CNhs14438_13571-146B7_forward Regulation 
COBLaRinderpestCInfection06hrBiolRep3_CNhs14437_tpm_rev Tc:COBL-aRinderpest(-C)_06hrBr3- COBL-a rinderpest(-C) infection, 06hr, biol_rep3_CNhs14437_13570-146B6_reverse Regulation 
COBLaRinderpestCInfection06hrBiolRep3_CNhs14437_tpm_fwd Tc:COBL-aRinderpest(-C)_06hrBr3+ COBL-a rinderpest(-C) infection, 06hr, biol_rep3_CNhs14437_13570-146B6_forward Regulation 
COBLaRinderpestCInfection06hrBiolRep2_CNhs14436_tpm_rev Tc:COBL-aRinderpest(-C)_06hrBr2- COBL-a rinderpest(-C) infection, 06hr, biol_rep2_CNhs14436_13569-146B5_reverse Regulation 
COBLaRinderpestCInfection06hrBiolRep2_CNhs14436_tpm_fwd Tc:COBL-aRinderpest(-C)_06hrBr2+ COBL-a rinderpest(-C) infection, 06hr, biol_rep2_CNhs14436_13569-146B5_forward Regulation 
COBLaRinderpestCInfection06hrBiolRep1_CNhs14435_tpm_rev Tc:COBL-aRinderpest(-C)_06hrBr1- COBL-a rinderpest(-C) infection, 06hr, biol_rep1_CNhs14435_13568-146B4_reverse Regulation 
COBLaRinderpestCInfection06hrBiolRep1_CNhs14435_tpm_fwd Tc:COBL-aRinderpest(-C)_06hrBr1+ COBL-a rinderpest(-C) infection, 06hr, biol_rep1_CNhs14435_13568-146B4_forward Regulation 
293SLAMRinderpestInfection24hrBiolRep3_CNhs14418_tpm_rev Tc:293SlamRinderpest_24hrBr3- 293SLAM rinderpest infection, 24hr, biol_rep3_CNhs14418_13552-145I6_reverse Regulation 
293SLAMRinderpestInfection24hrBiolRep3_CNhs14418_tpm_fwd Tc:293SlamRinderpest_24hrBr3+ 293SLAM rinderpest infection, 24hr, biol_rep3_CNhs14418_13552-145I6_forward Regulation 
293SLAMRinderpestInfection24hrBiolRep2_CNhs14417_tpm_rev Tc:293SlamRinderpest_24hrBr2- 293SLAM rinderpest infection, 24hr, biol_rep2_CNhs14417_13551-145I5_reverse Regulation 
293SLAMRinderpestInfection24hrBiolRep2_CNhs14417_tpm_fwd Tc:293SlamRinderpest_24hrBr2+ 293SLAM rinderpest infection, 24hr, biol_rep2_CNhs14417_13551-145I5_forward Regulation 
293SLAMRinderpestInfection24hrBiolRep1_CNhs14416_tpm_rev Tc:293SlamRinderpest_24hrBr1- 293SLAM rinderpest infection, 24hr, biol_rep1_CNhs14416_13550-145I4_reverse Regulation 
293SLAMRinderpestInfection24hrBiolRep1_CNhs14416_tpm_fwd Tc:293SlamRinderpest_24hrBr1+ 293SLAM rinderpest infection, 24hr, biol_rep1_CNhs14416_13550-145I4_forward Regulation 
293SLAMRinderpestInfection12hrBiolRep3_CNhs14415_tpm_rev Tc:293SlamRinderpest_12hrBr3- 293SLAM rinderpest infection, 12hr, biol_rep3_CNhs14415_13549-145I3_reverse Regulation 
293SLAMRinderpestInfection12hrBiolRep3_CNhs14415_tpm_fwd Tc:293SlamRinderpest_12hrBr3+ 293SLAM rinderpest infection, 12hr, biol_rep3_CNhs14415_13549-145I3_forward Regulation 
293SLAMRinderpestInfection12hrBiolRep2_CNhs14414_tpm_rev Tc:293SlamRinderpest_12hrBr2- 293SLAM rinderpest infection, 12hr, biol_rep2_CNhs14414_13548-145I2_reverse Regulation 
293SLAMRinderpestInfection12hrBiolRep2_CNhs14414_tpm_fwd Tc:293SlamRinderpest_12hrBr2+ 293SLAM rinderpest infection, 12hr, biol_rep2_CNhs14414_13548-145I2_forward Regulation 
293SLAMRinderpestInfection12hrBiolRep1_CNhs14413_tpm_rev Tc:293SlamRinderpest_12hrBr1- 293SLAM rinderpest infection, 12hr, biol_rep1_CNhs14413_13547-145I1_reverse Regulation 
293SLAMRinderpestInfection12hrBiolRep1_CNhs14413_tpm_fwd Tc:293SlamRinderpest_12hrBr1+ 293SLAM rinderpest infection, 12hr, biol_rep1_CNhs14413_13547-145I1_forward Regulation 
293SLAMRinderpestInfection06hrBiolRep3_CNhs14412_tpm_rev Tc:293SlamRinderpest_06hrBr3- 293SLAM rinderpest infection, 06hr, biol_rep3_CNhs14412_13546-145H9_reverse Regulation 
293SLAMRinderpestInfection06hrBiolRep3_CNhs14412_tpm_fwd Tc:293SlamRinderpest_06hrBr3+ 293SLAM rinderpest infection, 06hr, biol_rep3_CNhs14412_13546-145H9_forward Regulation 
293SLAMRinderpestInfection06hrBiolRep2_CNhs14411_tpm_rev Tc:293SlamRinderpest_06hrBr2- 293SLAM rinderpest infection, 06hr, biol_rep2_CNhs14411_13545-145H8_reverse Regulation 
293SLAMRinderpestInfection06hrBiolRep2_CNhs14411_tpm_fwd Tc:293SlamRinderpest_06hrBr2+ 293SLAM rinderpest infection, 06hr, biol_rep2_CNhs14411_13545-145H8_forward Regulation 
293SLAMRinderpestInfection06hrBiolRep1_CNhs14410_tpm_rev Tc:293SlamRinderpest_06hrBr1- 293SLAM rinderpest infection, 06hr, biol_rep1_CNhs14410_13544-145H7_reverse Regulation 
293SLAMRinderpestInfection06hrBiolRep1_CNhs14410_tpm_fwd Tc:293SlamRinderpest_06hrBr1+ 293SLAM rinderpest infection, 06hr, biol_rep1_CNhs14410_13544-145H7_forward Regulation 
293SLAMRinderpestInfection00hrBiolRep3_CNhs14408_tpm_rev Tc:293SlamRinderpest_00hrBr3- 293SLAM rinderpest infection, 00hr, biol_rep3_CNhs14408_13543-145H6_reverse Regulation 
293SLAMRinderpestInfection00hrBiolRep3_CNhs14408_tpm_fwd Tc:293SlamRinderpest_00hrBr3+ 293SLAM rinderpest infection, 00hr, biol_rep3_CNhs14408_13543-145H6_forward Regulation 
293SLAMRinderpestInfection00hrBiolRep2_CNhs14407_tpm_rev Tc:293SlamRinderpest_00hrBr2- 293SLAM rinderpest infection, 00hr, biol_rep2_CNhs14407_13542-145H5_reverse Regulation 
293SLAMRinderpestInfection00hrBiolRep2_CNhs14407_tpm_fwd Tc:293SlamRinderpest_00hrBr2+ 293SLAM rinderpest infection, 00hr, biol_rep2_CNhs14407_13542-145H5_forward Regulation 
293SLAMRinderpestInfection00hrBiolRep1_CNhs14406_tpm_rev Tc:293SlamRinderpest_00hrBr1- 293SLAM rinderpest infection, 00hr, biol_rep1_CNhs14406_13541-145H4_reverse Regulation 
293SLAMRinderpestInfection00hrBiolRep1_CNhs14406_tpm_fwd Tc:293SlamRinderpest_00hrBr1+ 293SLAM rinderpest infection, 00hr, biol_rep1_CNhs14406_13541-145H4_forward Regulation 
AdipocyteDifferentiationDay12Donor4_CNhs13419_tpm_rev Tc:AdipoDiff_Day12D4- Adipocyte differentiation, day12, donor4_CNhs13419_13030-139E6_reverse Regulation 
AdipocyteDifferentiationDay12Donor4_CNhs13419_tpm_fwd Tc:AdipoDiff_Day12D4+ Adipocyte differentiation, day12, donor4_CNhs13419_13030-139E6_forward Regulation 
AdipocyteDifferentiationDay12Donor3_CNhs13416_tpm_rev Tc:AdipoDiff_Day12D3- Adipocyte differentiation, day12, donor3_CNhs13416_13027-139E3_reverse Regulation 
AdipocyteDifferentiationDay12Donor3_CNhs13416_tpm_fwd Tc:AdipoDiff_Day12D3+ Adipocyte differentiation, day12, donor3_CNhs13416_13027-139E3_forward Regulation 
AdipocyteDifferentiationDay12Donor2_CNhs13412_tpm_rev Tc:AdipoDiff_Day12D2- Adipocyte differentiation, day12, donor2_CNhs13412_13024-139D9_reverse Regulation 
AdipocyteDifferentiationDay12Donor2_CNhs13412_tpm_fwd Tc:AdipoDiff_Day12D2+ Adipocyte differentiation, day12, donor2_CNhs13412_13024-139D9_forward Regulation 
AdipocyteDifferentiationDay12Donor1_CNhs13336_tpm_rev Tc:AdipoDiff_Day12D1- Adipocyte differentiation, day12, donor1_CNhs13336_13021-139D6_reverse Regulation 
AdipocyteDifferentiationDay12Donor1_CNhs13336_tpm_fwd Tc:AdipoDiff_Day12D1+ Adipocyte differentiation, day12, donor1_CNhs13336_13021-139D6_forward Regulation 
AdipocyteDifferentiationDay08Donor4_CNhs13418_tpm_rev Tc:AdipoDiff_Day08D4- Adipocyte differentiation, day08, donor4_CNhs13418_13029-139E5_reverse Regulation 
AdipocyteDifferentiationDay08Donor4_CNhs13418_tpm_fwd Tc:AdipoDiff_Day08D4+ Adipocyte differentiation, day08, donor4_CNhs13418_13029-139E5_forward Regulation 
AdipocyteDifferentiationDay08Donor3_CNhs13415_tpm_rev Tc:AdipoDiff_Day08D3- Adipocyte differentiation, day08, donor3_CNhs13415_13026-139E2_reverse Regulation 
AdipocyteDifferentiationDay08Donor3_CNhs13415_tpm_fwd Tc:AdipoDiff_Day08D3+ Adipocyte differentiation, day08, donor3_CNhs13415_13026-139E2_forward Regulation 
AdipocyteDifferentiationDay08Donor2_CNhs13411_tpm_rev Tc:AdipoDiff_Day08D2- Adipocyte differentiation, day08, donor2_CNhs13411_13023-139D8_reverse Regulation 
AdipocyteDifferentiationDay08Donor2_CNhs13411_tpm_fwd Tc:AdipoDiff_Day08D2+ Adipocyte differentiation, day08, donor2_CNhs13411_13023-139D8_forward Regulation 
AdipocyteDifferentiationDay08Donor1_CNhs12517_tpm_rev Tc:AdipoDiff_Day08D1- Adipocyte differentiation, day08, donor1_CNhs12517_13020-139D5_reverse Regulation 
AdipocyteDifferentiationDay08Donor1_CNhs12517_tpm_fwd Tc:AdipoDiff_Day08D1+ Adipocyte differentiation, day08, donor1_CNhs12517_13020-139D5_forward Regulation 
AdipocyteDifferentiationDay04Donor4_CNhs13417_tpm_rev Tc:AdipoDiff_Day04D4- Adipocyte differentiation, day04, donor4_CNhs13417_13028-139E4_reverse Regulation 
AdipocyteDifferentiationDay04Donor4_CNhs13417_tpm_fwd Tc:AdipoDiff_Day04D4+ Adipocyte differentiation, day04, donor4_CNhs13417_13028-139E4_forward Regulation 
AdipocyteDifferentiationDay04Donor3_CNhs13413_tpm_rev Tc:AdipoDiff_Day04D3- Adipocyte differentiation, day04, donor3_CNhs13413_13025-139E1_reverse Regulation 
AdipocyteDifferentiationDay04Donor3_CNhs13413_tpm_fwd Tc:AdipoDiff_Day04D3+ Adipocyte differentiation, day04, donor3_CNhs13413_13025-139E1_forward Regulation 
AdipocyteDifferentiationDay04Donor2_CNhs13410_tpm_rev Tc:AdipoDiff_Day04D2- Adipocyte differentiation, day04, donor2_CNhs13410_13022-139D7_reverse Regulation 
AdipocyteDifferentiationDay04Donor2_CNhs13410_tpm_fwd Tc:AdipoDiff_Day04D2+ Adipocyte differentiation, day04, donor2_CNhs13410_13022-139D7_forward Regulation 
AdipocyteDifferentiationDay04Donor1_CNhs12516_tpm_rev Tc:AdipoDiff_Day04D1- Adipocyte differentiation, day04, donor1_CNhs12516_13019-139D4_reverse Regulation 
AdipocyteDifferentiationDay04Donor1_CNhs12516_tpm_fwd Tc:AdipoDiff_Day04D1+ Adipocyte differentiation, day04, donor1_CNhs12516_13019-139D4_forward Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor3_CNhs14613_tpm_rev MyoblastToMyotubes_Day12D3- Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor3_CNhs14613_13522-145F3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor3_CNhs14585_tpm_rev MyoblastToMyotubes_Day12D3- Myoblast differentiation to myotubes, day12, control donor3_CNhs14585_13495-145C3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor3_CNhs14613_tpm_fwd MyoblastToMyotubes_Day12D3+ Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor3_CNhs14613_13522-145F3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor3_CNhs14585_tpm_fwd MyoblastToMyotubes_Day12D3+ Myoblast differentiation to myotubes, day12, control donor3_CNhs14585_13495-145C3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor2_CNhs14604_tpm_rev MyoblastToMyotubes_Day12D2- Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor2_CNhs14604_13513-145E3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor2_CNhs14576_tpm_rev MyoblastToMyotubes_Day12D2- Myoblast differentiation to myotubes, day12, control donor2_CNhs14576_13486-145B3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor2_CNhs14604_tpm_fwd MyoblastToMyotubes_Day12D2+ Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor2_CNhs14604_13513-145E3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor2_CNhs14576_tpm_fwd MyoblastToMyotubes_Day12D2+ Myoblast differentiation to myotubes, day12, control donor2_CNhs14576_13486-145B3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor1_CNhs14566_tpm_rev MyoblastToMyotubes_Day12D1- Myoblast differentiation to myotubes, day12, control donor1_CNhs14566_13477-145A3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor1_CNhs14595_tpm_rev MyoblastToMyotubes_Day12D1- Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor1_CNhs14595_13504-145D3_reverse Regulation 
MyoblastDifferentiationToMyotubesDay12ControlDonor1_CNhs14566_tpm_fwd MyoblastToMyotubes_Day12D1+ Myoblast differentiation to myotubes, day12, control donor1_CNhs14566_13477-145A3_forward Regulation 
MyoblastDifferentiationToMyotubesDay12DuchenneMuscularDystrophyDonor1_CNhs14595_tpm_fwd MyoblastToMyotubes_Day12D1+ Myoblast differentiation to myotubes, day12, Duchenne Muscular Dystrophy donor1_CNhs14595_13504-145D3_forward Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor3_CNhs14612_tpm_rev MyoblastToMyotubes_Day10D3- Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor3_CNhs14612_13521-145F2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor3_CNhs14612_tpm_fwd MyoblastToMyotubes_Day10D3+ Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor3_CNhs14612_13521-145F2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor2_CNhs14575_tpm_rev MyoblastToMyotubes_Day10D2- Myoblast differentiation to myotubes, day10, control donor2_CNhs14575_13485-145B2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor2_CNhs14603_tpm_rev MyoblastToMyotubes_Day10D2- Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor2_CNhs14603_13512-145E2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor2_CNhs14575_tpm_fwd MyoblastToMyotubes_Day10D2+ Myoblast differentiation to myotubes, day10, control donor2_CNhs14575_13485-145B2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor2_CNhs14603_tpm_fwd MyoblastToMyotubes_Day10D2+ Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor2_CNhs14603_13512-145E2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor1_CNhs14594_tpm_rev MyoblastToMyotubes_Day10D1- Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor1_CNhs14594_13503-145D2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor1_CNhs13854_tpm_rev MyoblastToMyotubes_Day10D1- Myoblast differentiation to myotubes, day10, control donor1_CNhs13854_13476-145A2_reverse Regulation 
MyoblastDifferentiationToMyotubesDay10DuchenneMuscularDystrophyDonor1_CNhs14594_tpm_fwd MyoblastToMyotubes_Day10D1+ Myoblast differentiation to myotubes, day10, Duchenne Muscular Dystrophy donor1_CNhs14594_13503-145D2_forward Regulation 
MyoblastDifferentiationToMyotubesDay10ControlDonor1_CNhs13854_tpm_fwd MyoblastToMyotubes_Day10D1+ Myoblast differentiation to myotubes, day10, control donor1_CNhs13854_13476-145A2_forward Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor3_CNhs14583_tpm_rev MyoblastToMyotubes_Day08D3- Myoblast differentiation to myotubes, day08, control donor3_CNhs14583_13493-145C1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor3_CNhs14611_tpm_rev MyoblastToMyotubes_Day08D3- Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor3_CNhs14611_13520-145F1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor3_CNhs14583_tpm_fwd MyoblastToMyotubes_Day08D3+ Myoblast differentiation to myotubes, day08, control donor3_CNhs14583_13493-145C1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor3_CNhs14611_tpm_fwd MyoblastToMyotubes_Day08D3+ Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor3_CNhs14611_13520-145F1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor2_CNhs14574_tpm_rev MyoblastToMyotubes_Day08D2- Myoblast differentiation to myotubes, day08, control donor2_CNhs14574_13484-145B1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor2_CNhs14602_tpm_rev MyoblastToMyotubes_Day08D2- Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor2_CNhs14602_13511-145E1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor2_CNhs14574_tpm_fwd MyoblastToMyotubes_Day08D2+ Myoblast differentiation to myotubes, day08, control donor2_CNhs14574_13484-145B1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor2_CNhs14602_tpm_fwd MyoblastToMyotubes_Day08D2+ Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor2_CNhs14602_13511-145E1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor1_CNhs14592_tpm_rev MyoblastToMyotubes_Day08D1- Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor1_CNhs14592_13502-145D1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor1_CNhs13853_tpm_rev MyoblastToMyotubes_Day08D1- Myoblast differentiation to myotubes, day08, control donor1_CNhs13853_13475-145A1_reverse Regulation 
MyoblastDifferentiationToMyotubesDay08DuchenneMuscularDystrophyDonor1_CNhs14592_tpm_fwd MyoblastToMyotubes_Day08D1+ Myoblast differentiation to myotubes, day08, Duchenne Muscular Dystrophy donor1_CNhs14592_13502-145D1_forward Regulation 
MyoblastDifferentiationToMyotubesDay08ControlDonor1_CNhs13853_tpm_fwd MyoblastToMyotubes_Day08D1+ Myoblast differentiation to myotubes, day08, control donor1_CNhs13853_13475-145A1_forward Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor3_CNhs14582_tpm_rev MyoblastToMyotubes_Day06D3- Myoblast differentiation to myotubes, day06, control donor3_CNhs14582_13492-145B9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor3_CNhs14610_tpm_rev MyoblastToMyotubes_Day06D3- Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor3_CNhs14610_13519-145E9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor3_CNhs14582_tpm_fwd MyoblastToMyotubes_Day06D3+ Myoblast differentiation to myotubes, day06, control donor3_CNhs14582_13492-145B9_forward Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor3_CNhs14610_tpm_fwd MyoblastToMyotubes_Day06D3+ Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor3_CNhs14610_13519-145E9_forward Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor2_CNhs14573_tpm_rev MyoblastToMyotubes_Day06D2- Myoblast differentiation to myotubes, day06, control donor2_CNhs14573_13483-145A9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor2_CNhs14573_tpm_fwd MyoblastToMyotubes_Day06D2+ Myoblast differentiation to myotubes, day06, control donor2_CNhs14573_13483-145A9_forward Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor1_CNhs14591_tpm_rev MyoblastToMyotubes_Day06D1- Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor1_CNhs14591_13501-145C9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor1_CNhs13852_tpm_rev MyoblastToMyotubes_Day06D1- Myoblast differentiation to myotubes, day06, control donor1_CNhs13852_13474-144I9_reverse Regulation 
MyoblastDifferentiationToMyotubesDay06DuchenneMuscularDystrophyDonor1_CNhs14591_tpm_fwd MyoblastToMyotubes_Day06D1+ Myoblast differentiation to myotubes, day06, Duchenne Muscular Dystrophy donor1_CNhs14591_13501-145C9_forward Regulation 
MyoblastDifferentiationToMyotubesDay06ControlDonor1_CNhs13852_tpm_fwd MyoblastToMyotubes_Day06D1+ Myoblast differentiation to myotubes, day06, control donor1_CNhs13852_13474-144I9_forward Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor3_CNhs14581_tpm_rev MyoblastToMyotubes_Day04D3- Myoblast differentiation to myotubes, day04, control donor3_CNhs14581_13491-145B8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor3_CNhs14609_tpm_rev MyoblastToMyotubes_Day04D3- Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor3_CNhs14609_13518-145E8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor3_CNhs14581_tpm_fwd MyoblastToMyotubes_Day04D3+ Myoblast differentiation to myotubes, day04, control donor3_CNhs14581_13491-145B8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor3_CNhs14609_tpm_fwd MyoblastToMyotubes_Day04D3+ Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor3_CNhs14609_13518-145E8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor2_CNhs14572_tpm_rev MyoblastToMyotubes_Day04D2- Myoblast differentiation to myotubes, day04, control donor2_CNhs14572_13482-145A8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor2_CNhs14600_tpm_rev MyoblastToMyotubes_Day04D2- Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor2_CNhs14600_13509-145D8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor2_CNhs14572_tpm_fwd MyoblastToMyotubes_Day04D2+ Myoblast differentiation to myotubes, day04, control donor2_CNhs14572_13482-145A8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor2_CNhs14600_tpm_fwd MyoblastToMyotubes_Day04D2+ Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor2_CNhs14600_13509-145D8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor1_CNhs13851_tpm_rev MyoblastToMyotubes_Day04D1- Myoblast differentiation to myotubes, day04, control donor1_CNhs13851_13473-144I8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor1_CNhs14590_tpm_rev MyoblastToMyotubes_Day04D1- Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor1_CNhs14590_13500-145C8_reverse Regulation 
MyoblastDifferentiationToMyotubesDay04ControlDonor1_CNhs13851_tpm_fwd MyoblastToMyotubes_Day04D1+ Myoblast differentiation to myotubes, day04, control donor1_CNhs13851_13473-144I8_forward Regulation 
MyoblastDifferentiationToMyotubesDay04DuchenneMuscularDystrophyDonor1_CNhs14590_tpm_fwd MyoblastToMyotubes_Day04D1+ Myoblast differentiation to myotubes, day04, Duchenne Muscular Dystrophy donor1_CNhs14590_13500-145C8_forward Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor3_CNhs14580_tpm_rev MyoblastToMyotubes_Day03D3- Myoblast differentiation to myotubes, day03, control donor3_CNhs14580_13490-145B7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor3_CNhs14580_tpm_fwd MyoblastToMyotubes_Day03D3+ Myoblast differentiation to myotubes, day03, control donor3_CNhs14580_13490-145B7_forward Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor2_CNhs14571_tpm_rev MyoblastToMyotubes_Day03D2- Myoblast differentiation to myotubes, day03, control donor2_CNhs14571_13481-145A7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03DuchenneMuscularDystrophyDonor2_CNhs14599_tpm_rev MyoblastToMyotubes_Day03D2- Myoblast differentiation to myotubes, day03, Duchenne Muscular Dystrophy donor2_CNhs14599_13508-145D7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor2_CNhs14571_tpm_fwd MyoblastToMyotubes_Day03D2+ Myoblast differentiation to myotubes, day03, control donor2_CNhs14571_13481-145A7_forward Regulation 
MyoblastDifferentiationToMyotubesDay03DuchenneMuscularDystrophyDonor2_CNhs14599_tpm_fwd MyoblastToMyotubes_Day03D2+ Myoblast differentiation to myotubes, day03, Duchenne Muscular Dystrophy donor2_CNhs14599_13508-145D7_forward Regulation 
MyoblastDifferentiationToMyotubesDay03DuchenneMuscularDystrophyDonor1_CNhs14589_tpm_rev MyoblastToMyotubes_Day03D1- Myoblast differentiation to myotubes, day03, Duchenne Muscular Dystrophy donor1_CNhs14589_13499-145C7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor1_CNhs13850_tpm_rev MyoblastToMyotubes_Day03D1- Myoblast differentiation to myotubes, day03, control donor1_CNhs13850_13472-144I7_reverse Regulation 
MyoblastDifferentiationToMyotubesDay03DuchenneMuscularDystrophyDonor1_CNhs14589_tpm_fwd MyoblastToMyotubes_Day03D1+ Myoblast differentiation to myotubes, day03, Duchenne Muscular Dystrophy donor1_CNhs14589_13499-145C7_forward Regulation 
MyoblastDifferentiationToMyotubesDay03ControlDonor1_CNhs13850_tpm_fwd MyoblastToMyotubes_Day03D1+ Myoblast differentiation to myotubes, day03, control donor1_CNhs13850_13472-144I7_forward Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor3_CNhs14607_tpm_rev MyoblastToMyotubes_Day02D3- Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor3_CNhs14607_13516-145E6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor3_CNhs14579_tpm_rev MyoblastToMyotubes_Day02D3- Myoblast differentiation to myotubes, day02, control donor3_CNhs14579_13489-145B6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor3_CNhs14607_tpm_fwd MyoblastToMyotubes_Day02D3+ Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor3_CNhs14607_13516-145E6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor3_CNhs14579_tpm_fwd MyoblastToMyotubes_Day02D3+ Myoblast differentiation to myotubes, day02, control donor3_CNhs14579_13489-145B6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor2_CNhs14570_tpm_rev MyoblastToMyotubes_Day02D2- Myoblast differentiation to myotubes, day02, control donor2_CNhs14570_13480-145A6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor2_CNhs14598_tpm_rev MyoblastToMyotubes_Day02D2- Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor2_CNhs14598_13507-145D6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor2_CNhs14570_tpm_fwd MyoblastToMyotubes_Day02D2+ Myoblast differentiation to myotubes, day02, control donor2_CNhs14570_13480-145A6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor2_CNhs14598_tpm_fwd MyoblastToMyotubes_Day02D2+ Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor2_CNhs14598_13507-145D6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor1_CNhs13849_tpm_rev MyoblastToMyotubes_Day02D1- Myoblast differentiation to myotubes, day02, control donor1_CNhs13849_13471-144I6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor1_CNhs14588_tpm_rev MyoblastToMyotubes_Day02D1- Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor1_CNhs14588_13498-145C6_reverse Regulation 
MyoblastDifferentiationToMyotubesDay02ControlDonor1_CNhs13849_tpm_fwd MyoblastToMyotubes_Day02D1+ Myoblast differentiation to myotubes, day02, control donor1_CNhs13849_13471-144I6_forward Regulation 
MyoblastDifferentiationToMyotubesDay02DuchenneMuscularDystrophyDonor1_CNhs14588_tpm_fwd MyoblastToMyotubes_Day02D1+ Myoblast differentiation to myotubes, day02, Duchenne Muscular Dystrophy donor1_CNhs14588_13498-145C6_forward Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor3_CNhs14606_tpm_rev MyoblastToMyotubes_Day01D3- Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor3_CNhs14606_13515-145E5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor3_CNhs14578_tpm_rev MyoblastToMyotubes_Day01D3- Myoblast differentiation to myotubes, day01, control donor3_CNhs14578_13488-145B5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor3_CNhs14606_tpm_fwd MyoblastToMyotubes_Day01D3+ Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor3_CNhs14606_13515-145E5_forward Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor3_CNhs14578_tpm_fwd MyoblastToMyotubes_Day01D3+ Myoblast differentiation to myotubes, day01, control donor3_CNhs14578_13488-145B5_forward Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor2_CNhs14597_tpm_rev MyoblastToMyotubes_Day01D2- Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor2_CNhs14597_13506-145D5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor2_CNhs14597_tpm_fwd MyoblastToMyotubes_Day01D2+ Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor2_CNhs14597_13506-145D5_forward Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor1_CNhs13848_tpm_rev MyoblastToMyotubes_Day01D1- Myoblast differentiation to myotubes, day01, control donor1_CNhs13848_13470-144I5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor1_CNhs14587_tpm_rev MyoblastToMyotubes_Day01D1- Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor1_CNhs14587_13497-145C5_reverse Regulation 
MyoblastDifferentiationToMyotubesDay01ControlDonor1_CNhs13848_tpm_fwd MyoblastToMyotubes_Day01D1+ Myoblast differentiation to myotubes, day01, control donor1_CNhs13848_13470-144I5_forward Regulation 
MyoblastDifferentiationToMyotubesDay01DuchenneMuscularDystrophyDonor1_CNhs14587_tpm_fwd MyoblastToMyotubes_Day01D1+ Myoblast differentiation to myotubes, day01, Duchenne Muscular Dystrophy donor1_CNhs14587_13497-145C5_forward Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor3_CNhs14605_tpm_rev MyoblastToMyotubes_Day00D3- Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor3_CNhs14605_13514-145E4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor3_CNhs14577_tpm_rev MyoblastToMyotubes_Day00D3- Myoblast differentiation to myotubes, day00, control donor3_CNhs14577_13487-145B4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor3_CNhs14605_tpm_fwd MyoblastToMyotubes_Day00D3+ Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor3_CNhs14605_13514-145E4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor3_CNhs14577_tpm_fwd MyoblastToMyotubes_Day00D3+ Myoblast differentiation to myotubes, day00, control donor3_CNhs14577_13487-145B4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor2_CNhs14567_tpm_rev MyoblastToMyotubes_Day00D2- Myoblast differentiation to myotubes, day00, control donor2_CNhs14567_13478-145A4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor2_CNhs14596_tpm_rev MyoblastToMyotubes_Day00D2- Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor2_CNhs14596_13505-145D4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor2_CNhs14567_tpm_fwd MyoblastToMyotubes_Day00D2+ Myoblast differentiation to myotubes, day00, control donor2_CNhs14567_13478-145A4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor2_CNhs14596_tpm_fwd MyoblastToMyotubes_Day00D2+ Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor2_CNhs14596_13505-145D4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor1_CNhs13847_tpm_rev MyoblastToMyotubes_Day00D1- Myoblast differentiation to myotubes, day00, control donor1_CNhs13847_13469-144I4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor1_CNhs14586_tpm_rev MyoblastToMyotubes_Day00D1- Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor1_CNhs14586_13496-145C4_reverse Regulation 
MyoblastDifferentiationToMyotubesDay00ControlDonor1_CNhs13847_tpm_fwd MyoblastToMyotubes_Day00D1+ Myoblast differentiation to myotubes, day00, control donor1_CNhs13847_13469-144I4_forward Regulation 
MyoblastDifferentiationToMyotubesDay00DuchenneMuscularDystrophyDonor1_CNhs14586_tpm_fwd MyoblastToMyotubes_Day00D1+ Myoblast differentiation to myotubes, day00, Duchenne Muscular Dystrophy donor1_CNhs14586_13496-145C4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS48hrDonor2T26Subject2_CNhs13405_tpm_rev Tc:MdmToLps_48hrD2- Monocyte-derived macrophages response to LPS, 48hr, donor2 (t26 Subject2)_CNhs13405_12821-136I4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS48hrDonor2T26Subject2_CNhs13405_tpm_fwd Tc:MdmToLps_48hrD2+ Monocyte-derived macrophages response to LPS, 48hr, donor2 (t26 Subject2)_CNhs13405_12821-136I4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS48hrDonor1T26Subject1_CNhs11942_tpm_rev Tc:MdmToLps_48hrD1- Monocyte-derived macrophages response to LPS, 48hr, donor1 (t26 Subject1)_CNhs11942_12723-135G5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS48hrDonor1T26Subject1_CNhs11942_tpm_fwd Tc:MdmToLps_48hrD1+ Monocyte-derived macrophages response to LPS, 48hr, donor1 (t26 Subject1)_CNhs11942_12723-135G5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor3T25Subject3_CNhs13335_tpm_rev Tc:MdmToLps_36hrD3- Monocyte-derived macrophages response to LPS, 36hr, donor3 (t25 Subject3)_CNhs13335_12918-138B2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor3T25Subject3_CNhs13335_tpm_fwd Tc:MdmToLps_36hrD3+ Monocyte-derived macrophages response to LPS, 36hr, donor3 (t25 Subject3)_CNhs13335_12918-138B2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor2T25Subject2_CNhs13404_tpm_rev Tc:MdmToLps_36hrD2- Monocyte-derived macrophages response to LPS, 36hr, donor2 (t25 Subject2)_CNhs13404_12820-136I3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor2T25Subject2_CNhs13404_tpm_fwd Tc:MdmToLps_36hrD2+ Monocyte-derived macrophages response to LPS, 36hr, donor2 (t25 Subject2)_CNhs13404_12820-136I3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor1T25Subject1_CNhs12933_tpm_rev Tc:MdmToLps_36hrD1- Monocyte-derived macrophages response to LPS, 36hr, donor1 (t25 Subject1)_CNhs12933_12722-135G4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS36hrDonor1T25Subject1_CNhs12933_tpm_fwd Tc:MdmToLps_36hrD1+ Monocyte-derived macrophages response to LPS, 36hr, donor1 (t25 Subject1)_CNhs12933_12722-135G4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor3T24Subject3_CNhs13334_tpm_rev Tc:MdmToLps_24hrD3- Monocyte-derived macrophages response to LPS, 24hr, donor3 (t24 Subject3)_CNhs13334_12917-138B1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor3T24Subject3_CNhs13334_tpm_fwd Tc:MdmToLps_24hrD3+ Monocyte-derived macrophages response to LPS, 24hr, donor3 (t24 Subject3)_CNhs13334_12917-138B1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor2T24Subject2_CNhs13403_tpm_rev Tc:MdmToLps_24hrD2- Monocyte-derived macrophages response to LPS, 24hr, donor2 (t24 Subject2)_CNhs13403_12819-136I2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor2T24Subject2_CNhs13403_tpm_fwd Tc:MdmToLps_24hrD2+ Monocyte-derived macrophages response to LPS, 24hr, donor2 (t24 Subject2)_CNhs13403_12819-136I2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor1T24Subject1_CNhs12932_tpm_rev Tc:MdmToLps_24hrD1- Monocyte-derived macrophages response to LPS, 24hr, donor1 (t24 Subject1)_CNhs12932_12721-135G3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS24hrDonor1T24Subject1_CNhs12932_tpm_fwd Tc:MdmToLps_24hrD1+ Monocyte-derived macrophages response to LPS, 24hr, donor1 (t24 Subject1)_CNhs12932_12721-135G3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor3T23Subject3_CNhs13333_tpm_rev Tc:MdmToLps_22hrD3- Monocyte-derived macrophages response to LPS, 22hr, donor3 (t23 Subject3)_CNhs13333_12916-138A9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor3T23Subject3_CNhs13333_tpm_fwd Tc:MdmToLps_22hrD3+ Monocyte-derived macrophages response to LPS, 22hr, donor3 (t23 Subject3)_CNhs13333_12916-138A9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor2T23Subject2_CNhs13402_tpm_rev Tc:MdmToLps_22hrD2- Monocyte-derived macrophages response to LPS, 22hr, donor2 (t23 Subject2)_CNhs13402_12818-136I1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor2T23Subject2_CNhs13402_tpm_fwd Tc:MdmToLps_22hrD2+ Monocyte-derived macrophages response to LPS, 22hr, donor2 (t23 Subject2)_CNhs13402_12818-136I1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor1T23Subject1_CNhs12815_tpm_rev Tc:MdmToLps_22hrD1- Monocyte-derived macrophages response to LPS, 22hr, donor1 (t23 Subject1)_CNhs12815_12720-135G2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS22hrDonor1T23Subject1_CNhs12815_tpm_fwd Tc:MdmToLps_22hrD1+ Monocyte-derived macrophages response to LPS, 22hr, donor1 (t23 Subject1)_CNhs12815_12720-135G2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor3T22Subject3_CNhs13332_tpm_rev Tc:MdmToLps_20hrD3- Monocyte-derived macrophages response to LPS, 20hr, donor3 (t22 Subject3)_CNhs13332_12915-138A8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor3T22Subject3_CNhs13332_tpm_fwd Tc:MdmToLps_20hrD3+ Monocyte-derived macrophages response to LPS, 20hr, donor3 (t22 Subject3)_CNhs13332_12915-138A8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor2T22Subject2_CNhs13401_tpm_rev Tc:MdmToLps_20hrD2- Monocyte-derived macrophages response to LPS, 20hr, donor2 (t22 Subject2)_CNhs13401_12817-136H9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor2T22Subject2_CNhs13401_tpm_fwd Tc:MdmToLps_20hrD2+ Monocyte-derived macrophages response to LPS, 20hr, donor2 (t22 Subject2)_CNhs13401_12817-136H9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor1T22Subject1_CNhs12931_tpm_rev Tc:MdmToLps_20hrD1- Monocyte-derived macrophages response to LPS, 20hr, donor1 (t22 Subject1)_CNhs12931_12719-135G1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS20hrDonor1T22Subject1_CNhs12931_tpm_fwd Tc:MdmToLps_20hrD1+ Monocyte-derived macrophages response to LPS, 20hr, donor1 (t22 Subject1)_CNhs12931_12719-135G1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor3T21Subject3_CNhs13331_tpm_rev Tc:MdmToLps_18hrD3- Monocyte-derived macrophages response to LPS, 18hr, donor3 (t21 Subject3)_CNhs13331_12914-138A7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor3T21Subject3_CNhs13331_tpm_fwd Tc:MdmToLps_18hrD3+ Monocyte-derived macrophages response to LPS, 18hr, donor3 (t21 Subject3)_CNhs13331_12914-138A7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor2T21Subject2_CNhs13400_tpm_rev Tc:MdmToLps_18hrD2- Monocyte-derived macrophages response to LPS, 18hr, donor2 (t21 Subject2)_CNhs13400_12816-136H8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor2T21Subject2_CNhs13400_tpm_fwd Tc:MdmToLps_18hrD2+ Monocyte-derived macrophages response to LPS, 18hr, donor2 (t21 Subject2)_CNhs13400_12816-136H8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor1T21Subject1_CNhs12814_tpm_rev Tc:MdmToLps_18hrD1- Monocyte-derived macrophages response to LPS, 18hr, donor1 (t21 Subject1)_CNhs12814_12718-135F9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS18hrDonor1T21Subject1_CNhs12814_tpm_fwd Tc:MdmToLps_18hrD1+ Monocyte-derived macrophages response to LPS, 18hr, donor1 (t21 Subject1)_CNhs12814_12718-135F9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor3T20Subject3_CNhs13330_tpm_rev Tc:MdmToLps_16hrD3- Monocyte-derived macrophages response to LPS, 16hr, donor3 (t20 Subject3)_CNhs13330_12913-138A6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor3T20Subject3_CNhs13330_tpm_fwd Tc:MdmToLps_16hrD3+ Monocyte-derived macrophages response to LPS, 16hr, donor3 (t20 Subject3)_CNhs13330_12913-138A6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor2T20Subject2_CNhs13399_tpm_rev Tc:MdmToLps_16hrD2- Monocyte-derived macrophages response to LPS, 16hr, donor2 (t20 Subject2)_CNhs13399_12815-136H7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS16hrDonor2T20Subject2_CNhs13399_tpm_fwd Tc:MdmToLps_16hrD2+ Monocyte-derived macrophages response to LPS, 16hr, donor2 (t20 Subject2)_CNhs13399_12815-136H7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor3T19Subject3_CNhs13329_tpm_rev Tc:MdmToLps_14hrD3- Monocyte-derived macrophages response to LPS, 14hr, donor3 (t19 Subject3)_CNhs13329_12912-138A5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor3T19Subject3_CNhs13329_tpm_fwd Tc:MdmToLps_14hrD3+ Monocyte-derived macrophages response to LPS, 14hr, donor3 (t19 Subject3)_CNhs13329_12912-138A5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor2T19Subject2_CNhs13398_tpm_rev Tc:MdmToLps_14hrD2- Monocyte-derived macrophages response to LPS, 14hr, donor2 (t19 Subject2)_CNhs13398_12814-136H6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor2T19Subject2_CNhs13398_tpm_fwd Tc:MdmToLps_14hrD2+ Monocyte-derived macrophages response to LPS, 14hr, donor2 (t19 Subject2)_CNhs13398_12814-136H6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor1T19Subject1_CNhs12929_tpm_rev Tc:MdmToLps_14hrD1- Monocyte-derived macrophages response to LPS, 14hr, donor1 (t19 Subject1)_CNhs12929_12716-135F7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS14hrDonor1T19Subject1_CNhs12929_tpm_fwd Tc:MdmToLps_14hrD1+ Monocyte-derived macrophages response to LPS, 14hr, donor1 (t19 Subject1)_CNhs12929_12716-135F7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor3T18Subject3_CNhs13328_tpm_rev Tc:MdmToLps_12hrD3- Monocyte-derived macrophages response to LPS, 12hr, donor3 (t18 Subject3)_CNhs13328_12911-138A4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor3T18Subject3_CNhs13328_tpm_fwd Tc:MdmToLps_12hrD3+ Monocyte-derived macrophages response to LPS, 12hr, donor3 (t18 Subject3)_CNhs13328_12911-138A4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor2T18Subject2_CNhs13397_tpm_rev Tc:MdmToLps_12hrD2- Monocyte-derived macrophages response to LPS, 12hr, donor2 (t18 Subject2)_CNhs13397_12813-136H5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor2T18Subject2_CNhs13397_tpm_fwd Tc:MdmToLps_12hrD2+ Monocyte-derived macrophages response to LPS, 12hr, donor2 (t18 Subject2)_CNhs13397_12813-136H5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor1T18Subject1_CNhs12813_tpm_rev Tc:MdmToLps_12hrD1- Monocyte-derived macrophages response to LPS, 12hr, donor1 (t18 Subject1)_CNhs12813_12715-135F6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS12hrDonor1T18Subject1_CNhs12813_tpm_fwd Tc:MdmToLps_12hrD1+ Monocyte-derived macrophages response to LPS, 12hr, donor1 (t18 Subject1)_CNhs12813_12715-135F6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor3T17Subject3_CNhs13327_tpm_rev Tc:MdmToLps_10hrD3- Monocyte-derived macrophages response to LPS, 10hr, donor3 (t17 Subject3)_CNhs13327_12910-138A3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor3T17Subject3_CNhs13327_tpm_fwd Tc:MdmToLps_10hrD3+ Monocyte-derived macrophages response to LPS, 10hr, donor3 (t17 Subject3)_CNhs13327_12910-138A3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor2T17Subject2_CNhs13396_tpm_rev Tc:MdmToLps_10hrD2- Monocyte-derived macrophages response to LPS, 10hr, donor2 (t17 Subject2)_CNhs13396_12812-136H4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS10hrDonor2T17Subject2_CNhs13396_tpm_fwd Tc:MdmToLps_10hrD2+ Monocyte-derived macrophages response to LPS, 10hr, donor2 (t17 Subject2)_CNhs13396_12812-136H4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor3T16Subject3_CNhs13326_tpm_rev Tc:MdmToLps_08hrD3- Monocyte-derived macrophages response to LPS, 08hr, donor3 (t16 Subject3)_CNhs13326_12909-138A2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor3T16Subject3_CNhs13326_tpm_fwd Tc:MdmToLps_08hrD3+ Monocyte-derived macrophages response to LPS, 08hr, donor3 (t16 Subject3)_CNhs13326_12909-138A2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor2T16Subject2_CNhs13395_tpm_rev Tc:MdmToLps_08hrD2- Monocyte-derived macrophages response to LPS, 08hr, donor2 (t16 Subject2)_CNhs13395_12811-136H3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor2T16Subject2_CNhs13395_tpm_fwd Tc:MdmToLps_08hrD2+ Monocyte-derived macrophages response to LPS, 08hr, donor2 (t16 Subject2)_CNhs13395_12811-136H3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor1T16Subject1_CNhs12927_tpm_rev Tc:MdmToLps_08hrD1- Monocyte-derived macrophages response to LPS, 08hr, donor1 (t16 Subject1)_CNhs12927_12713-135F4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS08hrDonor1T16Subject1_CNhs12927_tpm_fwd Tc:MdmToLps_08hrD1+ Monocyte-derived macrophages response to LPS, 08hr, donor1 (t16 Subject1)_CNhs12927_12713-135F4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor3T13Subject3_CNhs13186_tpm_rev Tc:MdmToLps_05hrD3- Monocyte-derived macrophages response to LPS, 05hr, donor3 (t13 Subject3)_CNhs13186_12906-137I8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor3T13Subject3_CNhs13186_tpm_fwd Tc:MdmToLps_05hrD3+ Monocyte-derived macrophages response to LPS, 05hr, donor3 (t13 Subject3)_CNhs13186_12906-137I8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor2T13Subject2_CNhs13392_tpm_rev Tc:MdmToLps_05hrD2- Monocyte-derived macrophages response to LPS, 05hr, donor2 (t13 Subject2)_CNhs13392_12808-136G9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor2T13Subject2_CNhs13392_tpm_fwd Tc:MdmToLps_05hrD2+ Monocyte-derived macrophages response to LPS, 05hr, donor2 (t13 Subject2)_CNhs13392_12808-136G9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor1T13Subject1_CNhs13155_tpm_rev Tc:MdmToLps_05hrD1- Monocyte-derived macrophages response to LPS, 05hr, donor1 (t13 Subject1)_CNhs13155_12710-135F1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS05hrDonor1T13Subject1_CNhs13155_tpm_fwd Tc:MdmToLps_05hrD1+ Monocyte-derived macrophages response to LPS, 05hr, donor1 (t13 Subject1)_CNhs13155_12710-135F1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor3T12Subject3_CNhs13185_tpm_rev Tc:MdmToLps_04hrD3- Monocyte-derived macrophages response to LPS, 04hr, donor3 (t12 Subject3)_CNhs13185_12905-137I7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor3T12Subject3_CNhs13185_tpm_fwd Tc:MdmToLps_04hrD3+ Monocyte-derived macrophages response to LPS, 04hr, donor3 (t12 Subject3)_CNhs13185_12905-137I7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor2T12Subject2_CNhs13391_tpm_rev Tc:MdmToLps_04hrD2- Monocyte-derived macrophages response to LPS, 04hr, donor2 (t12 Subject2)_CNhs13391_12807-136G8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS04hrDonor2T12Subject2_CNhs13391_tpm_fwd Tc:MdmToLps_04hrD2+ Monocyte-derived macrophages response to LPS, 04hr, donor2 (t12 Subject2)_CNhs13391_12807-136G8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor3T11Subject3_CNhs13184_tpm_rev Tc:MdmToLps_03hr30minD3- Monocyte-derived macrophages response to LPS, 03hr30min, donor3 (t11 Subject3)_CNhs13184_12904-137I6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor3T11Subject3_CNhs13184_tpm_fwd Tc:MdmToLps_03hr30minD3+ Monocyte-derived macrophages response to LPS, 03hr30min, donor3 (t11 Subject3)_CNhs13184_12904-137I6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor2T11Subject2_CNhs13389_tpm_rev Tc:MdmToLps_03hr30minD2- Monocyte-derived macrophages response to LPS, 03hr30min, donor2 (t11 Subject2)_CNhs13389_12806-136G7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr30minDonor2T11Subject2_CNhs13389_tpm_fwd Tc:MdmToLps_03hr30minD2+ Monocyte-derived macrophages response to LPS, 03hr30min, donor2 (t11 Subject2)_CNhs13389_12806-136G7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor3T10Subject3_CNhs13183_tpm_rev Tc:MdmToLps_03hr00minD3- Monocyte-derived macrophages response to LPS, 03hr00min, donor3 (t10 Subject3)_CNhs13183_12903-137I5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor3T10Subject3_CNhs13183_tpm_fwd Tc:MdmToLps_03hr00minD3+ Monocyte-derived macrophages response to LPS, 03hr00min, donor3 (t10 Subject3)_CNhs13183_12903-137I5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor2T10Subject2_CNhs13388_tpm_rev Tc:MdmToLps_03hr00minD2- Monocyte-derived macrophages response to LPS, 03hr00min, donor2 (t10 Subject2)_CNhs13388_12805-136G6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor2T10Subject2_CNhs13388_tpm_fwd Tc:MdmToLps_03hr00minD2+ Monocyte-derived macrophages response to LPS, 03hr00min, donor2 (t10 Subject2)_CNhs13388_12805-136G6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor1T10Subject1_CNhs12924_tpm_rev Tc:MdmToLps_03hr00minD1- Monocyte-derived macrophages response to LPS, 03hr00min, donor1 (t10 Subject1)_CNhs12924_12707-135E7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS03hr00minDonor1T10Subject1_CNhs12924_tpm_fwd Tc:MdmToLps_03hr00minD1+ Monocyte-derived macrophages response to LPS, 03hr00min, donor1 (t10 Subject1)_CNhs12924_12707-135E7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor3T9Subject3_CNhs13182_tpm_rev Tc:MdmToLps_02hr30minD3- Monocyte-derived macrophages response to LPS, 02hr30min, donor3 (t9 Subject3)_CNhs13182_12902-137I4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor3T9Subject3_CNhs13182_tpm_fwd Tc:MdmToLps_02hr30minD3+ Monocyte-derived macrophages response to LPS, 02hr30min, donor3 (t9 Subject3)_CNhs13182_12902-137I4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor2T9Subject2_CNhs13387_tpm_rev Tc:MdmToLps_02hr30minD2- Monocyte-derived macrophages response to LPS, 02hr30min, donor2 (t9 Subject2)_CNhs13387_12804-136G5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor2T9Subject2_CNhs13387_tpm_fwd Tc:MdmToLps_02hr30minD2+ Monocyte-derived macrophages response to LPS, 02hr30min, donor2 (t9 Subject2)_CNhs13387_12804-136G5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor1T9Subject1_CNhs13152_tpm_rev Tc:MdmToLps_02hr30minD1- Monocyte-derived macrophages response to LPS, 02hr30min, donor1 (t9 Subject1)_CNhs13152_12706-135E6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr30minDonor1T9Subject1_CNhs13152_tpm_fwd Tc:MdmToLps_02hr30minD1+ Monocyte-derived macrophages response to LPS, 02hr30min, donor1 (t9 Subject1)_CNhs13152_12706-135E6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor3T8Subject3_CNhs13181_tpm_rev Tc:MdmToLps_02hr00minD3- Monocyte-derived macrophages response to LPS, 02hr00min, donor3 (t8 Subject3)_CNhs13181_12901-137I3_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor3T8Subject3_CNhs13181_tpm_fwd Tc:MdmToLps_02hr00minD3+ Monocyte-derived macrophages response to LPS, 02hr00min, donor3 (t8 Subject3)_CNhs13181_12901-137I3_forward Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor2T8Subject2_CNhs13386_tpm_rev Tc:MdmToLps_02hr00minD2- Monocyte-derived macrophages response to LPS, 02hr00min, donor2 (t8 Subject2)_CNhs13386_12803-136G4_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS02hr00minDonor2T8Subject2_CNhs13386_tpm_fwd Tc:MdmToLps_02hr00minD2+ Monocyte-derived macrophages response to LPS, 02hr00min, donor2 (t8 Subject2)_CNhs13386_12803-136G4_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor3T6Subject3_CNhs13179_tpm_rev Tc:MdmToLps_01hr20minD3- Monocyte-derived macrophages response to LPS, 01hr20min, donor3 (t6 Subject3)_CNhs13179_12899-137I1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor3T6Subject3_CNhs13179_tpm_fwd Tc:MdmToLps_01hr20minD3+ Monocyte-derived macrophages response to LPS, 01hr20min, donor3 (t6 Subject3)_CNhs13179_12899-137I1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor2T6Subject2_CNhs13384_tpm_rev Tc:MdmToLps_01hr20minD2- Monocyte-derived macrophages response to LPS, 01hr20min, donor2 (t6 Subject2)_CNhs13384_12801-136G2_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr20minDonor2T6Subject2_CNhs13384_tpm_fwd Tc:MdmToLps_01hr20minD2+ Monocyte-derived macrophages response to LPS, 01hr20min, donor2 (t6 Subject2)_CNhs13384_12801-136G2_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor3T5Subject3_CNhs13178_tpm_rev Tc:MdmToLps_01hr00minD3- Monocyte-derived macrophages response to LPS, 01hr00min, donor3 (t5 Subject3)_CNhs13178_12898-137H9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor3T5Subject3_CNhs13178_tpm_fwd Tc:MdmToLps_01hr00minD3+ Monocyte-derived macrophages response to LPS, 01hr00min, donor3 (t5 Subject3)_CNhs13178_12898-137H9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor2T5Subject2_CNhs13383_tpm_rev Tc:MdmToLps_01hr00minD2- Monocyte-derived macrophages response to LPS, 01hr00min, donor2 (t5 Subject2)_CNhs13383_12800-136G1_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS01hr00minDonor2T5Subject2_CNhs13383_tpm_fwd Tc:MdmToLps_01hr00minD2+ Monocyte-derived macrophages response to LPS, 01hr00min, donor2 (t5 Subject2)_CNhs13383_12800-136G1_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor3T4Subject3_CNhs13177_tpm_rev Tc:MdmToLps_00hr45minD3- Monocyte-derived macrophages response to LPS, 00hr45min, donor3 (t4 Subject3)_CNhs13177_12897-137H8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor3T4Subject3_CNhs13177_tpm_fwd Tc:MdmToLps_00hr45minD3+ Monocyte-derived macrophages response to LPS, 00hr45min, donor3 (t4 Subject3)_CNhs13177_12897-137H8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor2T4Subject2_CNhs13382_tpm_rev Tc:MdmToLps_00hr45minD2- Monocyte-derived macrophages response to LPS, 00hr45min, donor2 (t4 Subject2)_CNhs13382_12799-136F9_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr45minDonor2T4Subject2_CNhs13382_tpm_fwd Tc:MdmToLps_00hr45minD2+ Monocyte-derived macrophages response to LPS, 00hr45min, donor2 (t4 Subject2)_CNhs13382_12799-136F9_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor3T3Subject3_CNhs13176_tpm_rev Tc:MdmToLps_00hr30minD3- Monocyte-derived macrophages response to LPS, 00hr30min, donor3 (t3 Subject3)_CNhs13176_12896-137H7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor3T3Subject3_CNhs13176_tpm_fwd Tc:MdmToLps_00hr30minD3+ Monocyte-derived macrophages response to LPS, 00hr30min, donor3 (t3 Subject3)_CNhs13176_12896-137H7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor2T3Subject2_CNhs13381_tpm_rev Tc:MdmToLps_00hr30minD2- Monocyte-derived macrophages response to LPS, 00hr30min, donor2 (t3 Subject2)_CNhs13381_12798-136F8_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr30minDonor2T3Subject2_CNhs13381_tpm_fwd Tc:MdmToLps_00hr30minD2+ Monocyte-derived macrophages response to LPS, 00hr30min, donor2 (t3 Subject2)_CNhs13381_12798-136F8_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor3T2Subject3_CNhs13175_tpm_rev Tc:MdmToLps_00hr15minD3- Monocyte-derived macrophages response to LPS, 00hr15min, donor3 (t2 Subject3)_CNhs13175_12895-137H6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor3T2Subject3_CNhs13175_tpm_fwd Tc:MdmToLps_00hr15minD3+ Monocyte-derived macrophages response to LPS, 00hr15min, donor3 (t2 Subject3)_CNhs13175_12895-137H6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor2T2Subject2_CNhs13380_tpm_rev Tc:MdmToLps_00hr15minD2- Monocyte-derived macrophages response to LPS, 00hr15min, donor2 (t2 Subject2)_CNhs13380_12797-136F7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr15minDonor2T2Subject2_CNhs13380_tpm_fwd Tc:MdmToLps_00hr15minD2+ Monocyte-derived macrophages response to LPS, 00hr15min, donor2 (t2 Subject2)_CNhs13380_12797-136F7_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor3T1Subject3_CNhs13174_tpm_rev Tc:MdmToLps_00hr00minD3- Monocyte-derived macrophages response to LPS, 00hr00min, donor3 (t1 Subject3)_CNhs13174_12894-137H5_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor3T1Subject3_CNhs13174_tpm_fwd Tc:MdmToLps_00hr00minD3+ Monocyte-derived macrophages response to LPS, 00hr00min, donor3 (t1 Subject3)_CNhs13174_12894-137H5_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor2T1Subject2_CNhs13379_tpm_rev Tc:MdmToLps_00hr00minD2- Monocyte-derived macrophages response to LPS, 00hr00min, donor2 (t1 Subject2)_CNhs13379_12796-136F6_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor2T1Subject2_CNhs13379_tpm_fwd Tc:MdmToLps_00hr00minD2+ Monocyte-derived macrophages response to LPS, 00hr00min, donor2 (t1 Subject2)_CNhs13379_12796-136F6_forward Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor1T1Subject1_CNhs11941_tpm_rev Tc:MdmToLps_00hr00minD1- Monocyte-derived macrophages response to LPS, 00hr00min, donor1 (t1 Subject1)_CNhs11941_12698-135D7_reverse Regulation 
MonocytederivedMacrophagesResponseToLPS00hr00minDonor1T1Subject1_CNhs11941_tpm_fwd Tc:MdmToLps_00hr00minD1+ Monocyte-derived macrophages response to LPS, 00hr00min, donor1 (t1 Subject1)_CNhs11941_12698-135D7_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor4227_121MI_24h_CNhs13644_tpm_rev Tc:MdmToMock_24hr00minD4- Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor4 (227_121:MI_24h)_CNhs13644_13315-143A3_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor4227_121MI_24h_CNhs13644_tpm_fwd Tc:MdmToMock_24hr00minD4+ Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor4 (227_121:MI_24h)_CNhs13644_13315-143A3_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor3536_119MI_24h_CNhs13652_tpm_rev Tc:MdmToMock_24hr00minD3- Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor3 (536_119:MI_24h)_CNhs13652_13327-143B6_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor3536_119MI_24h_CNhs13652_tpm_fwd Tc:MdmToMock_24hr00minD3+ Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor3 (536_119:MI_24h)_CNhs13652_13327-143B6_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor2150_120MI_24h_CNhs13648_tpm_rev Tc:MdmToMock_24hr00minD2- Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor2 (150_120:MI_24h)_CNhs13648_13321-143A9_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor2150_120MI_24h_CNhs13648_tpm_fwd Tc:MdmToMock_24hr00minD2+ Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor2 (150_120:MI_24h)_CNhs13648_13321-143A9_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor1868_121MI_24h_CNhs13693_tpm_rev Tc:MdmToMock_24hr00minD1- Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor1 (868_121:MI_24h)_CNhs13693_13309-142I6_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection24hr00minDonor1868_121MI_24h_CNhs13693_tpm_fwd Tc:MdmToMock_24hr00minD1+ Monocyte-derived macrophages response to mock influenza infection, 24hr00min, donor1 (868_121:MI_24h)_CNhs13693_13309-142I6_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor4227_121MI_0h_CNhs13638_tpm_rev Tc:MdmToMock_00hr00minD4- Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor4 (227_121:MI_0h)_CNhs13638_13310-142I7_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor4227_121MI_0h_CNhs13638_tpm_fwd Tc:MdmToMock_00hr00minD4+ Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor4 (227_121:MI_0h)_CNhs13638_13310-142I7_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor3536_119MI_0h_CNhs13649_tpm_rev Tc:MdmToMock_00hr00minD3- Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor3 (536_119:MI_0h)_CNhs13649_13322-143B1_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor3536_119MI_0h_CNhs13649_tpm_fwd Tc:MdmToMock_00hr00minD3+ Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor3 (536_119:MI_0h)_CNhs13649_13322-143B1_forward Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor2150_120MI_0h_CNhs13645_tpm_rev Tc:MdmToMock_00hr00minD2- Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor2 (150_120:MI_0h)_CNhs13645_13316-143A4_reverse Regulation 
MonocytederivedMacrophagesResponseToMockInfluenzaInfection00hr00minDonor2150_120MI_0h_CNhs13645_tpm_fwd Tc:MdmToMock_00hr00minD2+ Monocyte-derived macrophages response to mock influenza infection, 00hr00min, donor2 (150_120:MI_0h)_CNhs13645_13316-143A4_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor3536_119Ud_24h_CNhs13562_tpm_rev MonocyteMacrophageUdornInfluenza_24hr00minD3- Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor3 (536_119:Ud_24h)_CNhs13562_13326-143B5_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor3536_119Ud_24h_CNhs13562_tpm_fwd MonocyteMacrophageUdornInfluenza_24hr00minD3+ Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor3 (536_119:Ud_24h)_CNhs13562_13326-143B5_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor2150_120Ud_24h_CNhs13560_tpm_rev MonocyteMacrophageUdornInfluenza_24hr00minD2- Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor2 (150_120:Ud_24h)_CNhs13560_13320-143A8_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor2150_120Ud_24h_CNhs13560_tpm_fwd MonocyteMacrophageUdornInfluenza_24hr00minD2+ Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor2 (150_120:Ud_24h)_CNhs13560_13320-143A8_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor1868_121Ud_24h_CNhs13557_tpm_rev MonocyteMacrophageUdornInfluenza_24hr00minD1- Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor1 (868_121:Ud_24h)_CNhs13557_13308-142I5_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection24hr00minDonor1868_121Ud_24h_CNhs13557_tpm_fwd MonocyteMacrophageUdornInfluenza_24hr00minD1+ Monocyte-derived macrophages response to udorn influenza infection, 24hr00min, donor1 (868_121:Ud_24h)_CNhs13557_13308-142I5_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor4227_121Ud_7h_CNhs13641_tpm_rev MonocyteMacrophageUdornInfluenza_07hr00minD4- Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor4 (227_121:Ud_7h)_CNhs13641_13313-143A1_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor4227_121Ud_7h_CNhs13641_tpm_fwd MonocyteMacrophageUdornInfluenza_07hr00minD4+ Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor4 (227_121:Ud_7h)_CNhs13641_13313-143A1_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor3536_119Ud_7h_CNhs13561_tpm_rev MonocyteMacrophageUdornInfluenza_07hr00minD3- Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor3 (536_119:Ud_7h)_CNhs13561_13325-143B4_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor3536_119Ud_7h_CNhs13561_tpm_fwd MonocyteMacrophageUdornInfluenza_07hr00minD3+ Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor3 (536_119:Ud_7h)_CNhs13561_13325-143B4_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor2150_120Ud_7h_CNhs13559_tpm_rev MonocyteMacrophageUdornInfluenza_07hr00minD2- Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor2 (150_120:Ud_7h)_CNhs13559_13319-143A7_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor2150_120Ud_7h_CNhs13559_tpm_fwd MonocyteMacrophageUdornInfluenza_07hr00minD2+ Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor2 (150_120:Ud_7h)_CNhs13559_13319-143A7_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor1868_121Ud_7h_CNhs13556_tpm_rev MonocyteMacrophageUdornInfluenza_07hr00minD1- Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor1 (868_121:Ud_7h)_CNhs13556_13307-142I4_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection07hr00minDonor1868_121Ud_7h_CNhs13556_tpm_fwd MonocyteMacrophageUdornInfluenza_07hr00minD1+ Monocyte-derived macrophages response to udorn influenza infection, 07hr00min, donor1 (868_121:Ud_7h)_CNhs13556_13307-142I4_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor4227_121Ud_2h_CNhs13640_tpm_rev MonocyteMacrophageUdornInfluenza_02hr00minD4- Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor4 (227_121:Ud_2h)_CNhs13640_13312-142I9_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor4227_121Ud_2h_CNhs13640_tpm_fwd MonocyteMacrophageUdornInfluenza_02hr00minD4+ Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor4 (227_121:Ud_2h)_CNhs13640_13312-142I9_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor3536_119Ud_2h_CNhs13651_tpm_rev MonocyteMacrophageUdornInfluenza_02hr00minD3- Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor3 (536_119:Ud_2h)_CNhs13651_13324-143B3_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor3536_119Ud_2h_CNhs13651_tpm_fwd MonocyteMacrophageUdornInfluenza_02hr00minD3+ Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor3 (536_119:Ud_2h)_CNhs13651_13324-143B3_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor1868_121Ud_2h_CNhs13555_tpm_rev MonocyteMacrophageUdornInfluenza_02hr00minD1- Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor1 (868_121:Ud_2h)_CNhs13555_13306-142I3_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection02hr00minDonor1868_121Ud_2h_CNhs13555_tpm_fwd MonocyteMacrophageUdornInfluenza_02hr00minD1+ Monocyte-derived macrophages response to udorn influenza infection, 02hr00min, donor1 (868_121:Ud_2h)_CNhs13555_13306-142I3_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor4227_121Ud_0h_CNhs13639_tpm_rev MonocyteMacrophageUdornInfluenza_00hr00minD4- Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor4 (227_121:Ud_0h)_CNhs13639_13311-142I8_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor4227_121Ud_0h_CNhs13639_tpm_fwd MonocyteMacrophageUdornInfluenza_00hr00minD4+ Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor4 (227_121:Ud_0h)_CNhs13639_13311-142I8_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor3536_119Ud_0h_CNhs13650_tpm_rev MonocyteMacrophageUdornInfluenza_00hr00minD3- Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor3 (536_119:Ud_0h)_CNhs13650_13323-143B2_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor3536_119Ud_0h_CNhs13650_tpm_fwd MonocyteMacrophageUdornInfluenza_00hr00minD3+ Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor3 (536_119:Ud_0h)_CNhs13650_13323-143B2_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor2150_120Ud_0h_CNhs13646_tpm_rev MonocyteMacrophageUdornInfluenza_00hr00minD2- Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor2 (150_120:Ud_0h)_CNhs13646_13317-143A5_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor2150_120Ud_0h_CNhs13646_tpm_fwd MonocyteMacrophageUdornInfluenza_00hr00minD2+ Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor2 (150_120:Ud_0h)_CNhs13646_13317-143A5_forward Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor1868_121Ud_0h_CNhs13554_tpm_rev MonocyteMacrophageUdornInfluenza_00hr00minD1- Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor1 (868_121:Ud_0h)_CNhs13554_13305-142I2_reverse Regulation 
MonocytederivedMacrophagesResponseToUdornInfluenzaInfection00hr00minDonor1868_121Ud_0h_CNhs13554_tpm_fwd MonocyteMacrophageUdornInfluenza_00hr00minD1+ Monocyte-derived macrophages response to udorn influenza infection, 00hr00min, donor1 (868_121:Ud_0h)_CNhs13554_13305-142I2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep3_CNhs13632_tpm_rev MscAdipogenicInduction_Day14Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep3_CNhs13632_13279-142F3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep3_CNhs13632_tpm_fwd MscAdipogenicInduction_Day14Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep3_CNhs13632_13279-142F3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep1_CNhs13338_tpm_rev MscAdipogenicInduction_Day14Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep1_CNhs13338_13277-142F1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay14BiolRep1_CNhs13338_tpm_fwd MscAdipogenicInduction_Day14Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day14, biol_rep1_CNhs13338_13277-142F1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep3_CNhs13630_tpm_rev MscAdipogenicInduction_Day12Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep3_CNhs13630_13276-142E9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep3_CNhs13630_tpm_fwd MscAdipogenicInduction_Day12Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep3_CNhs13630_13276-142E9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep2_CNhs13629_tpm_rev MscAdipogenicInduction_Day12Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep2_CNhs13629_13275-142E8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep2_CNhs13629_tpm_fwd MscAdipogenicInduction_Day12Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep2_CNhs13629_13275-142E8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep1_CNhs13628_tpm_rev MscAdipogenicInduction_Day12Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep1_CNhs13628_13274-142E7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay12BiolRep1_CNhs13628_tpm_fwd MscAdipogenicInduction_Day12Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day12, biol_rep1_CNhs13628_13274-142E7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep3_CNhs13627_tpm_rev MscAdipogenicInduction_Day08Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep3_CNhs13627_13273-142E6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep3_CNhs13627_tpm_fwd MscAdipogenicInduction_Day08Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep3_CNhs13627_13273-142E6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep2_CNhs13626_tpm_rev MscAdipogenicInduction_Day08Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep2_CNhs13626_13272-142E5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep2_CNhs13626_tpm_fwd MscAdipogenicInduction_Day08Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep2_CNhs13626_13272-142E5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep1_CNhs13625_tpm_rev MscAdipogenicInduction_Day08Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep1_CNhs13625_13271-142E4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay08BiolRep1_CNhs13625_tpm_fwd MscAdipogenicInduction_Day08Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep1_CNhs13625_13271-142E4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep3_CNhs13624_tpm_rev MscAdipogenicInduction_Day04Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep3_CNhs13624_13270-142E3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep3_CNhs13624_tpm_fwd MscAdipogenicInduction_Day04Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep3_CNhs13624_13270-142E3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep1_CNhs13622_tpm_rev MscAdipogenicInduction_Day04Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep1_CNhs13622_13268-142E1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay04BiolRep1_CNhs13622_tpm_fwd MscAdipogenicInduction_Day04Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day04, biol_rep1_CNhs13622_13268-142E1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep3_CNhs13621_tpm_rev MscAdipogenicInduction_Day02Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep3_CNhs13621_13267-142D9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep3_CNhs13621_tpm_fwd MscAdipogenicInduction_Day02Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep3_CNhs13621_13267-142D9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep2_CNhs13620_tpm_rev MscAdipogenicInduction_Day02Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep2_CNhs13620_13266-142D8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep2_CNhs13620_tpm_fwd MscAdipogenicInduction_Day02Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep2_CNhs13620_13266-142D8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep1_CNhs13619_tpm_rev MscAdipogenicInduction_Day02Br1- mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep1_CNhs13619_13265-142D7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay02BiolRep1_CNhs13619_tpm_fwd MscAdipogenicInduction_Day02Br1+ mesenchymal stem cells (adipose derived), adipogenic induction, day02, biol_rep1_CNhs13619_13265-142D7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep3_CNhs13617_tpm_rev MscAdipogenicInduction_Day01Br3- mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep3_CNhs13617_13264-142D6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep3_CNhs13617_tpm_fwd MscAdipogenicInduction_Day01Br3+ mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep3_CNhs13617_13264-142D6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep2_CNhs13616_tpm_rev MscAdipogenicInduction_Day01Br2- mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep2_CNhs13616_13263-142D5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInductionDay01BiolRep2_CNhs13616_tpm_fwd MscAdipogenicInduction_Day01Br2+ mesenchymal stem cells (adipose derived), adipogenic induction, day01, biol_rep2_CNhs13616_13263-142D5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep3_CNhs13611_tpm_rev MscAdipogenicInduction_03hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep3_CNhs13611_13258-142C9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep3_CNhs13611_tpm_fwd MscAdipogenicInduction_03hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep3_CNhs13611_13258-142C9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep1_CNhs13609_tpm_rev MscAdipogenicInduction_03hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep1_CNhs13609_13256-142C7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction03hr00minBiolRep1_CNhs13609_tpm_fwd MscAdipogenicInduction_03hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 03hr00min, biol_rep1_CNhs13609_13256-142C7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep3_CNhs13608_tpm_rev MscAdipogenicInduction_02hr30minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep3_CNhs13608_13255-142C6_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep3_CNhs13608_tpm_fwd MscAdipogenicInduction_02hr30minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep3_CNhs13608_13255-142C6_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep1_CNhs13606_tpm_rev MscAdipogenicInduction_02hr30minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep1_CNhs13606_13253-142C4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr30minBiolRep1_CNhs13606_tpm_fwd MscAdipogenicInduction_02hr30minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr30min, biol_rep1_CNhs13606_13253-142C4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep2_CNhs13604_tpm_rev MscAdipogenicInduction_02hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep2_CNhs13604_13251-142C2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep2_CNhs13604_tpm_fwd MscAdipogenicInduction_02hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep2_CNhs13604_13251-142C2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep1_CNhs13603_tpm_rev MscAdipogenicInduction_02hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep1_CNhs13603_13250-142C1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction02hr00minBiolRep1_CNhs13603_tpm_fwd MscAdipogenicInduction_02hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 02hr00min, biol_rep1_CNhs13603_13250-142C1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep3_CNhs13602_tpm_rev MscAdipogenicInduction_01hr40minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep3_CNhs13602_13249-142B9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep3_CNhs13602_tpm_fwd MscAdipogenicInduction_01hr40minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep3_CNhs13602_13249-142B9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep2_CNhs13601_tpm_rev MscAdipogenicInduction_01hr40minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep2_CNhs13601_13248-142B8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep2_CNhs13601_tpm_fwd MscAdipogenicInduction_01hr40minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep2_CNhs13601_13248-142B8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep1_CNhs13600_tpm_rev MscAdipogenicInduction_01hr40minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep1_CNhs13600_13247-142B7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr40minBiolRep1_CNhs13600_tpm_fwd MscAdipogenicInduction_01hr40minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr40min, biol_rep1_CNhs13600_13247-142B7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep3_CNhs13433_tpm_rev MscAdipogenicInduction_01hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep3_CNhs13433_13243-142B3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep3_CNhs13433_tpm_fwd MscAdipogenicInduction_01hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep3_CNhs13433_13243-142B3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep2_CNhs13432_tpm_rev MscAdipogenicInduction_01hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep2_CNhs13432_13242-142B2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep2_CNhs13432_tpm_fwd MscAdipogenicInduction_01hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep2_CNhs13432_13242-142B2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep1_CNhs13431_tpm_rev MscAdipogenicInduction_01hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep1_CNhs13431_13241-142B1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction01hr00minBiolRep1_CNhs13431_tpm_fwd MscAdipogenicInduction_01hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 01hr00min, biol_rep1_CNhs13431_13241-142B1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep3_CNhs13430_tpm_rev MscAdipogenicInduction_00hr45minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep3_CNhs13430_13240-142A9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep3_CNhs13430_tpm_fwd MscAdipogenicInduction_00hr45minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep3_CNhs13430_13240-142A9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep2_CNhs13429_tpm_rev MscAdipogenicInduction_00hr45minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep2_CNhs13429_13239-142A8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep2_CNhs13429_tpm_fwd MscAdipogenicInduction_00hr45minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep2_CNhs13429_13239-142A8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep1_CNhs13428_tpm_rev MscAdipogenicInduction_00hr45minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep1_CNhs13428_13238-142A7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr45minBiolRep1_CNhs13428_tpm_fwd MscAdipogenicInduction_00hr45minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr45min, biol_rep1_CNhs13428_13238-142A7_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep2_CNhs13426_tpm_rev MscAdipogenicInduction_00hr30minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep2_CNhs13426_13236-142A5_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep2_CNhs13426_tpm_fwd MscAdipogenicInduction_00hr30minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep2_CNhs13426_13236-142A5_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep1_CNhs13425_tpm_rev MscAdipogenicInduction_00hr30minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep1_CNhs13425_13235-142A4_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr30minBiolRep1_CNhs13425_tpm_fwd MscAdipogenicInduction_00hr30minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr30min, biol_rep1_CNhs13425_13235-142A4_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep3_CNhs13424_tpm_rev MscAdipogenicInduction_00hr15minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep3_CNhs13424_13234-142A3_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep3_CNhs13424_tpm_fwd MscAdipogenicInduction_00hr15minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep3_CNhs13424_13234-142A3_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep2_CNhs13423_tpm_rev MscAdipogenicInduction_00hr15minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep2_CNhs13423_13233-142A2_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep2_CNhs13423_tpm_fwd MscAdipogenicInduction_00hr15minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep2_CNhs13423_13233-142A2_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep1_CNhs13422_tpm_rev MscAdipogenicInduction_00hr15minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep1_CNhs13422_13232-142A1_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr15minBiolRep1_CNhs13422_tpm_fwd MscAdipogenicInduction_00hr15minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr15min, biol_rep1_CNhs13422_13232-142A1_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep3_CNhs13421_tpm_rev MscAdipogenicInduction_00hr00minBr3- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep3_CNhs13421_13231-141I9_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep3_CNhs13421_tpm_fwd MscAdipogenicInduction_00hr00minBr3+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep3_CNhs13421_13231-141I9_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep2_CNhs13420_tpm_rev MscAdipogenicInduction_00hr00minBr2- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep2_CNhs13420_13230-141I8_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep2_CNhs13420_tpm_fwd MscAdipogenicInduction_00hr00minBr2+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep2_CNhs13420_13230-141I8_forward Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep1_CNhs13337_tpm_rev MscAdipogenicInduction_00hr00minBr1- mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep1_CNhs13337_13229-141I7_reverse Regulation 
MesenchymalStemCellsAdiposeDerivedAdipogenicInduction00hr00minBiolRep1_CNhs13337_tpm_fwd MscAdipogenicInduction_00hr00minBr1+ mesenchymal stem cells (adipose derived), adipogenic induction, 00hr00min, biol_rep1_CNhs13337_13229-141I7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep3_CNhs12768_tpm_rev Tc:Mcf7ToHrg_08hrBr3- MCF7 breast cancer cell line response to HRG, 08hr, biol_rep3_CNhs12768_13194-141E8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep3_CNhs12768_tpm_fwd Tc:Mcf7ToHrg_08hrBr3+ MCF7 breast cancer cell line response to HRG, 08hr, biol_rep3_CNhs12768_13194-141E8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep2_CNhs12667_tpm_rev Tc:Mcf7ToHrg_08hrBr2- MCF7 breast cancer cell line response to HRG, 08hr, biol_rep2_CNhs12667_13128-140G5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep2_CNhs12667_tpm_fwd Tc:Mcf7ToHrg_08hrBr2+ MCF7 breast cancer cell line response to HRG, 08hr, biol_rep2_CNhs12667_13128-140G5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep1_CNhs12740_tpm_rev Tc:Mcf7ToHrg_08hrBr1- MCF7 breast cancer cell line response to HRG, 08hr, biol_rep1_CNhs12740_13062-139I2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG08hrBiolRep1_CNhs12740_tpm_fwd Tc:Mcf7ToHrg_08hrBr1+ MCF7 breast cancer cell line response to HRG, 08hr, biol_rep1_CNhs12740_13062-139I2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep3_CNhs12767_tpm_rev Tc:Mcf7ToHrg_07hrBr3- MCF7 breast cancer cell line response to HRG, 07hr, biol_rep3_CNhs12767_13193-141E7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep3_CNhs12767_tpm_fwd Tc:Mcf7ToHrg_07hrBr3+ MCF7 breast cancer cell line response to HRG, 07hr, biol_rep3_CNhs12767_13193-141E7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep2_CNhs12666_tpm_rev Tc:Mcf7ToHrg_07hrBr2- MCF7 breast cancer cell line response to HRG, 07hr, biol_rep2_CNhs12666_13127-140G4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep2_CNhs12666_tpm_fwd Tc:Mcf7ToHrg_07hrBr2+ MCF7 breast cancer cell line response to HRG, 07hr, biol_rep2_CNhs12666_13127-140G4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep1_CNhs12448_tpm_rev Tc:Mcf7ToHrg_07hrBr1- MCF7 breast cancer cell line response to HRG, 07hr, biol_rep1_CNhs12448_13061-139I1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG07hrBiolRep1_CNhs12448_tpm_fwd Tc:Mcf7ToHrg_07hrBr1+ MCF7 breast cancer cell line response to HRG, 07hr, biol_rep1_CNhs12448_13061-139I1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep3_CNhs12766_tpm_rev Tc:Mcf7ToHrg_06hrBr3- MCF7 breast cancer cell line response to HRG, 06hr, biol_rep3_CNhs12766_13192-141E6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep3_CNhs12766_tpm_fwd Tc:Mcf7ToHrg_06hrBr3+ MCF7 breast cancer cell line response to HRG, 06hr, biol_rep3_CNhs12766_13192-141E6_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep2_CNhs12665_tpm_rev Tc:Mcf7ToHrg_06hrBr2- MCF7 breast cancer cell line response to HRG, 06hr, biol_rep2_CNhs12665_13126-140G3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep2_CNhs12665_tpm_fwd Tc:Mcf7ToHrg_06hrBr2+ MCF7 breast cancer cell line response to HRG, 06hr, biol_rep2_CNhs12665_13126-140G3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep1_CNhs12447_tpm_rev Tc:Mcf7ToHrg_06hrBr1- MCF7 breast cancer cell line response to HRG, 06hr, biol_rep1_CNhs12447_13060-139H9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG06hrBiolRep1_CNhs12447_tpm_fwd Tc:Mcf7ToHrg_06hrBr1+ MCF7 breast cancer cell line response to HRG, 06hr, biol_rep1_CNhs12447_13060-139H9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep3_CNhs12765_tpm_rev Tc:Mcf7ToHrg_05hrBr3- MCF7 breast cancer cell line response to HRG, 05hr, biol_rep3_CNhs12765_13191-141E5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep3_CNhs12765_tpm_fwd Tc:Mcf7ToHrg_05hrBr3+ MCF7 breast cancer cell line response to HRG, 05hr, biol_rep3_CNhs12765_13191-141E5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep2_CNhs12664_tpm_rev Tc:Mcf7ToHrg_05hrBr2- MCF7 breast cancer cell line response to HRG, 05hr, biol_rep2_CNhs12664_13125-140G2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep2_CNhs12664_tpm_fwd Tc:Mcf7ToHrg_05hrBr2+ MCF7 breast cancer cell line response to HRG, 05hr, biol_rep2_CNhs12664_13125-140G2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep1_CNhs12446_tpm_rev Tc:Mcf7ToHrg_05hrBr1- MCF7 breast cancer cell line response to HRG, 05hr, biol_rep1_CNhs12446_13059-139H8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG05hrBiolRep1_CNhs12446_tpm_fwd Tc:Mcf7ToHrg_05hrBr1+ MCF7 breast cancer cell line response to HRG, 05hr, biol_rep1_CNhs12446_13059-139H8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep3_CNhs12764_tpm_rev Tc:Mcf7ToHrg_04hrBr3- MCF7 breast cancer cell line response to HRG, 04hr, biol_rep3_CNhs12764_13190-141E4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep3_CNhs12764_tpm_fwd Tc:Mcf7ToHrg_04hrBr3+ MCF7 breast cancer cell line response to HRG, 04hr, biol_rep3_CNhs12764_13190-141E4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep2_CNhs12663_tpm_rev Tc:Mcf7ToHrg_04hrBr2- MCF7 breast cancer cell line response to HRG, 04hr, biol_rep2_CNhs12663_13124-140G1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep2_CNhs12663_tpm_fwd Tc:Mcf7ToHrg_04hrBr2+ MCF7 breast cancer cell line response to HRG, 04hr, biol_rep2_CNhs12663_13124-140G1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep1_CNhs12445_tpm_rev Tc:Mcf7ToHrg_04hrBr1- MCF7 breast cancer cell line response to HRG, 04hr, biol_rep1_CNhs12445_13058-139H7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG04hrBiolRep1_CNhs12445_tpm_fwd Tc:Mcf7ToHrg_04hrBr1+ MCF7 breast cancer cell line response to HRG, 04hr, biol_rep1_CNhs12445_13058-139H7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep3_CNhs12763_tpm_rev Tc:Mcf7ToHrg_03hr30minBr3- MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep3_CNhs12763_13189-141E3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep3_CNhs12763_tpm_fwd Tc:Mcf7ToHrg_03hr30minBr3+ MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep3_CNhs12763_13189-141E3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep2_CNhs12662_tpm_rev Tc:Mcf7ToHrg_03hr30minBr2- MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep2_CNhs12662_13123-140F9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep2_CNhs12662_tpm_fwd Tc:Mcf7ToHrg_03hr30minBr2+ MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep2_CNhs12662_13123-140F9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep1_CNhs12444_tpm_rev Tc:Mcf7ToHrg_03hr30minBr1- MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep1_CNhs12444_13057-139H6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr30minBiolRep1_CNhs12444_tpm_fwd Tc:Mcf7ToHrg_03hr30minBr1+ MCF7 breast cancer cell line response to HRG, 03hr30min, biol_rep1_CNhs12444_13057-139H6_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep3_CNhs12762_tpm_rev Tc:Mcf7ToHrg_03hr00minBr3- MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep3_CNhs12762_13188-141E2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep3_CNhs12762_tpm_fwd Tc:Mcf7ToHrg_03hr00minBr3+ MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep3_CNhs12762_13188-141E2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep2_CNhs12660_tpm_rev Tc:Mcf7ToHrg_03hr00minBr2- MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep2_CNhs12660_13122-140F8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep2_CNhs12660_tpm_fwd Tc:Mcf7ToHrg_03hr00minBr2+ MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep2_CNhs12660_13122-140F8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep1_CNhs12443_tpm_rev Tc:Mcf7ToHrg_03hr00minBr1- MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep1_CNhs12443_13056-139H5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG03hr00minBiolRep1_CNhs12443_tpm_fwd Tc:Mcf7ToHrg_03hr00minBr1+ MCF7 breast cancer cell line response to HRG, 03hr00min, biol_rep1_CNhs12443_13056-139H5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep3_CNhs12761_tpm_rev Tc:Mcf7ToHrg_02hr30minBr3- MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep3_CNhs12761_13187-141E1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep3_CNhs12761_tpm_fwd Tc:Mcf7ToHrg_02hr30minBr3+ MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep3_CNhs12761_13187-141E1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep2_CNhs12659_tpm_rev Tc:Mcf7ToHrg_02hr30minBr2- MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep2_CNhs12659_13121-140F7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep2_CNhs12659_tpm_fwd Tc:Mcf7ToHrg_02hr30minBr2+ MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep2_CNhs12659_13121-140F7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep1_CNhs12442_tpm_rev Tc:Mcf7ToHrg_02hr30minBr1- MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep1_CNhs12442_13055-139H4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr30minBiolRep1_CNhs12442_tpm_fwd Tc:Mcf7ToHrg_02hr30minBr1+ MCF7 breast cancer cell line response to HRG, 02hr30min, biol_rep1_CNhs12442_13055-139H4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep3_CNhs12760_tpm_rev Tc:Mcf7ToHrg_02hr00minBr3- MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep3_CNhs12760_13186-141D9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep3_CNhs12760_tpm_fwd Tc:Mcf7ToHrg_02hr00minBr3+ MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep3_CNhs12760_13186-141D9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep2_CNhs12658_tpm_rev Tc:Mcf7ToHrg_02hr00minBr2- MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep2_CNhs12658_13120-140F6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep2_CNhs12658_tpm_fwd Tc:Mcf7ToHrg_02hr00minBr2+ MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep2_CNhs12658_13120-140F6_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep1_CNhs12441_tpm_rev Tc:Mcf7ToHrg_02hr00minBr1- MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep1_CNhs12441_13054-139H3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG02hr00minBiolRep1_CNhs12441_tpm_fwd Tc:Mcf7ToHrg_02hr00minBr1+ MCF7 breast cancer cell line response to HRG, 02hr00min, biol_rep1_CNhs12441_13054-139H3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep3_CNhs12759_tpm_rev Tc:Mcf7ToHrg_01hr40minBr3- MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep3_CNhs12759_13185-141D8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep3_CNhs12759_tpm_fwd Tc:Mcf7ToHrg_01hr40minBr3+ MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep3_CNhs12759_13185-141D8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep2_CNhs12657_tpm_rev Tc:Mcf7ToHrg_01hr40minBr2- MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep2_CNhs12657_13119-140F5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep2_CNhs12657_tpm_fwd Tc:Mcf7ToHrg_01hr40minBr2+ MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep2_CNhs12657_13119-140F5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep1_CNhs12440_tpm_rev Tc:Mcf7ToHrg_01hr40minBr1- MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep1_CNhs12440_13053-139H2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr40minBiolRep1_CNhs12440_tpm_fwd Tc:Mcf7ToHrg_01hr40minBr1+ MCF7 breast cancer cell line response to HRG, 01hr40min, biol_rep1_CNhs12440_13053-139H2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep3_CNhs12758_tpm_rev Tc:Mcf7ToHrg_01hr20minBr3- MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep3_CNhs12758_13184-141D7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep3_CNhs12758_tpm_fwd Tc:Mcf7ToHrg_01hr20minBr3+ MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep3_CNhs12758_13184-141D7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep2_CNhs12656_tpm_rev Tc:Mcf7ToHrg_01hr20minBr2- MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep2_CNhs12656_13118-140F4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep2_CNhs12656_tpm_fwd Tc:Mcf7ToHrg_01hr20minBr2+ MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep2_CNhs12656_13118-140F4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep1_CNhs12439_tpm_rev Tc:Mcf7ToHrg_01hr20minBr1- MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep1_CNhs12439_13052-139H1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr20minBiolRep1_CNhs12439_tpm_fwd Tc:Mcf7ToHrg_01hr20minBr1+ MCF7 breast cancer cell line response to HRG, 01hr20min, biol_rep1_CNhs12439_13052-139H1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep3_CNhs12757_tpm_rev Tc:Mcf7ToHrg_01hr00minBr3- MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep3_CNhs12757_13183-141D6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep3_CNhs12757_tpm_fwd Tc:Mcf7ToHrg_01hr00minBr3+ MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep3_CNhs12757_13183-141D6_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep2_CNhs12655_tpm_rev Tc:Mcf7ToHrg_01hr00minBr2- MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep2_CNhs12655_13117-140F3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep2_CNhs12655_tpm_fwd Tc:Mcf7ToHrg_01hr00minBr2+ MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep2_CNhs12655_13117-140F3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep1_CNhs12438_tpm_rev Tc:Mcf7ToHrg_01hr00minBr1- MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep1_CNhs12438_13051-139G9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG01hr00minBiolRep1_CNhs12438_tpm_fwd Tc:Mcf7ToHrg_01hr00minBr1+ MCF7 breast cancer cell line response to HRG, 01hr00min, biol_rep1_CNhs12438_13051-139G9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep3_CNhs12756_tpm_rev Tc:Mcf7ToHrg_00hr45minBr3- MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep3_CNhs12756_13182-141D5_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep3_CNhs12756_tpm_fwd Tc:Mcf7ToHrg_00hr45minBr3+ MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep3_CNhs12756_13182-141D5_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep2_CNhs12654_tpm_rev Tc:Mcf7ToHrg_00hr45minBr2- MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep2_CNhs12654_13116-140F2_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep2_CNhs12654_tpm_fwd Tc:Mcf7ToHrg_00hr45minBr2+ MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep2_CNhs12654_13116-140F2_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep1_CNhs12437_tpm_rev Tc:Mcf7ToHrg_00hr45minBr1- MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep1_CNhs12437_13050-139G8_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr45minBiolRep1_CNhs12437_tpm_fwd Tc:Mcf7ToHrg_00hr45minBr1+ MCF7 breast cancer cell line response to HRG, 00hr45min, biol_rep1_CNhs12437_13050-139G8_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep3_CNhs12755_tpm_rev Tc:Mcf7ToHrg_00hr30minBr3- MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep3_CNhs12755_13181-141D4_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep3_CNhs12755_tpm_fwd Tc:Mcf7ToHrg_00hr30minBr3+ MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep3_CNhs12755_13181-141D4_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep2_CNhs12653_tpm_rev Tc:Mcf7ToHrg_00hr30minBr2- MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep2_CNhs12653_13115-140F1_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep2_CNhs12653_tpm_fwd Tc:Mcf7ToHrg_00hr30minBr2+ MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep2_CNhs12653_13115-140F1_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep1_CNhs12436_tpm_rev Tc:Mcf7ToHrg_00hr30minBr1- MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep1_CNhs12436_13049-139G7_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr30minBiolRep1_CNhs12436_tpm_fwd Tc:Mcf7ToHrg_00hr30minBr1+ MCF7 breast cancer cell line response to HRG, 00hr30min, biol_rep1_CNhs12436_13049-139G7_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep3_CNhs12754_tpm_rev Tc:Mcf7ToHrg_00hr15minBr3- MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep3_CNhs12754_13180-141D3_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep3_CNhs12754_tpm_fwd Tc:Mcf7ToHrg_00hr15minBr3+ MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep3_CNhs12754_13180-141D3_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep2_CNhs12652_tpm_rev Tc:Mcf7ToHrg_00hr15minBr2- MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep2_CNhs12652_13114-140E9_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep2_CNhs12652_tpm_fwd Tc:Mcf7ToHrg_00hr15minBr2+ MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep2_CNhs12652_13114-140E9_forward Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep1_CNhs12435_tpm_rev Tc:Mcf7ToHrg_00hr15minBr1- MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep1_CNhs12435_13048-139G6_reverse Regulation 
MCF7BreastCancerCellLineResponseToHRG00hr15minBiolRep1_CNhs12435_tpm_fwd Tc:Mcf7ToHrg_00hr15minBr1+ MCF7 breast cancer cell line response to HRG, 00hr15min, biol_rep1_CNhs12435_13048-139G6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep3_CNhs12753_tpm_rev Mcf7ToEgf1_08hrBr3- MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep3_CNhs12753_13178-141D1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep3_CNhs12753_tpm_fwd Mcf7ToEgf1_08hrBr3+ MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep3_CNhs12753_13178-141D1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep2_CNhs12491_tpm_rev Mcf7ToEgf1_08hrBr2- MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep2_CNhs12491_13112-140E7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep2_CNhs12491_tpm_fwd Mcf7ToEgf1_08hrBr2+ MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep2_CNhs12491_13112-140E7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep3_CNhs12752_tpm_rev Mcf7ToEgf1_07hrBr3- MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep3_CNhs12752_13177-141C9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep3_CNhs12752_tpm_fwd Mcf7ToEgf1_07hrBr3+ MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep3_CNhs12752_13177-141C9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep2_CNhs12490_tpm_rev Mcf7ToEgf1_07hrBr2- MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep2_CNhs12490_13111-140E6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep2_CNhs12490_tpm_fwd Mcf7ToEgf1_07hrBr2+ MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep2_CNhs12490_13111-140E6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep1_CNhs12434_tpm_rev Mcf7ToEgf1_07hrBr1- MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep1_CNhs12434_13045-139G3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF107hrBiolRep1_CNhs12434_tpm_fwd Mcf7ToEgf1_07hrBr1+ MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep1_CNhs12434_13045-139G3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep3_CNhs12751_tpm_rev Mcf7ToEgf1_06hrBr3- MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep3_CNhs12751_13176-141C8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep3_CNhs12751_tpm_fwd Mcf7ToEgf1_06hrBr3+ MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep3_CNhs12751_13176-141C8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep2_CNhs12489_tpm_rev Mcf7ToEgf1_06hrBr2- MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep2_CNhs12489_13110-140E5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep2_CNhs12489_tpm_fwd Mcf7ToEgf1_06hrBr2+ MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep2_CNhs12489_13110-140E5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep1_CNhs12432_tpm_rev Mcf7ToEgf1_06hrBr1- MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep1_CNhs12432_13044-139G2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF106hrBiolRep1_CNhs12432_tpm_fwd Mcf7ToEgf1_06hrBr1+ MCF7 breast cancer cell line response to EGF1, 06hr, biol_rep1_CNhs12432_13044-139G2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep3_CNhs12750_tpm_rev Mcf7ToEgf1_05hrBr3- MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep3_CNhs12750_13175-141C7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep3_CNhs12750_tpm_fwd Mcf7ToEgf1_05hrBr3+ MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep3_CNhs12750_13175-141C7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep2_CNhs12488_tpm_rev Mcf7ToEgf1_05hrBr2- MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep2_CNhs12488_13109-140E4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep2_CNhs12488_tpm_fwd Mcf7ToEgf1_05hrBr2+ MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep2_CNhs12488_13109-140E4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep1_CNhs12431_tpm_rev Mcf7ToEgf1_05hrBr1- MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep1_CNhs12431_13043-139G1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF105hrBiolRep1_CNhs12431_tpm_fwd Mcf7ToEgf1_05hrBr1+ MCF7 breast cancer cell line response to EGF1, 05hr, biol_rep1_CNhs12431_13043-139G1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep3_CNhs12749_tpm_rev Mcf7ToEgf1_04hrBr3- MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep3_CNhs12749_13174-141C6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep3_CNhs12749_tpm_fwd Mcf7ToEgf1_04hrBr3+ MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep3_CNhs12749_13174-141C6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep2_CNhs12487_tpm_rev Mcf7ToEgf1_04hrBr2- MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep2_CNhs12487_13108-140E3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep2_CNhs12487_tpm_fwd Mcf7ToEgf1_04hrBr2+ MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep2_CNhs12487_13108-140E3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep1_CNhs12430_tpm_rev Mcf7ToEgf1_04hrBr1- MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep1_CNhs12430_13042-139F9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF104hrBiolRep1_CNhs12430_tpm_fwd Mcf7ToEgf1_04hrBr1+ MCF7 breast cancer cell line response to EGF1, 04hr, biol_rep1_CNhs12430_13042-139F9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep3_CNhs12748_tpm_rev Mcf7ToEgf1_03hr30minBr3- MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep3_CNhs12748_13173-141C5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep3_CNhs12748_tpm_fwd Mcf7ToEgf1_03hr30minBr3+ MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep3_CNhs12748_13173-141C5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep2_CNhs12486_tpm_rev Mcf7ToEgf1_03hr30minBr2- MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep2_CNhs12486_13107-140E2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep2_CNhs12486_tpm_fwd Mcf7ToEgf1_03hr30minBr2+ MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep2_CNhs12486_13107-140E2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep1_CNhs12429_tpm_rev Mcf7ToEgf1_03hr30minBr1- MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep1_CNhs12429_13041-139F8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr30minBiolRep1_CNhs12429_tpm_fwd Mcf7ToEgf1_03hr30minBr1+ MCF7 breast cancer cell line response to EGF1, 03hr30min, biol_rep1_CNhs12429_13041-139F8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep3_CNhs12747_tpm_rev Mcf7ToEgf1_03hr00minBr3- MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep3_CNhs12747_13172-141C4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep3_CNhs12747_tpm_fwd Mcf7ToEgf1_03hr00minBr3+ MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep3_CNhs12747_13172-141C4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep2_CNhs12485_tpm_rev Mcf7ToEgf1_03hr00minBr2- MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep2_CNhs12485_13106-140E1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep2_CNhs12485_tpm_fwd Mcf7ToEgf1_03hr00minBr2+ MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep2_CNhs12485_13106-140E1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep1_CNhs12428_tpm_rev Mcf7ToEgf1_03hr00minBr1- MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep1_CNhs12428_13040-139F7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF103hr00minBiolRep1_CNhs12428_tpm_fwd Mcf7ToEgf1_03hr00minBr1+ MCF7 breast cancer cell line response to EGF1, 03hr00min, biol_rep1_CNhs12428_13040-139F7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep3_CNhs12746_tpm_rev Mcf7ToEgf1_02hr30minBr3- MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep3_CNhs12746_13171-141C3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep3_CNhs12746_tpm_fwd Mcf7ToEgf1_02hr30minBr3+ MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep3_CNhs12746_13171-141C3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep2_CNhs12484_tpm_rev Mcf7ToEgf1_02hr30minBr2- MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep2_CNhs12484_13105-140D9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep2_CNhs12484_tpm_fwd Mcf7ToEgf1_02hr30minBr2+ MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep2_CNhs12484_13105-140D9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep1_CNhs12427_tpm_rev Mcf7ToEgf1_02hr30minBr1- MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep1_CNhs12427_13039-139F6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr30minBiolRep1_CNhs12427_tpm_fwd Mcf7ToEgf1_02hr30minBr1+ MCF7 breast cancer cell line response to EGF1, 02hr30min, biol_rep1_CNhs12427_13039-139F6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep3_CNhs12744_tpm_rev Mcf7ToEgf1_02hr00minBr3- MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep3_CNhs12744_13170-141C2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep3_CNhs12744_tpm_fwd Mcf7ToEgf1_02hr00minBr3+ MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep3_CNhs12744_13170-141C2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep2_CNhs12483_tpm_rev Mcf7ToEgf1_02hr00minBr2- MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep2_CNhs12483_13104-140D8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep2_CNhs12483_tpm_fwd Mcf7ToEgf1_02hr00minBr2+ MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep2_CNhs12483_13104-140D8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep1_CNhs12426_tpm_rev Mcf7ToEgf1_02hr00minBr1- MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep1_CNhs12426_13038-139F5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF102hr00minBiolRep1_CNhs12426_tpm_fwd Mcf7ToEgf1_02hr00minBr1+ MCF7 breast cancer cell line response to EGF1, 02hr00min, biol_rep1_CNhs12426_13038-139F5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep3_CNhs12743_tpm_rev Mcf7ToEgf1_01hr40minBr3- MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep3_CNhs12743_13169-141C1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep3_CNhs12743_tpm_fwd Mcf7ToEgf1_01hr40minBr3+ MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep3_CNhs12743_13169-141C1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep2_CNhs12482_tpm_rev Mcf7ToEgf1_01hr40minBr2- MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep2_CNhs12482_13103-140D7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep2_CNhs12482_tpm_fwd Mcf7ToEgf1_01hr40minBr2+ MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep2_CNhs12482_13103-140D7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep1_CNhs12425_tpm_rev Mcf7ToEgf1_01hr40minBr1- MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep1_CNhs12425_13037-139F4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr40minBiolRep1_CNhs12425_tpm_fwd Mcf7ToEgf1_01hr40minBr1+ MCF7 breast cancer cell line response to EGF1, 01hr40min, biol_rep1_CNhs12425_13037-139F4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep3_CNhs12742_tpm_rev Mcf7ToEgf1_01hr20minBr3- MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep3_CNhs12742_13168-141B9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep3_CNhs12742_tpm_fwd Mcf7ToEgf1_01hr20minBr3+ MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep3_CNhs12742_13168-141B9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep2_CNhs12480_tpm_rev Mcf7ToEgf1_01hr20minBr2- MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep2_CNhs12480_13102-140D6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep2_CNhs12480_tpm_fwd Mcf7ToEgf1_01hr20minBr2+ MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep2_CNhs12480_13102-140D6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep1_CNhs12424_tpm_rev Mcf7ToEgf1_01hr20minBr1- MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep1_CNhs12424_13036-139F3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr20minBiolRep1_CNhs12424_tpm_fwd Mcf7ToEgf1_01hr20minBr1+ MCF7 breast cancer cell line response to EGF1, 01hr20min, biol_rep1_CNhs12424_13036-139F3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep3_CNhs12705_tpm_rev Mcf7ToEgf1_01hr00minBr3- MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep3_CNhs12705_13167-141B8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep3_CNhs12705_tpm_fwd Mcf7ToEgf1_01hr00minBr3+ MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep3_CNhs12705_13167-141B8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep2_CNhs12479_tpm_rev Mcf7ToEgf1_01hr00minBr2- MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep2_CNhs12479_13101-140D5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep2_CNhs12479_tpm_fwd Mcf7ToEgf1_01hr00minBr2+ MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep2_CNhs12479_13101-140D5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep1_CNhs12423_tpm_rev Mcf7ToEgf1_01hr00minBr1- MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep1_CNhs12423_13035-139F2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF101hr00minBiolRep1_CNhs12423_tpm_fwd Mcf7ToEgf1_01hr00minBr1+ MCF7 breast cancer cell line response to EGF1, 01hr00min, biol_rep1_CNhs12423_13035-139F2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep3_CNhs12739_tpm_rev Mcf7ToEgf1_00hr45minBr3- MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep3_CNhs12739_13166-141B7_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep3_CNhs12739_tpm_fwd Mcf7ToEgf1_00hr45minBr3+ MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep3_CNhs12739_13166-141B7_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep2_CNhs12478_tpm_rev Mcf7ToEgf1_00hr45minBr2- MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep2_CNhs12478_13100-140D4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep2_CNhs12478_tpm_fwd Mcf7ToEgf1_00hr45minBr2+ MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep2_CNhs12478_13100-140D4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep1_CNhs12422_tpm_rev Mcf7ToEgf1_00hr45minBr1- MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep1_CNhs12422_13034-139F1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr45minBiolRep1_CNhs12422_tpm_fwd Mcf7ToEgf1_00hr45minBr1+ MCF7 breast cancer cell line response to EGF1, 00hr45min, biol_rep1_CNhs12422_13034-139F1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep3_CNhs12738_tpm_rev Mcf7ToEgf1_00hr30minBr3- MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep3_CNhs12738_13165-141B6_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep3_CNhs12738_tpm_fwd Mcf7ToEgf1_00hr30minBr3+ MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep3_CNhs12738_13165-141B6_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep2_CNhs12477_tpm_rev Mcf7ToEgf1_00hr30minBr2- MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep2_CNhs12477_13099-140D3_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep2_CNhs12477_tpm_fwd Mcf7ToEgf1_00hr30minBr2+ MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep2_CNhs12477_13099-140D3_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep1_CNhs12421_tpm_rev Mcf7ToEgf1_00hr30minBr1- MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep1_CNhs12421_13033-139E9_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr30minBiolRep1_CNhs12421_tpm_fwd Mcf7ToEgf1_00hr30minBr1+ MCF7 breast cancer cell line response to EGF1, 00hr30min, biol_rep1_CNhs12421_13033-139E9_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep3_CNhs12704_tpm_rev Mcf7ToEgf1_00hr15minBr3- MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep3_CNhs12704_13164-141B5_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep3_CNhs12704_tpm_fwd Mcf7ToEgf1_00hr15minBr3+ MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep3_CNhs12704_13164-141B5_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep2_CNhs12476_tpm_rev Mcf7ToEgf1_00hr15minBr2- MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep2_CNhs12476_13098-140D2_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep2_CNhs12476_tpm_fwd Mcf7ToEgf1_00hr15minBr2+ MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep2_CNhs12476_13098-140D2_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep1_CNhs12420_tpm_rev Mcf7ToEgf1_00hr15minBr1- MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep1_CNhs12420_13032-139E8_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr15minBiolRep1_CNhs12420_tpm_fwd Mcf7ToEgf1_00hr15minBr1+ MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep1_CNhs12420_13032-139E8_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep3_CNhs12703_tpm_rev Mcf7ToEgf1_00hr00minBr3- MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep3_CNhs12703_13163-141B4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep3_CNhs12703_tpm_fwd Mcf7ToEgf1_00hr00minBr3+ MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep3_CNhs12703_13163-141B4_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep2_CNhs12475_tpm_rev Mcf7ToEgf1_00hr00minBr2- MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep2_CNhs12475_13097-140D1_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF100hr00minBiolRep2_CNhs12475_tpm_fwd Mcf7ToEgf1_00hr00minBr2+ MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep2_CNhs12475_13097-140D1_forward Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep1_CNhs12565_tpm_rev Mcf7ToEgf1_08hrBr1- MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep1_CNhs12565_13046-139G4_reverse Regulation 
MCF7BreastCancerCellLineResponseToEGF108hrBiolRep1_CNhs12565_tpm_fwd Mcf7ToEgf1_08hrBr1+ MCF7 breast cancer cell line response to EGF1, 08hr, biol_rep1_CNhs12565_13046-139G4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep3MMXXII16_CNhs13291_tpm_rev LymphaticEndothelialCellsToVegfc_08hrBr3- Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep3 (MM XXII - 16)_CNhs13291_12519-133B8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep3MMXXII16_CNhs13291_tpm_fwd LymphaticEndothelialCellsToVegfc_08hrBr3+ Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep3 (MM XXII - 16)_CNhs13291_12519-133B8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep2MMXIV16_CNhs13173_tpm_rev LymphaticEndothelialCellsToVegfc_08hrBr2- Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep2 (MM XIV - 16)_CNhs13173_12397-131G3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep2MMXIV16_CNhs13173_tpm_fwd LymphaticEndothelialCellsToVegfc_08hrBr2+ Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep2 (MM XIV - 16)_CNhs13173_12397-131G3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep1MMXIX16_CNhs11937_tpm_rev LymphaticEndothelialCellsToVegfc_08hrBr1- Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep1 (MM XIX - 16)_CNhs11937_12275-130B7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC08hrBiolRep1MMXIX16_CNhs11937_tpm_fwd LymphaticEndothelialCellsToVegfc_08hrBr1+ Lymphatic Endothelial cells response to VEGFC, 08hr, biol_rep1 (MM XIX - 16)_CNhs11937_12275-130B7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep3MMXXII15_CNhs13290_tpm_rev LymphaticEndothelialCellsToVegfc_07hrBr3- Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep3 (MM XXII - 15)_CNhs13290_12518-133B7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep3MMXXII15_CNhs13290_tpm_fwd LymphaticEndothelialCellsToVegfc_07hrBr3+ Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep3 (MM XXII - 15)_CNhs13290_12518-133B7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep2MMXIV15_CNhs13172_tpm_rev LymphaticEndothelialCellsToVegfc_07hrBr2- Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep2 (MM XIV - 15)_CNhs13172_12396-131G2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep2MMXIV15_CNhs13172_tpm_fwd LymphaticEndothelialCellsToVegfc_07hrBr2+ Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep2 (MM XIV - 15)_CNhs13172_12396-131G2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep1MMXIX15_CNhs13113_tpm_rev LymphaticEndothelialCellsToVegfc_07hrBr1- Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep1 (MM XIX - 15)_CNhs13113_12274-130B6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC07hrBiolRep1MMXIX15_CNhs13113_tpm_fwd LymphaticEndothelialCellsToVegfc_07hrBr1+ Lymphatic Endothelial cells response to VEGFC, 07hr, biol_rep1 (MM XIX - 15)_CNhs13113_12274-130B6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep3MMXXII14_CNhs13289_tpm_rev LymphaticEndothelialCellsToVegfc_06hrBr3- Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep3 (MM XXII - 14)_CNhs13289_12517-133B6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep3MMXXII14_CNhs13289_tpm_fwd LymphaticEndothelialCellsToVegfc_06hrBr3+ Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep3 (MM XXII - 14)_CNhs13289_12517-133B6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep2MMXIV14_CNhs13171_tpm_rev LymphaticEndothelialCellsToVegfc_06hrBr2- Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep2 (MM XIV - 14)_CNhs13171_12395-131G1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep2MMXIV14_CNhs13171_tpm_fwd LymphaticEndothelialCellsToVegfc_06hrBr2+ Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep2 (MM XIV - 14)_CNhs13171_12395-131G1_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep1MMXIX14_CNhs13112_tpm_rev LymphaticEndothelialCellsToVegfc_06hrBr1- Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep1 (MM XIX - 14)_CNhs13112_12273-130B5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC06hrBiolRep1MMXIX14_CNhs13112_tpm_fwd LymphaticEndothelialCellsToVegfc_06hrBr1+ Lymphatic Endothelial cells response to VEGFC, 06hr, biol_rep1 (MM XIX - 14)_CNhs13112_12273-130B5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep3MMXXII13_CNhs13288_tpm_rev LymphaticEndothelialCellsToVegfc_05hrBr3- Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep3 (MM XXII - 13)_CNhs13288_12516-133B5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep3MMXXII13_CNhs13288_tpm_fwd LymphaticEndothelialCellsToVegfc_05hrBr3+ Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep3 (MM XXII - 13)_CNhs13288_12516-133B5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep2MMXIV13_CNhs13170_tpm_rev LymphaticEndothelialCellsToVegfc_05hrBr2- Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep2 (MM XIV - 13)_CNhs13170_12394-131F9_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep2MMXIV13_CNhs13170_tpm_fwd LymphaticEndothelialCellsToVegfc_05hrBr2+ Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep2 (MM XIV - 13)_CNhs13170_12394-131F9_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep1MMXIX13_CNhs13111_tpm_rev LymphaticEndothelialCellsToVegfc_05hrBr1- Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep1 (MM XIX - 13)_CNhs13111_12272-130B4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC05hrBiolRep1MMXIX13_CNhs13111_tpm_fwd LymphaticEndothelialCellsToVegfc_05hrBr1+ Lymphatic Endothelial cells response to VEGFC, 05hr, biol_rep1 (MM XIX - 13)_CNhs13111_12272-130B4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep3MMXXII12_CNhs13287_tpm_rev LymphaticEndothelialCellsToVegfc_04hrBr3- Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep3 (MM XXII - 12)_CNhs13287_12515-133B4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep3MMXXII12_CNhs13287_tpm_fwd LymphaticEndothelialCellsToVegfc_04hrBr3+ Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep3 (MM XXII - 12)_CNhs13287_12515-133B4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep2MMXIV12_CNhs13169_tpm_rev LymphaticEndothelialCellsToVegfc_04hrBr2- Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep2 (MM XIV - 12)_CNhs13169_12393-131F8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep2MMXIV12_CNhs13169_tpm_fwd LymphaticEndothelialCellsToVegfc_04hrBr2+ Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep2 (MM XIV - 12)_CNhs13169_12393-131F8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep1MMXIX12_CNhs13110_tpm_rev LymphaticEndothelialCellsToVegfc_04hrBr1- Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep1 (MM XIX - 12)_CNhs13110_12271-130B3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC04hrBiolRep1MMXIX12_CNhs13110_tpm_fwd LymphaticEndothelialCellsToVegfc_04hrBr1+ Lymphatic Endothelial cells response to VEGFC, 04hr, biol_rep1 (MM XIX - 12)_CNhs13110_12271-130B3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep3MMXXII11_CNhs13286_tpm_rev LymphaticEndothelialCellsToVegfc_03hr30minBr3- Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep3 (MM XXII - 11)_CNhs13286_12514-133B3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep3MMXXII11_CNhs13286_tpm_fwd LymphaticEndothelialCellsToVegfc_03hr30minBr3+ Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep3 (MM XXII - 11)_CNhs13286_12514-133B3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep2MMXIV11_CNhs13168_tpm_rev LymphaticEndothelialCellsToVegfc_03hr30minBr2- Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep2 (MM XIV - 11)_CNhs13168_12392-131F7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep2MMXIV11_CNhs13168_tpm_fwd LymphaticEndothelialCellsToVegfc_03hr30minBr2+ Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep2 (MM XIV - 11)_CNhs13168_12392-131F7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep1MMXIX11_CNhs13109_tpm_rev LymphaticEndothelialCellsToVegfc_03hr30minBr1- Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep1 (MM XIX - 11)_CNhs13109_12270-130B2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr30minBiolRep1MMXIX11_CNhs13109_tpm_fwd LymphaticEndothelialCellsToVegfc_03hr30minBr1+ Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep1 (MM XIX - 11)_CNhs13109_12270-130B2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep3MMXXII10_CNhs13285_tpm_rev LymphaticEndothelialCellsToVegfc_03hr00minBr3- Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep3 (MM XXII - 10)_CNhs13285_12513-133B2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep3MMXXII10_CNhs13285_tpm_fwd LymphaticEndothelialCellsToVegfc_03hr00minBr3+ Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep3 (MM XXII - 10)_CNhs13285_12513-133B2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep2MMXIV10_CNhs13166_tpm_rev LymphaticEndothelialCellsToVegfc_03hr00minBr2- Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep2 (MM XIV - 10)_CNhs13166_12391-131F6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep2MMXIV10_CNhs13166_tpm_fwd LymphaticEndothelialCellsToVegfc_03hr00minBr2+ Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep2 (MM XIV - 10)_CNhs13166_12391-131F6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep1MMXIX10_CNhs13108_tpm_rev LymphaticEndothelialCellsToVegfc_03hr00minBr1- Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep1 (MM XIX - 10)_CNhs13108_12269-130B1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC03hr00minBiolRep1MMXIX10_CNhs13108_tpm_fwd LymphaticEndothelialCellsToVegfc_03hr00minBr1+ Lymphatic Endothelial cells response to VEGFC, 03hr00min, biol_rep1 (MM XIX - 10)_CNhs13108_12269-130B1_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep3MMXXII9_CNhs13284_tpm_rev LymphaticEndothelialCellsToVegfc_02hr30minBr3- Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep3 (MM XXII - 9)_CNhs13284_12512-133B1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep3MMXXII9_CNhs13284_tpm_fwd LymphaticEndothelialCellsToVegfc_02hr30minBr3+ Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep3 (MM XXII - 9)_CNhs13284_12512-133B1_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep2MMXIV9_CNhs13165_tpm_rev LymphaticEndothelialCellsToVegfc_02hr30minBr2- Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep2 (MM XIV - 9)_CNhs13165_12390-131F5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep2MMXIV9_CNhs13165_tpm_fwd LymphaticEndothelialCellsToVegfc_02hr30minBr2+ Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep2 (MM XIV - 9)_CNhs13165_12390-131F5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep1MMXIX9_CNhs13107_tpm_rev LymphaticEndothelialCellsToVegfc_02hr30minBr1- Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep1 (MM XIX - 9)_CNhs13107_12268-130A9_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr30minBiolRep1MMXIX9_CNhs13107_tpm_fwd LymphaticEndothelialCellsToVegfc_02hr30minBr1+ Lymphatic Endothelial cells response to VEGFC, 02hr30min, biol_rep1 (MM XIX - 9)_CNhs13107_12268-130A9_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep3MMXXII8_CNhs13283_tpm_rev LymphaticEndothelialCellsToVegfc_02hr00minBr3- Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep3 (MM XXII - 8)_CNhs13283_12511-133A9_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep3MMXXII8_CNhs13283_tpm_fwd LymphaticEndothelialCellsToVegfc_02hr00minBr3+ Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep3 (MM XXII - 8)_CNhs13283_12511-133A9_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep2MMXIV8_CNhs13164_tpm_rev LymphaticEndothelialCellsToVegfc_02hr00minBr2- Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep2 (MM XIV - 8)_CNhs13164_12389-131F4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep2MMXIV8_CNhs13164_tpm_fwd LymphaticEndothelialCellsToVegfc_02hr00minBr2+ Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep2 (MM XIV - 8)_CNhs13164_12389-131F4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep1MMXIX8_CNhs13106_tpm_rev LymphaticEndothelialCellsToVegfc_02hr00minBr1- Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep1 (MM XIX - 8)_CNhs13106_12267-130A8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC02hr00minBiolRep1MMXIX8_CNhs13106_tpm_fwd LymphaticEndothelialCellsToVegfc_02hr00minBr1+ Lymphatic Endothelial cells response to VEGFC, 02hr00min, biol_rep1 (MM XIX - 8)_CNhs13106_12267-130A8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep3MMXXII7_CNhs13282_tpm_rev LymphaticEndothelialCellsToVegfc_01hr40minBr3- Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep3 (MM XXII - 7)_CNhs13282_12510-133A8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep3MMXXII7_CNhs13282_tpm_fwd LymphaticEndothelialCellsToVegfc_01hr40minBr3+ Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep3 (MM XXII - 7)_CNhs13282_12510-133A8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep2MMXIV7_CNhs13163_tpm_rev LymphaticEndothelialCellsToVegfc_01hr40minBr2- Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep2 (MM XIV - 7)_CNhs13163_12388-131F3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep2MMXIV7_CNhs13163_tpm_fwd LymphaticEndothelialCellsToVegfc_01hr40minBr2+ Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep2 (MM XIV - 7)_CNhs13163_12388-131F3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep1MMXIX7_CNhs13105_tpm_rev LymphaticEndothelialCellsToVegfc_01hr40minBr1- Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep1 (MM XIX - 7)_CNhs13105_12266-130A7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr40minBiolRep1MMXIX7_CNhs13105_tpm_fwd LymphaticEndothelialCellsToVegfc_01hr40minBr1+ Lymphatic Endothelial cells response to VEGFC, 01hr40min, biol_rep1 (MM XIX - 7)_CNhs13105_12266-130A7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep3MMXXII6_CNhs13281_tpm_rev LymphaticEndothelialCellsToVegfc_01hr20minBr3- Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep3 (MM XXII - 6)_CNhs13281_12509-133A7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep3MMXXII6_CNhs13281_tpm_fwd LymphaticEndothelialCellsToVegfc_01hr20minBr3+ Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep3 (MM XXII - 6)_CNhs13281_12509-133A7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep2MMXIV6_CNhs13162_tpm_rev LymphaticEndothelialCellsToVegfc_01hr20minBr2- Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep2 (MM XIV - 6)_CNhs13162_12387-131F2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep2MMXIV6_CNhs13162_tpm_fwd LymphaticEndothelialCellsToVegfc_01hr20minBr2+ Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep2 (MM XIV - 6)_CNhs13162_12387-131F2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep1MMXIX6_CNhs13104_tpm_rev LymphaticEndothelialCellsToVegfc_01hr20minBr1- Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep1 (MM XIX - 6)_CNhs13104_12265-130A6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr20minBiolRep1MMXIX6_CNhs13104_tpm_fwd LymphaticEndothelialCellsToVegfc_01hr20minBr1+ Lymphatic Endothelial cells response to VEGFC, 01hr20min, biol_rep1 (MM XIX - 6)_CNhs13104_12265-130A6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep3MMXXII5_CNhs13280_tpm_rev LymphaticEndothelialCellsToVegfc_01hr00minBr3- Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep3 (MM XXII - 5)_CNhs13280_12508-133A6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep3MMXXII5_CNhs13280_tpm_fwd LymphaticEndothelialCellsToVegfc_01hr00minBr3+ Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep3 (MM XXII - 5)_CNhs13280_12508-133A6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep2MMXIV5_CNhs13161_tpm_rev LymphaticEndothelialCellsToVegfc_01hr00minBr2- Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep2 (MM XIV - 5)_CNhs13161_12386-131F1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep2MMXIV5_CNhs13161_tpm_fwd LymphaticEndothelialCellsToVegfc_01hr00minBr2+ Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep2 (MM XIV - 5)_CNhs13161_12386-131F1_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep1MMXIX5_CNhs13103_tpm_rev LymphaticEndothelialCellsToVegfc_01hr00minBr1- Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep1 (MM XIX - 5)_CNhs13103_12264-130A5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC01hr00minBiolRep1MMXIX5_CNhs13103_tpm_fwd LymphaticEndothelialCellsToVegfc_01hr00minBr1+ Lymphatic Endothelial cells response to VEGFC, 01hr00min, biol_rep1 (MM XIX - 5)_CNhs13103_12264-130A5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep3MMXXII4_CNhs13279_tpm_rev LymphaticEndothelialCellsToVegfc_00hr45minBr3- Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep3 (MM XXII - 4)_CNhs13279_12507-133A5_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep3MMXXII4_CNhs13279_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr45minBr3+ Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep3 (MM XXII - 4)_CNhs13279_12507-133A5_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep2MMXIV4_CNhs13160_tpm_rev LymphaticEndothelialCellsToVegfc_00hr45minBr2- Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep2 (MM XIV - 4)_CNhs13160_12385-131E9_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep2MMXIV4_CNhs13160_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr45minBr2+ Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep2 (MM XIV - 4)_CNhs13160_12385-131E9_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep1MMXIX4_CNhs13102_tpm_rev LymphaticEndothelialCellsToVegfc_00hr45minBr1- Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep1 (MM XIX - 4)_CNhs13102_12263-130A4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr45minBiolRep1MMXIX4_CNhs13102_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr45minBr1+ Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep1 (MM XIX - 4)_CNhs13102_12263-130A4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep3MMXXII3_CNhs13278_tpm_rev LymphaticEndothelialCellsToVegfc_00hr30minBr3- Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep3 (MM XXII - 3)_CNhs13278_12506-133A4_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep3MMXXII3_CNhs13278_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr30minBr3+ Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep3 (MM XXII - 3)_CNhs13278_12506-133A4_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep2MMXIV3_CNhs13159_tpm_rev LymphaticEndothelialCellsToVegfc_00hr30minBr2- Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep2 (MM XIV - 3)_CNhs13159_12384-131E8_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep2MMXIV3_CNhs13159_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr30minBr2+ Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep2 (MM XIV - 3)_CNhs13159_12384-131E8_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep1MMXIX3_CNhs13101_tpm_rev LymphaticEndothelialCellsToVegfc_00hr30minBr1- Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep1 (MM XIX - 3)_CNhs13101_12262-130A3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr30minBiolRep1MMXIX3_CNhs13101_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr30minBr1+ Lymphatic Endothelial cells response to VEGFC, 00hr30min, biol_rep1 (MM XIX - 3)_CNhs13101_12262-130A3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep3MMXXII2_CNhs13277_tpm_rev LymphaticEndothelialCellsToVegfc_00hr15minBr3- Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep3 (MM XXII - 2)_CNhs13277_12505-133A3_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep3MMXXII2_CNhs13277_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr15minBr3+ Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep3 (MM XXII - 2)_CNhs13277_12505-133A3_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep2MMXIV2_CNhs13158_tpm_rev LymphaticEndothelialCellsToVegfc_00hr15minBr2- Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep2 (MM XIV - 2)_CNhs13158_12383-131E7_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep2MMXIV2_CNhs13158_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr15minBr2+ Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep2 (MM XIV - 2)_CNhs13158_12383-131E7_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep1MMXIX2_CNhs13100_tpm_rev LymphaticEndothelialCellsToVegfc_00hr15minBr1- Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep1 (MM XIX - 2)_CNhs13100_12261-130A2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr15minBiolRep1MMXIX2_CNhs13100_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr15minBr1+ Lymphatic Endothelial cells response to VEGFC, 00hr15min, biol_rep1 (MM XIX - 2)_CNhs13100_12261-130A2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep3MMXXII1_CNhs13276_tpm_rev LymphaticEndothelialCellsToVegfc_00hr00minBr3- Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep3 (MM XXII - 1 )_CNhs13276_12504-133A2_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep3MMXXII1_CNhs13276_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr00minBr3+ Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep3 (MM XXII - 1 )_CNhs13276_12504-133A2_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep2MMXIV1_CNhs13157_tpm_rev LymphaticEndothelialCellsToVegfc_00hr00minBr2- Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep2 (MM XIV - 1)_CNhs13157_12382-131E6_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep2MMXIV1_CNhs13157_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr00minBr2+ Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep2 (MM XIV - 1)_CNhs13157_12382-131E6_forward Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep1MMXIX1_CNhs11936_tpm_rev LymphaticEndothelialCellsToVegfc_00hr00minBr1- Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep1 (MM XIX - 1)_CNhs11936_12260-130A1_reverse Regulation 
LymphaticEndothelialCellsResponseToVEGFC00hr00minBiolRep1MMXIX1_CNhs11936_tpm_fwd LymphaticEndothelialCellsToVegfc_00hr00minBr1+ Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep1 (MM XIX - 1)_CNhs11936_12260-130A1_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep3_CNhs14055_tpm_rev IpsToNeuronControlDnC11-CRL2429Day18R3- iPS differentiation to neuron, control donor C32-CRL1502, day18, rep3_CNhs14055_13444-144F6_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep3_CNhs14055_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day18R3+ iPS differentiation to neuron, control donor C32-CRL1502, day18, rep3_CNhs14055_13444-144F6_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep2_CNhs13842_tpm_rev IpsToNeuronControlDnC11-CRL2429Day18R2- iPS differentiation to neuron, control donor C32-CRL1502, day18, rep2_CNhs13842_13440-144F2_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep2_CNhs13842_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day18R2+ iPS differentiation to neuron, control donor C32-CRL1502, day18, rep2_CNhs13842_13440-144F2_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep1_CNhs13829_tpm_rev IpsToNeuronControlDnC11-CRL2429Day18R1- iPS differentiation to neuron, control donor C32-CRL1502, day18, rep1_CNhs13829_13436-144E7_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day18Rep1_CNhs13829_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day18R1+ iPS differentiation to neuron, control donor C32-CRL1502, day18, rep1_CNhs13829_13436-144E7_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep3_CNhs14054_tpm_rev IpsToNeuronControlDnC11-CRL2429Day12R3- iPS differentiation to neuron, control donor C32-CRL1502, day12, rep3_CNhs14054_13443-144F5_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep3_CNhs14054_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day12R3+ iPS differentiation to neuron, control donor C32-CRL1502, day12, rep3_CNhs14054_13443-144F5_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep2_CNhs13841_tpm_rev IpsToNeuronControlDnC11-CRL2429Day12R2- iPS differentiation to neuron, control donor C32-CRL1502, day12, rep2_CNhs13841_13439-144F1_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep2_CNhs13841_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day12R2+ iPS differentiation to neuron, control donor C32-CRL1502, day12, rep2_CNhs13841_13439-144F1_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep1_CNhs13828_tpm_rev IpsToNeuronControlDnC11-CRL2429Day12R1- iPS differentiation to neuron, control donor C32-CRL1502, day12, rep1_CNhs13828_13435-144E6_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day12Rep1_CNhs13828_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day12R1+ iPS differentiation to neuron, control donor C32-CRL1502, day12, rep1_CNhs13828_13435-144E6_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep3_CNhs14053_tpm_rev IpsToNeuronControlDnC11-CRL2429Day06R3- iPS differentiation to neuron, control donor C32-CRL1502, day06, rep3_CNhs14053_13442-144F4_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep3_CNhs14053_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day06R3+ iPS differentiation to neuron, control donor C32-CRL1502, day06, rep3_CNhs14053_13442-144F4_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep2_CNhs13840_tpm_rev IpsToNeuronControlDnC11-CRL2429Day06R2- iPS differentiation to neuron, control donor C32-CRL1502, day06, rep2_CNhs13840_13438-144E9_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep2_CNhs13840_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day06R2+ iPS differentiation to neuron, control donor C32-CRL1502, day06, rep2_CNhs13840_13438-144E9_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep1_CNhs13827_tpm_rev IpsToNeuronControlDnC11-CRL2429Day06R1- iPS differentiation to neuron, control donor C32-CRL1502, day06, rep1_CNhs13827_13434-144E5_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day06Rep1_CNhs13827_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day06R1+ iPS differentiation to neuron, control donor C32-CRL1502, day06, rep1_CNhs13827_13434-144E5_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep3_CNhs14052_tpm_rev IpsToNeuronControlDnC11-CRL2429Day00R3- iPS differentiation to neuron, control donor C32-CRL1502, day00, rep3_CNhs14052_13441-144F3_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep3_CNhs14052_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day00R3+ iPS differentiation to neuron, control donor C32-CRL1502, day00, rep3_CNhs14052_13441-144F3_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep2_CNhs13839_tpm_rev IpsToNeuronControlDnC11-CRL2429Day00R2- iPS differentiation to neuron, control donor C32-CRL1502, day00, rep2_CNhs13839_13437-144E8_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep2_CNhs13839_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day00R2+ iPS differentiation to neuron, control donor C32-CRL1502, day00, rep2_CNhs13839_13437-144E8_forward Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep1_CNhs13826_tpm_rev IpsToNeuronControlDnC11-CRL2429Day00R1- iPS differentiation to neuron, control donor C32-CRL1502, day00, rep1_CNhs13826_13433-144E4_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC32CRL1502Day00Rep1_CNhs13826_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day00R1+ iPS differentiation to neuron, control donor C32-CRL1502, day00, rep1_CNhs13826_13433-144E4_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep3_CNhs13917_tpm_rev IpsToNeuronControlDnC11-CRL2429Day18R3- iPS differentiation to neuron, control donor C11-CRL2429, day18, rep3_CNhs13917_13432-144E3_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep3_CNhs13917_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day18R3+ iPS differentiation to neuron, control donor C11-CRL2429, day18, rep3_CNhs13917_13432-144E3_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep2_CNhs13825_tpm_rev IpsToNeuronControlDnC11-CRL2429Day18R2- iPS differentiation to neuron, control donor C11-CRL2429, day18, rep2_CNhs13825_13428-144D8_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep2_CNhs13825_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day18R2+ iPS differentiation to neuron, control donor C11-CRL2429, day18, rep2_CNhs13825_13428-144D8_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep1_CNhs13916_tpm_rev IpsToNeuronControlDnC11-CRL2429Day18R1- iPS differentiation to neuron, control donor C11-CRL2429, day18, rep1_CNhs13916_13424-144D4_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day18Rep1_CNhs13916_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day18R1+ iPS differentiation to neuron, control donor C11-CRL2429, day18, rep1_CNhs13916_13424-144D4_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep3_CNhs14051_tpm_rev IpsToNeuronControlDnC11-CRL2429Day12R3- iPS differentiation to neuron, control donor C11-CRL2429, day12, rep3_CNhs14051_13431-144E2_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep3_CNhs14051_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day12R3+ iPS differentiation to neuron, control donor C11-CRL2429, day12, rep3_CNhs14051_13431-144E2_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep2_CNhs13824_tpm_rev IpsToNeuronControlDnC11-CRL2429Day12R2- iPS differentiation to neuron, control donor C11-CRL2429, day12, rep2_CNhs13824_13427-144D7_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep2_CNhs13824_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day12R2+ iPS differentiation to neuron, control donor C11-CRL2429, day12, rep2_CNhs13824_13427-144D7_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep1_CNhs14047_tpm_rev IpsToNeuronControlDnC11-CRL2429Day12R1- iPS differentiation to neuron, control donor C11-CRL2429, day12, rep1_CNhs14047_13423-144D3_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day12Rep1_CNhs14047_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day12R1+ iPS differentiation to neuron, control donor C11-CRL2429, day12, rep1_CNhs14047_13423-144D3_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep3_CNhs14050_tpm_rev IpsToNeuronControlDnC11-CRL2429Day06R3- iPS differentiation to neuron, control donor C11-CRL2429, day06, rep3_CNhs14050_13430-144E1_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep3_CNhs14050_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day06R3+ iPS differentiation to neuron, control donor C11-CRL2429, day06, rep3_CNhs14050_13430-144E1_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep2_CNhs13823_tpm_rev IpsToNeuronControlDnC11-CRL2429Day06R2- iPS differentiation to neuron, control donor C11-CRL2429, day06, rep2_CNhs13823_13426-144D6_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep2_CNhs13823_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day06R2+ iPS differentiation to neuron, control donor C11-CRL2429, day06, rep2_CNhs13823_13426-144D6_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep1_CNhs14046_tpm_rev IpsToNeuronControlDnC11-CRL2429Day06R1- iPS differentiation to neuron, control donor C11-CRL2429, day06, rep1_CNhs14046_13422-144D2_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day06Rep1_CNhs14046_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day06R1+ iPS differentiation to neuron, control donor C11-CRL2429, day06, rep1_CNhs14046_13422-144D2_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep3_CNhs14049_tpm_rev IpsToNeuronControlDnC11-CRL2429Day00R3- iPS differentiation to neuron, control donor C11-CRL2429, day00, rep3_CNhs14049_13429-144D9_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep3_CNhs14049_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day00R3+ iPS differentiation to neuron, control donor C11-CRL2429, day00, rep3_CNhs14049_13429-144D9_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep2_CNhs13822_tpm_rev IpsToNeuronControlDnC11-CRL2429Day00R2- iPS differentiation to neuron, control donor C11-CRL2429, day00, rep2_CNhs13822_13425-144D5_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep2_CNhs13822_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day00R2+ iPS differentiation to neuron, control donor C11-CRL2429, day00, rep2_CNhs13822_13425-144D5_forward Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep1_CNhs14045_tpm_rev IpsToNeuronControlDnC11-CRL2429Day00R1- iPS differentiation to neuron, control donor C11-CRL2429, day00, rep1_CNhs14045_13421-144D1_reverse Regulation 
IPSDifferentiationToNeuronControlDonorC11CRL2429Day00Rep1_CNhs14045_tpm_fwd IpsToNeuronControlDnC11-CRL2429Day00R1+ iPS differentiation to neuron, control donor C11-CRL2429, day00, rep1_CNhs14045_13421-144D1_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep3_CNhs14066_tpm_rev Tc:iPStoNeuronDs_Day18R3- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep3_CNhs14066_13468-144I3_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep3_CNhs14066_tpm_fwd Tc:iPStoNeuronDs_Day18R3+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep3_CNhs14066_13468-144I3_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep2_CNhs13922_tpm_rev Tc:iPStoNeuronDs_Day18R2- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep2_CNhs13922_13464-144H8_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep2_CNhs13922_tpm_fwd Tc:iPStoNeuronDs_Day18R2+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep2_CNhs13922_13464-144H8_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep1_CNhs13838_tpm_rev Tc:iPStoNeuronDs_Day18R1- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep1_CNhs13838_13460-144H4_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day18Rep1_CNhs13838_tpm_fwd Tc:iPStoNeuronDs_Day18R1+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day18, rep1_CNhs13838_13460-144H4_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep3_CNhs14065_tpm_rev Tc:iPStoNeuronDs_Day12R3- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep3_CNhs14065_13467-144I2_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep3_CNhs14065_tpm_fwd Tc:iPStoNeuronDs_Day12R3+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep3_CNhs14065_13467-144I2_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep2_CNhs14062_tpm_rev Tc:iPStoNeuronDs_Day12R2- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep2_CNhs14062_13463-144H7_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep2_CNhs14062_tpm_fwd Tc:iPStoNeuronDs_Day12R2+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep2_CNhs14062_13463-144H7_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep1_CNhs13837_tpm_rev Tc:iPStoNeuronDs_Day12R1- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep1_CNhs13837_13459-144H3_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day12Rep1_CNhs13837_tpm_fwd Tc:iPStoNeuronDs_Day12R1+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day12, rep1_CNhs13837_13459-144H3_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep3_CNhs14064_tpm_rev Tc:iPStoNeuronDs_Day06R3- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep3_CNhs14064_13466-144I1_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep3_CNhs14064_tpm_fwd Tc:iPStoNeuronDs_Day06R3+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep3_CNhs14064_13466-144I1_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep2_CNhs14061_tpm_rev Tc:iPStoNeuronDs_Day06R2- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep2_CNhs14061_13462-144H6_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep2_CNhs14061_tpm_fwd Tc:iPStoNeuronDs_Day06R2+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep2_CNhs14061_13462-144H6_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep1_CNhs13836_tpm_rev Tc:iPStoNeuronDs_Day06R1- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep1_CNhs13836_13458-144H2_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day06Rep1_CNhs13836_tpm_fwd Tc:iPStoNeuronDs_Day06R1+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day06, rep1_CNhs13836_13458-144H2_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep3_CNhs14063_tpm_rev Tc:iPStoNeuronDs_Day00R3- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep3_CNhs14063_13465-144H9_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep3_CNhs14063_tpm_fwd Tc:iPStoNeuronDs_Day00R3+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep3_CNhs14063_13465-144H9_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep2_CNhs14060_tpm_rev Tc:iPStoNeuronDs_Day00R2- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep2_CNhs14060_13461-144H5_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep2_CNhs14060_tpm_fwd Tc:iPStoNeuronDs_Day00R2+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep2_CNhs14060_13461-144H5_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep1_CNhs13835_tpm_rev Tc:iPStoNeuronDs_Day00R1- iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep1_CNhs13835_13457-144H1_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC18CCL54Day00Rep1_CNhs13835_tpm_fwd Tc:iPStoNeuronDs_Day00R1+ iPS differentiation to neuron, down-syndrome donor C18-CCL54, day00, rep1_CNhs13835_13457-144H1_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep3_CNhs14059_tpm_rev Tc:iPStoNeuronDs_Day18R3- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep3_CNhs14059_13456-144G9_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep3_CNhs14059_tpm_fwd Tc:iPStoNeuronDs_Day18R3+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep3_CNhs14059_13456-144G9_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep2_CNhs13846_tpm_rev Tc:iPStoNeuronDs_Day18R2- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep2_CNhs13846_13452-144G5_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep2_CNhs13846_tpm_fwd Tc:iPStoNeuronDs_Day18R2+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep2_CNhs13846_13452-144G5_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep1_CNhs13833_tpm_rev Tc:iPStoNeuronDs_Day18R1- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep1_CNhs13833_13448-144G1_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day18Rep1_CNhs13833_tpm_fwd Tc:iPStoNeuronDs_Day18R1+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day18, rep1_CNhs13833_13448-144G1_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep3_CNhs14058_tpm_rev Tc:iPStoNeuronDs_Day12R3- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep3_CNhs14058_13455-144G8_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep3_CNhs14058_tpm_fwd Tc:iPStoNeuronDs_Day12R3+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep3_CNhs14058_13455-144G8_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep2_CNhs13845_tpm_rev Tc:iPStoNeuronDs_Day12R2- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep2_CNhs13845_13451-144G4_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep2_CNhs13845_tpm_fwd Tc:iPStoNeuronDs_Day12R2+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep2_CNhs13845_13451-144G4_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep1_CNhs13832_tpm_rev Tc:iPStoNeuronDs_Day12R1- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep1_CNhs13832_13447-144F9_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day12Rep1_CNhs13832_tpm_fwd Tc:iPStoNeuronDs_Day12R1+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day12, rep1_CNhs13832_13447-144F9_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep3_CNhs14057_tpm_rev Tc:iPStoNeuronDs_Day06R3- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep3_CNhs14057_13454-144G7_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep3_CNhs14057_tpm_fwd Tc:iPStoNeuronDs_Day06R3+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep3_CNhs14057_13454-144G7_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep2_CNhs13844_tpm_rev Tc:iPStoNeuronDs_Day06R2- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep2_CNhs13844_13450-144G3_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep2_CNhs13844_tpm_fwd Tc:iPStoNeuronDs_Day06R2+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep2_CNhs13844_13450-144G3_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep1_CNhs13831_tpm_rev Tc:iPStoNeuronDs_Day06R1- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep1_CNhs13831_13446-144F8_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day06Rep1_CNhs13831_tpm_fwd Tc:iPStoNeuronDs_Day06R1+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day06, rep1_CNhs13831_13446-144F8_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep3_CNhs14056_tpm_rev Tc:iPStoNeuronDs_Day00R3- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep3_CNhs14056_13453-144G6_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep3_CNhs14056_tpm_fwd Tc:iPStoNeuronDs_Day00R3+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep3_CNhs14056_13453-144G6_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep2_CNhs13843_tpm_rev Tc:iPStoNeuronDs_Day00R2- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep2_CNhs13843_13449-144G2_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep2_CNhs13843_tpm_fwd Tc:iPStoNeuronDs_Day00R2+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep2_CNhs13843_13449-144G2_forward Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep1_CNhs13830_tpm_rev Tc:iPStoNeuronDs_Day00R1- iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep1_CNhs13830_13445-144F7_reverse Regulation 
IPSDifferentiationToNeuronDownsyndromeDonorC11CCL54Day00Rep1_CNhs13830_tpm_fwd Tc:iPStoNeuronDs_Day00R1+ iPS differentiation to neuron, down-syndrome donor C11-CCL54, day00, rep1_CNhs13830_13445-144F7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep3_CNhs14543_tpm_rev Tc:ARPE-19Emt_60hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep3_CNhs14543_13687-147F6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep3_CNhs14543_tpm_fwd Tc:ARPE-19Emt_60hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep3_CNhs14543_13687-147F6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep2_CNhs14542_tpm_rev Tc:ARPE-19Emt_60hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep2_CNhs14542_13686-147F5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep2_CNhs14542_tpm_fwd Tc:ARPE-19Emt_60hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep2_CNhs14542_13686-147F5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep1_CNhs14541_tpm_rev Tc:ARPE-19Emt_60hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep1_CNhs14541_13685-147F4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha60hr00minBiolRep1_CNhs14541_tpm_fwd Tc:ARPE-19Emt_60hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 60hr00min, biol_rep1_CNhs14541_13685-147F4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep3_CNhs14540_tpm_rev Tc:ARPE-19Emt_42hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep3_CNhs14540_13684-147F3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep3_CNhs14540_tpm_fwd Tc:ARPE-19Emt_42hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep3_CNhs14540_13684-147F3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep2_CNhs14539_tpm_rev Tc:ARPE-19Emt_42hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep2_CNhs14539_13683-147F2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep2_CNhs14539_tpm_fwd Tc:ARPE-19Emt_42hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep2_CNhs14539_13683-147F2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep1_CNhs14538_tpm_rev Tc:ARPE-19Emt_42hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep1_CNhs14538_13682-147F1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha42hr00minBiolRep1_CNhs14538_tpm_fwd Tc:ARPE-19Emt_42hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 42hr00min, biol_rep1_CNhs14538_13682-147F1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep3_CNhs14537_tpm_rev Tc:ARPE-19Emt_24hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep3_CNhs14537_13681-147E9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep3_CNhs14537_tpm_fwd Tc:ARPE-19Emt_24hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep3_CNhs14537_13681-147E9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep1_CNhs14535_tpm_rev Tc:ARPE-19Emt_24hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep1_CNhs14535_13679-147E7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha24hr00minBiolRep1_CNhs14535_tpm_fwd Tc:ARPE-19Emt_24hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep1_CNhs14535_13679-147E7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep3_CNhs14534_tpm_rev Tc:ARPE-19Emt_16hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep3_CNhs14534_13678-147E6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep3_CNhs14534_tpm_fwd Tc:ARPE-19Emt_16hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep3_CNhs14534_13678-147E6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep2_CNhs14533_tpm_rev Tc:ARPE-19Emt_16hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep2_CNhs14533_13677-147E5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep2_CNhs14533_tpm_fwd Tc:ARPE-19Emt_16hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep2_CNhs14533_13677-147E5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep1_CNhs14532_tpm_rev Tc:ARPE-19Emt_16hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep1_CNhs14532_13676-147E4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha16hr00minBiolRep1_CNhs14532_tpm_fwd Tc:ARPE-19Emt_16hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 16hr00min, biol_rep1_CNhs14532_13676-147E4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha12hr00minBiolRep3_CNhs14531_tpm_rev Tc:ARPE-19Emt_12hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 12hr00min, biol_rep3_CNhs14531_13675-147E3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha12hr00minBiolRep3_CNhs14531_tpm_fwd Tc:ARPE-19Emt_12hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 12hr00min, biol_rep3_CNhs14531_13675-147E3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha12hr00minBiolRep2_CNhs14530_tpm_rev Tc:ARPE-19Emt_12hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 12hr00min, biol_rep2_CNhs14530_13674-147E2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha12hr00minBiolRep2_CNhs14530_tpm_fwd Tc:ARPE-19Emt_12hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 12hr00min, biol_rep2_CNhs14530_13674-147E2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep3_CNhs14528_tpm_rev Tc:ARPE-19Emt_08hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep3_CNhs14528_13672-147D9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep3_CNhs14528_tpm_fwd Tc:ARPE-19Emt_08hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep3_CNhs14528_13672-147D9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep2_CNhs14527_tpm_rev Tc:ARPE-19Emt_08hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep2_CNhs14527_13671-147D8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep2_CNhs14527_tpm_fwd Tc:ARPE-19Emt_08hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep2_CNhs14527_13671-147D8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep1_CNhs14526_tpm_rev Tc:ARPE-19Emt_08hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep1_CNhs14526_13670-147D7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha08hr00minBiolRep1_CNhs14526_tpm_fwd Tc:ARPE-19Emt_08hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 08hr00min, biol_rep1_CNhs14526_13670-147D7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep3_CNhs14525_tpm_rev Tc:ARPE-19Emt_07hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep3_CNhs14525_13669-147D6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep3_CNhs14525_tpm_fwd Tc:ARPE-19Emt_07hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep3_CNhs14525_13669-147D6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep2_CNhs14524_tpm_rev Tc:ARPE-19Emt_07hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep2_CNhs14524_13668-147D5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep2_CNhs14524_tpm_fwd Tc:ARPE-19Emt_07hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep2_CNhs14524_13668-147D5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep1_CNhs14523_tpm_rev Tc:ARPE-19Emt_07hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep1_CNhs14523_13667-147D4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha07hr00minBiolRep1_CNhs14523_tpm_fwd Tc:ARPE-19Emt_07hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 07hr00min, biol_rep1_CNhs14523_13667-147D4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep3_CNhs14522_tpm_rev Tc:ARPE-19Emt_06hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep3_CNhs14522_13666-147D3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep3_CNhs14522_tpm_fwd Tc:ARPE-19Emt_06hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep3_CNhs14522_13666-147D3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep1_CNhs14519_tpm_rev Tc:ARPE-19Emt_06hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep1_CNhs14519_13664-147D1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha06hr00minBiolRep1_CNhs14519_tpm_fwd Tc:ARPE-19Emt_06hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep1_CNhs14519_13664-147D1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep3_CNhs14518_tpm_rev Tc:ARPE-19Emt_05hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep3_CNhs14518_13663-147C9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep3_CNhs14518_tpm_fwd Tc:ARPE-19Emt_05hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep3_CNhs14518_13663-147C9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep2_CNhs14501_tpm_rev Tc:ARPE-19Emt_05hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep2_CNhs14501_13662-147C8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep2_CNhs14501_tpm_fwd Tc:ARPE-19Emt_05hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep2_CNhs14501_13662-147C8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep1_CNhs14500_tpm_rev Tc:ARPE-19Emt_05hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep1_CNhs14500_13661-147C7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha05hr00minBiolRep1_CNhs14500_tpm_fwd Tc:ARPE-19Emt_05hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 05hr00min, biol_rep1_CNhs14500_13661-147C7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep3_CNhs14499_tpm_rev Tc:ARPE-19Emt_04hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep3_CNhs14499_13660-147C6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep3_CNhs14499_tpm_fwd Tc:ARPE-19Emt_04hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep3_CNhs14499_13660-147C6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep2_CNhs14498_tpm_rev Tc:ARPE-19Emt_04hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep2_CNhs14498_13659-147C5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep2_CNhs14498_tpm_fwd Tc:ARPE-19Emt_04hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep2_CNhs14498_13659-147C5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep1_CNhs14497_tpm_rev Tc:ARPE-19Emt_04hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep1_CNhs14497_13658-147C4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha04hr00minBiolRep1_CNhs14497_tpm_fwd Tc:ARPE-19Emt_04hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 04hr00min, biol_rep1_CNhs14497_13658-147C4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep3_CNhs14496_tpm_rev Tc:ARPE-19Emt_03hr30minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep3_CNhs14496_13657-147C3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep3_CNhs14496_tpm_fwd Tc:ARPE-19Emt_03hr30minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep3_CNhs14496_13657-147C3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep2_CNhs14495_tpm_rev Tc:ARPE-19Emt_03hr30minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep2_CNhs14495_13656-147C2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep2_CNhs14495_tpm_fwd Tc:ARPE-19Emt_03hr30minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep2_CNhs14495_13656-147C2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep1_CNhs14494_tpm_rev Tc:ARPE-19Emt_03hr30minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep1_CNhs14494_13655-147C1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr30minBiolRep1_CNhs14494_tpm_fwd Tc:ARPE-19Emt_03hr30minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr30min, biol_rep1_CNhs14494_13655-147C1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep3_CNhs14493_tpm_rev Tc:ARPE-19Emt_03hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep3_CNhs14493_13654-147B9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep3_CNhs14493_tpm_fwd Tc:ARPE-19Emt_03hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep3_CNhs14493_13654-147B9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep2_CNhs14492_tpm_rev Tc:ARPE-19Emt_03hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep2_CNhs14492_13653-147B8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep2_CNhs14492_tpm_fwd Tc:ARPE-19Emt_03hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep2_CNhs14492_13653-147B8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep1_CNhs14491_tpm_rev Tc:ARPE-19Emt_03hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep1_CNhs14491_13652-147B7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha03hr00minBiolRep1_CNhs14491_tpm_fwd Tc:ARPE-19Emt_03hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 03hr00min, biol_rep1_CNhs14491_13652-147B7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep3_CNhs14490_tpm_rev Tc:ARPE-19Emt_02hr30minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep3_CNhs14490_13651-147B6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep3_CNhs14490_tpm_fwd Tc:ARPE-19Emt_02hr30minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep3_CNhs14490_13651-147B6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep2_CNhs14489_tpm_rev Tc:ARPE-19Emt_02hr30minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep2_CNhs14489_13650-147B5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep2_CNhs14489_tpm_fwd Tc:ARPE-19Emt_02hr30minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep2_CNhs14489_13650-147B5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep1_CNhs14488_tpm_rev Tc:ARPE-19Emt_02hr30minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep1_CNhs14488_13649-147B4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr30minBiolRep1_CNhs14488_tpm_fwd Tc:ARPE-19Emt_02hr30minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr30min, biol_rep1_CNhs14488_13649-147B4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep3_CNhs14487_tpm_rev Tc:ARPE-19Emt_02hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep3_CNhs14487_13648-147B3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep3_CNhs14487_tpm_fwd Tc:ARPE-19Emt_02hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep3_CNhs14487_13648-147B3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep2_CNhs14486_tpm_rev Tc:ARPE-19Emt_02hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep2_CNhs14486_13647-147B2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep2_CNhs14486_tpm_fwd Tc:ARPE-19Emt_02hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep2_CNhs14486_13647-147B2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep1_CNhs14485_tpm_rev Tc:ARPE-19Emt_02hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep1_CNhs14485_13646-147B1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha02hr00minBiolRep1_CNhs14485_tpm_fwd Tc:ARPE-19Emt_02hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 02hr00min, biol_rep1_CNhs14485_13646-147B1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep3_CNhs14484_tpm_rev Tc:ARPE-19Emt_01hr40minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep3_CNhs14484_13645-147A9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep3_CNhs14484_tpm_fwd Tc:ARPE-19Emt_01hr40minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep3_CNhs14484_13645-147A9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep2_CNhs14483_tpm_rev Tc:ARPE-19Emt_01hr40minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep2_CNhs14483_13644-147A8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep2_CNhs14483_tpm_fwd Tc:ARPE-19Emt_01hr40minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep2_CNhs14483_13644-147A8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep1_CNhs14482_tpm_rev Tc:ARPE-19Emt_01hr40minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep1_CNhs14482_13643-147A7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr40minBiolRep1_CNhs14482_tpm_fwd Tc:ARPE-19Emt_01hr40minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr40min, biol_rep1_CNhs14482_13643-147A7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep3_CNhs14480_tpm_rev Tc:ARPE-19Emt_01hr20minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep3_CNhs14480_13642-147A6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep3_CNhs14480_tpm_fwd Tc:ARPE-19Emt_01hr20minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep3_CNhs14480_13642-147A6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep2_CNhs14479_tpm_rev Tc:ARPE-19Emt_01hr20minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep2_CNhs14479_13641-147A5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep2_CNhs14479_tpm_fwd Tc:ARPE-19Emt_01hr20minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep2_CNhs14479_13641-147A5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep1_CNhs14478_tpm_rev Tc:ARPE-19Emt_01hr20minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep1_CNhs14478_13640-147A4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr20minBiolRep1_CNhs14478_tpm_fwd Tc:ARPE-19Emt_01hr20minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr20min, biol_rep1_CNhs14478_13640-147A4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep3_CNhs14477_tpm_rev Tc:ARPE-19Emt_01hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep3_CNhs14477_13639-147A3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep3_CNhs14477_tpm_fwd Tc:ARPE-19Emt_01hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep3_CNhs14477_13639-147A3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep2_CNhs14476_tpm_rev Tc:ARPE-19Emt_01hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep2_CNhs14476_13638-147A2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep2_CNhs14476_tpm_fwd Tc:ARPE-19Emt_01hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep2_CNhs14476_13638-147A2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep1_CNhs14475_tpm_rev Tc:ARPE-19Emt_01hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep1_CNhs14475_13637-147A1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha01hr00minBiolRep1_CNhs14475_tpm_fwd Tc:ARPE-19Emt_01hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 01hr00min, biol_rep1_CNhs14475_13637-147A1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep3_CNhs14474_tpm_rev Tc:ARPE-19Emt_00hr45minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep3_CNhs14474_13636-146I9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep3_CNhs14474_tpm_fwd Tc:ARPE-19Emt_00hr45minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep3_CNhs14474_13636-146I9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep2_CNhs14473_tpm_rev Tc:ARPE-19Emt_00hr45minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep2_CNhs14473_13635-146I8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep2_CNhs14473_tpm_fwd Tc:ARPE-19Emt_00hr45minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep2_CNhs14473_13635-146I8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep1_CNhs14472_tpm_rev Tc:ARPE-19Emt_00hr45minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep1_CNhs14472_13634-146I7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr45minBiolRep1_CNhs14472_tpm_fwd Tc:ARPE-19Emt_00hr45minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr45min, biol_rep1_CNhs14472_13634-146I7_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep3_CNhs14471_tpm_rev Tc:ARPE-19Emt_00hr30minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep3_CNhs14471_13633-146I6_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep3_CNhs14471_tpm_fwd Tc:ARPE-19Emt_00hr30minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep3_CNhs14471_13633-146I6_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep2_CNhs14470_tpm_rev Tc:ARPE-19Emt_00hr30minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep2_CNhs14470_13632-146I5_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep2_CNhs14470_tpm_fwd Tc:ARPE-19Emt_00hr30minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep2_CNhs14470_13632-146I5_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep1_CNhs14469_tpm_rev Tc:ARPE-19Emt_00hr30minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep1_CNhs14469_13631-146I4_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr30minBiolRep1_CNhs14469_tpm_fwd Tc:ARPE-19Emt_00hr30minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr30min, biol_rep1_CNhs14469_13631-146I4_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep3_CNhs14468_tpm_rev Tc:ARPE-19Emt_00hr15minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep3_CNhs14468_13630-146I3_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep3_CNhs14468_tpm_fwd Tc:ARPE-19Emt_00hr15minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep3_CNhs14468_13630-146I3_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep2_CNhs14467_tpm_rev Tc:ARPE-19Emt_00hr15minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep2_CNhs14467_13629-146I2_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep2_CNhs14467_tpm_fwd Tc:ARPE-19Emt_00hr15minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep2_CNhs14467_13629-146I2_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep1_CNhs14466_tpm_rev Tc:ARPE-19Emt_00hr15minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep1_CNhs14466_13628-146I1_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr15minBiolRep1_CNhs14466_tpm_fwd Tc:ARPE-19Emt_00hr15minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr15min, biol_rep1_CNhs14466_13628-146I1_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep3_CNhs14465_tpm_rev Tc:ARPE-19Emt_00hr00minBr3- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep3_CNhs14465_13627-146H9_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep3_CNhs14465_tpm_fwd Tc:ARPE-19Emt_00hr00minBr3+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep3_CNhs14465_13627-146H9_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep2_CNhs14464_tpm_rev Tc:ARPE-19Emt_00hr00minBr2- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep2_CNhs14464_13626-146H8_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep2_CNhs14464_tpm_fwd Tc:ARPE-19Emt_00hr00minBr2+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep2_CNhs14464_13626-146H8_forward Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep1_CNhs14463_tpm_rev Tc:ARPE-19Emt_00hr00minBr1- ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep1_CNhs14463_13625-146H7_reverse Regulation 
ARPE19EMTInducedWithTGFbetaAndTNFalpha00hr00minBiolRep1_CNhs14463_tpm_fwd Tc:ARPE-19Emt_00hr00minBr1+ ARPE-19 EMT induced with TGF-beta and TNF-alpha, 00hr00min, biol_rep1_CNhs14463_13625-146H7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep3H9EB3D41_CNhs12950_tpm_rev H9MelanocyticInduction_Day41Br3- H9 Embryoid body cells, melanocytic induction, day41, biol_rep3 (H9EB-3 d41)_CNhs12950_12836-137B1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep3H9EB3D41_CNhs12950_tpm_fwd H9MelanocyticInduction_Day41Br3+ H9 Embryoid body cells, melanocytic induction, day41, biol_rep3 (H9EB-3 d41)_CNhs12950_12836-137B1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep2H9EB2D41_CNhs12907_tpm_rev H9MelanocyticInduction_Day41Br2- H9 Embryoid body cells, melanocytic induction, day41, biol_rep2 (H9EB-2 d41)_CNhs12907_12738-135I2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep2H9EB2D41_CNhs12907_tpm_fwd H9MelanocyticInduction_Day41Br2+ H9 Embryoid body cells, melanocytic induction, day41, biol_rep2 (H9EB-2 d41)_CNhs12907_12738-135I2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep1H9EB1D41_CNhs12905_tpm_rev H9MelanocyticInduction_Day41Br1- H9 Embryoid body cells, melanocytic induction, day41, biol_rep1 (H9EB-1 d41)_CNhs12905_12640-134G3_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay41BiolRep1H9EB1D41_CNhs12905_tpm_fwd H9MelanocyticInduction_Day41Br1+ H9 Embryoid body cells, melanocytic induction, day41, biol_rep1 (H9EB-1 d41)_CNhs12905_12640-134G3_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep3H9EB3D34_CNhs12919_tpm_rev H9MelanocyticInduction_Day34Br3- H9 Embryoid body cells, melanocytic induction, day34, biol_rep3 (H9EB-3 d34)_CNhs12919_12835-137A9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep3H9EB3D34_CNhs12919_tpm_fwd H9MelanocyticInduction_Day34Br3+ H9 Embryoid body cells, melanocytic induction, day34, biol_rep3 (H9EB-3 d34)_CNhs12919_12835-137A9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep2H9EB2D34_CNhs12906_tpm_rev H9MelanocyticInduction_Day34Br2- H9 Embryoid body cells, melanocytic induction, day34, biol_rep2 (H9EB-2 d34)_CNhs12906_12737-135I1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep2H9EB2D34_CNhs12906_tpm_fwd H9MelanocyticInduction_Day34Br2+ H9 Embryoid body cells, melanocytic induction, day34, biol_rep2 (H9EB-2 d34)_CNhs12906_12737-135I1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep1H9EB1D34_CNhs12904_tpm_rev H9MelanocyticInduction_Day34Br1- H9 Embryoid body cells, melanocytic induction, day34, biol_rep1 (H9EB-1 d34)_CNhs12904_12639-134G2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay34BiolRep1H9EB1D34_CNhs12904_tpm_fwd H9MelanocyticInduction_Day34Br1+ H9 Embryoid body cells, melanocytic induction, day34, biol_rep1 (H9EB-1 d34)_CNhs12904_12639-134G2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep3H9EB3D30_CNhs12918_tpm_rev H9MelanocyticInduction_Day30Br3- H9 Embryoid body cells, melanocytic induction, day30, biol_rep3 (H9EB-3 d30)_CNhs12918_12834-137A8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep3H9EB3D30_CNhs12918_tpm_fwd H9MelanocyticInduction_Day30Br3+ H9 Embryoid body cells, melanocytic induction, day30, biol_rep3 (H9EB-3 d30)_CNhs12918_12834-137A8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep2H9EB2D30_CNhs12836_tpm_rev H9MelanocyticInduction_Day30Br2- H9 Embryoid body cells, melanocytic induction, day30, biol_rep2 (H9EB-2 d30)_CNhs12836_12736-135H9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep2H9EB2D30_CNhs12836_tpm_fwd H9MelanocyticInduction_Day30Br2+ H9 Embryoid body cells, melanocytic induction, day30, biol_rep2 (H9EB-2 d30)_CNhs12836_12736-135H9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep1H9EB1D30_CNhs12903_tpm_rev H9MelanocyticInduction_Day30Br1- H9 Embryoid body cells, melanocytic induction, day30, biol_rep1 (H9EB-1 d30)_CNhs12903_12638-134G1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay30BiolRep1H9EB1D30_CNhs12903_tpm_fwd H9MelanocyticInduction_Day30Br1+ H9 Embryoid body cells, melanocytic induction, day30, biol_rep1 (H9EB-1 d30)_CNhs12903_12638-134G1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep3H9EB3D27_CNhs12917_tpm_rev H9MelanocyticInduction_Day27Br3- H9 Embryoid body cells, melanocytic induction, day27, biol_rep3 (H9EB-3 d27)_CNhs12917_12833-137A7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep3H9EB3D27_CNhs12917_tpm_fwd H9MelanocyticInduction_Day27Br3+ H9 Embryoid body cells, melanocytic induction, day27, biol_rep3 (H9EB-3 d27)_CNhs12917_12833-137A7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep2H9EB2D27_CNhs12835_tpm_rev H9MelanocyticInduction_Day27Br2- H9 Embryoid body cells, melanocytic induction, day27, biol_rep2 (H9EB-2 d27)_CNhs12835_12735-135H8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep2H9EB2D27_CNhs12835_tpm_fwd H9MelanocyticInduction_Day27Br2+ H9 Embryoid body cells, melanocytic induction, day27, biol_rep2 (H9EB-2 d27)_CNhs12835_12735-135H8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep1H9EB1D27_CNhs12902_tpm_rev H9MelanocyticInduction_Day27Br1- H9 Embryoid body cells, melanocytic induction, day27, biol_rep1 (H9EB-1 d27)_CNhs12902_12637-134F9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay27BiolRep1H9EB1D27_CNhs12902_tpm_fwd H9MelanocyticInduction_Day27Br1+ H9 Embryoid body cells, melanocytic induction, day27, biol_rep1 (H9EB-1 d27)_CNhs12902_12637-134F9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep3H9EB3D24_CNhs12916_tpm_rev H9MelanocyticInduction_Day24Br3- H9 Embryoid body cells, melanocytic induction, day24, biol_rep3 (H9EB-3 d24)_CNhs12916_12832-137A6_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep3H9EB3D24_CNhs12916_tpm_fwd H9MelanocyticInduction_Day24Br3+ H9 Embryoid body cells, melanocytic induction, day24, biol_rep3 (H9EB-3 d24)_CNhs12916_12832-137A6_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep2H9EB2D24_CNhs12834_tpm_rev H9MelanocyticInduction_Day24Br2- H9 Embryoid body cells, melanocytic induction, day24, biol_rep2 (H9EB-2 d24)_CNhs12834_12734-135H7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep2H9EB2D24_CNhs12834_tpm_fwd H9MelanocyticInduction_Day24Br2+ H9 Embryoid body cells, melanocytic induction, day24, biol_rep2 (H9EB-2 d24)_CNhs12834_12734-135H7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep1H9EB1D24_CNhs12901_tpm_rev H9MelanocyticInduction_Day24Br1- H9 Embryoid body cells, melanocytic induction, day24, biol_rep1 (H9EB-1 d24)_CNhs12901_12636-134F8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay24BiolRep1H9EB1D24_CNhs12901_tpm_fwd H9MelanocyticInduction_Day24Br1+ H9 Embryoid body cells, melanocytic induction, day24, biol_rep1 (H9EB-1 d24)_CNhs12901_12636-134F8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep3H9EB3D21_CNhs12915_tpm_rev H9MelanocyticInduction_Day21Br3- H9 Embryoid body cells, melanocytic induction, day21, biol_rep3 (H9EB-3 d21)_CNhs12915_12831-137A5_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep3H9EB3D21_CNhs12915_tpm_fwd H9MelanocyticInduction_Day21Br3+ H9 Embryoid body cells, melanocytic induction, day21, biol_rep3 (H9EB-3 d21)_CNhs12915_12831-137A5_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep2H9EB2D21_CNhs12833_tpm_rev H9MelanocyticInduction_Day21Br2- H9 Embryoid body cells, melanocytic induction, day21, biol_rep2 (H9EB-2 d21)_CNhs12833_12733-135H6_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep2H9EB2D21_CNhs12833_tpm_fwd H9MelanocyticInduction_Day21Br2+ H9 Embryoid body cells, melanocytic induction, day21, biol_rep2 (H9EB-2 d21)_CNhs12833_12733-135H6_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep1H9EB1D21_CNhs12900_tpm_rev H9MelanocyticInduction_Day21Br1- H9 Embryoid body cells, melanocytic induction, day21, biol_rep1 (H9EB-1 d21)_CNhs12900_12635-134F7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay21BiolRep1H9EB1D21_CNhs12900_tpm_fwd H9MelanocyticInduction_Day21Br1+ H9 Embryoid body cells, melanocytic induction, day21, biol_rep1 (H9EB-1 d21)_CNhs12900_12635-134F7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep3H9EB3D18_CNhs12914_tpm_rev H9MelanocyticInduction_Day18Br3- H9 Embryoid body cells, melanocytic induction, day18, biol_rep3 (H9EB-3 d18)_CNhs12914_12830-137A4_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep3H9EB3D18_CNhs12914_tpm_fwd H9MelanocyticInduction_Day18Br3+ H9 Embryoid body cells, melanocytic induction, day18, biol_rep3 (H9EB-3 d18)_CNhs12914_12830-137A4_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep2H9EB2D18_CNhs12832_tpm_rev H9MelanocyticInduction_Day18Br2- H9 Embryoid body cells, melanocytic induction, day18, biol_rep2 (H9EB-2 d18)_CNhs12832_12732-135H5_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep2H9EB2D18_CNhs12832_tpm_fwd H9MelanocyticInduction_Day18Br2+ H9 Embryoid body cells, melanocytic induction, day18, biol_rep2 (H9EB-2 d18)_CNhs12832_12732-135H5_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep1H9EB1D18_CNhs12899_tpm_rev H9MelanocyticInduction_Day18Br1- H9 Embryoid body cells, melanocytic induction, day18, biol_rep1 (H9EB-1 d18)_CNhs12899_12634-134F6_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay18BiolRep1H9EB1D18_CNhs12899_tpm_fwd H9MelanocyticInduction_Day18Br1+ H9 Embryoid body cells, melanocytic induction, day18, biol_rep1 (H9EB-1 d18)_CNhs12899_12634-134F6_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep3H9EB3D15_CNhs12912_tpm_rev H9MelanocyticInduction_Day15Br3- H9 Embryoid body cells, melanocytic induction, day15, biol_rep3 (H9EB-3 d15)_CNhs12912_12829-137A3_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep3H9EB3D15_CNhs12912_tpm_fwd H9MelanocyticInduction_Day15Br3+ H9 Embryoid body cells, melanocytic induction, day15, biol_rep3 (H9EB-3 d15)_CNhs12912_12829-137A3_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep2H9EB2D15_CNhs12831_tpm_rev H9MelanocyticInduction_Day15Br2- H9 Embryoid body cells, melanocytic induction, day15, biol_rep2 (H9EB-2 d15)_CNhs12831_12731-135H4_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep2H9EB2D15_CNhs12831_tpm_fwd H9MelanocyticInduction_Day15Br2+ H9 Embryoid body cells, melanocytic induction, day15, biol_rep2 (H9EB-2 d15)_CNhs12831_12731-135H4_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep1H9EB1D15_CNhs12898_tpm_rev H9MelanocyticInduction_Day15Br1- H9 Embryoid body cells, melanocytic induction, day15, biol_rep1 (H9EB-1 d15)_CNhs12898_12633-134F5_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay15BiolRep1H9EB1D15_CNhs12898_tpm_fwd H9MelanocyticInduction_Day15Br1+ H9 Embryoid body cells, melanocytic induction, day15, biol_rep1 (H9EB-1 d15)_CNhs12898_12633-134F5_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep3H9EB3D12_CNhs12995_tpm_rev H9MelanocyticInduction_Day12Br3- H9 Embryoid body cells, melanocytic induction, day12, biol_rep3 (H9EB-3 d12)_CNhs12995_12828-137A2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep3H9EB3D12_CNhs12949_tpm_rev H9MelanocyticInduction_Day12Br3- H9 Embryoid body cells, melanocytic induction, day12, biol_rep3 (H9EB-3 d12)_CNhs12949_12828-137A2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep3H9EB3D12_CNhs12995_tpm_fwd H9MelanocyticInduction_Day12Br3+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep3 (H9EB-3 d12)_CNhs12995_12828-137A2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep3H9EB3D12_CNhs12949_tpm_fwd H9MelanocyticInduction_Day12Br3+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep3 (H9EB-3 d12)_CNhs12949_12828-137A2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep2H9EB2D12_CNhs12830_tpm_rev H9MelanocyticInduction_Day12Br2- H9 Embryoid body cells, melanocytic induction, day12, biol_rep2 (H9EB-2 d12)_CNhs12830_12730-135H3_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep2H9EB2D12_CNhs12830_tpm_fwd H9MelanocyticInduction_Day12Br2+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep2 (H9EB-2 d12)_CNhs12830_12730-135H3_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep1H9EB1D12_CNhs12994_tpm_rev H9MelanocyticInduction_Day12Br1- H9 Embryoid body cells, melanocytic induction, day12, biol_rep1 (H9EB-1 d12)_CNhs12994_12632-134F4_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep1H9EB1D12_CNhs12948_tpm_rev H9MelanocyticInduction_Day12Br1- H9 Embryoid body cells, melanocytic induction, day12, biol_rep1 (H9EB-1 d12)_CNhs12948_12632-134F4_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep1H9EB1D12_CNhs12994_tpm_fwd H9MelanocyticInduction_Day12Br1+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep1 (H9EB-1 d12)_CNhs12994_12632-134F4_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay12BiolRep1H9EB1D12_CNhs12948_tpm_fwd H9MelanocyticInduction_Day12Br1+ H9 Embryoid body cells, melanocytic induction, day12, biol_rep1 (H9EB-1 d12)_CNhs12948_12632-134F4_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep3H9EB3D9_CNhs12951_tpm_rev H9MelanocyticInduction_Day09Br3- H9 Embryoid body cells, melanocytic induction, day09, biol_rep3 (H9EB-3 d9)_CNhs12951_12827-137A1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep3H9EB3D9_CNhs12951_tpm_fwd H9MelanocyticInduction_Day09Br3+ H9 Embryoid body cells, melanocytic induction, day09, biol_rep3 (H9EB-3 d9)_CNhs12951_12827-137A1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep2H9EB2D9_CNhs12829_tpm_rev H9MelanocyticInduction_Day09Br2- H9 Embryoid body cells, melanocytic induction, day09, biol_rep2 (H9EB-2 d9)_CNhs12829_12729-135H2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep2H9EB2D9_CNhs12829_tpm_fwd H9MelanocyticInduction_Day09Br2+ H9 Embryoid body cells, melanocytic induction, day09, biol_rep2 (H9EB-2 d9)_CNhs12829_12729-135H2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep1H9EB1D9_CNhs12897_tpm_rev H9MelanocyticInduction_Day09Br1- H9 Embryoid body cells, melanocytic induction, day09, biol_rep1 (H9EB-1 d9)_CNhs12897_12631-134F3_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay09BiolRep1H9EB1D9_CNhs12897_tpm_fwd H9MelanocyticInduction_Day09Br1+ H9 Embryoid body cells, melanocytic induction, day09, biol_rep1 (H9EB-1 d9)_CNhs12897_12631-134F3_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep3H9EB3D6_CNhs12911_tpm_rev H9MelanocyticInduction_Day06Br3- H9 Embryoid body cells, melanocytic induction, day06, biol_rep3 (H9EB-3 d6)_CNhs12911_12826-136I9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep3H9EB3D6_CNhs12911_tpm_fwd H9MelanocyticInduction_Day06Br3+ H9 Embryoid body cells, melanocytic induction, day06, biol_rep3 (H9EB-3 d6)_CNhs12911_12826-136I9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep2H9EB2D6_CNhs12828_tpm_rev H9MelanocyticInduction_Day06Br2- H9 Embryoid body cells, melanocytic induction, day06, biol_rep2 (H9EB-2 d6)_CNhs12828_12728-135H1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep2H9EB2D6_CNhs12828_tpm_fwd H9MelanocyticInduction_Day06Br2+ H9 Embryoid body cells, melanocytic induction, day06, biol_rep2 (H9EB-2 d6)_CNhs12828_12728-135H1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep1H9EB1D6_CNhs12896_tpm_rev H9MelanocyticInduction_Day06Br1- H9 Embryoid body cells, melanocytic induction, day06, biol_rep1 (H9EB-1 d6)_CNhs12896_12630-134F2_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay06BiolRep1H9EB1D6_CNhs12896_tpm_fwd H9MelanocyticInduction_Day06Br1+ H9 Embryoid body cells, melanocytic induction, day06, biol_rep1 (H9EB-1 d6)_CNhs12896_12630-134F2_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep3H9EB3D3_CNhs12910_tpm_rev H9MelanocyticInduction_Day03Br3- H9 Embryoid body cells, melanocytic induction, day03, biol_rep3 (H9EB-3 d3)_CNhs12910_12825-136I8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep3H9EB3D3_CNhs12910_tpm_fwd H9MelanocyticInduction_Day03Br3+ H9 Embryoid body cells, melanocytic induction, day03, biol_rep3 (H9EB-3 d3)_CNhs12910_12825-136I8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep2H9EB2D3_CNhs12827_tpm_rev H9MelanocyticInduction_Day03Br2- H9 Embryoid body cells, melanocytic induction, day03, biol_rep2 (H9EB-2 d3)_CNhs12827_12727-135G9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep2H9EB2D3_CNhs12827_tpm_fwd H9MelanocyticInduction_Day03Br2+ H9 Embryoid body cells, melanocytic induction, day03, biol_rep2 (H9EB-2 d3)_CNhs12827_12727-135G9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep1H9EB1D3_CNhs12895_tpm_rev H9MelanocyticInduction_Day03Br1- H9 Embryoid body cells, melanocytic induction, day03, biol_rep1 (H9EB-1 d3)_CNhs12895_12629-134F1_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay03BiolRep1H9EB1D3_CNhs12895_tpm_fwd H9MelanocyticInduction_Day03Br1+ H9 Embryoid body cells, melanocytic induction, day03, biol_rep1 (H9EB-1 d3)_CNhs12895_12629-134F1_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep3H9EB3D1_CNhs12909_tpm_rev H9MelanocyticInduction_Day01Br3- H9 Embryoid body cells, melanocytic induction, day01, biol_rep3 (H9EB-3 d1)_CNhs12909_12824-136I7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep3H9EB3D1_CNhs12909_tpm_fwd H9MelanocyticInduction_Day01Br3+ H9 Embryoid body cells, melanocytic induction, day01, biol_rep3 (H9EB-3 d1)_CNhs12909_12824-136I7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep2H9EB2D1_CNhs12826_tpm_rev H9MelanocyticInduction_Day01Br2- H9 Embryoid body cells, melanocytic induction, day01, biol_rep2 (H9EB-2 d1)_CNhs12826_12726-135G8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep2H9EB2D1_CNhs12826_tpm_fwd H9MelanocyticInduction_Day01Br2+ H9 Embryoid body cells, melanocytic induction, day01, biol_rep2 (H9EB-2 d1)_CNhs12826_12726-135G8_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep1H9EB1D1_CNhs12823_tpm_rev H9MelanocyticInduction_Day01Br1- H9 Embryoid body cells, melanocytic induction, day01, biol_rep1 (H9EB-1 d1)_CNhs12823_12628-134E9_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay01BiolRep1H9EB1D1_CNhs12823_tpm_fwd H9MelanocyticInduction_Day01Br1+ H9 Embryoid body cells, melanocytic induction, day01, biol_rep1 (H9EB-1 d1)_CNhs12823_12628-134E9_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep3H9EB3D0_CNhs12908_tpm_rev H9MelanocyticInduction_Day00Br3- H9 Embryoid body cells, melanocytic induction, day00, biol_rep3 (H9EB-3 d0)_CNhs12908_12823-136I6_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep3H9EB3D0_CNhs12908_tpm_fwd H9MelanocyticInduction_Day00Br3+ H9 Embryoid body cells, melanocytic induction, day00, biol_rep3 (H9EB-3 d0)_CNhs12908_12823-136I6_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep2H9EB2D0_CNhs12825_tpm_rev H9MelanocyticInduction_Day00Br2- H9 Embryoid body cells, melanocytic induction, day00, biol_rep2 (H9EB-2 d0)_CNhs12825_12725-135G7_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep2H9EB2D0_CNhs12825_tpm_fwd H9MelanocyticInduction_Day00Br2+ H9 Embryoid body cells, melanocytic induction, day00, biol_rep2 (H9EB-2 d0)_CNhs12825_12725-135G7_forward Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep1H9EB1D0_CNhs12822_tpm_rev H9MelanocyticInduction_Day00Br1- H9 Embryoid body cells, melanocytic induction, day00, biol_rep1 (H9EB-1 d0)_CNhs12822_12627-134E8_reverse Regulation 
H9EmbryoidBodyCellsMelanocyticInductionDay00BiolRep1H9EB1D0_CNhs12822_tpm_fwd H9MelanocyticInduction_Day00Br1+ H9 Embryoid body cells, melanocytic induction, day00, biol_rep1 (H9EB-1 d0)_CNhs12822_12627-134E8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep3_CNhs13736_tpm_rev Hes3-gfpCardiomyocyticInduction_Day12Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep3_CNhs13736_13363-143F6_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep3_CNhs13736_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day12Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep3_CNhs13736_13363-143F6_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep2_CNhs13724_tpm_rev Hes3-gfpCardiomyocyticInduction_Day12Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep2_CNhs13724_13351-143E3_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep2_CNhs13724_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day12Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep2_CNhs13724_13351-143E3_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep1_CNhs13711_tpm_rev Hes3-gfpCardiomyocyticInduction_Day12Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep1_CNhs13711_13339-143C9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay12BiolRep1_CNhs13711_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day12Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day12, biol_rep1_CNhs13711_13339-143C9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep3_CNhs13735_tpm_rev Hes3-gfpCardiomyocyticInduction_Day11Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep3_CNhs13735_13362-143F5_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep3_CNhs13735_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day11Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep3_CNhs13735_13362-143F5_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep2_CNhs13723_tpm_rev Hes3-gfpCardiomyocyticInduction_Day11Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep2_CNhs13723_13350-143E2_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep2_CNhs13723_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day11Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep2_CNhs13723_13350-143E2_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep1_CNhs13710_tpm_rev Hes3-gfpCardiomyocyticInduction_Day11Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep1_CNhs13710_13338-143C8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay11BiolRep1_CNhs13710_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day11Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day11, biol_rep1_CNhs13710_13338-143C8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep3_CNhs13734_tpm_rev Hes3-gfpCardiomyocyticInduction_Day10Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep3_CNhs13734_13361-143F4_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep3_CNhs13734_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day10Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep3_CNhs13734_13361-143F4_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep2_CNhs13722_tpm_rev Hes3-gfpCardiomyocyticInduction_Day10Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep2_CNhs13722_13349-143E1_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep2_CNhs13722_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day10Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep2_CNhs13722_13349-143E1_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep1_CNhs13662_tpm_rev Hes3-gfpCardiomyocyticInduction_Day10Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep1_CNhs13662_13337-143C7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay10BiolRep1_CNhs13662_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day10Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day10, biol_rep1_CNhs13662_13337-143C7_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep3_CNhs13733_tpm_rev Hes3-gfpCardiomyocyticInduction_Day09Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep3_CNhs13733_13360-143F3_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep3_CNhs13733_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day09Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep3_CNhs13733_13360-143F3_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep2_CNhs13721_tpm_rev Hes3-gfpCardiomyocyticInduction_Day09Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep2_CNhs13721_13348-143D9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep2_CNhs13721_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day09Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep2_CNhs13721_13348-143D9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep1_CNhs13661_tpm_rev Hes3-gfpCardiomyocyticInduction_Day09Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep1_CNhs13661_13336-143C6_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay09BiolRep1_CNhs13661_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day09Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day09, biol_rep1_CNhs13661_13336-143C6_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep3_CNhs13732_tpm_rev Hes3-gfpCardiomyocyticInduction_Day08Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep3_CNhs13732_13359-143F2_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep3_CNhs13732_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day08Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep3_CNhs13732_13359-143F2_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep2_CNhs13720_tpm_rev Hes3-gfpCardiomyocyticInduction_Day08Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep2_CNhs13720_13347-143D8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep2_CNhs13720_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day08Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep2_CNhs13720_13347-143D8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep1_CNhs13660_tpm_rev Hes3-gfpCardiomyocyticInduction_Day08Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep1_CNhs13660_13335-143C5_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay08BiolRep1_CNhs13660_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day08Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day08, biol_rep1_CNhs13660_13335-143C5_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep3_CNhs13731_tpm_rev Hes3-gfpCardiomyocyticInduction_Day07Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep3_CNhs13731_13358-143F1_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep3_CNhs13731_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day07Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep3_CNhs13731_13358-143F1_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep2_CNhs13719_tpm_rev Hes3-gfpCardiomyocyticInduction_Day07Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep2_CNhs13719_13346-143D7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay07BiolRep2_CNhs13719_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day07Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day07, biol_rep2_CNhs13719_13346-143D7_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep3_CNhs13730_tpm_rev Hes3-gfpCardiomyocyticInduction_Day06Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep3_CNhs13730_13357-143E9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep3_CNhs13730_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day06Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep3_CNhs13730_13357-143E9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep2_CNhs13718_tpm_rev Hes3-gfpCardiomyocyticInduction_Day06Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep2_CNhs13718_13345-143D6_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep2_CNhs13718_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day06Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep2_CNhs13718_13345-143D6_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep1_CNhs13658_tpm_rev Hes3-gfpCardiomyocyticInduction_Day06Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep1_CNhs13658_13333-143C3_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay06BiolRep1_CNhs13658_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day06Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day06, biol_rep1_CNhs13658_13333-143C3_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep3_CNhs13729_tpm_rev Hes3-gfpCardiomyocyticInduction_Day05Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep3_CNhs13729_13356-143E8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep3_CNhs13729_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day05Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep3_CNhs13729_13356-143E8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep2_CNhs13717_tpm_rev Hes3-gfpCardiomyocyticInduction_Day05Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep2_CNhs13717_13344-143D5_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep2_CNhs13717_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day05Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep2_CNhs13717_13344-143D5_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep1_CNhs13657_tpm_rev Hes3-gfpCardiomyocyticInduction_Day05Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep1_CNhs13657_13332-143C2_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay05BiolRep1_CNhs13657_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day05Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day05, biol_rep1_CNhs13657_13332-143C2_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep3_CNhs13728_tpm_rev Hes3-gfpCardiomyocyticInduction_Day04Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep3_CNhs13728_13355-143E7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep3_CNhs13728_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day04Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep3_CNhs13728_13355-143E7_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep2_CNhs13716_tpm_rev Hes3-gfpCardiomyocyticInduction_Day04Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep2_CNhs13716_13343-143D4_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep2_CNhs13716_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day04Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep2_CNhs13716_13343-143D4_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep1_CNhs13656_tpm_rev Hes3-gfpCardiomyocyticInduction_Day04Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep1_CNhs13656_13331-143C1_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay04BiolRep1_CNhs13656_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day04Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day04, biol_rep1_CNhs13656_13331-143C1_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep3_CNhs13727_tpm_rev Hes3-gfpCardiomyocyticInduction_Day03Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep3_CNhs13727_13354-143E6_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep3_CNhs13727_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day03Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep3_CNhs13727_13354-143E6_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep2_CNhs13715_tpm_rev Hes3-gfpCardiomyocyticInduction_Day03Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep2_CNhs13715_13342-143D3_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep2_CNhs13715_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day03Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep2_CNhs13715_13342-143D3_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep1_CNhs13655_tpm_rev Hes3-gfpCardiomyocyticInduction_Day03Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep1_CNhs13655_13330-143B9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay03BiolRep1_CNhs13655_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day03Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day03, biol_rep1_CNhs13655_13330-143B9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep3_CNhs13726_tpm_rev Hes3-gfpCardiomyocyticInduction_Day02Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep3_CNhs13726_13353-143E5_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep3_CNhs13726_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day02Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep3_CNhs13726_13353-143E5_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep2_CNhs13714_tpm_rev Hes3-gfpCardiomyocyticInduction_Day02Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep2_CNhs13714_13341-143D2_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep2_CNhs13714_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day02Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep2_CNhs13714_13341-143D2_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep1_CNhs13654_tpm_rev Hes3-gfpCardiomyocyticInduction_Day02Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep1_CNhs13654_13329-143B8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay02BiolRep1_CNhs13654_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day02Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day02, biol_rep1_CNhs13654_13329-143B8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep3_CNhs13725_tpm_rev Hes3-gfpCardiomyocyticInduction_Day01Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep3_CNhs13725_13352-143E4_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep3_CNhs13725_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day01Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep3_CNhs13725_13352-143E4_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep2_CNhs13712_tpm_rev Hes3-gfpCardiomyocyticInduction_Day01Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep2_CNhs13712_13340-143D1_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep2_CNhs13712_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day01Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep2_CNhs13712_13340-143D1_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep1_CNhs13653_tpm_rev Hes3-gfpCardiomyocyticInduction_Day01Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep1_CNhs13653_13328-143B7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay01BiolRep1_CNhs13653_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day01Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day01, biol_rep1_CNhs13653_13328-143B7_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep3UH3_CNhs13738_tpm_rev Hes3-gfpCardiomyocyticInduction_Day00Br3- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep3 (UH-3)_CNhs13738_13366-143F9_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep3UH3_CNhs13738_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day00Br3+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep3 (UH-3)_CNhs13738_13366-143F9_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep2UH2_CNhs13695_tpm_rev Hes3-gfpCardiomyocyticInduction_Day00Br2- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep2 (UH-2)_CNhs13695_13365-143F8_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep2UH2_CNhs13695_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day00Br2+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep2 (UH-2)_CNhs13695_13365-143F8_forward Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep1UH1_CNhs13694_tpm_rev Hes3-gfpCardiomyocyticInduction_Day00Br1- HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep1 (UH-1)_CNhs13694_13364-143F7_reverse Regulation 
HES3GFPEmbryonicStemCellsCardiomyocyticInductionDay00BiolRep1UH1_CNhs13694_tpm_fwd Hes3-gfpCardiomyocyticInduction_Day00Br1+ HES3-GFP Embryonic Stem cells, cardiomyocytic induction, day00, biol_rep1 (UH-1)_CNhs13694_13364-143F7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep3LK60_CNhs13586_tpm_rev AorticSmsToIL1b_06hrBr3- Aortic smooth muscle cell response to IL1b, 06hr, biol_rep3 (LK60)_CNhs13586_12857-137D4_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep3LK60_CNhs13586_tpm_fwd AorticSmsToIL1b_06hrBr3+ Aortic smooth muscle cell response to IL1b, 06hr, biol_rep3 (LK60)_CNhs13586_12857-137D4_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep2LK59_CNhs13378_tpm_rev AorticSmsToIL1b_06hrBr2- Aortic smooth muscle cell response to IL1b, 06hr, biol_rep2 (LK59)_CNhs13378_12759-136B5_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep2LK59_CNhs13378_tpm_fwd AorticSmsToIL1b_06hrBr2+ Aortic smooth muscle cell response to IL1b, 06hr, biol_rep2 (LK59)_CNhs13378_12759-136B5_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_tpm_rev AorticSmsToIL1b_06hrBr1- Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b06hrBiolRep1LK58_CNhs13357_tpm_fwd AorticSmsToIL1b_06hrBr1+ Aortic smooth muscle cell response to IL1b, 06hr, biol_rep1 (LK58)_CNhs13357_12661-134I6_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_tpm_rev AorticSmsToIL1b_05hrBr2- Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep2LK56_CNhs13377_tpm_fwd AorticSmsToIL1b_05hrBr2+ Aortic smooth muscle cell response to IL1b, 05hr, biol_rep2 (LK56)_CNhs13377_12758-136B4_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_tpm_rev AorticSmsToIL1b_05hrBr1- Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b05hrBiolRep1LK55_CNhs13356_tpm_fwd AorticSmsToIL1b_05hrBr1+ Aortic smooth muscle cell response to IL1b, 05hr, biol_rep1 (LK55)_CNhs13356_12660-134I5_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_tpm_rev AorticSmsToIL1b_04hrBr3- Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep3LK54_CNhs13584_tpm_fwd AorticSmsToIL1b_04hrBr3+ Aortic smooth muscle cell response to IL1b, 04hr, biol_rep3 (LK54)_CNhs13584_12855-137D2_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_tpm_rev AorticSmsToIL1b_04hrBr2- Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep2LK53_CNhs13376_tpm_fwd AorticSmsToIL1b_04hrBr2+ Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)_CNhs13376_12757-136B3_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_tpm_rev AorticSmsToIL1b_04hrBr1- Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b04hrBiolRep1LK52_CNhs13682_tpm_fwd AorticSmsToIL1b_04hrBr1+ Aortic smooth muscle cell response to IL1b, 04hr, biol_rep1 (LK52)_CNhs13682_12659-134I4_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_tpm_rev AorticSmsToIL1b_03hrBr2- Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep2LK50_CNhs13375_tpm_fwd AorticSmsToIL1b_03hrBr2+ Aortic smooth muscle cell response to IL1b, 03hr, biol_rep2 (LK50)_CNhs13375_12756-136B2_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_tpm_rev AorticSmsToIL1b_03hrBr1- Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b03hrBiolRep1LK49_CNhs13355_tpm_fwd AorticSmsToIL1b_03hrBr1+ Aortic smooth muscle cell response to IL1b, 03hr, biol_rep1 (LK49)_CNhs13355_12658-134I3_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_tpm_rev AorticSmsToIL1b_02hrBr3- Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep3LK48_CNhs13582_tpm_fwd AorticSmsToIL1b_02hrBr3+ Aortic smooth muscle cell response to IL1b, 02hr, biol_rep3 (LK48)_CNhs13582_12853-137C9_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_tpm_rev AorticSmsToIL1b_02hrBr2- Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b02hrBiolRep2LK47_CNhs13374_tpm_fwd AorticSmsToIL1b_02hrBr2+ Aortic smooth muscle cell response to IL1b, 02hr, biol_rep2 (LK47)_CNhs13374_12755-136B1_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_tpm_rev AorticSmsToIL1b_01hrBr2- Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep2LK44_CNhs13373_tpm_fwd AorticSmsToIL1b_01hrBr2+ Aortic smooth muscle cell response to IL1b, 01hr, biol_rep2 (LK44)_CNhs13373_12754-136A9_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_tpm_rev AorticSmsToIL1b_01hrBr1- Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b01hrBiolRep1LK43_CNhs13353_tpm_fwd AorticSmsToIL1b_01hrBr1+ Aortic smooth muscle cell response to IL1b, 01hr, biol_rep1 (LK43)_CNhs13353_12656-134I1_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_tpm_rev AorticSmsToIL1b_00hr45minBr3- Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep3LK42_CNhs13580_tpm_fwd AorticSmsToIL1b_00hr45minBr3+ Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep3 (LK42)_CNhs13580_12851-137C7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_tpm_rev AorticSmsToIL1b_00hr45minBr2- Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep2LK41_CNhs13372_tpm_fwd AorticSmsToIL1b_00hr45minBr2+ Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep2 (LK41)_CNhs13372_12753-136A8_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_tpm_rev AorticSmsToIL1b_00hr45minBr1- Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr45minBiolRep1LK40_CNhs13352_tpm_fwd AorticSmsToIL1b_00hr45minBr1+ Aortic smooth muscle cell response to IL1b, 00hr45min, biol_rep1 (LK40)_CNhs13352_12655-134H9_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_tpm_rev AorticSmsToIL1b_00hr30minBr3- Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep3LK39_CNhs13579_tpm_fwd AorticSmsToIL1b_00hr30minBr3+ Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep3 (LK39)_CNhs13579_12850-137C6_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_tpm_rev AorticSmsToIL1b_00hr30minBr2- Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep2LK38_CNhs13371_tpm_fwd AorticSmsToIL1b_00hr30minBr2+ Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep2 (LK38)_CNhs13371_12752-136A7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_tpm_rev AorticSmsToIL1b_00hr30minBr1- Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr30minBiolRep1LK37_CNhs13351_tpm_fwd AorticSmsToIL1b_00hr30minBr1+ Aortic smooth muscle cell response to IL1b, 00hr30min, biol_rep1 (LK37)_CNhs13351_12654-134H8_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_tpm_rev AorticSmsToIL1b_00hr15minBr3- Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep3LK36_CNhs13578_tpm_fwd AorticSmsToIL1b_00hr15minBr3+ Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep3 (LK36)_CNhs13578_12849-137C5_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_tpm_rev AorticSmsToIL1b_00hr15minBr2- Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep2LK35_CNhs13370_tpm_fwd AorticSmsToIL1b_00hr15minBr2+ Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep2 (LK35)_CNhs13370_12751-136A6_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_tpm_rev AorticSmsToIL1b_00hr15minBr1- Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr15minBiolRep1LK34_CNhs13350_tpm_fwd AorticSmsToIL1b_00hr15minBr1+ Aortic smooth muscle cell response to IL1b, 00hr15min, biol_rep1 (LK34)_CNhs13350_12653-134H7_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_tpm_rev AorticSmsToIL1b_00hr00minBr3- Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep3LK33_CNhs13577_tpm_fwd AorticSmsToIL1b_00hr00minBr3+ Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep3 (LK33)_CNhs13577_12848-137C4_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_tpm_rev AorticSmsToIL1b_00hr00minBr2- Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep2LK32_CNhs13369_tpm_fwd AorticSmsToIL1b_00hr00minBr2+ Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_forward Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_tpm_rev AorticSmsToIL1b_00hr00minBr1- Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_reverse Regulation 
AorticSmoothMuscleCellResponseToIL1b00hr00minBiolRep1LK31_CNhs13349_tpm_fwd AorticSmsToIL1b_00hr00minBr1+ Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_forward Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_tpm_rev AorticSmsToFgf2_06hrBr3- Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep3LK30_CNhs13576_tpm_fwd AorticSmsToFgf2_06hrBr3+ Aortic smooth muscle cell response to FGF2, 06hr, biol_rep3 (LK30)_CNhs13576_12847-137C3_forward Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_tpm_rev AorticSmsToFgf2_06hrBr2- Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep2LK29_CNhs13368_tpm_fwd AorticSmsToFgf2_06hrBr2+ Aortic smooth muscle cell response to FGF2, 06hr, biol_rep2 (LK29)_CNhs13368_12749-136A4_forward Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_tpm_rev AorticSmsToFgf2_06hrBr1- Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF206hrBiolRep1LK28_CNhs13348_tpm_fwd AorticSmsToFgf2_06hrBr1+ Aortic smooth muscle cell response to FGF2, 06hr, biol_rep1 (LK28)_CNhs13348_12651-134H5_forward Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_tpm_rev AorticSmsToFgf2_05hrBr3- Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep3LK27_CNhs13575_tpm_fwd AorticSmsToFgf2_05hrBr3+ Aortic smooth muscle cell response to FGF2, 05hr, biol_rep3 (LK27)_CNhs13575_12846-137C2_forward Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_tpm_rev AorticSmsToFgf2_05hrBr2- Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep2LK26_CNhs13367_tpm_fwd AorticSmsToFgf2_05hrBr2+ Aortic smooth muscle cell response to FGF2, 05hr, biol_rep2 (LK26)_CNhs13367_12748-136A3_forward Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_tpm_rev AorticSmsToFgf2_05hrBr1- Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF205hrBiolRep1LK25_CNhs13347_tpm_fwd AorticSmsToFgf2_05hrBr1+ Aortic smooth muscle cell response to FGF2, 05hr, biol_rep1 (LK25)_CNhs13347_12650-134H4_forward Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_tpm_rev AorticSmsToFgf2_03hrBr3- Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep3LK21_CNhs13573_tpm_fwd AorticSmsToFgf2_03hrBr3+ Aortic smooth muscle cell response to FGF2, 03hr, biol_rep3 (LK21)_CNhs13573_12844-137B9_forward Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep2LK20_CNhs13364_tpm_rev AorticSmsToFgf2_03hrBr2- Aortic smooth muscle cell response to FGF2, 03hr, biol_rep2 (LK20)_CNhs13364_12746-136A1_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep2LK20_CNhs13364_tpm_fwd AorticSmsToFgf2_03hrBr2+ Aortic smooth muscle cell response to FGF2, 03hr, biol_rep2 (LK20)_CNhs13364_12746-136A1_forward Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep1LK19_CNhs13345_tpm_rev AorticSmsToFgf2_03hrBr1- Aortic smooth muscle cell response to FGF2, 03hr, biol_rep1 (LK19)_CNhs13345_12648-134H2_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF203hrBiolRep1LK19_CNhs13345_tpm_fwd AorticSmsToFgf2_03hrBr1+ Aortic smooth muscle cell response to FGF2, 03hr, biol_rep1 (LK19)_CNhs13345_12648-134H2_forward Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep3LK18_CNhs13572_tpm_rev AorticSmsToFgf2_02hrBr3- Aortic smooth muscle cell response to FGF2, 02hr, biol_rep3 (LK18)_CNhs13572_12843-137B8_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep3LK18_CNhs13572_tpm_fwd AorticSmsToFgf2_02hrBr3+ Aortic smooth muscle cell response to FGF2, 02hr, biol_rep3 (LK18)_CNhs13572_12843-137B8_forward Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep2LK17_CNhs13363_tpm_rev AorticSmsToFgf2_02hrBr2- Aortic smooth muscle cell response to FGF2, 02hr, biol_rep2 (LK17)_CNhs13363_12745-135I9_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep2LK17_CNhs13363_tpm_fwd AorticSmsToFgf2_02hrBr2+ Aortic smooth muscle cell response to FGF2, 02hr, biol_rep2 (LK17)_CNhs13363_12745-135I9_forward Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep1LK16_CNhs13344_tpm_rev AorticSmsToFgf2_02hrBr1- Aortic smooth muscle cell response to FGF2, 02hr, biol_rep1 (LK16)_CNhs13344_12647-134H1_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF202hrBiolRep1LK16_CNhs13344_tpm_fwd AorticSmsToFgf2_02hrBr1+ Aortic smooth muscle cell response to FGF2, 02hr, biol_rep1 (LK16)_CNhs13344_12647-134H1_forward Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep3LK15_CNhs13683_tpm_rev AorticSmsToFgf2_01hrBr3- Aortic smooth muscle cell response to FGF2, 01hr, biol_rep3 (LK15)_CNhs13683_12842-137B7_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep3LK15_CNhs13683_tpm_fwd AorticSmsToFgf2_01hrBr3+ Aortic smooth muscle cell response to FGF2, 01hr, biol_rep3 (LK15)_CNhs13683_12842-137B7_forward Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep1LK13_CNhs12741_tpm_rev AorticSmsToFgf2_01hrBr1- Aortic smooth muscle cell response to FGF2, 01hr, biol_rep1 (LK13)_CNhs12741_12646-134G9_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF201hrBiolRep1LK13_CNhs12741_tpm_fwd AorticSmsToFgf2_01hrBr1+ Aortic smooth muscle cell response to FGF2, 01hr, biol_rep1 (LK13)_CNhs12741_12646-134G9_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep3LK12_CNhs13571_tpm_rev AorticSmsToFgf2_00hr45minBr3- Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep3 (LK12)_CNhs13571_12841-137B6_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep3LK12_CNhs13571_tpm_fwd AorticSmsToFgf2_00hr45minBr3+ Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep3 (LK12)_CNhs13571_12841-137B6_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep2LK11_CNhs13361_tpm_rev AorticSmsToFgf2_00hr45minBr2- Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep2 (LK11)_CNhs13361_12743-135I7_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep2LK11_CNhs13361_tpm_fwd AorticSmsToFgf2_00hr45minBr2+ Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep2 (LK11)_CNhs13361_12743-135I7_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep1LK10_CNhs13343_tpm_rev AorticSmsToFgf2_00hr45minBr1- Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep1 (LK10)_CNhs13343_12645-134G8_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr45minBiolRep1LK10_CNhs13343_tpm_fwd AorticSmsToFgf2_00hr45minBr1+ Aortic smooth muscle cell response to FGF2, 00hr45min, biol_rep1 (LK10)_CNhs13343_12645-134G8_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep3LK9_CNhs13569_tpm_rev AorticSmsToFgf2_00hr30minBr3- Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep3 (LK9)_CNhs13569_12840-137B5_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep3LK9_CNhs13569_tpm_fwd AorticSmsToFgf2_00hr30minBr3+ Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep3 (LK9)_CNhs13569_12840-137B5_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep2LK8_CNhs13360_tpm_rev AorticSmsToFgf2_00hr30minBr2- Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep2 (LK8)_CNhs13360_12742-135I6_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep2LK8_CNhs13360_tpm_fwd AorticSmsToFgf2_00hr30minBr2+ Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep2 (LK8)_CNhs13360_12742-135I6_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep1LK7_CNhs13341_tpm_rev AorticSmsToFgf2_00hr30minBr1- Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep1 (LK7)_CNhs13341_12644-134G7_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr30minBiolRep1LK7_CNhs13341_tpm_fwd AorticSmsToFgf2_00hr30minBr1+ Aortic smooth muscle cell response to FGF2, 00hr30min, biol_rep1 (LK7)_CNhs13341_12644-134G7_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep3LK6_CNhs13568_tpm_rev AorticSmsToFgf2_00hr15minBr3- Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep3 (LK6)_CNhs13568_12839-137B4_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep3LK6_CNhs13568_tpm_fwd AorticSmsToFgf2_00hr15minBr3+ Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep3 (LK6)_CNhs13568_12839-137B4_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_tpm_rev AorticSmsToFgf2_00hr15minBr2- Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep2LK5_CNhs13359_tpm_fwd AorticSmsToFgf2_00hr15minBr2+ Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep2 (LK5)_CNhs13359_12741-135I5_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_tpm_rev AorticSmsToFgf2_00hr15minBr1- Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr15minBiolRep1LK4_CNhs13340_tpm_fwd AorticSmsToFgf2_00hr15minBr1+ Aortic smooth muscle cell response to FGF2, 00hr15min, biol_rep1 (LK4)_CNhs13340_12643-134G6_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep2LK2_CNhs13358_tpm_rev AorticSmsToFgf2_00hr00minBr2- Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep2LK2_CNhs13358_tpm_fwd AorticSmsToFgf2_00hr00minBr2+ Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_forward Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_tpm_rev AorticSmsToFgf2_00hr00minBr1- Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_reverse Regulation 
AorticSmoothMuscleCellResponseToFGF200hr00minBiolRep1LK1_CNhs13339_tpm_fwd AorticSmsToFgf2_00hr00minBr1+ Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_forward Regulation 
wgEncodeOpenChromSynth Open Chrom Synth GSE40833 None DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA) Regulation Description These tracks display a synthesis of evidence from different assays as part of the four Open Chromatin track sets. This track displays open chromatin regions and/or transcription factor binding sites identified in multiple cell types by one or more complementary methodologies: DNaseI hypersensitivity (HS) (Duke DNaseI HS), Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (UNC FAIRE), and chromatin immunoprecipitation (ChIP) for select regulatory factors (UTA TFBS). Each methodology was performed on the same cell type using identical growth conditions. (Note: Data for some or all ChIP experiments may not be available for all cell types). Regions that overlap between methodologies identify regulatory elements that are cross-validated indicating high confidence regions. In addition, multiple lines of evidence suggest that regions detected by a single assay (e.g., DNase-only or FAIRE-only) are also biologically relevant (Song et al., submitted). DNaseI HS data: DNaseI is an enzyme that has long been used to map general chromatin accessibility, and DNaseI "hypersensitivity" is a feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions, and novel elements. DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome. FAIRE data: FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) is a method to isolate and identify nucleosome-depleted regions of the genome. FAIRE was initially discovered in yeast and subsequently shown to identify active regulatory elements in human cells (Giresi et al., 2007). Similar to DNaseI HS, FAIRE appears to identify functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions and novel elements. ChIP data: ChIP (Chromatin Immunoprecipitation) is a method to identify the specific location of proteins that are directly or indirectly bound to genomic DNA. By identifying the binding location of sequence-specific transcription factors, general transcription machinery components, and chromatin factors, ChIP can help in the functional annotation of the open chromatin regions identified by DNaseI HS mapping and FAIRE. Input data: As a background control experiment, the input genomic DNA sample that was used for ChIP was sequenced. Crosslinked chromatin is sheared and the crosslinks are reversed without carrying out the immunoprecipitation step. This sample is otherwise processed in a manner identical to the ChIP sample as described below. The input track is useful in revealing potential artifacts arising from the sequence alignment process such as copy number differences between the reference genome and the sequenced samples, as well as regions of poor sequence alignability. Display Conventions and Configuration This track contains multiple subtracks representing different cell types that display individually on the browser. Instructions for configuring tracks with multiple subtracks are here. To facilitate analyses, each region has been assigned an Open Chromatin Code (OC Code), based on the assay(s) by which it was detected, and a color, based on its level of validation (which was determined by the combination of its OC Code and its statistical significance): Validated, OC Code = 1: Black: Regions identified as peaks by both the DNaseI HS assay and FAIRE assay. Peaks for DNaseI HS have DNase peak calling p-values &lt; 0.05 (-log10(p-value) &gt; 1.3) and peaks for FAIRE have FAIRE peak calling p-values &lt; 0.1 (-log10(p-value) &gt; 1.0). Open Chromatin, OC Code = 2 or 3: Blue (high significance): Regions not identified as peaks in both DNaseI HS and FAIRE, but for which the combination of peak calling p-values from these assays using Fisher's combined probability test results in a p-value &lt; 0.01 (-log10(p-value) &gt; 2). DNase, OC Code = 2: Green (low significance): Regions identified by DNaseI HS as peaks (DNase peak calling p-value &lt; 0.05 (-log10(p-value) &gt; 1.3)) and not identified by FAIRE as peaks (FAIRE peak calling p-value &lt; 0.1 (-log10(p-value) &gt; 1.0)), and with a Fisher's combined DNaseI HS and FAIRE p-value &gt;= 0.01 (-log10(p-value) &lt;= 2). Blue (high significance): see Open Chromatin above. FAIRE, OC Code = 3: Dark Red (low significance): Regions identified by FAIRE as peaks (FAIRE peak calling p-value &lt; 0.1 (-log10(p-value) &gt; 1.0)) and not identified by DNaseI HS as peaks (DNase peak calling p-value &lt; 0.05 (-log10(p-value) &gt; 1.3)), and with a Fisher's combined DNaseI HS and FAIRE p-value &gt;= 0.01 (-log10(p-value) &lt;= 2). Blue (high significance): see Open Chromatin above. ChIP-seq, OC Code = 4: Pink: Regions identified by ChIP-seq as peaks (at least one of the peak calling p-values for the three ChIP experiments are &lt; 0.05 (-log10(p-value) &gt; 1.3)) indicating binding sites for one or more of RNA Pol II, CTCF, and c-Myc described here and not identified by DNaseI HS or FAIRE as peaks. Peaks for ChIP-seq have p-values &lt; 0.05 (-log10(p-value) &gt; 1.3). For RNA Pol II, only sites that overlap annotated transcription start sites by the UCSC Genes track are considered. All signal values, -log10(p-values), and the OC Code are displayed on the detail page for each element and are available in the corresponding bed file. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods For each site, the maximum F-Seq Density Signal value has been calculated for each assay that was performed in that cell type. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Significant regions, or peaks, were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05 (DNaseI HS, ChIP) or 0.1 (FAIRE) threshold were considered significant. See assay specific description pages (Duke DNaseI HS, UNC FAIRE and UTA TFBS) for more details. A Fisher's Combined P-value for DNaseI HS and FAIRE was calculated using Fisher's combined probability test. First, a test statistic is calculated using the formula: X2 = -2&#8721;loge(pi) where pi are the p-values calculated for DNaseI HS and FAIRE. X2 follows a chi-squared distribution, thus a combined p-value can be assigned to this test statistic. Enhancer and Insulator Functional assays: A subset of DNaseI and FAIRE regions were cloned into functional tissue culture reporter assays to test for enhancer and insulator activity. Coordinates and results from these experiments can be found here. Release Notes This is release 2 (Feb 2012) of this track and is based upon these three Open Chromatin tracks: Duke DNaseI HS, UNC FAIRE, and UTA TFBS. Release 2 brings in synthesis analysis for 10 samples: Gliobla, GM12891, GM12892, GM18507, GM19239, HeLa-S3/IFNa4h, HTR8svn, Medullo, PanIslets, Urothelia. Credits These data and annotations were created by a collaboration of multiple institutions (contact: Terry Furey): Duke University's Institute for Genome Sciences & Policy (IGSP): Zhancheng Zhang, Lingyun Song, Terry Furey, and Greg Crawford University of North Carolina at Chapel Hill: Paul Giresi and Jason Lieb Universty of Texas at Austin: Zheng Liu, Ryan McDaniell, Bum-Kyu Lee, and Vishy Iyer European Bioinformatics Insitute: Paul Flicek, Damian Keefe, and Ewan Birney University of Cambridge, Department of Oncology and CR-UK Cambridge Research Institute (CRI): Stefan Graf References Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res. 2007 Jun;17(6):910-6. Birney E, Stamatoyannopoulos JA, Dutta A, Guig&#243; R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008 Jan 25;132(2):311-22. Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8. Buck MJ, Nobel AB, Lieb JD. ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 2005;6(11):R97. Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods. 2006 Jul;3(7):503-9. Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123-31. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007 Jun;17(6):877-885. Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods. 2009 Jul;48(3):233-9. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Nov;18(11):1851-8. Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeOpenChromSynthPanisletsPk Pan Islets Syn Pk PanIslets Combined ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002261 2261 GSM1002652 Crawford Duke 1.0 wgEncodeOpenChromSynthPanisletsPk None Peaks pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment PanIslets DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthNhekPk NHEK Syn Pk NHEK Combined ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001329 1329 GSM1002658 Crawford Duke 1.0 wgEncodeOpenChromSynthNhekPk None Peaks epidermal keratinocytes Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment NHEK DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthMedulloPk Medullo Syn Pk Medullo Combined ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002260 2260 GSM1002667 Crawford Duke 1.0 wgEncodeOpenChromSynthMedulloPk None Peaks medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment Medullo DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthHtr8Pk HTR8svn Syn Pk HTR8svn Combined ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002258 2258 GSM1002661 Crawford Duke 1.0 wgEncodeOpenChromSynthHtr8Pk None Peaks trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment HTR8svn DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthGm19239Pk GM19239 Syn Pk GM19239 Combined ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002256 2256 GSM1002663 Crawford Duke 1.0 wgEncodeOpenChromSynthGm19239Pk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment GM19239 DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthGm18507Pk GM18507 Syn Pk GM18507 Combined ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002255 2255 GSM1002664 Crawford Duke 1.0 wgEncodeOpenChromSynthGm18507Pk None Peaks lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment GM18507 DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthGm12892Pk GM12892 Syn Pk GM12892 Combined ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002254 2254 GSM1002665 Crawford Duke 1.0 wgEncodeOpenChromSynthGm12892Pk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment GM12892 DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthGm12891Pk GM12891 Syn Pk GM12891 Combined ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002253 2253 GSM1002666 Crawford Duke 1.0 wgEncodeOpenChromSynthGm12891Pk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment GM12891 DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthGlioblaPk Gliobla Syn Pk Gliobla Combined ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002257 2257 GSM1002662 Crawford Duke 1.0 wgEncodeOpenChromSynthGlioblaPk None Peaks glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment Gliobla DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthHuvecPk HUVEC Syn Pk HUVEC Combined ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001325 1325 GSM1002656 Crawford Duke 1.0 wgEncodeOpenChromSynthHuvecPk None Peaks umbilical vein endothelial cells Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment HUVEC DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthHepg2Pk HepG2 Syn Pk HepG2 Combined ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001327 1327 GSM1002654 Crawford Duke 1.0 wgEncodeOpenChromSynthHepg2Pk None Peaks hepatocellular carcinoma Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment HepG2 DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthHelas3Pk HeLa-S3 Syn Pk HeLa-S3 Combined ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001326 1326 GSM1002653 Crawford Duke 1.0 wgEncodeOpenChromSynthHelas3Pk None Peaks cervical carcinoma Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment HeLa-S3 DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthHelas3Ifna4hPk HeLa-S3 Syn Pk HeLa-S3 Combined ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002259 2259 GSM1002660 Crawford Duke 1.0 wgEncodeOpenChromSynthHelas3Ifna4hPk IFNa4h Peaks cervical carcinoma Multi-assay Synthesis Crawford Crawford - Duke University 4 hours of 500 U/ml Interferon alpha (Crawford) Regions of enriched signal in experiment HeLa-S3 IFNa4h DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthK562Pk K562 Syn Pk K562 Combined ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001328 1328 GSM1002657 Crawford Duke 1.0 wgEncodeOpenChromSynthK562Pk None Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment K562 DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthH1hescPk H1-hESC Syn Pk H1-hESC Combined ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001324 1324 GSM1002655 Crawford Duke 1.0 wgEncodeOpenChromSynthH1hescPk None Peaks embryonic stem cells Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment H1-hESC DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
wgEncodeOpenChromSynthGm12878Pk GM12878 Syn Pk GM12878 Combined ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001323 1323 GSM1002651 Crawford Duke 1.0 wgEncodeOpenChromSynthGm12878Pk None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Multi-assay Synthesis Crawford Crawford - Duke University Regions of enriched signal in experiment GM12878 DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom Regulation 
affyU95 Affy U95 Alignments of Affymetrix Consensus/Exemplars from HG-U95 Expression Description This track shows the location of the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U95Av2 chip. For this chip, probes are predominantly designed from consensus sequences. Methods Consensus and exemplar sequences were downloaded from the Affymetrix Product Support and mapped to the genome using blat followed by pslReps with the parameters: -minCover=0.3 -minAli=0.95 -nearTop=0.005 Credits Thanks to Affymetrix for the data underlying this track. 
evoCpg Evo Cpg Weizmann Evolutionary CpG Islands Comparative Genomics Description Evolutionary analysis of CpG-rich regions reveals that several distinct processes generate and maintain CpG islands. One central evolutionary regime resulting in enriched CpG content is driven by low levels of DNA methylation and consequentially low rates of deamination (C &#8594; T). Another major force forming CpG islands is biased gene conversion, which stabilizes constitutively methylated CpG islands by balancing rapid deamination with G/C fixation, indirectly increasing the CpG frequency. This track classifies contiguous CpG rich regions according to their inferred evolutionary dynamics. Analysis of different epigenetic marks (DNA methylation and others) should usually be performed separately for the different evolutionary classes. Display Conventions The track shows contiguous (100bp or more) genomic elements with CpG content greater than 3%, color-coded according to their classification of evolutionary dynamics. Green elements represent CpG islands that have low rates of C&#8594;T deamination and are typically unmethylated. Red elements represent CpG rich regions that gain G/C quickly and are in many cases constitutively methylated. Blue elements represent CpG rich loci that overlap exons (where stabilization of CpGs can be explained by indirect selective pressure on coding sequence). A probabilistic score for each CpG island indicates the specificity of the evolutionary behavior; positive values indicate hypo-deamination and negative values indicate high rates of G/C gain.The intensity of the CpG island classification score is also represented in the shade of the CpG island element (shades of green for hypodeaminated elements, and shades of red for constitutively methylated islands). Note: CpG islands in chromosomes X and Y and islands that cannot be aligned to other primate genomes are currently ignored. Methods A parameter-rich evolutionary model was used to infer substitution dynamics over genomic bins of 50bp and clustering analysis identified two major types of genomic behaviors (as described in Mendelson Cohen, Kenigsberg and Tanay, Cell 2011). The distributions of evolutionary parameters in each cluster (Figure 3 in the paper) were used to compute a log-odds score for each 50bp genomic bin. Bins with CpG content higher than 3% (smoothed over 500bp) were then assembled into contiguous segments as follows: Adjacent bins from the same cluster were merged. Ambiguously classified bins were merged with any adjacent non-ambiguous bins. Bins of the same class with gaps of up to 50bp were merged. Short intervals (&lt;200bp) at a distance less than 100bp were also merged. Intervals shorter than 100bp were discarded. All merged intervals were reclassified according to the mean log-odds score spanning the entire interval. The Evo CpG data of hg18 was lifted to hg19 by Weizmann Institute of Science. The raw inferred evolutionary statistics and cluster distributions are available upon request (amos.tanay@weizmann.ac.il) Credits Thanks to Amos Tanay's lab at the Weizmann Institute of Science for the evolutionary model and classification scheme. References Cohen NM, Kenigsberg E, Tanay A. Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell. 2011 May 27;145(5):773-86. PMID: 21620139 
HInvGeneMrna H-Inv H-Invitational Genes mRNA Alignments mRNA and EST Description This track shows alignments of full-length cDNAs that were used as the basis of the H-Invitational Gene Database (HInv-DB). The HInv-DB is a human gene database containing human-curated annotation of 41,118 full-length cDNA clones representing 21,037 cDNA clusters. The project was initiated in 2002 and the database became publicly available in April 2004. HInv-DB entries describe the following entities: gene structures functions novel alternative splicing isoforms non-coding functional RNAs functional domains sub-cellular localizations metabolic pathways predictions of protein 3D structure mapping of SNPs and microsatellite repeat motifs in relation with orphan diseases gene expression profiling comparative results with mouse full-length cDNAs gene structures Methods To cluster redundant cDNAs and alternative splicing variants within the H-Inv cDNAs, a total of 41,118 H-Inv cDNAs were mapped to the human genome using the mapping pipeline developed by the Japan Biological Information Research Center (JBIRC). The mapping yielded 40,140 cDNAs that were aligned against the genome using the stringent criteria of at least 95% identity and 90% length coverage. These 40,140 cDNAs were clustered to 20,190 loci, resulting in an average of 2.0 cDNAs per locus. For the remaining 978 unmapped cDNAs, cDNA-based clustering was applied, yielding 847 clusters. In total, 21,037 clusters (20,190 mapped and 847 unmapped) were identified and integrated into H-InvDB. H-Inv cluster IDs (e.g. HIX0000001) were assigned to these clusters. A representative sequence was selected from each cluster and used for further analyses and annotation. A full description of the construction of the HInv-DB is contained in the report by the H-Inv Consortium (see References section). Credits The H-InvDB is hosted at the JBIRC. The human-curated annotations were produced during invitational annotation meetings held in Japan during the summer of 2002, with a follow-up meeting in November 2004. Participants included 158 scientists representing 67 institutions from 12 countries. The full-length cDNA clones and sequences were produced by the Chinese National Human Genome Center (CHGC), the Deutsches Krebsforschungszentrum (DKFZ/MIPS), Helix Research Institute, Inc. (HRI), the Institute of Medical Science in the University of Tokyo (IMSUT), the Kazusa DNA Research Institute (KDRI), the Mammalian Gene Collection (MGC/NIH) and the Full-Length Long Japan (FLJ) project. References Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi- Kabata Y, Tanino M et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2004 Jun;2(6):e162. PMID: 15103394; PMC: PMC393292 
affyU133 Affy U133 Alignments of Affymetrix Consensus/Exemplars from HG-U133 Expression Description This track shows the location of the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U133A and HG-U133B chips. Methods Consensus and exemplar sequences were downloaded from the Affymetrix Product Support and mapped to the genome using blat followed by pslReps with the parameters: -minCover=0.5 -minAli=0.97 -nearTop=0.005 Credits Thanks to Affymetrix for the data underlying this track. 
knownGeneV45lift37 GENCODE V45lift37 GENCODE V45lift37 Genes and Gene Predictions Description The GENCODE Genes track (version 45, January 2024) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. By default, only the basic gene set is displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts that GENCODE believes will be useful to the majority of users. The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes are not displayed by default. It contains annotations on the reference chromosomes as well as assembly patches and alternative loci (haplotypes). Statistics for the v45 release can be found in the GENCODE site for this build. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. It includes options to display the entire GENCODE set and pseudogenes. To customize these options, the respective boxes can be checked or unchecked at the top of this description page. This track also includes a variety of labels which identify the transcripts when visibility is set to &quot;full&quot; or &quot;pack&quot;. Gene symbols (e.g. NIPA1) are displayed by default, but additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene and transcript names can be found in our FAQ. This track, in general, follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. Coloring for the gene annotations is based on the annotation type: coding: protein coding transcripts, including polymorphic pseudogenes non-coding: non-protein coding transcripts pseudogene: pseudogene transcript annotations problem: problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. There is also an option to display the data as a density graph, which can be helpful for visualizing the distribution of items over a region. Squishy-pack Display Within a gene using the pack display mode, transcripts below a specified rank will be condensed into a view similar to squish mode. The transcript ranking approach is preliminary and will change in future releases. The transcripts rankings are defined by the following criteria for protein-coding and non-coding genes: Protein_coding genes MANE or Ensembl canonical 1st: MANE Select / Ensembl canonical 2nd: MANE Plus Clinical Coding biotypes 1st: protein_coding and protein_coding_LoF 2nd: NMDs and NSDs 3rd: retained intron and protein_coding_CDS_not_defined Completeness 1st: full length 2nd: CDS start/end not found CARS score (only for coding transcripts) Transcript genomic span and length (only for non-coding transcripts) Non-coding genes Transcript biotype 1st: transcript biotype identical to gene biotype Ensembl canonical GENCODE basic Transcript genomic span Transcript length Methods The GENCODE v45 track was built from the GENCODE downloads file gencode.v45.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources were correlated with the GENCODE data to build association tables. Related Data The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a downloadable file. One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list is then available on the table menu. Data access GENCODE Genes and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. The genePred format files for hg38 are available from our downloads directory or in our GTF download directory. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. Credits The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a computational pipeline developed by Jim Kent and Brian Raney. This version of the track was generated by Jonathan Casper. References Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. PMID: 36420896; PMC: PMC9825462 A full list of GENCODE publications is available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
knownGeneArchive Genes Archive Previous versions of GENCODE/UCSC Genes (knownGene) Genes and Gene Predictions Description This super track contains previous versions of the GENCODE primary gene set. 
allHg19RS_BW GERP GERP Scores for Mammalian Alignments Comparative Genomics Description Genomic Evolutionary Rate Profiling (GERP) is a method for producing position-specific estimates of evolutionary constraint using maximum likelihood evolutionary rate estimation. It also discovers "constrained elements" where multiple positions combine to give a signal that is indicative of a putative functional element; this track shows the position-specific scores only, not the element predictions. Constraint intensity at each individual alignment position is quantified in terms of a "rejected substitutions" (RS) score, defined as the number of substitutions expected under neutrality minus the number of substitutions "observed" at the position. This concept was described, and a first implementation of GERP was presented, in Cooper et al (2005). GERP++ as described in Davydov et al (2010) uses a more rigorous set of algorithms to calculate site-specific RS scores and to discover evolutionarily constrained elements. Sites are scored independently. Positive scores represent a substitution deficit (i.e., fewer substitutions than the average neutral site) and thus indicate that a site may be under evolutionary constraint. Negative scores indicate that a site is probably evolving neutrally; negative scores should not be interpreted as evidence of accelerated rates of evolution because of too many strong confounders, such as alignment uncertainty or rate variance. Positive scores scale with the level of constraint, such that the greater the score, the greater the level of evolutionary constraint inferred to be acting on that site. We applied GERP, as implemented in the GERP++ software package, to quantify the level of evolutionary constraint acting on each site in hg19, based on an alignment of 35 mammals to hg19 with a maximum phylogenetic scope of 6.18 substitutions per neutral site. Gaps in the alignment are treated as missing data, which means that the number of substitutions per neutral site will be less than 6.18 in sites where one or more species has a gap. Thus, RS scores range from a maximum of 6.18 down to a below-zero minimum, which we cap at -12.36. RS scores will vary with alignment depth and level of sequence conservation. A score of 0 indicates that the alignment was too shallow at that position to get a meaningful estimate of constraint. Should classification into "constrained" and "unconstrained" sites be desired, a threshold may be chosen above which sites are considered "constrained". In practice, we find that a RS score threshold of 2 provides high sensitivity while still strongly enriching for truly constrained sites. Methods Given a multiple sequence alignment and a phylogenetic tree with branch lengths representing the neutral rate between the species within that alignment, GERP++ quantifies constraint intensity at each individual position in terms of rejected substitutions, the difference between the neutral rate and the estimated evolutionary rate at the position. GERP++ begins with a pre-defined neutral tree relating the genomes present within the alignment that supplies both the total neutral rate across the entire tree and the relative length of each individual branch. For each alignment column, we estimate a scaling factor, applied uniformly to all branches of the tree, that maximizes the probability of the observed nucleotides in the alignment column. The product of the scaling factor and the neutral rate defines the 'observed' rate of evolution at each position. GERP++ uses the HKY85 model of evolution with the transition/transversion ratio set to 2.0 and nucleotide frequencies estimated from the multiple alignment. To generate RS scores for each position in the human genome, we used GERP++ to analyze the TBA alignment of hg19 to 35 other mammalian species (listed here: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz46way/), spanning over 3 billion positions (see the description for the 'Conservation' track for details of this alignment). The alignment was compressed to remove gaps in the human sequence, and GERP++ scores were computed for every position with at least 3 ungapped species present. Importantly, the human sequence was removed from the alignment and not included in either the neutral rate estimation or the site-specific "observed" estimates, and therefore is not included in the RS score. This is consistent with the published work on GERP, and is done to eliminate the confounding influence of deleterious derived alleles segregating in the human population that are present in the reference sequence. The phylogenetic tree used was the generally accepted topology. Neutral branch lengths were estimated from 4-fold degenerate sites in the alignment. Credits The RS scores were generated by David Goode, Dept. of Genetics, Stanford University. GERP++ was developed by Eugene Davydov and Serafim Batzoglou, Dept. of Computer Science, Stanford University; Arend Sidow, Depts. of Pathology and Genetics, Stanford University; and Gregory Cooper, HudsonAlpha Institute for Biotechnology, Huntsville, AL. References Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++ . PLoS Comput Biol. 2010 Dec 2;6(12):e1001025. Cooper GM, Stone EA, Asimenos G; NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence . Genome Res. 2005 Jul;15(7):901-13. For more information on using GERP to detect putatively functional genetic variation: Cooper GM, Goode DL, Ng SB, Sidow A, Bamshad MJ, Shendure J, Nickerson DA. Single-nucleotide evolutionary constraint scores highlight disease-causing mutations . Nature Methods. 2010 Apr;7(4):250-1. Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM, Sidow A. Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes . Genome Res. 2010 Mar;20(3):301-10. 
est Human ESTs Human ESTs Including Unspliced mRNA and EST Description This track shows alignments between human expressed sequence tags (ESTs) in GenBank and the genome. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. NOTE: As of April, 2007, we no longer include GenBank sequences that contain the following URL as part of the record: http://fulllength.invitrogen.com Some of these entries are the result of alignment to pseudogenes, followed by &quot;correction&quot; of the EST to match the genomic sequence. It is therefore not the sequence of the actual EST and makes it appear that the EST is transcribed. Invitrogen no longer sells the clones. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the EST display. For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only ESTs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, ESTs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display ESTs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those ESTs that match the filter criteria. This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods To make an EST, RNA is isolated from cells and reverse transcribed into cDNA. Typically, the cDNA is cloned into a plasmid vector and a read is taken from the 5' and/or 3' primer. For most &mdash; but not all &mdash; ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. The reverse transcriptase may or may not make it to the 5' end of the mRNA, which may or may not be degraded. In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. Some of the newer cap-selected libraries cover transcription start reasonably well. Before the cap-selection techniques emerged, some projects used random rather than poly-A priming in an attempt to retrieve sequence distant from the 3' end. These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. Even outside of the random-primed projects, there is a degree of non-mRNA contamination. Because of this, a single unspliced EST should be viewed with considerable skepticism. To generate this track, human ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from EST sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. Kent WJ. BLAT - The BLAST-Like Alignment Tool. Genome Res. 2002 Apr;12(4):656-64. 
knownGeneKent UCSC Genes 2013 Legacy UCSC Genes track (knownGene) from 2013 Genes and Gene Predictions Description The UCSC Genes track is a set of gene predictions based on data from RefSeq, GenBank, CCDS, Rfam, and the tRNA Genes track. The track includes both protein-coding genes and non-coding RNA genes. Both types of genes can produce non-coding transcripts, but non-coding RNA genes do not produce protein-coding transcripts. This is a moderately conservative set of predictions. Transcripts of protein-coding genes require the support of one RefSeq RNA, or one GenBank RNA sequence plus at least one additional line of evidence. Transcripts of non-coding RNA genes require the support of one Rfam or tRNA prediction. Compared to RefSeq, this gene set has generally about 10% more protein-coding genes, approximately four times as many putative non-coding genes, and about twice as many splice variants. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track in general follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. The following color key is used: Black -- feature has a corresponding entry in the Protein Data Bank (PDB) Dark blue -- transcript has been reviewed or validated by either the RefSeq, SwissProt or CCDS staff Medium blue -- other RefSeq transcripts Light blue -- non-RefSeq transcripts This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. Methods The UCSC Genes are built using a multi-step pipeline: RefSeq and GenBank RNAs are aligned to the genome with BLAT, keeping only the best alignments for each RNA. Alignments are discarded if they do not meet certain sequence identity and coverage filters. All sequences must align with high (98%) identity. The sequence coverage must be at least 90% for shorter sequences (those with 2500 or fewer bases), with the coverage threshold progressively relaxed for longer sequences. Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out. A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge. Gene models from the Consensus CDS project (CCDS) are also added to the graph. A similar splicing graph is created in the mouse, based on mouse RNA and ESTs. If the mouse graph has an edge that is orthologous to an edge in the human graph, that is added to the evidence for the human edge. If an edge in the splicing graph is supported by two or more human ESTs, it is added as evidence for the edge. If there is an Exoniphy prediction for an exon, that is added as evidence. The graph is traversed to generate all unique transcripts. The traversal is guided by the initial RNAs to avoid a combinatorial explosion in alternative splicing. All RefSeq transcripts are output. For other multi-exon transcripts to be output, an edge supported by at least one additional line of evidence beyond the RNA is required. Single-exon genes require either two RNAs or two additional lines of evidence beyond the single RNA. Alignments are merged in from the hg19 tRNA Genes track and from Rfam in regions that are syntenic with the mm9 mouse genome. Protein predictions are generated. For non-RefSeq transcripts we use the txCdsPredict program to determine if the transcript is protein-coding, and if so, the locations of the start and stop codons. The program weighs as positive evidence the length of the protein, the presence of a Kozak consensus sequence at the start codon, and the length of the orthologous predicted protein in other species. As negative evidence it considers nonsense-mediated decay and start codons in any frame upstream of the predicted start codon. For RefSeq transcripts the RefSeq protein prediction is used directly instead of this procedure. For CCDS proteins the CCDS protein is used directly. The corresponding UniProt protein is found, if any. The transcript is assigned a permanent &quot;uc&quot; accession. If the transcript was not in the previous release of UCSC Genes, the accession ends with the suffix &quot;.1&quot; indicating that this is the first version of this transcript. If the transcript is identical to some transcript in the previous release of UCSC Genes, the accession is re-used with the same version number. If the transcript is not identical to any transcript in the previous release but it overlaps a similar transcript with a compatible structure, the previous accession is re-used with the version number incremented. Related Data The UCSC Genes transcripts are annotated in numerous tables, each of which is also available as a downloadable file. These include tables that link UCSC Genes transcripts to external datasets (such as knownToLocusLink, which maps UCSC Genes transcripts to Entrez identifiers, previously known as Locus Link identifiers), and tables that detail some property of UCSC Genes transcript sequences (such as knownToPfam, which identifies any Pfam domains found in the UCSC Genes protein-coding transcripts). One can see a full list of the associated tables in the Table Browser by selecting UCSC Genes at the track menu; this list is then available at the table menu. Note that some of these tables refer to UCSC Genes by its former name of Known Genes, sometimes abbreviated as known or kg. While the complete set of annotation tables is too long to describe, some of the more important tables are described below. kgXref identifies the RefSeq, SwissProt, Rfam, or tRNA sequences (if any) on which each transcript was based. knownToRefSeq identifies the RefSeq transcript that each UCSC Genes transcript is most closely associated with. That RefSeq transcript is either the RefSeq on which the UCSC Genes transcript was based, if there is one, or it's the RefSeq transcript that the UCSC Genes transcript overlaps at the most bases. knownGeneMrna contains the mRNA sequence that represents each UCSC Genes transcript. If the transcript is based on a RefSeq transcript, then this table contains the RefSeq transcript, including any portions that do not align to the genome. knownGeneTxMrna contains mRNA sequences for each UCSC Genes transcript. In contrast to the sequencess in knownGeneMrna, these sequences are derived by obtaining the sequences for each exon from the reference genome and concatenating these exonic sequences. knownGenePep contains the protein sequences derived from the knownGeneMrna transcript sequences. Any protein-level annotations, such as the contents of the knownToPfam table, are based on these sequences. knownGeneTxPep contains the protein translation (if any) of each mRNA sequence in knownGeneTxMrna. knownIsoforms maps each transcript to a cluster ID, a cluster of isoforms of the same gene. knownCanonical identifies the canonical isoform of each cluster ID, or gene. Generally, this is the longest isoform. Data access UCSC Genes (knownGene for hg19) can be explored interactively using the REST API, the Table Browser or the Data Integrator. The genePred files for hg19 are available in our downloads directory or in our genes downloads directory in GTF format. All the tables can also be queried directly from our public MySQL servers. Information on accessing this data through MySQL can be found on our help page as well as on our blog. Credits The UCSC Genes track was produced at UCSC using a computational pipeline developed by Jim Kent, Chuck Sugnet, Melissa Cline and Mark Diekhans. It is based on data from NCBI RefSeq, UniProt (including TrEMBL and TrEMBL-NEW), CCDS, and GenBank as well as data from Rfam and the Todd Lowe lab. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them. References Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009 Jan;37(Database issue):D93-7. PMID: 18984615; PMC: PMC2686519 Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR et al. Rfam: Wikipedia, clans and the &quot;decimal&quot; release. Nucleic Acids Res. 2011 Jan;39(Database issue):D141-5. PMID: 21062808; PMC: PMC3013711 Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics. 2006 May 1;22(9):1036-46. PMID: 16500937 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955-64. PMID: 9023104; PMC: PMC146525 UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. PMID: 22102590; PMC: PMC3245120 
mrna Human mRNAs Human mRNAs from GenBank mRNA and EST Description The mRNA track shows alignments between human mRNAs in GenBank and the genome. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only mRNAs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, mRNAs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display mRNAs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those mRNAs that match the filter criteria. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods GenBank human mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
affyU133Plus2 Affy U133Plus2 Alignments of Affymetrix Consensus/Exemplars from HG-U133 Plus 2.0 Expression Description This track shows the location of the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U133 Plus 2.0 chip. Methods Consensus and exemplar sequences were downloaded from the Affymetrix Product Support and mapped to the genome using blat followed by pslReps with the parameters: -minCover=0.3 -minAli=0.95 -nearTop=0.005 Credits Thanks to Affymetrix for the data underlying this track. 
darned Human RNA Editing Human RNA Editing from the DAtabase of RNa EDiting mRNA and EST Description This track provides information on RNA nucleotides that are edited after transcription and their corresponding genomic coordinates. Only post-transcriptional editing that results in small changes to the identity of a nucleic acid are included in this track; it does not include other RNA processing such as splicing or methylation. The track contains information on A-to-I (adenosine-to-inosine) and C-to-U (cytidine-to-uridine) editing that occur due to deamination by ADAR and APOBEC enzymes, respectively. Most of the data in this track are on A-to-I editing, which is known to be highly abundant in humans. Display Track items are colored depending on their occurrence within RNA transcripts: Dark Green: 5' UTR Blue: CDS Red: Intron Deep Pink: 3' UTR Black: Other (exon/intron status is unclear or unknown) Methods The data were obtained from several research papers on RNA editing and were mapped to the reference genome. More information can be obtained from DARNED database. References: Kiran A, Baranov PV. DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics. 2010 Jul 15;26(14):1772-6. PMID: 20547637 
phastBias phastBias gBGC phastBias gBGC predictions Comparative Genomics Description The phastBias gBGC tracks show regions predicted to be influenced by GC-biased gene conversion (gBGC). gBGC is a process in which GC/AT (strong/weak) heterozygotes are preferentially resolved to the strong allele during gene conversion. This confers an advantage to G and C alleles that mimics positive selection, without conferring any known functional advantage. Therefore, some regions of the genome identified to be under positive selection may be better explained by gBGC. gBGC has also been hypothesized to be an important contributor to variation in GC content and the fixation of deleterious mutations. PhastBias is a prediction method that captures gBGC's signature in multiple-genome alignments: clusters of weak-to-strong substitutions amidst a deficit of strong-to-weak substitutions. Due to the short life of recombination hotspots, phastBias searches for gBGC tracts on a single foreground branch. PhastBias is designed to pick up gBGC tracts of arbitrary length and to be robust to variations in local mutation rate and GC content. It uses a hidden Markov model (HMM) that can be thought of as an extension to the phastCons model. Whereas phastCons predicts conserved elements using an HMM with two states (conserved and neutral), phastBias predicts gBGC tracts using a four-state HMM (conserved, neutral, conserved with gBGC, neutral with gBGC). One of the main parameters of the phastBias model is B, which represents the strength of gBGC and the degree to which weak-to-strong and strong-to-weak substitution rates are skewed on the foreground branch. The tracks presented here were created with B=3, which was chosen for being sensitive while still having a low false positive rate. Simulation experiments suggest that phastBias has reasonable power to pick up tracts with length &gt; 1000bp, and very good power for tracts &gt; 2000bp. Nonetheless, other lines of evidence suggest that phastBias only identifies approximately 25-50% of bases influenced by gBGC, so the tract predictions should not be considered exhaustive. Display Conventions The phastBias tracks display separate predictions for both human and chimp lineages of the phylogenetic tree (from the human-chimp ancestor). For each lineage, two tracks are available: a wiggle showing raw posterior probabilities, and a BED track showing regions predicted to be affected by gBGC. The posterior probability track shows the probability that each base is assigned to either of the gBGC states under the phastBias HMM. The phastBias tracts show regions predicted to be affected by gBGC on a particular lineage. These are simply defined as all regions with posterior probability &gt; 0.5. Methods The phastBias tracks were predicted using the phastBias program, available as part of the PHAST software package. The phastBias tracks represent two separate result sets; one predicting gBGC on the branch leading from the human-chimp ancestor to human, and the other on the opposite branch leading to chimp. The software was run on human-referenced alignments of hg18, panTro2, ponAbe2, and rheMac2, which were extracted from the hg18 44-way multiple alignment. Details are available in Capra et al., 2013 (cited below). Briefly, the gBGC bias parameter B was set to 3, the mean expected tract length was set to 1/1000, and the transition rate into gBGC states was estimated by expectation-maximization. Most other parameter settings were set to the same values used for UCSC's mammalian conservation tracts. Relative branch lengths came from this placental mammal tree model, the conservation scale factor was set to 0.31, expected length of conserved elements to 45, and expected coverage of conserved elements to 0.3. The alignment was split into 10 Mb chunks; for each chunk, a scaling factor for the neutral tree, the transition/transversion rate ratio, and the background base frequencies were re-estimated using the PHAST program phyloFit. The final tracts were filtered to remove elements with length &ge; 5000bp, as these are likely due to artifacts unrelated to gBGC (repeats, alignment error). The method was re-run on hg19 data, extracting hg19, panTro2, rheMac2, and ponAbe2 from the 46-way alignments. The chimp tracks were not re-created for hg19, since interest in them is lower. References Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genet. 2013 Aug;9(8):e1003684. PMID: 23966869; PMC: PMC3744432 Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 2011 Jan;12(1):41-51. PMID: 21278375; PMC: PMC3030812 Duret L, Galtier N. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet. 2009;10:285-311. PMID: 19630562 
phastBiasTracts Tracts phastBias gBGC predictions Comparative Genomics 
phastBiasTracts3 human tracts phastBias gBGC human tracts Comparative Genomics 
phastBiasPosteriors Posteriors phastBias gBGC predictions Comparative Genomics 
phastBiasPosteriors3 human posterior phastBias gBGC posterior probability on human branch Comparative Genomics 
allenBrainAli Allen Brain Allen Brain Atlas Probes Expression Description This track provides a link into the Allen Brain Atlas (ABA) images for this probe. The ABA is an extensive database of high resolution in-situ hybridization images of adult male mouse brains covering the majority of genes. Methods The ABA created a platform for high-throughput in situ hybridization (ISH) that allows a highly systematic approach to analyzing gene expression in the brain. ISH is a technique that allows the cellular localization of mRNA transcripts for specific genes. Labeled antisense probes, specific to a particular gene, are hybridized to cellular (sense) transcripts and subsequent detection of the bound probe produces specific labeling in those cells expressing the particular gene. This method involves tagged nucleotides detected by colorimetric methods. The platform used for the ABA utilizes this non-isotopic approach, with digoxigenin-labeled nucleotides incorporated into a riboprobe produced by in vitro transcription. This method produces a label that fills the cell body, in contrast to autoradiography that produces scattered silver grains surrounding each labeled cell. To enhance the ability to detect low level expression, the ABA has incorporated a tyramide signal amplification step into the protocol that greatly increases sensitivity. The specific methodology is described in detail within the ABA Data Production Processes document. Credits Thanks to the Allen Institute for Brain Science in general, and Susan Sunkin in particular, for coordinating with UCSC on this annotation. 
xenoEst Other ESTs Non-Human ESTs from GenBank mRNA and EST Description This track displays translated blat alignments of expressed sequence tags (ESTs) in GenBank from organisms other than human. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The strand information (+/-) for this track is in two parts. The first + or - indicates the orientation of the query sequence whose translated protein produced the match. The second + or - indicates the orientation of the matching translated genomic sequence. Because the two orientations of a DNA sequence give different predicted protein sequences, there are four combinations. ++ is not the same as --, nor is +- the same as -+. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the EST display. For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only ESTs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, ESTs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display ESTs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those ESTs that match the filter criteria. This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, go to the Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods To generate this track, the ESTs were aligned against the genome using blat. When a single EST aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from EST sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
primateChainNet Primate Chain/Net Primate Genomes, Chain and Net Alignments Comparative Genomics Description Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to other genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and the other genome simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the other assembly or an insertion in the human assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the other genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/other chain for every part of the other genome. It is useful for finding orthologous regions and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/other split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single chromosome from the other genome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following lastz matrix was usedfor the alignments to: Chimp, Gorilla, Orangutan, Gibbon,Rhesus, Baboon and Marmoset &nbsp;ACGT A90-330-236-356 C-330100-318-236 G-236-318100-330 T-356-236-33090 &nbsp; The following lastz matrix was usedfor the alignments to: Tarsier, Mouse Lemur and Bushbaby &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 For the alignments to: Chimp, Gorilla, Orangutan, Gibbon, Rhesus, Baboon and Marmoset, chains scoring below a minimum score of '5000' were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 For the alignments to: Tarsier, Mouse Lemur and Bushbaby, chains scoring below a minimum score of '3000' were discarded; the remaining chains are displayed in this track. The same linear gap matrix show above was used with axtChain. Chains for low-coverage assemblies for which no browser has been built (Gorilla, Baboon, Tarsier, Mouse Lemur and Bushbaby) are not available as browser tracks, but only from downloads. See also: lastz parameters and other details (e.g., update time) and chain minimum score and gap parameters used in these alignments. Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
primateChainNetViewnet Nets Primate Genomes, Chain and Net Alignments Comparative Genomics 
netCalJac3 Marmoset Net Marmoset (March 2009 (WUGSC 3.2/calJac3)) Alignment Net Comparative Genomics 
netRheMac10 Rhesus Net Rhesus (Feb. 2019 (Mmul_10/rheMac10)) Alignment Net Comparative Genomics 
netMacFas5 Crab-eating macaque Net Crab-eating macaque (Jun. 2013 (Macaca_fascicularis_5.0/macFas5)) Alignment Net Comparative Genomics 
netNomLeu3 Gibbon Net Gibbon (Oct. 2012 (GGSC Nleu3.0/nomLeu3)) Alignment Net Comparative Genomics 
netPonAbe2 Orangutan Net Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Alignment Net Comparative Genomics 
netGorGor3 Gorilla Net Gorilla (May 2011 (gorGor3.1/gorGor3)) Alignment Net Comparative Genomics 
netPanTro4 Chimp Net Chimp (Feb. 2011 (CSAC 2.1.4/panTro4)) Alignment Net Comparative Genomics 
primateChainNetViewchain Chains Primate Genomes, Chain and Net Alignments Comparative Genomics 
chainCalJac3 Marmoset Chain Marmoset (March 2009 (WUGSC 3.2/calJac3)) Chained Alignments Comparative Genomics 
chainRheMac10 Rhesus Chain Rhesus (Feb. 2019 (Mmul_10/rheMac10)) Chained Alignments Comparative Genomics 
chainMacFas5 Crab-eating macaque Chain Crab-eating macaque (Jun. 2013 (Macaca_fascicularis_5.0/macFas5)) Chained Alignments Comparative Genomics 
chainNomLeu3 Gibbon Chain Gibbon (Oct. 2012 (GGSC Nleu3.0/nomLeu3)) Chained Alignments Comparative Genomics 
chainPonAbe2 Orangutan Chain Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Chained Alignments Comparative Genomics 
chainGorGor3 Gorilla Chain Gorilla (May 2011 (gorGor3.1/gorGor3)) Chained Alignments Comparative Genomics 
chainPanTro4 Chimp Chain Chimp (Feb. 2011 (CSAC 2.1.4/panTro4)) Chained Alignments Comparative Genomics 
burgeRnaSeqGemMapperAlign Burge RNA-seq Burge Lab RNA-seq Aligned by GEM Mapper Expression Description RNA-Seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly. RNA-Seq was performed by reverse-transcribing an RNA sample into cDNA, followed by high throughput DNA sequencing on an Illumina Genome Analyser. This track shows the RNA-seq data published by Chris Burge's lab (Wang et al.,2008) mapped to the genome using GEM Mapper by the Guig&oacute; lab at the Center for Genomic Regulation (CRG). The subtracks display RNA-seq data from various tissues/cell lines: Brain Liver Heart Muscle Colon Adipose Testes Lymph Node Breast BT474 - Breast Tumour Cell Line HME - Human Mammary Epithelial Cell Line MCF7 - Breast Adenocarcinoma Cell Line MB-435 - Breast Ductal Adenocarcinoma Cell Line* T-47D - Breast Ductal Carcinoma Cell Line Tissues were obtained from unrelated anonymous donors. HME is a mammary epithelial cell line immortalized with telomerase reverse transcriptase (TERT). The other cell lines are breast cancer cell lines produced from invasive ductal carcinomas (ATCC). *NOTE: studies have shown that the MDA-MB-435 cell line appears to have been contaminated with the M14 melanoma cell line. See this entry on the American Type Culture Collection (ATCC) website for more details. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. The following views are in this track: Raw Signal Density graph (bedGraph) of signal enrichment based on a normalized aligned read density (counts per million mapped reads for each subtrack). This normalized measure assists in visualizing the relative amount of a given transcript across multiple samples. Alignments The Alignments view shows reads mapped to the genome. Methods The group at CRG obtained RNA-seq reads, generated by Wang et al. (2008), from the Short Read Archive section of GEO at NCBI under accession number GSE12946. Using their GEM mapper program, CRG mapped the RNA-seq reads to the genome and transcriptome (GENCODE Release 3, October 2009 Freeze). GEM mapper was run using default parameters and allowing up to two mismatches in the read alignments. Since mapping to the transcriptome depends on length of the reads mapped, reads were only mapped for the 14 tissues or cell lines where reads were of length 32 bp. This excluded reads from MAQC human cell lines (mixed human brain) and MAQC UHR (mixed human cell lines). Credits These data were generated by Chris Burge's lab at the Massachusetts Institute of Technology and by Roderic Guig&oacute;'s lab at the Center for Genomic Regulation (CRG) in Barcelona, Spain. GTF files of the mapped data were provided by Thomas Derrien and Paolo Ribeca from CRG. GEM mapper software can be obtained here. References Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008 Nov 27;456(7221):470-6. PMID: 18978772; PMC: PMC2593745 
burgeRnaSeqGemMapperAlignViewRawSignal All Raw Signal Burge Lab RNA-seq Aligned by GEM Mapper Expression 
burgeRnaSeqGemMapperAlignTestesAllRawSignal RNA-seq Testes Sig Burge Lab RNA-seq 32mer Reads from Testes, Raw Signal Expression 
burgeRnaSeqGemMapperAlignSkelMuscleAllRawSignal RNA-seq Muscle Sig Burge Lab RNA-seq 32mer Reads from Skeletal Muscle, Raw Signal Expression 
burgeRnaSeqGemMapperAlignLymphNodeAllRawSignal RNA-seq Lymph Node Sig Burge Lab RNA-seq 32mer Reads from Lymph Node, Raw Signal Expression 
burgeRnaSeqGemMapperAlignLiverAllRawSignal RNA-seq Liver Sig Burge Lab RNA-seq 32mer Reads from Liver, Raw Signal Expression 
burgeRnaSeqGemMapperAlignHeartAllRawSignal RNA-seq Heart Sig Burge Lab RNA-seq 32mer Reads from Heart, Raw Signal Expression 
burgeRnaSeqGemMapperAlignColonAllRawSignal RNA-seq Colon Sig Burge Lab RNA-seq 32mer Reads from Colon, Raw Signal Expression 
burgeRnaSeqGemMapperAlignBreastAllRawSignal RNA-seq Breast Sig Burge Lab RNA-seq 32mer Reads from Breast, Raw Signal Expression 
burgeRnaSeqGemMapperAlignBrainAllRawSignal RNA-seq Brain Sig Burge Lab RNA-seq 32mer Reads from Brain, Raw Signal Expression 
burgeRnaSeqGemMapperAlignAdiposeAllRawSignal RNA-seq Adipose Sig Burge Lab RNA-seq 32mer Reads from Adipose, Raw Signal Expression 
burgeRnaSeqGemMapperAlignT47DAllRawSignal RNA-seq T47D Sig Burge Lab RNA-seq 32mer Reads from T-47D Breast Ductal Carcinoma Cell Line, Raw Signal Expression 
burgeRnaSeqGemMapperAlignMCF7AllRawSignal RNA-seq MCF7 Sig Burge Lab RNA-seq 32mer Reads from MCF-7 Breast Adenocarcinoma Cell Line, Raw Signal Expression 
burgeRnaSeqGemMapperAlignMB435AllRawSignal RNA-seq MB435 Sig Burge Lab RNA-seq 32mer Reads from MB-435 Cell Line, Raw Signal Expression 
burgeRnaSeqGemMapperAlignHMEAllRawSignal RNA-seq HME Sig Burge Lab RNA-seq 32mer Reads from HME (Human Mammary Epithelial) Cell Line, Raw Signal Expression 
burgeRnaSeqGemMapperAlignBT474AllRawSignal RNA-seq BT474 Sig Burge Lab RNA-seq 32mer Reads from BT474 Breast Tumour Cell Line, Raw Signal Expression 
burgeRnaSeqGemMapperAlignViewAlignments Alignments Burge Lab RNA-seq Aligned by GEM Mapper Expression 
burgeRnaSeqGemMapperAlignTestes RNA-seq Testes Burge Lab RNA-seq 32mer Reads from Testes Expression 
burgeRnaSeqGemMapperAlignSkelMuscle RNA-seq Muscle Burge Lab RNA-seq 32mer Reads from Skeletal Muscle Expression 
burgeRnaSeqGemMapperAlignLymphNode RNA-seq Lymph Node Burge Lab RNA-seq 32mer Reads from Lymph Node Expression 
burgeRnaSeqGemMapperAlignLiver RNA-seq Liver Burge Lab RNA-seq 32mer Reads from Liver Expression 
burgeRnaSeqGemMapperAlignHeart RNA-seq Heart Burge Lab RNA-seq 32mer Reads from Heart Expression 
burgeRnaSeqGemMapperAlignColon RNA-seq Colon Burge Lab RNA-seq 32mer Reads from Colon Expression 
burgeRnaSeqGemMapperAlignBreast RNA-seq Breast Burge Lab RNA-seq 32mer Reads from Breast Expression 
burgeRnaSeqGemMapperAlignBrain RNA-seq Brain Burge Lab RNA-seq 32mer Reads from Brain Expression 
burgeRnaSeqGemMapperAlignAdipose RNA-seq Adipose Burge Lab RNA-seq 32mer Reads from Adipose Expression 
burgeRnaSeqGemMapperAlignT47D RNA-seq T47D Burge Lab RNA-seq 32mer Reads from T-47D Breast Ductal Carcinoma Cell Line Expression 
burgeRnaSeqGemMapperAlignMCF7 RNA-seq MCF7 Burge Lab RNA-seq 32mer Reads from MCF-7 Breast Adenocarcinoma Cell Line Expression 
burgeRnaSeqGemMapperAlignMB435 RNA-seq MB435 Burge Lab RNA-seq 32mer Reads from MB-435 Cell Line Expression 
burgeRnaSeqGemMapperAlignHME RNA-seq HME Burge Lab RNA-seq 32mer Reads from HME (Human Mammary Epithelial) Cell Line Expression 
burgeRnaSeqGemMapperAlignBT474 RNA-seq BT474 Burge Lab RNA-seq 32mer Reads from BT474 Breast Tumor Cell Line Expression 
xenoMrna Other mRNAs Non-Human mRNAs from GenBank mRNA and EST Description This track displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank from organisms other than human. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The strand information (+/-) for this track is in two parts. The first + indicates the orientation of the query sequence whose translated protein produced the match (here always 5' to 3', hence +). The second + or - indicates the orientation of the matching translated genomic sequence. Because the two orientations of a DNA sequence give different predicted protein sequences, there are four combinations. ++ is not the same as --, nor is +- the same as -+. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only mRNAs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, mRNAs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display mRNAs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those mRNAs that match the filter criteria. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods The mRNAs were aligned against the human genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept. Credits The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
placentalChainNet Placental Chain/Net Non-primate Placental Mammal Genomes, Chain and Net Alignments Comparative Genomics Description Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to other genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and the other genome simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the other assembly or an insertion in the human assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the other genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/other chain for every part of the other genome. It is useful for finding orthologous regions and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/other split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single chromosome from the other genome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. Chains scoring below a minimum score of '5000' were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 See also: lastz parameters used in these alignments, and chain minimum score and gap parameters used in these alignments. Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
placentalChainNetViewnet Nets Non-primate Placental Mammal Genomes, Chain and Net Alignments Comparative Genomics 
netLoxAfr3 Elephant Net Elephant (Jul. 2009 (Broad/loxAfr3)) Alignment Net Comparative Genomics 
netEchTel2 Tenrec Net Tenrec (Nov. 2012 (Broad/echTel2)) Alignment Net Comparative Genomics 
netEquCab2 Horse Net Horse (Sep. 2007 (Broad/equCab2)) Alignment Net Comparative Genomics 
netCerSim1 White rhinoceros Net White rhinoceros (May 2012 (CerSimSim1.0/cerSim1)) Alignment Net Comparative Genomics 
netSorAra2 Shrew Net Shrew (Aug. 2008 (Broad/sorAra2)) Alignment Net Comparative Genomics 
netEriEur2 Hedgehog Net Hedgehog (May 2012 (EriEur2.0/eriEur2)) Alignment Net Comparative Genomics 
netVicPac2 Alpaca Net Alpaca (Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2)) Alignment Net Comparative Genomics 
netSusScr2 susScr2 Net Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) Alignment Net Comparative Genomics 
netOviAri3 Sheep Net Sheep (Aug. 2012 (ISGC Oar_v3.1/oviAri3)) Alignment Net Comparative Genomics 
netBosTau7 Cow Net Cow (Oct. 2011 (Baylor Btau_4.6.1/bosTau7)) Alignment Net Comparative Genomics 
netFelCat5 felCat5 Net Cat (Sep. 2011 (ICGSC Felis_catus 6.2/felCat5)) Alignment Net Comparative Genomics 
netCanFam3 Dog Net Dog (Sep. 2011 (Broad CanFam3.1/canFam3)) Alignment Net Comparative Genomics 
netAilMel1 Panda Net Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) Alignment Net Comparative Genomics 
netRn4 rn4 Net Rat (Nov. 2004 (Baylor 3.4/rn4)) Alignment Net Comparative Genomics 
netOryCun2 Rabbit Net Rabbit (Apr. 2009 (Broad/oryCun2)) Alignment Net Comparative Genomics 
netOchPri3 Pika Net Pika (May 2012 (OchPri3.0/ochPri3)) Alignment Net Comparative Genomics 
netMm10 Mouse Net Mouse (Dec. 2011 (GRCm38/mm10)) Alignment Net Comparative Genomics 
netCriGri1 Chinese hamster Net Chinese hamster (Jul. 2013 (C_griseus_v1.0/criGri1)) Alignment Net Comparative Genomics 
netCavPor3 Guinea pig Net Guinea pig (Feb. 2008 (Broad/cavPor3)) Alignment Net Comparative Genomics 
placentalChainNetViewchain Chains Non-primate Placental Mammal Genomes, Chain and Net Alignments Comparative Genomics 
chainLoxAfr3 Elephant Chain Elephant (Jul. 2009 (Broad/loxAfr3)) Chained Alignments Comparative Genomics 
chainEchTel2 Tenrec Chain Tenrec (Nov. 2012 (Broad/echTel2)) Chained Alignments Comparative Genomics 
chainEquCab2 Horse Chain Horse (Sep. 2007 (Broad/equCab2)) Chained Alignments Comparative Genomics 
chainCerSim1 White rhinoceros Chain White rhinoceros (May 2012 (CerSimSim1.0/cerSim1)) Chained Alignments Comparative Genomics 
chainSorAra2 Shrew Chain Shrew (Aug. 2008 (Broad/sorAra2)) Chained Alignments Comparative Genomics 
chainEriEur2 Hedgehog Chain Hedgehog (May 2012 (EriEur2.0/eriEur2)) Chained Alignments Comparative Genomics 
chainVicPac2 Alpaca Chain Alpaca (Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2)) Chained Alignments Comparative Genomics 
chainSusScr2 susScr2 Chain Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) Chained Alignments Comparative Genomics 
chainOviAri3 Sheep Chain Sheep (Aug. 2012 (ISGC Oar_v3.1/oviAri3)) Chained Alignments Comparative Genomics 
chainBosTau7 bosTau7 Chain Cow (Oct. 2011 (Baylor Btau_4.6.1/bosTau7)) Chained Alignments Comparative Genomics 
chainFelCat5 Cat Chain Cat (Sep. 2011 (ICGSC Felis_catus 6.2/felCat5)) Chained Alignments Comparative Genomics 
chainCanFam3 Dog Chain Dog (Sep. 2011 (Broad CanFam3.1/canFam3)) Chained Alignments Comparative Genomics 
chainAilMel1 Panda Chain Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) Chained Alignments Comparative Genomics 
chainRn4 Rat Chain Rat (Nov. 2004 (Baylor 3.4/rn4)) Chained Alignments Comparative Genomics 
chainOryCun2 Rabbit Chain Rabbit (Apr. 2009 (Broad/oryCun2)) Chained Alignments Comparative Genomics 
chainOchPri3 Pika Chain Pika (May 2012 (OchPri3.0/ochPri3)) Chained Alignments Comparative Genomics 
chainMm10 Mouse Chain Mouse (Dec. 2011 (GRCm38/mm10)) Chained Alignments Comparative Genomics 
chainCriGri1 Chinese hamster Chain Chinese hamster (Jul. 2013 (C_griseus_v1.0/criGri1)) Chained Alignments Comparative Genomics 
chainCavPor3 Guinea pig Chain Guinea pig (Feb. 2008 (Broad/cavPor3)) Chained Alignments Comparative Genomics 
wgEncodeCshlShortRnaSeq CSHL Small RNA-seq GSE24565 Small RNA-seq from ENCODE/Cold Spring Harbor Lab Expression Description The Cold Spring Harbor Lab (CSHL) small RNA track depicts short total RNA sequencing data from ENCODE tissues or sub-cellular compartments of ENCODE cell lines. The protocol used to generate these data produced directional reads from the 5' end of short RNAs, RNAs shorter than 200 nucleotides in length. Libraries were sequenced using an Illumina GAIIx. These data were generated by Cold Spring Harbor Laboratories as a part of the ENCODE Consortium. The ENCODE project seeks to identify and characterize all functional elements in the human genome. In many cases there are datasets of Cap Analysis of Gene Expression (CAGE, see the RIKEN CAGE Loc track), Long RNA-seq (RNAs longer than 200 nucleotides, see the CSHL Long RNA-seq track) and Pair-End di-TAG-RNA (PET-RNA, see the GIS RNA PET track) available from the same biological replicates. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Color differences among the views provide a visual cue for distinguishing between the different cell types and compartments. This track contains the following views: Contigs The Contigs are BED format files representing blocks of overlapping mapped reads from pooled biological replicates. The corresponding number of mapped reads, the RPKM (Reads Per kb per Million reads) value, and the non-parametric Irreproducible Discovery Rate (np-IDR) are reported for each contig. Plus and Minus Signal The Signal view shows the density of mapped reads on the plus and minus strands (wiggle format). Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. More views may be found on the Downloads Page. Methods Experimental Procedures Cells were grown according to the approved ENCODE cell culture protocols. Short RNAs between 20 and 200 nucleotides were isolated from total RNA using a Qiagen RNeasy kit (Qiagen #74204) according to the manufacturer's protocol. Purified small RNAs were depleted of ribosomal RNA. To clone different populations the RNA was either left untreated (5' monophosphate RNAs), treated with Tobacco Alkaline Pyrophosphatase (both 5' monophosphate and capped RNAs), or treated with Calf Intestinal Alkaline Phosphatase followed by Tobacco Alkaline Pyrophosphatase (capped RNAs) prior to ligation of a 5' linker. The 3' ends were polyadenylated in vitro (or polycytidylated in the case of Generation 0 data) using Poly-A Polymerase. Anchored oligo-dT was used to prime the reverse transcriptase reaction and sequencing compatible ends were added in a subsequent PCR step. The libraries were sequenced on the Illumina GAIIx of Hi-Seq from the 5' ends for a total of either 36 or 101 cycles. Complete protocols are available in the Downloads Page. Data Processing and Analysis Data from the Gingeras and Guigo labs were preprocessed to remove experimentally derived poly-A tails and Illumina 3' linkers from raw reads. The best alignment to the Illumina 3' linker for each read was determined. If the number of mismatches in the alignment was less than 20% of the aligned length, the read was clipped from the first aligned base. Pre-processed reads were mapped using the STAR algorithm. For a description of STAR, the source code and mapping parameters used, see the STAR project website. Reads mapping 10 times or less are reported in the Signal and Alignment files. Mapped reads were discarded if they fell into one of the following categories: 1) it contained five or more consecutive A's, 2) it was less than 16 nucleotides in length, 3) it mapped to more than one genomic position (multiply-mapped reads), 4) it mapped upstream of genomically encoded poly-A sequences. The remaining reads were used both to call contigs and to produce expression values over GENCODE V7 exons. Contigs were generated from overlapping reads in pooled biological replicates. Generation 0 data: Reads were trimmed to discard any bases following a quality score less than or equal to 20 and converted into FASTA format, thereby discarding quality information for the rest of the pipeline. As a result, the sequence quality scores in the BAM output are all displayed as "40" to indicate no quality information. The read lengths may exceed the insert sizes and consequently introduce 3' adapter sequence into the 3' end of the reads. The 3' sequencing adapter was removed from the reads using a custom clipper program (available at http://hannonlab.cshl.edu/fastx_toolkit/), which aligned the adapter sequence to the short-reads using up to two mismatches and no indels (insertions or deletions).. Regions that aligned were clipped off from the read. Terminal C nucleotides introduced at the 3' end of the RNA via the cloning procedure were also trimmed. Reads were aligned to the human genome (version hg19, using the gender build appropriate to the sample in question - female/male) using Bowtie (Langmead B et al., 2009). Reads that mapped 20 or fewer times with two or less mismatches were reported. See Release Notes for more information on Generation 0 datasets. Verification The mapped data were visually inspected to verify the majority of the reads were mapping the 5' ends of annotated small RNA classes. Release Notes This is Release 3 (July 2012) of CSHL Small RNA-seq with new data from the Gingeras lab. It includes twenty-two new cell lines: CD20+, CD34+_Mobilized, HAoAF, HAoEC, HCH, HFDPC, HMEpC, hMSC-AT, hMSC-UC, HOB, HPC-PL, HPIEpC, HSaVEC, HVMF, HWP, IMR90, Monocytes-CD14+, NHDF, NHEM.f_M2, NHEM_M2, SkMC, SK-N-SH. There are 53 new experiments in total. Release 3 data includes two new variations in protocol (CIP-TAP and untreated) to create different RNA populations. Many of the datasets produced by the Hannon lab (Generation 0 datasets) in Release 1 have been replaced by newly generated data from the Gingeras lab in Release 2. Of all Generation 0 datasets, only data from K562 and Prostate tissue are still displayed. All Generation 0 datasets are still available for download. Discrepancies between hg18 and hg19 versions of Generation 0 CSHL small RNA data: The alignment pipeline for the CSHL small RNA data was updated upon the release of the human genome version hg19, resulting in a few noteworthy discrepancies with the hg18 dataset. First, mapping was conducted with the open-source Bowtie algorithm (http://bowtie-bio.sourceforge.net/index.shtml) rather than the custom NexAlign software. As each algorithm uses different strategies to perform alignments, the mapping results may vary even in genomic regions that do not differ between builds. The read processing pipeline also varies slightly in that we no longer retain information regarding whether a read was clipped off an adapter sequence. Credits Hannon lab members: Katalin Fejes-Toth, Vihra Sotirova, Gordon Assaf, Jon Preall Gingeras and Guigo laboratories: Carrie A. Davis, Lei-Hoon See, Wei Lin Contacts: Jonathan Preall (Generation 0 Data from Hannon Lab) Carrie Davis (experimental) Alex Dobin (computational) Wei Lin (computational) Tom Gingeras (primary investigator) References Fejes-Toth K, Sotirova V, Sachidanandam R, Assaf G, Hannon GJ, Kapranov P, Foissac S, Willingham AT, Duttagupta R, Dumais E, Gingeras TR. Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature. 2009;457(7232):1028-32. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Mortazavi A, Williams BA, McCue K, Schaeffer L, and Wold BJ. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods. 2008 Jul; 5(7):621-628. --> Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column in the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeCshlShortRnaSeqViewPlusSignal Plus Signal Small RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapPlusRawRep2 SKRA cell TAP + 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001094 1094 GSM897070 Gingeras CSHL LID20748 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapPlusRawRep2 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH_RA TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapPlusRawRep1 SKRA cell TAP + 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001094 1094 GSM897070 Gingeras CSHL LID20747 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapPlusRawRep1 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH_RA TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSkmc812190217CellTapPlusRep2 SkMC cell TAP + 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002884 2884 GSM977039 Gingeras CSHL LID47240 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSkmc812190217CellTapPlusRep2 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSkmc9011302CellShorttotalTapPlusRep1 SkMC cell TAP + 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002884 2884 GSM977039 Gingeras CSHL LID47239 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSkmc9011302CellShorttotalTapPlusRep1 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqProstateCellTotalPlusRaw Pros cell TAP + 1 prostate RnaSeq ENCODE Jan 2011 Freeze 2010-06-30 2009-09-23 2010-06-23 wgEncodeEH000211 211 GSM605626 Gingeras CSHL crg-61 Produced by Hannon Lab cell hg18 TAP-Only shortTotal wgEncodeCshlShortRnaSeqProstateCellTotalPlusRaw PlusSignal prostate tissue purchased for CSHL project Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Graphs the base-by-base density of tags on the plus strand Prostate TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemm2CellTapPlusRep2 NHEM cell TAP + 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002897 2897 GSM977047 Gingeras CSHL LID47614 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemm2CellTapPlusRep2 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM_M2 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemm2CellTapPlusRep1 NHEM cell TAP + 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002897 2897 GSM977047 Gingeras CSHL LID47613 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemm2CellTapPlusRep1 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM_M2 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemfm2CellTapPlusRep2 NHEf cell TAP + 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002895 2895 GSM977045 Gingeras CSHL LID47612 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemfm2CellTapPlusRep2 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f_M2 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemfm2CellTapPlusRep1 NHEf cell TAP + 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002895 2895 GSM977045 Gingeras CSHL LID47611 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemfm2CellTapPlusRep1 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f_M2 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapPlusRawRep4 NHEK nucl TAP + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001093 1093 GSM897076 Gingeras CSHL LID21003 nucleus TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapPlusRawRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapPlusRawRep3 NHEK nucl TAP + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001093 1093 GSM897076 Gingeras CSHL LID21001 nucleus TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapPlusRawRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapPlusRawRep4 NHEK cyto TAP + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001092 1092 GSM897078 Gingeras CSHL LID21004 cytosol TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapPlusRawRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapPlusRawRep3 NHEK cyto TAP + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001092 1092 GSM897078 Gingeras CSHL LID21002 cytosol TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapPlusRawRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK TAP-only cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep2 NHEK cell TAP + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001091 1091 GSM897086 Gingeras CSHL LID21000 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep2 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep1 NHEK cell TAP + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001091 1091 GSM897086 Gingeras CSHL LID20999 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep1 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhdf00608013CellShorttotalTapPlusRep2 NHDF cell TAP + 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002883 2883 GSM977034 Gingeras CSHL LID47242 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhdf00608013CellShorttotalTapPlusRep2 PlusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhdf70717012CellShorttotalTapPlusRep1 NHDF cell TAP + 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002883 2883 GSM977034 Gingeras CSHL LID47241 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhdf70717012CellShorttotalTapPlusRep1 PlusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHwpCellTapPlusRep2 HWP cell TAP + 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002894 2894 GSM977046 Gingeras CSHL LID47610 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHwpCellTapPlusRep2 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHwpCellTapPlusRep1 HWP cell TAP + 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002894 2894 GSM977046 Gingeras CSHL LID47609 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHwpCellTapPlusRep1 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHvmf61004013CellShorttotalTapPlusRep2 HVMF cell TAP + 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002882 2882 GSM977033 Gingeras CSHL LID47244 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHvmf61004013CellShorttotalTapPlusRep2 PlusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHvmf60912033CellShorttotalTapPlusRep1 HVMF cell TAP + 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002882 2882 GSM977033 Gingeras CSHL LID47243 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHvmf60912033CellShorttotalTapPlusRep1 PlusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHsavecCellTapPlusRep2 HSaV cell TAP + 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002893 2893 GSM977051 Gingeras CSHL LID47616 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHsavecCellTapPlusRep2 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHsavecCellTapPlusRep1 HSaV cell TAP + 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002893 2893 GSM977051 Gingeras CSHL LID47615 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHsavecCellTapPlusRep1 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpiepcCellTapPlusRep2 HPIE cell TAP + 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002892 2892 GSM977052 Gingeras CSHL LID47520 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpiepcCellTapPlusRep2 PlusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpiepcCellTapPlusRep1 HPIE cell TAP + 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002892 2892 GSM977052 Gingeras CSHL LID47519 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpiepcCellTapPlusRep1 PlusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpcplCellTapPlusRep2 HPCP cell TAP + 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002891 2891 GSM977049 Gingeras CSHL LID47518 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpcplCellTapPlusRep2 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpcplCellTapPlusRep1 HPCP cell TAP + 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002891 2891 GSM977049 Gingeras CSHL LID47517 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpcplCellTapPlusRep1 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHob00902021CellShorttotalTapPlusRep2 HOB cell TAP + 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002881 2881 GSM977036 Gingeras CSHL LID47432 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHob00902021CellShorttotalTapPlusRep2 PlusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHobCellTapPlusRawRep1 HOB cell TAP + 1 HOB RnaSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH002881 2881 GSM977036 Gingeras CSHL LID47431 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHobCellTapPlusRawRep1 PlusRawSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscucCellTapPlusRep2 hMUC cell TAP + 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002896 2896 GSM977048 Gingeras CSHL LID47516 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscucCellTapPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscucCellTapPlusRep1 hMUC cell TAP + 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002896 2896 GSM977048 Gingeras CSHL LID47515 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscucCellTapPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscbmCellTapPlusRawRep2 hMBM cell TAP + 2 hMSC-BM RnaSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH002946 2946 GSM977028 Gingeras CSHL LID47659 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscbmCellTapPlusRawRep2 PlusRawSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscbmCellTapPlusRawRep1 hMBM cell TAP + 1 hMSC-BM RnaSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH002946 2946 GSM977028 Gingeras CSHL LID47658 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscbmCellTapPlusRawRep1 PlusRawSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscat906160112CellTapPlusRep2 hMAT cell TAP + 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002888 2888 GSM977041 Gingeras CSHL LID47480 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscat906160112CellTapPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscat010260412CellTapPlusRep1 hMAT cell TAP + 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002888 2888 GSM977041 Gingeras CSHL LID47479 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscat010260412CellTapPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmepcCellTapPlusRep1 HMEC cell TAP + 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002890 2890 GSM977050 Gingeras CSHL LID47657 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmepcCellTapPlusRep1 PlusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HMEpC TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHfdpc01005032CellTapPlusRep2 HFDC cell TAP + 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002887 2887 GSM977038 Gingeras CSHL LID47478 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHfdpc01005032CellTapPlusRep2 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHfdpc01027033CellTapPlusRep1 HFDC cell TAP + 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002887 2887 GSM977038 Gingeras CSHL LID47477 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHfdpc01027033CellTapPlusRep1 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHch81008082CellShorttotalTapPlusRep2 HCH cell TAP + 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002886 2886 GSM977037 Gingeras CSHL LID47476 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHch81008082CellShorttotalTapPlusRep2 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHch00113082pCellShorttotalTapPlusRep1 HCH cell TAP + 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002886 2886 GSM977037 Gingeras CSHL LID47475 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHch00113082pCellShorttotalTapPlusRep1 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoec80611021CellTapPlusRep2 HAEC cell TAP + 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002885 2885 GSM977040 Gingeras CSHL LID47436 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoec80611021CellTapPlusRep2 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoec70717061CellTapPlusRep1 HAEC cell TAP + 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002885 2885 GSM977040 Gingeras CSHL LID47435 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoec70717061CellTapPlusRep1 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoaf609010111CellTapPlusRep2 HAAF cell TAP + 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002880 2880 GSM977035 Gingeras CSHL LID47434 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoaf609010111CellTapPlusRep2 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoaf61113019CellTapPlusRep1 HAAF cell TAP + 1 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002880 2880 GSM977035 Gingeras CSHL LID47433 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoaf61113019CellTapPlusRep1 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellTapPlusRawRep2 H1ne cell TAP + 2 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002945 2945 GSM977029 Gingeras CSHL LID48356 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellTapPlusRawRep2 PlusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand H1-neurons TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellTapPlusRawRep1 H1ne cell TAP + 1 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002945 2945 GSM977029 Gingeras CSHL LID48355 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellTapPlusRawRep1 PlusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand H1-neurons TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellPlusRawRep2 H1ne cell + 2 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-20 2013-03-19 wgEncodeEH002943 2943 GSM977031 Gingeras CSHL LID48358 cell None 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellPlusRawRep2 PlusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand H1-neurons whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellPlusRawRep1 H1ne cell + 1 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002943 2943 GSM977031 Gingeras CSHL LID48357 cell None 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellPlusRawRep1 PlusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand H1-neurons whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellCiptapPlusRawRep2 H1ne cell CIP + 2 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002944 2944 GSM977030 Gingeras CSHL LID48354 cell CIP-TAP 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellCiptapPlusRawRep2 PlusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand H1-neurons CIP-TAP whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellCiptapPlusRawRep1 H1ne cell CIP + 1 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002944 2944 GSM977030 Gingeras CSHL LID48353 cell CIP-TAP 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellCiptapPlusRawRep1 PlusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand H1-neurons CIP-TAP whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqCd34mobilizedCellTapPlusRep1 CD34 cell TAP + 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002604 2604 GSM973662 Gingeras CSHL LID46197 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqCd34mobilizedCellTapPlusRep1 PlusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand CD34+ TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqBjCellShorttotalTapPlusRawRep2 BJ cell TAP + 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001079 1079 GSM897077 Gingeras CSHL LID20910 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqBjCellShorttotalTapPlusRawRep2 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqBjCellShorttotalTapPlusRawRep1 BJ cell TAP + 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001079 1079 GSM897077 Gingeras CSHL LID20909 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqBjCellShorttotalTapPlusRawRep1 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapPlusRawRep2 AG50 cell TAP + 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001081 1081 GSM897074 Gingeras CSHL LID20746 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapPlusRawRep2 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapPlusRawRep1 AG50 cell TAP + 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001081 1081 GSM897074 Gingeras CSHL LID20745 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapPlusRawRep1 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapPlusRep4 SKSH nucl TAP + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002469 2469 GSM973689 Gingeras CSHL LID46961 nucleus TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapPlusRep3 SKSH nucl TAP + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002469 2469 GSM973689 Gingeras CSHL LID46960 nucleus TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalPlusRep4 SKSH nucl + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002613 2613 GSM973665 Gingeras CSHL LID46204 nucleus None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalPlusRep3 SKSH nucl + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002613 2613 GSM973665 Gingeras CSHL LID46203 nucleus None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapPlusRep4 SKSH nucl CIP + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002615 2615 GSM973663 Gingeras CSHL LID46273 nucleus CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH CIP-TAP nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapPlusRep3 SKSH nucl CIP + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002615 2615 GSM973663 Gingeras CSHL LID46272 nucleus CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH CIP-TAP nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapPlusRep4 SKSH cyto TAP + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002468 2468 GSM973688 Gingeras CSHL LID46959 cytosol TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapPlusRep3 SKSH cyto TAP + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002468 2468 GSM973688 Gingeras CSHL LID46958 cytosol TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH TAP-only cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalPlusRep4 SKSH cyto + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002612 2612 GSM973666 Gingeras CSHL LID46206 cytosol None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalPlusRep3 SKSH cyto + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002612 2612 GSM973666 Gingeras CSHL LID46205 cytosol None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapPlusRep4 SKSH cyto CIP + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002614 2614 GSM973692 Gingeras CSHL LID46275 cytosol CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH CIP-TAP cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapPlusRep3 SKSH cyto CIP + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002614 2614 GSM973692 Gingeras CSHL LID46274 cytosol CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH CIP-TAP cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalTapPlusRep4 SKSH cell TAP + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002470 2470 GSM973667 Gingeras CSHL LID46957 cell TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalTapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalTapPlusRep3 SKSH cell TAP + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002470 2470 GSM973667 Gingeras CSHL LID46956 cell TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalTapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalPlusRep4 SKSH cell + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002622 2622 GSM973675 Gingeras CSHL LID46202 cell None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalPlusRep3 SKSH cell + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002622 2622 GSM973675 Gingeras CSHL LID46201 cell None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep4 SKSH cell CIP + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002616 2616 GSM973677 Gingeras CSHL LID46271 cell CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH CIP-TAP whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep3 SKSH cell CIP + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002616 2616 GSM973677 Gingeras CSHL LID46270 cell CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH CIP-TAP whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMonocd14CellTapPlusRep2 CD14 cell TAP + 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002898 2898 GSM977044 Gingeras CSHL LID44361 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqMonocd14CellTapPlusRep2 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD14+ TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMonocd14CellTapPlusRep1 CD14 cell TAP + 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002898 2898 GSM977044 Gingeras CSHL LID44360 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqMonocd14CellTapPlusRep1 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD14+ TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep4 MCF7 nucl TAP + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002467 2467 GSM973682 Gingeras CSHL LID47165 nucleus TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep3 MCF7 nucl TAP + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002467 2467 GSM973682 Gingeras CSHL LID47164 nucleus TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep4 MCF7 nucl + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002608 2608 GSM973687 Gingeras CSHL LID46314 nucleus None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep3 MCF7 nucl + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002608 2608 GSM973687 Gingeras CSHL LID46313 nucleus None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep4 MCF7 cyto TAP + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH002466 2466 GSM973681 Gingeras CSHL LID47163 cytosol TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep3 MCF7 cyto TAP + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002466 2466 GSM973681 Gingeras CSHL LID47162 cytosol TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 TAP-only cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep4 MCF7 cyto + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002607 2607 GSM973672 Gingeras CSHL LID46316 cytosol None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep3 MCF7 cyto + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002607 2607 GSM973672 Gingeras CSHL LID46315 cytosol None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRep2V2 MCF7 cell TAP + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2011-01-19 2011-10-19 wgEncodeEH001090 1090 GSM897081 Gingeras CSHL LID47161 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRep2V2 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRep1V2 MCF7 cell TAP + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2011-01-19 2011-10-19 wgEncodeEH001090 1090 GSM897081 Gingeras CSHL LID47160 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRep1V2 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep4 MCF7 cell + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002609 2609 GSM973690 Gingeras CSHL LID46312 cell None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep3 MCF7 cell + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002609 2609 GSM973690 Gingeras CSHL LID46311 cell None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep4 MCF7 cell CIP + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002610 2610 GSM973676 Gingeras CSHL LID46459 cell CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 CIP-TAP whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep3 MCF7 cell CIP + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002610 2610 GSM973676 Gingeras CSHL LID46458 cell CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 CIP-TAP whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapPlusRep2 IMR9 nucl TAP + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH002464 2464 GSM973679 Gingeras CSHL LID47267 nucleus TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapPlusRep1 IMR9 nucl TAP + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002464 2464 GSM973679 Gingeras CSHL LID47266 nucleus TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalPlusRep2 IMR9 nucl + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002606 2606 GSM973678 Gingeras CSHL LID45956 nucleus None 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalPlusRep1 IMR9 nucl + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002606 2606 GSM973678 Gingeras CSHL LID45955 nucleus None 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapPlusRep2 IMR9 nucl CIP + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002605 2605 GSM973673 Gingeras CSHL LID45887 nucleus CIP-TAP 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 CIP-TAP nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapPlusRep1 IMR9 nucl CIP + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002605 2605 GSM973673 Gingeras CSHL LID45886 nucleus CIP-TAP 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 CIP-TAP nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapPlusRep2 IMR9 cyto TAP + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002463 2463 GSM973686 Gingeras CSHL LID47265 cytosol TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapPlusRep1 IMR9 cyto TAP + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002463 2463 GSM973686 Gingeras CSHL LID47264 cytosol TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 TAP-only cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalPlusRep2 IMR9 cyto + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002618 2618 GSM973671 Gingeras CSHL LID45958 cytosol None 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalPlusRep1 IMR9 cyto + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002618 2618 GSM973671 Gingeras CSHL LID45957 cytosol None 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapPlusRep2 IMR9 cyto CIP + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002619 2619 GSM973670 Gingeras CSHL LID45889 cytosol CIP-TAP 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 CIP-TAP cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapPlusRep1 IMR9 cyto CIP + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002619 2619 GSM973670 Gingeras CSHL LID45888 cytosol CIP-TAP 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 CIP-TAP cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalTapPlusRep2 IMR9 cell TAP + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002465 2465 GSM973680 Gingeras CSHL LID47263 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalTapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalTapPlusRep1 IMR9 cell TAP + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002465 2465 GSM973680 Gingeras CSHL LID47262 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalTapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalPlusRep2 IMR9 cell + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002620 2620 GSM973691 Gingeras CSHL LID45110 cell None 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalPlusRep1 IMR9 cell + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002620 2620 GSM973691 Gingeras CSHL LID45107 cell None 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapPlusRep2 IMR9 cell CIP + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002621 2621 GSM973693 Gingeras CSHL LID45111 cell CIP-TAP 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 CIP-TAP whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapPlusRep1 IMR9 cell CIP + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002621 2621 GSM973693 Gingeras CSHL LID45108 cell CIP-TAP 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 CIP-TAP whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep4 HUVE nucl TAP + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001080 1080 GSM897075 Gingeras CSHL LID21058 nucleus TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep3 HUVE nucl TAP + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001080 1080 GSM897075 Gingeras CSHL LID21056 nucleus TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep2 HepG nucl TAP + 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001742 1742 GSM897085 Gingeras CSHL LID44463 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep1 HepG nucl TAP + 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001742 1742 GSM897085 Gingeras CSHL LID44462 nucleus TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapPlusRawRep2 HepG cyto TAP + 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001743 1743 GSM897082 Gingeras CSHL LID44465 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapPlusRawRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapPlusRawRep1 HepG cyto TAP + 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH001743 1743 GSM897082 Gingeras CSHL LID44464 cytosol TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapPlusRawRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 TAP-only cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapPlusRawRep2 HepG cell TAP + 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEH001741 1741 GSM897084 Gingeras CSHL LID44461 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapPlusRawRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapPlusRawRep1 HepG cell TAP + 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEH001741 1741 GSM897084 Gingeras CSHL LID44460 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapPlusRawRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapPlusRawRep2 HeLa nucl TAP + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001088 1088 GSM897080 Gingeras CSHL LID21147 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapPlusRawRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapPlusRawRep1 HeLa nucl TAP + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001088 1088 GSM897080 Gingeras CSHL LID21144 nucleus TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapPlusRawRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapPlusRawRep2 HeLa cyto TAP + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001087 1087 GSM897069 Gingeras CSHL LID21148 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapPlusRawRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapPlusRawRep1 HeLa cyto TAP + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001087 1087 GSM897069 Gingeras CSHL LID21145 cytosol TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapPlusRawRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 TAP-only cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapPlusRawRep2 HeLa cell TAP + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001089 1089 GSM897079 Gingeras CSHL LID21146 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapPlusRawRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapPlusRawRep1 HeLa cell TAP + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001089 1089 GSM897079 Gingeras CSHL LID21143 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapPlusRawRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqCd20ro01778CellShorttotalTapPlusRep2 CD20 cell TAP + 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002879 2879 GSM977043 Gingeras CSHL LID44363 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqCd20ro01778CellShorttotalTapPlusRep2 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqCd20ro01794CellShorttotalTapPlusRep1 CD20 cell TAP + 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002879 2879 GSM977043 Gingeras CSHL LID44362 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqCd20ro01794CellShorttotalTapPlusRep1 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapPlusRep4 A549 nucl TAP + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002462 2462 GSM973685 Gingeras CSHL LID47044 nucleus TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapPlusRep3 A549 nucl TAP + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002462 2462 GSM973685 Gingeras CSHL LID47043 nucleus TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalPlusRep4 A549 nucl + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002600 2600 GSM973683 Gingeras CSHL LID46061 nucleus None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalPlusRep3 A549 nucl + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002600 2600 GSM973683 Gingeras CSHL LID46060 nucleus None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapPlusRep4 A549 nucl CIP + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002617 2617 GSM973661 Gingeras CSHL LID46101 nucleus CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 CIP-TAP nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapPlusRep3 A549 nucl CIP + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002617 2617 GSM973661 Gingeras CSHL LID46100 nucleus CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 CIP-TAP nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapPlusRep4 A549 cyto TAP + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002461 2461 GSM973684 Gingeras CSHL LID47042 cytosol TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapPlusRep3 A549 cyto TAP + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002461 2461 GSM973684 Gingeras CSHL LID47041 cytosol TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 TAP-only cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalPlusRep4 A549 cyto + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002597 2597 GSM973664 Gingeras CSHL LID46063 cytosol None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalPlusRep3 A549 cyto + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002597 2597 GSM973664 Gingeras CSHL LID46062 cytosol None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapPlusRep4 A549 cyto CIP + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002599 2599 GSM973669 Gingeras CSHL LID46103 cytosol CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 CIP-TAP cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapPlusRep3 A549 cyto CIP + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002599 2599 GSM973669 Gingeras CSHL LID46102 cytosol CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 CIP-TAP cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalTapPlusRep2V2 A549 cell TAP + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2011-05-11 2012-02-11 wgEncodeEH001740 1740 GSM897083 Gingeras CSHL LID47040 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalTapPlusRep2V2 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalTapPlusRep1V2 A549 cell TAP + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2011-05-11 2012-02-11 wgEncodeEH001740 1740 GSM897083 Gingeras CSHL LID47039 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalTapPlusRep1V2 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalPlusRep4 A549 cell + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002598 2598 GSM973668 Gingeras CSHL LID46059 cell None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalPlusRep3 A549 cell + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002598 2598 GSM973668 Gingeras CSHL LID46058 cell None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapPlusRep4 A549 cell CIP + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002601 2601 GSM973674 Gingeras CSHL LID46099 cell CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 CIP-TAP whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapPlusRep3 A549 cell CIP + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002601 2601 GSM973674 Gingeras CSHL LID46098 cell CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 CIP-TAP whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562PolysomeShortPlusRaw K562 psom TAP + 1 K562 RnaSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-23 2010-06-23 wgEncodeEH000210 210 GSM605631 Gingeras CSHL crg-44 Produced by Hannon Lab polysome hg18 TAP-Only shortTotal wgEncodeCshlShortRnaSeqK562PolysomeShortPlusRaw PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Strand of mRNA with ribosomes attached This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Graphs the base-by-base density of tags on the plus strand K562 TAP-only polysome small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapPlusRawRep2 K562 nucl TAP + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000209 209 GSM605635 Gingeras CSHL LID10569 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapPlusRawRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapPlusRawRep1 K562 nucl TAP + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000209 209 GSM605635 Gingeras CSHL LID10570 nucleus TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapPlusRawRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep4 K562 nplm TAP + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000208 208 GSM605634 Gingeras CSHL LID18559 nucleoplasm TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only nucleoplasm small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep3 K562 nplm TAP + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000208 208 GSM605634 Gingeras CSHL LID8929 nucleoplasm TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep3 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only nucleoplasm small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapPlusRawRep4 K562 nlus TAP + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000207 207 GSM605628 Gingeras CSHL LID18558 nucleolus TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapPlusRawRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only nucleolus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapPlusRawRep3 K562 nlus TAP + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000207 207 GSM605628 Gingeras CSHL LID8928 nucleolus TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapPlusRawRep3 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only nucleolus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep2 K562 cyto TAP + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000206 206 GSM605629 Gingeras CSHL LID10571 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep1 K562 cyto TAP + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000206 206 GSM605629 Gingeras CSHL LID10572 cytosol TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapPlusRawRep4 K562 chrm TAP + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000205 205 GSM605632 Gingeras CSHL LID18560 chromatin TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapPlusRawRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only chromatin small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapPlusRawRep3 K562 chrm TAP + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000205 205 GSM605632 Gingeras CSHL LID8930 chromatin TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapPlusRawRep3 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only chromatin small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CellShorttotalTapPlusRawRep2 K562 cell TAP + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000213 213 GSM605630 Gingeras CSHL LID10568 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CellShorttotalTapPlusRawRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CellShorttotalTapPlusRawRep1 K562 cell TAP + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000213 213 GSM605630 Gingeras CSHL LID10567 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CellShorttotalTapPlusRawRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapPlusRawRep2 H1ES nucl TAP + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001084 1084 GSM897071 Gingeras CSHL LID20907 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapPlusRawRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapPlusRawRep2 H1ES cyto TAP + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001083 1083 GSM897072 Gingeras CSHL LID20908 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapPlusRawRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapPlusRawRep2 H1ES cell TAP + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001082 1082 GSM897073 Gingeras CSHL LID20906 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapPlusRawRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapPlusRawRep1 H1ES cell TAP + 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001082 1082 GSM897073 Gingeras CSHL LID20905 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapPlusRawRep1 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep2 GM78 nucl TAP + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000204 204 GSM605633 Gingeras CSHL LID20903 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only nucleus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep1 GM78 nucl TAP + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000204 204 GSM605633 Gingeras CSHL LID20900 nucleus TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only nucleus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep4 GM78 nlus TAP + 2 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002942 2942 GSM977032 Gingeras CSHL LID47654 nucleolus TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep4 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only nucleolus small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep3 GM78 nlus TAP + 1 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-20 2013-03-19 wgEncodeEH002942 2942 GSM977032 Gingeras CSHL LID47653 nucleolus TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep3 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only nucleolus small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep2 GM78 cyto TAP + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000203 203 GSM605627 Gingeras CSHL LID20904 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only cytosol small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep1 GM78 cyto TAP + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000203 203 GSM605627 Gingeras CSHL LID20901 cytosol TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only cytosol small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878ChromatinTapPlusRep4 GM78 chrm TAP + 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002889 2889 GSM977042 Gingeras CSHL LID47656 chromatin TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878ChromatinTapPlusRep4 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only chromatin small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878ChromatinTapPlusRep3 GM78 chrm TAP + 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002889 2889 GSM977042 Gingeras CSHL LID47655 chromatin TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878ChromatinTapPlusRep3 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only chromatin small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapPlusRawRep2 GM78 cell TAP + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000212 212 GSM605625 Gingeras CSHL LID20902 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapPlusRawRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only whole cell small RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapPlusRawRep1 GM78 cell TAP + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000212 212 GSM605625 Gingeras CSHL LID20899 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapPlusRawRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 TAP-only whole cell small RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqViewMinusSignal Minus Signal Small RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapMinusRawRep2 SKRA cell TAP - 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001094 1094 GSM897070 Gingeras CSHL LID20748 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapMinusRawRep2 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH_RA TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapMinusRawRep1 SKRA cell TAP - 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001094 1094 GSM897070 Gingeras CSHL LID20747 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapMinusRawRep1 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH_RA TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSkmc812190217CellTapMinusRep2 SkMC cell TAP - 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002884 2884 GSM977039 Gingeras CSHL LID47240 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSkmc812190217CellTapMinusRep2 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSkmc9011302CellShorttotalTapMinusRep1 SkMC cell TAP - 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002884 2884 GSM977039 Gingeras CSHL LID47239 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSkmc9011302CellShorttotalTapMinusRep1 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqProstateCellTotalMinusRaw Pros cell TAP - 1 prostate RnaSeq ENCODE Jan 2011 Freeze 2010-06-30 2009-09-23 2010-06-23 wgEncodeEH000211 211 GSM605626 Gingeras CSHL crg-61 Produced by Hannon Lab cell hg18 TAP-Only shortTotal wgEncodeCshlShortRnaSeqProstateCellTotalMinusRaw MinusSignal prostate tissue purchased for CSHL project Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Graphs the base-by-base density of tags on the minus strand Prostate TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemm2CellTapMinusRep2 NHEM cell TAP - 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002897 2897 GSM977047 Gingeras CSHL LID47614 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemm2CellTapMinusRep2 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM_M2 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemm2CellTapMinusRep1 NHEM cell TAP - 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002897 2897 GSM977047 Gingeras CSHL LID47613 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemm2CellTapMinusRep1 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM_M2 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemfm2CellTapMinusRep2 NHEf cell TAP - 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002895 2895 GSM977045 Gingeras CSHL LID47612 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemfm2CellTapMinusRep2 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f_M2 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemfm2CellTapMinusRep1 NHEf cell TAP - 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002895 2895 GSM977045 Gingeras CSHL LID47611 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemfm2CellTapMinusRep1 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f_M2 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapMinusRawRep4 NHEK nucl TAP - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001093 1093 GSM897076 Gingeras CSHL LID21003 nucleus TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapMinusRawRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapMinusRawRep3 NHEK nucl TAP - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001093 1093 GSM897076 Gingeras CSHL LID21001 nucleus TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapMinusRawRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapMinusRawRep4 NHEK cyto TAP - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001092 1092 GSM897078 Gingeras CSHL LID21004 cytosol TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapMinusRawRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapMinusRawRep3 NHEK cyto TAP - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001092 1092 GSM897078 Gingeras CSHL LID21002 cytosol TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapMinusRawRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK TAP-only cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep2 NHEK cell TAP - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001091 1091 GSM897086 Gingeras CSHL LID21000 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep2 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep1 NHEK cell TAP - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001091 1091 GSM897086 Gingeras CSHL LID20999 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep1 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhdf00608013CellShorttotalTapMinusRep2 NHDF cell TAP - 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002883 2883 GSM977034 Gingeras CSHL LID47242 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhdf00608013CellShorttotalTapMinusRep2 MinusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhdf70717012CellShorttotalTapMinusRep1 NHDF cell TAP - 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002883 2883 GSM977034 Gingeras CSHL LID47241 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhdf70717012CellShorttotalTapMinusRep1 MinusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHwpCellTapMinusRep2 HWP cell TAP - 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002894 2894 GSM977046 Gingeras CSHL LID47610 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHwpCellTapMinusRep2 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHwpCellTapMinusRep1 HWP cell TAP - 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002894 2894 GSM977046 Gingeras CSHL LID47609 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHwpCellTapMinusRep1 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHvmf61004013CellShorttotalTapMinusRep2 HVMF cell TAP - 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002882 2882 GSM977033 Gingeras CSHL LID47244 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHvmf61004013CellShorttotalTapMinusRep2 MinusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHvmf60912033CellShorttotalTapMinusRep1 HVMF cell TAP - 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002882 2882 GSM977033 Gingeras CSHL LID47243 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHvmf60912033CellShorttotalTapMinusRep1 MinusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHsavecCellTapMinusRep2 HSaV cell TAP - 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002893 2893 GSM977051 Gingeras CSHL LID47616 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHsavecCellTapMinusRep2 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHsavecCellTapMinusRep1 HSaV cell TAP - 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002893 2893 GSM977051 Gingeras CSHL LID47615 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHsavecCellTapMinusRep1 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpiepcCellTapMinusRep2 HPIE cell TAP - 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002892 2892 GSM977052 Gingeras CSHL LID47520 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpiepcCellTapMinusRep2 MinusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpiepcCellTapMinusRep1 HPIE cell TAP - 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002892 2892 GSM977052 Gingeras CSHL LID47519 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpiepcCellTapMinusRep1 MinusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpcplCellTapMinusRep2 HPCP cell TAP - 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002891 2891 GSM977049 Gingeras CSHL LID47518 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpcplCellTapMinusRep2 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpcplCellTapMinusRep1 HPCP cell TAP - 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002891 2891 GSM977049 Gingeras CSHL LID47517 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpcplCellTapMinusRep1 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHob00902021CellShorttotalTapMinusRep2 HOB cell TAP - 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002881 2881 GSM977036 Gingeras CSHL LID47432 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHob00902021CellShorttotalTapMinusRep2 MinusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHobCellTapMinusRawRep1 HOB cell TAP - 1 HOB RnaSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH002881 2881 GSM977036 Gingeras CSHL LID47431 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHobCellTapMinusRawRep1 MinusRawSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscucCellTapMinusRep2 hMUC cell TAP - 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002896 2896 GSM977048 Gingeras CSHL LID47516 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscucCellTapMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscucCellTapMinusRep1 hMUC cell TAP - 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002896 2896 GSM977048 Gingeras CSHL LID47515 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscucCellTapMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscbmCellTapMinusRawRep2 hMBM cell TAP - 2 hMSC-BM RnaSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH002946 2946 GSM977028 Gingeras CSHL LID47659 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscbmCellTapMinusRawRep2 MinusRawSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscbmCellTapMinusRawRep1 hMBM cell TAP - 1 hMSC-BM RnaSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH002946 2946 GSM977028 Gingeras CSHL LID47658 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscbmCellTapMinusRawRep1 MinusRawSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscat906160112CellTapMinusRep2 hMAT cell TAP - 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002888 2888 GSM977041 Gingeras CSHL LID47480 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscat906160112CellTapMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscat010260412CellTapMinusRep1 hMAT cell TAP - 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002888 2888 GSM977041 Gingeras CSHL LID47479 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscat010260412CellTapMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmepcCellTapMinusRep1 HMEC cell TAP - 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002890 2890 GSM977050 Gingeras CSHL LID47657 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmepcCellTapMinusRep1 MinusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HMEpC TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHfdpc01005032CellTapMinusRep2 HFDC cell TAP - 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002887 2887 GSM977038 Gingeras CSHL LID47478 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHfdpc01005032CellTapMinusRep2 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHfdpc01027033CellTapMinusRep1 HFDC cell TAP - 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002887 2887 GSM977038 Gingeras CSHL LID47477 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHfdpc01027033CellTapMinusRep1 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHch81008082CellShorttotalTapMinusRep2 HCH cell TAP - 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002886 2886 GSM977037 Gingeras CSHL LID47476 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHch81008082CellShorttotalTapMinusRep2 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHch00113082pCellShorttotalTapMinusRep1 HCH cell TAP - 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002886 2886 GSM977037 Gingeras CSHL LID47475 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHch00113082pCellShorttotalTapMinusRep1 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoec80611021CellTapMinusRep2 HAEC cell TAP - 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002885 2885 GSM977040 Gingeras CSHL LID47436 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoec80611021CellTapMinusRep2 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoec70717061CellTapMinusRep1 HAEC cell TAP - 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002885 2885 GSM977040 Gingeras CSHL LID47435 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoec70717061CellTapMinusRep1 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoaf609010111CellTapMinusRep2 HAAF cell TAP - 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002880 2880 GSM977035 Gingeras CSHL LID47434 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoaf609010111CellTapMinusRep2 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoaf61113019CellTapMinusRep1 HAAF cell TAP - 1 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002880 2880 GSM977035 Gingeras CSHL LID47433 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoaf61113019CellTapMinusRep1 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellTapMinusRawRep2 H1ne cell TAP - 2 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002945 2945 GSM977029 Gingeras CSHL LID48356 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellTapMinusRawRep2 MinusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand H1-neurons TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellTapMinusRawRep1 H1ne cell TAP - 1 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002945 2945 GSM977029 Gingeras CSHL LID48355 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellTapMinusRawRep1 MinusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand H1-neurons TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellMinusRawRep2 H1ne cell - 2 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-20 2013-03-19 wgEncodeEH002943 2943 GSM977031 Gingeras CSHL LID48358 cell None 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellMinusRawRep2 MinusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand H1-neurons whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellMinusRawRep1 H1ne cell - 1 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002943 2943 GSM977031 Gingeras CSHL LID48357 cell None 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellMinusRawRep1 MinusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand H1-neurons whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellCiptapMinusRawRep2 H1ne cell CIP - 2 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002944 2944 GSM977030 Gingeras CSHL LID48354 cell CIP-TAP 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellCiptapMinusRawRep2 MinusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand H1-neurons CIP-TAP whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellCiptapMinusRawRep1 H1ne cell CIP - 1 H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002944 2944 GSM977030 Gingeras CSHL LID48353 cell CIP-TAP 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellCiptapMinusRawRep1 MinusRawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand H1-neurons CIP-TAP whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqCd34mobilizedCellTapMinusRep1 CD34 cell TAP - 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002604 2604 GSM973662 Gingeras CSHL LID46197 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqCd34mobilizedCellTapMinusRep1 MinusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand CD34+ TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqBjCellShorttotalTapMinusRawRep2 BJ cell TAP - 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001079 1079 GSM897077 Gingeras CSHL LID20910 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqBjCellShorttotalTapMinusRawRep2 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqBjCellShorttotalTapMinusRawRep1 BJ cell TAP - 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001079 1079 GSM897077 Gingeras CSHL LID20909 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqBjCellShorttotalTapMinusRawRep1 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapMinusRawRep2 AG50 cell TAP - 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001081 1081 GSM897074 Gingeras CSHL LID20746 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapMinusRawRep2 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapMinusRawRep1 AG50 cell TAP - 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001081 1081 GSM897074 Gingeras CSHL LID20745 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapMinusRawRep1 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapMinusRep4 SKSH nucl TAP - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002469 2469 GSM973689 Gingeras CSHL LID46961 nucleus TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapMinusRep3 SKSH nucl TAP - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002469 2469 GSM973689 Gingeras CSHL LID46960 nucleus TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalMinusRep4 SKSH nucl - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002613 2613 GSM973665 Gingeras CSHL LID46204 nucleus None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalMinusRep3 SKSH nucl - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002613 2613 GSM973665 Gingeras CSHL LID46203 nucleus None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapMinusRep4 SKSH nucl CIP - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002615 2615 GSM973663 Gingeras CSHL LID46273 nucleus CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH CIP-TAP nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapMinusRep3 SKSH nucl CIP - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002615 2615 GSM973663 Gingeras CSHL LID46272 nucleus CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH CIP-TAP nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapMinusRep4 SKSH cyto TAP - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002468 2468 GSM973688 Gingeras CSHL LID46959 cytosol TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapMinusRep3 SKSH cyto TAP - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002468 2468 GSM973688 Gingeras CSHL LID46958 cytosol TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH TAP-only cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalMinusRep4 SKSH cyto - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002612 2612 GSM973666 Gingeras CSHL LID46206 cytosol None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalMinusRep3 SKSH cyto - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002612 2612 GSM973666 Gingeras CSHL LID46205 cytosol None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapMinusRep4 SKSH cyto CIP - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002614 2614 GSM973692 Gingeras CSHL LID46275 cytosol CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH CIP-TAP cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapMinusRep3 SKSH cyto CIP - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002614 2614 GSM973692 Gingeras CSHL LID46274 cytosol CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH CIP-TAP cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalTapMinusRep4 SKSH cell TAP - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002470 2470 GSM973667 Gingeras CSHL LID46957 cell TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalTapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalTapMinusRep3 SKSH cell TAP - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002470 2470 GSM973667 Gingeras CSHL LID46956 cell TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalTapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalMinusRep4 SKSH cell - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002622 2622 GSM973675 Gingeras CSHL LID46202 cell None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalMinusRep3 SKSH cell - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002622 2622 GSM973675 Gingeras CSHL LID46201 cell None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep4 SKSH cell CIP - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002616 2616 GSM973677 Gingeras CSHL LID46271 cell CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH CIP-TAP whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep3 SKSH cell CIP - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002616 2616 GSM973677 Gingeras CSHL LID46270 cell CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH CIP-TAP whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMonocd14CellTapMinusRep2 CD14 cell TAP - 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002898 2898 GSM977044 Gingeras CSHL LID44361 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqMonocd14CellTapMinusRep2 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD14+ TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMonocd14CellTapMinusRep1 CD14 cell TAP - 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002898 2898 GSM977044 Gingeras CSHL LID44360 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqMonocd14CellTapMinusRep1 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD14+ TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep4 MCF7 nucl TAP - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002467 2467 GSM973682 Gingeras CSHL LID47165 nucleus TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep3 MCF7 nucl TAP - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002467 2467 GSM973682 Gingeras CSHL LID47164 nucleus TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep4 MCF7 nucl - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002608 2608 GSM973687 Gingeras CSHL LID46314 nucleus None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep3 MCF7 nucl - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002608 2608 GSM973687 Gingeras CSHL LID46313 nucleus None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep4 MCF7 cyto TAP - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH002466 2466 GSM973681 Gingeras CSHL LID47163 cytosol TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep3 MCF7 cyto TAP - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002466 2466 GSM973681 Gingeras CSHL LID47162 cytosol TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 TAP-only cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep4 MCF7 cyto - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002607 2607 GSM973672 Gingeras CSHL LID46316 cytosol None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep3 MCF7 cyto - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002607 2607 GSM973672 Gingeras CSHL LID46315 cytosol None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRep2V2 MCF7 cell TAP - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2011-01-19 2011-10-19 wgEncodeEH001090 1090 GSM897081 Gingeras CSHL LID47161 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRep2V2 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRep1V2 MCF7 cell TAP - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2011-01-19 2011-10-19 wgEncodeEH001090 1090 GSM897081 Gingeras CSHL LID47160 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRep1V2 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep4 MCF7 cell - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002609 2609 GSM973690 Gingeras CSHL LID46312 cell None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep3 MCF7 cell - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002609 2609 GSM973690 Gingeras CSHL LID46311 cell None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep4 MCF7 cell CIP - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002610 2610 GSM973676 Gingeras CSHL LID46459 cell CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 CIP-TAP whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep3 MCF7 cell CIP - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002610 2610 GSM973676 Gingeras CSHL LID46458 cell CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 CIP-TAP whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapMinusRep2 IMR9 nucl TAP - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH002464 2464 GSM973679 Gingeras CSHL LID47267 nucleus TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapMinusRep1 IMR9 nucl TAP - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002464 2464 GSM973679 Gingeras CSHL LID47266 nucleus TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalMinusRep2 IMR9 nucl - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002606 2606 GSM973678 Gingeras CSHL LID45956 nucleus None 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalMinusRep1 IMR9 nucl - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002606 2606 GSM973678 Gingeras CSHL LID45955 nucleus None 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapMinusRep2 IMR9 nucl CIP - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002605 2605 GSM973673 Gingeras CSHL LID45887 nucleus CIP-TAP 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 CIP-TAP nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapMinusRep1 IMR9 nucl CIP - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002605 2605 GSM973673 Gingeras CSHL LID45886 nucleus CIP-TAP 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 CIP-TAP nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapMinusRep2 IMR9 cyto TAP - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002463 2463 GSM973686 Gingeras CSHL LID47265 cytosol TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapMinusRep1 IMR9 cyto TAP - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002463 2463 GSM973686 Gingeras CSHL LID47264 cytosol TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 TAP-only cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalMinusRep2 IMR9 cyto - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002618 2618 GSM973671 Gingeras CSHL LID45958 cytosol None 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalMinusRep1 IMR9 cyto - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002618 2618 GSM973671 Gingeras CSHL LID45957 cytosol None 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapMinusRep2 IMR9 cyto CIP - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002619 2619 GSM973670 Gingeras CSHL LID45889 cytosol CIP-TAP 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 CIP-TAP cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapMinusRep1 IMR9 cyto CIP - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-19 wgEncodeEH002619 2619 GSM973670 Gingeras CSHL LID45888 cytosol CIP-TAP 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 CIP-TAP cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalTapMinusRep2 IMR9 cell TAP - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002465 2465 GSM973680 Gingeras CSHL LID47263 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalTapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalTapMinusRep1 IMR9 cell TAP - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002465 2465 GSM973680 Gingeras CSHL LID47262 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalTapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalMinusRep2 IMR9 cell - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002620 2620 GSM973691 Gingeras CSHL LID45110 cell None 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalMinusRep1 IMR9 cell - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002620 2620 GSM973691 Gingeras CSHL LID45107 cell None 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapMinusRep2 IMR9 cell CIP - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002621 2621 GSM973693 Gingeras CSHL LID45111 cell CIP-TAP 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 CIP-TAP whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapMinusRep1 IMR9 cell CIP - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002621 2621 GSM973693 Gingeras CSHL LID45108 cell CIP-TAP 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 CIP-TAP whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep4 HUVE nucl TAP - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001080 1080 GSM897075 Gingeras CSHL LID21058 nucleus TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep3 HUVE nucl TAP - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001080 1080 GSM897075 Gingeras CSHL LID21056 nucleus TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep2 HepG nucl TAP - 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001742 1742 GSM897085 Gingeras CSHL LID44463 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep1 HepG nucl TAP - 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001742 1742 GSM897085 Gingeras CSHL LID44462 nucleus TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapMinusRawRep2 HepG cyto TAP - 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001743 1743 GSM897082 Gingeras CSHL LID44465 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapMinusRawRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapMinusRawRep1 HepG cyto TAP - 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH001743 1743 GSM897082 Gingeras CSHL LID44464 cytosol TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapMinusRawRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 TAP-only cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapMinusRawRep2 HepG cell TAP - 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEH001741 1741 GSM897084 Gingeras CSHL LID44461 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapMinusRawRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapMinusRawRep1 HepG cell TAP - 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEH001741 1741 GSM897084 Gingeras CSHL LID44460 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapMinusRawRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapMinusRawRep2 HeLa nucl TAP - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001088 1088 GSM897080 Gingeras CSHL LID21147 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapMinusRawRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapMinusRawRep1 HeLa nucl TAP - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001088 1088 GSM897080 Gingeras CSHL LID21144 nucleus TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapMinusRawRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapMinusRawRep2 HeLa cyto TAP - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001087 1087 GSM897069 Gingeras CSHL LID21148 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapMinusRawRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapMinusRawRep1 HeLa cyto TAP - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001087 1087 GSM897069 Gingeras CSHL LID21145 cytosol TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapMinusRawRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 TAP-only cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapMinusRawRep2 HeLa cell TAP - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001089 1089 GSM897079 Gingeras CSHL LID21146 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapMinusRawRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapMinusRawRep1 HeLa cell TAP - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001089 1089 GSM897079 Gingeras CSHL LID21143 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapMinusRawRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqCd20ro01778CellShorttotalTapMinusRep2 CD20 cell TAP - 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002879 2879 GSM977043 Gingeras CSHL LID44363 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqCd20ro01778CellShorttotalTapMinusRep2 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqCd20ro01794CellShorttotalTapMinusRep1 CD20 cell TAP - 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002879 2879 GSM977043 Gingeras CSHL LID44362 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqCd20ro01794CellShorttotalTapMinusRep1 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapMinusRep4 A549 nucl TAP - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002462 2462 GSM973685 Gingeras CSHL LID47044 nucleus TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapMinusRep3 A549 nucl TAP - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002462 2462 GSM973685 Gingeras CSHL LID47043 nucleus TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalMinusRep4 A549 nucl - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002600 2600 GSM973683 Gingeras CSHL LID46061 nucleus None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalMinusRep3 A549 nucl - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002600 2600 GSM973683 Gingeras CSHL LID46060 nucleus None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapMinusRep4 A549 nucl CIP - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002617 2617 GSM973661 Gingeras CSHL LID46101 nucleus CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 CIP-TAP nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapMinusRep3 A549 nucl CIP - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002617 2617 GSM973661 Gingeras CSHL LID46100 nucleus CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 CIP-TAP nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapMinusRep4 A549 cyto TAP - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEH002461 2461 GSM973684 Gingeras CSHL LID47042 cytosol TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapMinusRep3 A549 cyto TAP - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEH002461 2461 GSM973684 Gingeras CSHL LID47041 cytosol TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 TAP-only cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalMinusRep4 A549 cyto - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002597 2597 GSM973664 Gingeras CSHL LID46063 cytosol None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalMinusRep3 A549 cyto - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002597 2597 GSM973664 Gingeras CSHL LID46062 cytosol None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapMinusRep4 A549 cyto CIP - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002599 2599 GSM973669 Gingeras CSHL LID46103 cytosol CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 CIP-TAP cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapMinusRep3 A549 cyto CIP - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002599 2599 GSM973669 Gingeras CSHL LID46102 cytosol CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 CIP-TAP cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalTapMinusRep2V2 A549 cell TAP - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2011-05-11 2012-02-11 wgEncodeEH001740 1740 GSM897083 Gingeras CSHL LID47040 cell TAP-Only 1x101 2 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalTapMinusRep2V2 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalTapMinusRep1V2 A549 cell TAP - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2011-05-11 2012-02-11 wgEncodeEH001740 1740 GSM897083 Gingeras CSHL LID47039 cell TAP-Only 1x101 1 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalTapMinusRep1V2 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalMinusRep4 A549 cell - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002598 2598 GSM973668 Gingeras CSHL LID46059 cell None 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalMinusRep3 A549 cell - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002598 2598 GSM973668 Gingeras CSHL LID46058 cell None 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapMinusRep4 A549 cell CIP - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-18 wgEncodeEH002601 2601 GSM973674 Gingeras CSHL LID46099 cell CIP-TAP 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 CIP-TAP whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapMinusRep3 A549 cell CIP - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-19 2012-11-18 wgEncodeEH002601 2601 GSM973674 Gingeras CSHL LID46098 cell CIP-TAP 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 CIP-TAP whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562PolysomeShortMinusRaw K562 psom TAP - 1 K562 RnaSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-23 2010-06-23 wgEncodeEH000210 210 GSM605631 Gingeras CSHL crg-44 Produced by Hannon Lab polysome hg18 TAP-Only shortTotal wgEncodeCshlShortRnaSeqK562PolysomeShortMinusRaw MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Strand of mRNA with ribosomes attached This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Graphs the base-by-base density of tags on the minus strand K562 TAP-only polysome small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapMinusRawRep2 K562 nucl TAP - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000209 209 GSM605635 Gingeras CSHL LID10569 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapMinusRawRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapMinusRawRep1 K562 nucl TAP - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000209 209 GSM605635 Gingeras CSHL LID10570 nucleus TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapMinusRawRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep4 K562 nplm TAP - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000208 208 GSM605634 Gingeras CSHL LID18559 nucleoplasm TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only nucleoplasm small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep3 K562 nplm TAP - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000208 208 GSM605634 Gingeras CSHL LID8929 nucleoplasm TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep3 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only nucleoplasm small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapMinusRawRep4 K562 nlus TAP - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000207 207 GSM605628 Gingeras CSHL LID18558 nucleolus TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapMinusRawRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only nucleolus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapMinusRawRep3 K562 nlus TAP - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000207 207 GSM605628 Gingeras CSHL LID8928 nucleolus TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapMinusRawRep3 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only nucleolus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep2 K562 cyto TAP - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000206 206 GSM605629 Gingeras CSHL LID10571 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep1 K562 cyto TAP - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000206 206 GSM605629 Gingeras CSHL LID10572 cytosol TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapMinusRawRep4 K562 chrm TAP - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000205 205 GSM605632 Gingeras CSHL LID18560 chromatin TAP-Only 1x36 4 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapMinusRawRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only chromatin small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapMinusRawRep3 K562 chrm TAP - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000205 205 GSM605632 Gingeras CSHL LID8930 chromatin TAP-Only 1x36 3 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapMinusRawRep3 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only chromatin small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CellShorttotalTapMinusRawRep2 K562 cell TAP - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000213 213 GSM605630 Gingeras CSHL LID10568 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CellShorttotalTapMinusRawRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CellShorttotalTapMinusRawRep1 K562 cell TAP - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000213 213 GSM605630 Gingeras CSHL LID10567 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CellShorttotalTapMinusRawRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapMinusRawRep2 H1ES nucl TAP - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001084 1084 GSM897071 Gingeras CSHL LID20907 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapMinusRawRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapMinusRawRep2 H1ES cyto TAP - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001083 1083 GSM897072 Gingeras CSHL LID20908 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapMinusRawRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapMinusRawRep2 H1ES cell TAP - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001082 1082 GSM897073 Gingeras CSHL LID20906 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapMinusRawRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapMinusRawRep1 H1ES cell TAP - 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001082 1082 GSM897073 Gingeras CSHL LID20905 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapMinusRawRep1 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep2 GM78 nucl TAP - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH000204 204 GSM605633 Gingeras CSHL LID20903 nucleus TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only nucleus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep1 GM78 nucl TAP - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000204 204 GSM605633 Gingeras CSHL LID20900 nucleus TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only nucleus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep4 GM78 nlus TAP - 2 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH002942 2942 GSM977032 Gingeras CSHL LID47654 nucleolus TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep4 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only nucleolus small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep3 GM78 nlus TAP - 1 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-20 2013-03-19 wgEncodeEH002942 2942 GSM977032 Gingeras CSHL LID47653 nucleolus TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep3 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only nucleolus small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapMinusRawRep2 GM78 cyto TAP - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000203 203 GSM605627 Gingeras CSHL LID20904 cytosol TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapMinusRawRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only cytosol small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapMinusRawRep1 GM78 cyto TAP - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000203 203 GSM605627 Gingeras CSHL LID20901 cytosol TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapMinusRawRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only cytosol small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878ChromatinTapMinusRep4 GM78 chrm TAP - 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002889 2889 GSM977042 Gingeras CSHL LID47656 chromatin TAP-Only 1x101 4 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878ChromatinTapMinusRep4 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only chromatin small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878ChromatinTapMinusRep3 GM78 chrm TAP - 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-12-20 wgEncodeEH002889 2889 GSM977042 Gingeras CSHL LID47655 chromatin TAP-Only 1x101 3 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878ChromatinTapMinusRep3 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only chromatin small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapMinusRawRep2 GM78 cell TAP - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000212 212 GSM605625 Gingeras CSHL LID20902 cell TAP-Only 1x36 2 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapMinusRawRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only whole cell small RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapMinusRawRep1 GM78 cell TAP - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000212 212 GSM605625 Gingeras CSHL LID20899 cell TAP-Only 1x36 1 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapMinusRawRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 TAP-only whole cell small RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqViewContigs Contigs Small RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapContigs SKRA cell TAP C SK-N-SH_RA RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001094 1094 GSM897070 Gingeras CSHL LID20747,LID20748 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapContigs Contigs neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH_RA TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSkmcCellTapContigs SkMC cell TAP C SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002884 2884 GSM977039 Gingeras CSHL LID47239,LID47240 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSkmcCellTapContigs Contigs Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SkMC TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemm2CellTapContigs NHEM cell TAP C NHEM_M2 RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002897 2897 GSM977047 Gingeras CSHL LID47613,LID47614 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemm2CellTapContigs Contigs Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEM_M2 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhemfm2CellTapContigs NHEf cell TAP C NHEM.f_M2 RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002895 2895 GSM977045 Gingeras CSHL LID47611,LID47612 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhemfm2CellTapContigs Contigs Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEM.f_M2 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekNucleusTapContigs NHEK nucl TAP C NHEK RnaSeq ENCODE Jul 2012 Freeze 2012-05-07 2013-02-07 wgEncodeEH001093 1093 GSM897076 Gingeras CSHL LID21001,LID21003 iIDR nucleus TAP-Only 1x36 shortTotal Illumina_GA2x F wgEncodeCshlShortRnaSeqNhekNucleusTapContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Female Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapContigs NHEK cyto TAP C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001092 1092 GSM897078 Gingeras CSHL LID21002,LID21004 iIDR cytosol TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhekCellShorttotalTapContigs NHEK cell TAP C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001091 1091 GSM897086 Gingeras CSHL LID20999,LID21000 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqNhekCellShorttotalTapContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqNhdfCellTapContigs NHDF cell TAP C NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002883 2883 GSM977034 Gingeras CSHL LID47241,LID47242 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqNhdfCellTapContigs Contigs Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHDF TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHwpCellTapContigs HWP cell TAP C HWP RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002894 2894 GSM977046 Gingeras CSHL LID47609,LID47610 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHwpCellTapContigs Contigs Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HWP TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHvmfCellTapContigs HVMF cell TAP C HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002882 2882 GSM977033 Gingeras CSHL LID47243,LID47244 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHvmfCellTapContigs Contigs villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HVMF TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHsavecCellTapContigs HSaV cell TAP C HSaVEC RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002893 2893 GSM977051 Gingeras CSHL LID47615,LID47616 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHsavecCellTapContigs Contigs Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSaVEC TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpiepcCellTapContigs HPIE cell TAP C HPIEpC RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002892 2892 GSM977052 Gingeras CSHL LID47519,LID47520 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpiepcCellTapContigs Contigs Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HPIEpC TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHpcplCellTapContigs HPCP cell TAP C HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002891 2891 GSM977049 Gingeras CSHL LID47517,LID47518 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHpcplCellTapContigs Contigs Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HPC-PL TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHobCellTapContigs HOB cell TAP C HOB RnaSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH002881 2881 GSM977036 Gingeras CSHL LID47431,LID47432 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHobCellTapContigs Contigs Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HOB TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscucCellTapContigs hMUC cell TAP C hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002896 2896 GSM977048 Gingeras CSHL LID47515,LID47516 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscucCellTapContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-UC TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscbmCellTapContigs hMBM cell TAP C hMSC-BM RnaSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH002946 2946 GSM977028 Gingeras CSHL LID47658,LID47659 cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscbmCellTapContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-BM TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmscatCellTapContigs hMAT cell TAP C hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002888 2888 GSM977041 Gingeras CSHL LID47479,LID47480 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmscatCellTapContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-AT TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHmepcCellTapContigs HMEC cell TAP C HMEpC RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002890 2890 GSM977050 Gingeras CSHL LID47657 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHmepcCellTapContigs Contigs Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEpC TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHfdpcCellTapContigs HFDC cell TAP C HFDPC RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002887 2887 GSM977038 Gingeras CSHL LID47477,LID47478 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHfdpcCellTapContigs Contigs Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HFDPC TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHchCellTapContigs HCH cell TAP C HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002886 2886 GSM977037 Gingeras CSHL LID47475,LID47476 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHchCellTapContigs Contigs Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HCH TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoecCellTapContigs HAEC cell TAP C HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002885 2885 GSM977040 Gingeras CSHL LID47435,LID47436 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoecCellTapContigs Contigs Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HAoEC TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHaoafCellTapContigs HAAF cell TAP C HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002880 2880 GSM977035 Gingeras CSHL LID47433,LID47434 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqHaoafCellTapContigs Contigs Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HAoAF TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellTapContigs H1ne cell TAP C H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002945 2945 GSM977029 Gingeras CSHL LID48355,LID48356 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellTapContigs Contigs neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-neurons TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellContigs H1ne cell C H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002943 2943 GSM977031 Gingeras CSHL LID48357,LID48358 iIDR cell None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellContigs Contigs neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-neurons whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1neuronsCellCiptapContigs H1ne cell CIP C H1-neurons RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002944 2944 GSM977030 Gingeras CSHL LID48353,LID48354 iIDR cell CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqH1neuronsCellCiptapContigs Contigs neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-neurons CIP-TAP whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqCd34mobilizedCellTapContigs CD34 cell TAP C CD34+_Mobilized RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002604 2604 GSM973662 Gingeras CSHL LID46197 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqCd34mobilizedCellTapContigs Contigs hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD34+ TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqBjCellShorttotalTapContigs BJ cell TAP C BJ RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001079 1079 GSM897077 Gingeras CSHL LID20909,LID20910 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqBjCellShorttotalTapContigs Contigs skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). BJ TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapContigs AG50 cell TAP C AG04450 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001081 1081 GSM897074 Gingeras CSHL LID20745,LID20746 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqAg04450CellShorttotalTapContigs Contigs fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). AG04450 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusTapContigs SKSH nucl TAP C SK-N-SH RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002469 2469 GSM973689 Gingeras CSHL LID46960,LID46961 iIDR nucleus TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusTapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusContigs SKSH nucl C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002613 2613 GSM973665 Gingeras CSHL LID46203,LID46204 iIDR nucleus None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshNucleusCiptapContigs SKSH nucl CIP C SK-N-SH RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002615 2615 GSM973663 Gingeras CSHL LID46272,LID46273 iIDR nucleus CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshNucleusCiptapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH CIP-TAP nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolTapContigs SKSH cyto TAP C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002468 2468 GSM973688 Gingeras CSHL LID46958,LID46959 iIDR cytosol TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolTapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolContigs SKSH cyto C SK-N-SH RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002612 2612 GSM973666 Gingeras CSHL LID46205,LID46206 iIDR cytosol None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCytosolCiptapContigs SKSH cyto CIP C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002614 2614 GSM973692 Gingeras CSHL LID46274,LID46275 iIDR cytosol CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCytosolCiptapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH CIP-TAP cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellTapContigs SKSH cell TAP C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002470 2470 GSM973667 Gingeras CSHL LID46956,LID46957 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellTapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellContigs SKSH cell C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002622 2622 GSM973675 Gingeras CSHL LID46201,LID46202 iIDR cell None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqSknshCellCiptapContigs SKSH cell CIP C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002616 2616 GSM973677 Gingeras CSHL LID46270,LID46271 iIDR cell CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqSknshCellCiptapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH CIP-TAP whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMonocd14CellTapContigs CD14 cell TAP C Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002898 2898 GSM977044 Gingeras CSHL LID44360,LID44361 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqMonocd14CellTapContigs Contigs Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD14+ TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusTapContigs MCF7 nucl TAP C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002467 2467 GSM973682 Gingeras CSHL LID47164,LID47165 iIDR nucleus TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusTapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7NucleusContigs MCF7 nucl C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002608 2608 GSM973687 Gingeras CSHL LID46313,LID46314 iIDR nucleus None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7NucleusContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolTapContigs MCF7 cyto TAP C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002466 2466 GSM973681 Gingeras CSHL LID47162,LID47163 iIDR cytosol TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolTapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CytosolContigs MCF7 cyto C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002607 2607 GSM973672 Gingeras CSHL LID46315,LID46316 iIDR cytosol None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CytosolContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellTapContigsV2 MCF7 cell TAP C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2011-01-19 2011-10-19 wgEncodeEH001090 1090 GSM897081 Gingeras CSHL LID47160,LID47161 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellTapContigsV2 Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellContigs MCF7 cell C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002609 2609 GSM973690 Gingeras CSHL LID46311,LID46312 iIDR cell None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqMcf7CellCiptapContigs MCF7 cell CIP C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002610 2610 GSM973676 Gingeras CSHL LID46458,LID46459 iIDR cell CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqMcf7CellCiptapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 CIP-TAP whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusTapContigs IMR9 nucl TAP C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002464 2464 GSM973679 Gingeras CSHL LID47266,LID47267 iIDR nucleus TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusTapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusContigs IMR9 nucl C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002606 2606 GSM973678 Gingeras CSHL LID45955,LID45956 iIDR nucleus None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90NucleusCiptapContigs IMR9 nucl CIP C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002605 2605 GSM973673 Gingeras CSHL LID45886,LID45887 iIDR nucleus CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90NucleusCiptapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 CIP-TAP nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolTapContigs IMR9 cyto TAP C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002463 2463 GSM973686 Gingeras CSHL LID47264,LID47265 iIDR cytosol TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolTapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolContigs IMR9 cyto C IMR90 RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002618 2618 GSM973671 Gingeras CSHL LID45957,LID45958 iIDR cytosol None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CytosolCiptapContigs IMR9 cyto CIP C IMR90 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002619 2619 GSM973670 Gingeras CSHL LID45888,LID45889 iIDR cytosol CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CytosolCiptapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 CIP-TAP cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellTapContigs IMR9 cell TAP C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002465 2465 GSM973680 Gingeras CSHL LID47262,LID47263 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellTapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellContigs IMR9 cell C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002620 2620 GSM973691 Gingeras CSHL LID45107,LID45110 iIDR cell None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqImr90CellCiptapContigs IMR9 cell CIP C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002621 2621 GSM973693 Gingeras CSHL LID45108,LID45111 iIDR cell CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqImr90CellCiptapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 CIP-TAP whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapContigs HUVE nucl TAP C HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001080 1080 GSM897075 Gingeras CSHL LID21056,LID21058 iIDR nucleus TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapContigs HepG nucl TAP C HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001742 1742 GSM897085 Gingeras CSHL LID44462,LID44463 iIDR nucleus TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapContigs HepG cyto TAP C HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001743 1743 GSM897082 Gingeras CSHL LID44464,LID44465 iIDR cytosol TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapContigs HepG cell TAP C HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001741 1741 GSM897084 Gingeras CSHL LID44460,LID44461 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapContigs HeLa nucl TAP C HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001088 1088 GSM897080 Gingeras CSHL LID21144,LID21147 iIDR nucleus TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapContigs HeLa cyto TAP C HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001087 1087 GSM897069 Gingeras CSHL LID21145,LID21148 iIDR cytosol TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapContigs HeLa cell TAP C HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001089 1089 GSM897079 Gingeras CSHL LID21143,LID21146 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqCd20CellTapContigs CD20 cell TAP C CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002879 2879 GSM977043 Gingeras CSHL LID44362,LID44363 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqCd20CellTapContigs Contigs B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD20+ TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusTapContigs A549 nucl TAP C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002462 2462 GSM973685 Gingeras CSHL LID47043,LID47044 iIDR nucleus TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusTapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusContigs A549 nucl C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002600 2600 GSM973683 Gingeras CSHL LID46060,LID46061 iIDR nucleus None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549NucleusCiptapContigs A549 nucl CIP C A549 RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002617 2617 GSM973661 Gingeras CSHL LID46100,LID46101 iIDR nucleus CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549NucleusCiptapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 CIP-TAP nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolTapContigs A549 cyto TAP C A549 RnaSeq ENCODE Jul 2012 Freeze 2012-06-20 2013-03-20 wgEncodeEH002461 2461 GSM973684 Gingeras CSHL LID47041,LID47042 iIDR cytosol TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolTapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolContigs A549 cyto C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002597 2597 GSM973664 Gingeras CSHL LID46062,LID46063 iIDR cytosol None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CytosolCiptapContigs A549 cyto CIP C A549 RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002599 2599 GSM973669 Gingeras CSHL LID46102,LID46103 iIDR cytosol CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CytosolCiptapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 CIP-TAP cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellTapContigsV2 A549 cell TAP C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2011-05-11 2012-02-11 wgEncodeEH001740 1740 GSM897083 Gingeras CSHL LID47039,LID47040 iIDR cell TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellTapContigsV2 Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellContigs A549 cell C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002598 2598 GSM973668 Gingeras CSHL LID46058,LID46059 iIDR cell None 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqA549CellCiptapContigs A549 cell CIP C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002601 2601 GSM973674 Gingeras CSHL LID46098,LID46099 iIDR cell CIP-TAP 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqA549CellCiptapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 CIP-TAP whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapContigs K562 nucl TAP C K562 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH000209 209 GSM605635 Gingeras CSHL LID10570,LID10569 iIDR nucleus TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapContigs K562 nplm TAP C K562 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH000208 208 GSM605634 Gingeras CSHL LID8929,LID18559 iIDR nucleoplasm TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 TAP-only nucleoplasm small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapContigs K562 nlus TAP C K562 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH000207 207 GSM605628 Gingeras CSHL LID8928,LID18558 iIDR nucleolus TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 TAP-only nucleolus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapContigs K562 cyto TAP C K562 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH000206 206 GSM605629 Gingeras CSHL LID10572,LID10571 iIDR cytosol TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapContigs K562 chrm TAP C K562 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH000205 205 GSM605632 Gingeras CSHL LID8930,LID18560 iIDR chromatin TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 TAP-only chromatin small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqK562CellShorttotalTapContigs K562 cell TAP C K562 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH000213 213 GSM605630 Gingeras CSHL LID10567,LID10568 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqK562CellShorttotalTapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapContigsV2 H1ES nucl TAP C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001084 1084 GSM897071 Gingeras CSHL LID20907 iIDR nucleus TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapContigsV2 H1ES cyto TAP C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001083 1083 GSM897072 Gingeras CSHL LID20908 iIDR cytosol TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapContigs H1ES cell TAP C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH001082 1082 GSM897073 Gingeras CSHL LID20905,LID20906 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapContigs Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapContigs GM78 nucl TAP C GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH000204 204 GSM605633 Gingeras CSHL LID20900,LID20903 iIDR nucleus TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 TAP-only nucleus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878NucleolusTapContigs GM78 nlus TAP C GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002942 2942 GSM977032 Gingeras CSHL LID47653,LID47654 iIDR nucleolus TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878NucleolusTapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 TAP-only nucleolus small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapContigs GM78 cyto TAP C GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH000203 203 GSM605627 Gingeras CSHL LID20901,LID20904 iIDR cytosol TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 TAP-only cytosol small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878ChromatinTapContigs GM78 chrm TAP C GM12878 RnaSeq ENCODE Freeze 2012-04-23 2013-01-23 wgEncodeEH002889 2889 GSM977042 Gingeras CSHL LID47655,LID47656 iIDR chromatin TAP-Only 1x101 shortTotal Illumina_HiSeq_2000 wgEncodeCshlShortRnaSeqGm12878ChromatinTapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 101 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 TAP-only chromatin small RNA-seq Contigs from ENCODE/CSHL Expression 
wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapContigs GM78 cell TAP C GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-02-07 2011-07-12 2012-04-12 wgEncodeEH000212 212 GSM605625 Gingeras CSHL LID20899,LID20902 iIDR cell TAP-Only 1x36 shortTotal Illumina_GA2x wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. Single 36 nt reads Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 TAP-only whole cell small RNA-seq Contigs from ENCODE/CSHL Expression 
polyA Poly(A) Poly(A) Sites, Both Reported and Predicted mRNA and EST Description The polyA_DB database is a set of human mRNA polyadenlyation sites based on EST/cDNA evidence. A site is a single base denoting the beginning of a poly(A) tail in a nascent mRNA transcript and is typically 10-30 nucleotides downstream of a polyadenylation signal (most commonly AAUAAA). The polyA_DB web server is found at http://exon.umdnj.edu/polya_db/. The Poly(A) composite track consists of two subtracks: a polyA_DB subtrack that displays reported poly(A) sites, and a poly(A) prediction subtrack that displays poly(A) sites predicted using a support vector machine (SVM). The poly(A) predictions are made using 1500-base DNA sequences centered at the end of each RefSeq gene. The sequences serve as input into the SVM described in Cheng et al., 2006. The SVM scores each base using a model derived from 15 different cis-elements and reports an E-value for a region of DNA between 0 (excellent) and 0.5 (worst). This E-value is then normalized to an integer value between 0 (worst) and 1000 (excellent). High-scoring regions are highlighted, with the highest-scoring base indicated by a thicker line. The median length of these regions is 48 bases. References Cheng Y, Miura RM, Tian B. Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics. 2006 Oct 1;22(19):2320-5. PMID: 16870936 Zhang H, Hu J, Recce M, Tian B. PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D116-20. PMID: 15608159; PMC: PMC540009 
polyaPredict Poly(A) Predicted Poly(A) Sites Using an SVM mRNA and EST 
polyaDb PolyA_DB Reported Poly(A) Sites from PolyA_DB mRNA and EST 
vertebrateChainNet Vertebrate Chain/Net Non-placental Vertebrate Genomes, Chain and Net Alignments Comparative Genomics Description Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to other genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and the other genome simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the other assembly or an insertion in the human assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the other genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/other chain for every part of the other genome. It is useful for finding orthologous regions and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/other split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single chromosome from the other genome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following lastz matrix was usedfor the alignments to: Wallaby, Tasmanian Devil &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 &nbsp; The following lastz matrix was usedfor the alignments to: American Alligator, Medium Ground Finch, Opossum, Platypus, Chicken, Zebra Finch, Lizard, X. tropicalis, Stickleback, Fugu, Zebrafish, Tetraodon, Medaka, Lamprey &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 For the Wallaby alignment, chains scoring below a minimum score of '3000' were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 For the alignments to: American Alligator, Medium Ground Finch, Tasmanian Devil, Opossum, Platypus, Chicken, Zebra Finch, Lizard, X. tropicalis, Stickleback, Fugu, Zebrafish, Tetraodon, Medaka and Lamprey, chains scoring below a minimum score of '5000' were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 See also: lastz parameters used in these alignments, and chain minimum score and gap parameters used in these alignments. Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
vertebrateChainNetViewnet Nets Non-placental Vertebrate Genomes, Chain and Net Alignments Comparative Genomics 
netPetMar2 Lamprey Net Lamprey (Sep. 2010 (WUGSC 7.0/petMar2)) Alignment Net Comparative Genomics 
netTetNig2 Tetraodon Net Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Alignment Net Comparative Genomics 
netFr2 Fugu Net Fugu (Oct. 2004 (JGI 4.0/fr2)) Alignment Net Comparative Genomics 
netOryLat2 Medaka Net Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) Alignment Net Comparative Genomics 
netGasAcu1 Stickleback Net Stickleback (Feb. 2006 (Broad/gasAcu1)) Alignment Net Comparative Genomics 
netDanRer7 Zebrafish Net Zebrafish (Jul. 2010 (Zv9/danRer7)) Alignment Net Comparative Genomics 
netXenTro3 X. tropicalis Net X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) Alignment Net Comparative Genomics 
netAnoCar2 Lizard Net Lizard (May 2010 (Broad AnoCar2.0/anoCar2)) Alignment Net Comparative Genomics 
netAllMis1 American alligator Net American alligator (Aug. 2012 (allMis0.2/allMis1)) Alignment Net Comparative Genomics 
netTaeGut2 Zebra finch Net Zebra finch (Feb. 2013 (WashU taeGut324/taeGut2)) Alignment Net Comparative Genomics 
netGeoFor1 Medium ground finch Net Medium ground finch (Apr. 2012 (GeoFor_1.0/geoFor1)) Alignment Net Comparative Genomics 
netGalGal3 Chicken Net Chicken (May 2006 (WUGSC 2.1/galGal3)) Alignment Net Comparative Genomics 
netMelGal1 Turkey Net Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) Alignment Net Comparative Genomics 
netOrnAna1 Platypus Net Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Alignment Net Comparative Genomics 
netMonDom5 Opossum Net Opossum (Oct. 2006 (Broad/monDom5)) Alignment Net Comparative Genomics 
netSarHar1 Tasmanian devil Net Tasmanian devil (Feb. 2011 (WTSI Devil_ref v7.0/sarHar1)) Alignment Net Comparative Genomics 
vertebrateChainNetViewchain Chains Non-placental Vertebrate Genomes, Chain and Net Alignments Comparative Genomics 
chainPetMar2 Lamprey Chain Lamprey (Sep. 2010 (WUGSC 7.0/petMar2)) Chained Alignments Comparative Genomics 
chainTetNig2 Tetraodon Chain Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Chained Alignments Comparative Genomics 
chainFr2 Fugu Chain Fugu (Oct. 2004 (JGI 4.0/fr2)) Chained Alignments Comparative Genomics 
chainOryLat2 Medaka Chain Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) Chained Alignments Comparative Genomics 
chainGasAcu1 Stickleback Chain Stickleback (Feb. 2006 (Broad/gasAcu1)) Chained Alignments Comparative Genomics 
chainDanRer7 Zebrafish Chain Zebrafish (Jul. 2010 (Zv9/danRer7)) Chained Alignments Comparative Genomics 
chainXenTro3 X. tropicalis Chain X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) Chained Alignments Comparative Genomics 
chainAnoCar2 Lizard Chain Lizard (May 2010 (Broad AnoCar2.0/anoCar2)) Chained Alignments Comparative Genomics 
chainAllMis1 American alligator Chain American alligator (Aug. 2012 (allMis0.2/allMis1)) Chained Alignments Comparative Genomics 
chainTaeGut2 Zebra finch Chain Zebra finch (Feb. 2013 (WashU taeGut324/taeGut2)) Chained Alignments Comparative Genomics 
chainGeoFor1 Medium ground finch Chain Medium ground finch (Apr. 2012 (GeoFor_1.0/geoFor1)) Chained Alignments Comparative Genomics 
chainGalGal3 Chicken Chain Chicken (May 2006 (WUGSC 2.1/galGal3)) Chained Alignments Comparative Genomics 
chainMelGal1 Turkey Chain Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) Chained Alignments Comparative Genomics 
chainOrnAna1 Platypus Chain Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Chained Alignments Comparative Genomics 
chainMonDom5 Opossum Chain Opossum (Oct. 2006 (Broad/monDom5)) Chained Alignments Comparative Genomics 
chainSarHar1 Tasmanian devil Chain Tasmanian devil (Feb. 2011 (WTSI Devil_ref v7.0/sarHar1)) Chained Alignments Comparative Genomics 
mtrScores MTR Scores MTR - Missense Tolerance Ratio Scores by base Phenotype and Literature Description The "Constraint scores" container track includes several subtracks showing the results of constraint prediction algorithms. These try to find regions of negative selection, where variations likely have functional impact. The algorithms do not use multi-species alignments to derive evolutionary constraint, but use primarily human variation, usually from variants collected by gnomAD (see the gnomAD V2 or V3 tracks on hg19 and hg38) or TOPMED (contained in our dbSNP tracks and available as a filter). One of the subtracks is based on UK Biobank variants, which are not available publicly, so we have no track with the raw data. The number of human genomes that are used as the input for these scores are 76k, 53k and 110k for gnomAD, TOPMED and UK Biobank, respectively. Note that another important constraint score, gnomAD constraint, is not part of this container track but can be found in the hg38 gnomAD track. The algorithms included in this track are: JARVIS - "Junk" Annotation genome-wide Residual Variation Intolerance Score: JARVIS scores were created by first scanning the entire genome with a sliding-window approach (using a 1-nucleotide step), recording the number of all TOPMED variants and common variants, irrespective of their predicted effect, within each window, to eventually calculate a single-nucleotide resolution genome-wide residual variation intolerance score (gwRVIS). That score, gwRVIS was then combined with primary genomic sequence context, and additional genomic annotations with a multi-module deep learning framework to infer pathogenicity of noncoding regions that still remains naive to existing phylogenetic conservation metrics. The higher the score, the more deleterious the prediction. This score covers the entire genome, except the gaps. HMC - Homologous Missense Constraint: Homologous Missense Constraint (HMC) is a amino acid level measure of genetic intolerance of missense variants within human populations. For all assessable amino-acid positions in Pfam domains, the number of missense substitutions directly observed in gnomAD (Observed) was counted and compared to the expected value under a neutral evolution model (Expected). The upper limit of a 95% confidence interval for the Observed/Expected ratio is defined as the HMC score. Missense variants disrupting the amino-acid positions with HMC&lt;0.8 are predicted to be likely deleterious. This score only covers PFAM domains within coding regions. MetaDome - Tolerance Landscape Score (hg19 only): MetaDome Tolerance Landscape scores are computed as a missense over synonymous variant count ratio, which is calculated in a sliding window (with a size of 21 codons/residues) to provide a per-position indication of regional tolerance to missense variation. The variant database was gnomAD and the score corrected for codon composition. Scores &lt;0.7 are considered intolerant. This score covers only coding regions. MTR - Missense Tolerance Ratio (hg19 only): Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence. It is estimated across sliding windows of 31 codons (default) and uses observed standing variation data from the WES component of gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores were computed using Ensembl v95 release. The number of gnomAD 2 exomes used here is higher than the number of gnomAD 3 samples (125 exoms versus 76k full genomes), but this score only covers coding regions. UK Biobank depletion rank score (hg38 only): Halldorsson et al. tabulated the number of UK Biobank variants in each 500bp window of the genome and compared this number to an expected number given the heptamer nucleotide composition of the window and the fraction of heptamers with a sequence variant across the genome and their mutational classes. A variant depletion score was computed for every overlapping set of 500-bp windows in the genome with a 50-bp step size. They then assigned a rank (depletion rank (DR)) from 0 (most depletion) to 100 (least depletion) for each 500-bp window. Since the windows are overlapping, we plot the value only in the central 50bp of the 500bp window, following advice from the author of the score, Hakon Jonsson, deCODE Genetics. He suggested that the value of the central window, rather than the worst possible score of all overlapping windows, is the most informative for a position. This score covers almost the entire genome, only very few regions were excluded, where the genome sequence had too many gap characters. Display Conventions and Configuration JARVIS JARVIS scores are shown as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The scores were downloaded and converted to a single bigWig file. Move the mouse over the bars to display the exact values. A horizontal line is shown at the 0.733 value which signifies the 90th percentile. See hg19 makeDoc and hg38 makeDoc. Interpretation: The authors offer a suggested guideline of > 0.9998 for identifying higher confidence calls and minimizing false positives. In addition to that strict threshold, the following two more relaxed cutoffs can be used to explore additional hits. Note that these thresholds are offered as guidelines and are not necessarily representative of pathogenicity. PercentileJARVIS score threshold 99th0.9998 95th0.9826 90th0.7338 HMC HMC scores are displayed as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The highly-constrained cutoff of 0.8 is indicated with a line. Interpretation: A protein residue with HMC score &lt;1 indicates that missense variants affecting the homologous residues are significantly under negative selection (P-value &lt; 0.05) and likely to be deleterious. A more stringent score threshold of HMC&lt;0.8 is recommended to prioritize predicted disease-associated variants. MetaDome MetaDome data can be found on two tracks, MetaDome and MetaDome All Data. The MetaDome track should be used by default for data exploration. In this track the raw data containing the MetaDome tolerance scores were converted into a signal ("wiggle") track. Since this data was computed on the proteome, there was a small amount of coordinate overlap, roughly 0.42%. In these regions the lowest possible score was chosen for display in the track to maintain sensitivity. For this reason, if a protein variant is being evaluated, the MetaDome All Data track can be used to validate the score. More information on this data can be found in the MetaDome FAQ. Interpretation: The authors suggest the following guidelines for evaluating intolerance. By default, the MetaDome track displays a horizontal line at 0.7 which signifies the first intolerant bin. For more information see the MetaDome publication. ClassificationMetaDome Tolerance Score Highly intolerant&le; 0.175 Intolerant&le; 0.525 Slightly intolerant&le; 0.7 MTR MTR data can be found on two tracks, MTR All data and MTR Scores. In the MTR Scores track the data has been converted into 4 separate signal tracks representing each base pair mutation, with the lowest possible score shown when multiple transcripts overlap at a position. Overlaps can happen since this score is derived from transcripts and multiple transcripts can overlap. A horizontal line is drawn on the 0.8 score line to roughly represent the 25th percentile, meaning the items below may be of particular interest. It is recommended that the data be explored using this version of the track, as it condenses the information substantially while retaining the magnitude of the data. Any specific point mutations of interest can then be researched in the MTR All data track. This track contains all of the information from MTRV2 including more than 3 possible scores per base when transcripts overlap. A mouse-over on this track shows the ref and alt allele, as well as the MTR score and the MTR score percentile. Filters are available for MTR score, False Discovery Rate (FDR), MTR percentile, and variant consequence. By default, only items in the bottom 25 percentile are shown. Items in the track are colored according to their MTR percentile: Green items MTR percentiles over 75 Black items MTR percentiles between 25 and 75 Red items MTR percentiles below 25 Blue items No MTR score Interpretation: Regions with low MTR scores were seen to be enriched with pathogenic variants. For example, ClinVar pathogenic variants were seen to have an average score of 0.77 whereas ClinVar benign variants had an average score of 0.92. Further validation using the FATHMM cancer-associated training dataset saw that scores less than 0.5 contained 8.6% of the pathogenic variants while only containing 0.9% of neutral variants. In summary, lower scores are more likely to represent pathogenic variants whereas higher scores could be pathogenic, but have a higher chance to be a false positive. For more information see the MTR-Viewer publication. Methods JARVIS Scores were downloaded and converted to a single bigWig file. See the hg19 makeDoc and the hg38 makeDoc for more info. HMC Scores were downloaded and converted to .bedGraph files with a custom Python script. The bedGraph files were then converted to bigWig files, as documented in our makeDoc hg19 build log. MetaDome The authors provided a bed file containing codon coordinates along with the scores. This file was parsed with a python script to create the two tracks. For the first track the scores were aggregated for each coordinate, then the lowest score chosen for any overlaps and the result written out to bedGraph format. The file was then converted to bigWig with the bedGraphToBigWig utility. For the second track the file was reorganized into a bed 4+3 and conveted to bigBed with the bedToBigBed utility. See the hg19 makeDoc for details including the build script. The raw MetaDome data can also be accessed via their Zenodo handle. MTR V2 file was downloaded and columns were reshuffled as well as itemRgb added for the MTR All data track. For the MTR Scores track the file was parsed with a python script to pull out the highest possible MTR score for each of the 3 possible mutations at each base pair and 4 tracks built out of these values representing each mutation. See the hg19 makeDoc entry on MTR for more info. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/hmc/hmc.bw stdout Please refer to our Data Access FAQ for more information. Credits Thanks to Jean-Madeleine Desainteagathe (APHP Paris, France) for suggesting the JARVIS, MTR, HMC tracks. Thanks to Xialei Zhang for providing the HMC data file and to Dimitrios Vitsios and Slave Petrovski for helping clean up the hg38 JARVIS files for providing guidance on interpretation. Additional thanks to Laurens van de Wiel for providing the MetaDome data as well as guidance on the track development and interpretation. References Vitsios D, Dhindsa RS, Middleton L, Gussow AB, Petrovski S. Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. Nat Commun. 2021 Mar 8;12(1):1504. PMID: 33686085; PMC: PMC7940646 Xiaolei Zhang, Pantazis I. Theotokis, Nicholas Li, the SHaRe Investigators, Caroline F. Wright, Kaitlin E. Samocha, Nicola Whiffin, James S. Ware Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery. Medrxiv 2022.02.16.22271023 Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat. 2019 Aug;40(8):1030-1038. PMID: 31116477; PMC: PMC6772141 Silk M, Petrovski S, Ascher DB. MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 2019 Jul 2;47(W1):W121-W126. PMID: 31170280; PMC: PMC6602522 Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO et al. The sequences of 150,119 genomes in the UK Biobank. Nature. 2022 Jul;607(7920):732-740. PMID: 35859178; PMC: PMC9329122 
mtrT Mutation: T MTR Score: Mutation is T Phenotype and Literature 
mtrG Mutation: G MTR Score: Mutation is G Phenotype and Literature 
mtrC Mutation: C MTR Score: Mutation is C Phenotype and Literature 
mtrA Mutation: A MTR Score: Mutation is A Phenotype and Literature 
mtrBed MTR All Data MTR -  Missense Tolerance Ratio Scores all annotations Phenotype and Literature Description The "Constraint scores" container track includes several subtracks showing the results of constraint prediction algorithms. These try to find regions of negative selection, where variations likely have functional impact. The algorithms do not use multi-species alignments to derive evolutionary constraint, but use primarily human variation, usually from variants collected by gnomAD (see the gnomAD V2 or V3 tracks on hg19 and hg38) or TOPMED (contained in our dbSNP tracks and available as a filter). One of the subtracks is based on UK Biobank variants, which are not available publicly, so we have no track with the raw data. The number of human genomes that are used as the input for these scores are 76k, 53k and 110k for gnomAD, TOPMED and UK Biobank, respectively. Note that another important constraint score, gnomAD constraint, is not part of this container track but can be found in the hg38 gnomAD track. The algorithms included in this track are: JARVIS - "Junk" Annotation genome-wide Residual Variation Intolerance Score: JARVIS scores were created by first scanning the entire genome with a sliding-window approach (using a 1-nucleotide step), recording the number of all TOPMED variants and common variants, irrespective of their predicted effect, within each window, to eventually calculate a single-nucleotide resolution genome-wide residual variation intolerance score (gwRVIS). That score, gwRVIS was then combined with primary genomic sequence context, and additional genomic annotations with a multi-module deep learning framework to infer pathogenicity of noncoding regions that still remains naive to existing phylogenetic conservation metrics. The higher the score, the more deleterious the prediction. This score covers the entire genome, except the gaps. HMC - Homologous Missense Constraint: Homologous Missense Constraint (HMC) is a amino acid level measure of genetic intolerance of missense variants within human populations. For all assessable amino-acid positions in Pfam domains, the number of missense substitutions directly observed in gnomAD (Observed) was counted and compared to the expected value under a neutral evolution model (Expected). The upper limit of a 95% confidence interval for the Observed/Expected ratio is defined as the HMC score. Missense variants disrupting the amino-acid positions with HMC&lt;0.8 are predicted to be likely deleterious. This score only covers PFAM domains within coding regions. MetaDome - Tolerance Landscape Score (hg19 only): MetaDome Tolerance Landscape scores are computed as a missense over synonymous variant count ratio, which is calculated in a sliding window (with a size of 21 codons/residues) to provide a per-position indication of regional tolerance to missense variation. The variant database was gnomAD and the score corrected for codon composition. Scores &lt;0.7 are considered intolerant. This score covers only coding regions. MTR - Missense Tolerance Ratio (hg19 only): Missense Tolerance Ratio (MTR) scores aim to quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence. It is estimated across sliding windows of 31 codons (default) and uses observed standing variation data from the WES component of gnomAD / the Exome Aggregation Consortium Database (ExAC), version 2.0. Scores were computed using Ensembl v95 release. The number of gnomAD 2 exomes used here is higher than the number of gnomAD 3 samples (125 exoms versus 76k full genomes), but this score only covers coding regions. UK Biobank depletion rank score (hg38 only): Halldorsson et al. tabulated the number of UK Biobank variants in each 500bp window of the genome and compared this number to an expected number given the heptamer nucleotide composition of the window and the fraction of heptamers with a sequence variant across the genome and their mutational classes. A variant depletion score was computed for every overlapping set of 500-bp windows in the genome with a 50-bp step size. They then assigned a rank (depletion rank (DR)) from 0 (most depletion) to 100 (least depletion) for each 500-bp window. Since the windows are overlapping, we plot the value only in the central 50bp of the 500bp window, following advice from the author of the score, Hakon Jonsson, deCODE Genetics. He suggested that the value of the central window, rather than the worst possible score of all overlapping windows, is the most informative for a position. This score covers almost the entire genome, only very few regions were excluded, where the genome sequence had too many gap characters. Display Conventions and Configuration JARVIS JARVIS scores are shown as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The scores were downloaded and converted to a single bigWig file. Move the mouse over the bars to display the exact values. A horizontal line is shown at the 0.733 value which signifies the 90th percentile. See hg19 makeDoc and hg38 makeDoc. Interpretation: The authors offer a suggested guideline of > 0.9998 for identifying higher confidence calls and minimizing false positives. In addition to that strict threshold, the following two more relaxed cutoffs can be used to explore additional hits. Note that these thresholds are offered as guidelines and are not necessarily representative of pathogenicity. PercentileJARVIS score threshold 99th0.9998 95th0.9826 90th0.7338 HMC HMC scores are displayed as a signal ("wiggle") track, with one score per genome position. Mousing over the bars displays the exact values. The highly-constrained cutoff of 0.8 is indicated with a line. Interpretation: A protein residue with HMC score &lt;1 indicates that missense variants affecting the homologous residues are significantly under negative selection (P-value &lt; 0.05) and likely to be deleterious. A more stringent score threshold of HMC&lt;0.8 is recommended to prioritize predicted disease-associated variants. MetaDome MetaDome data can be found on two tracks, MetaDome and MetaDome All Data. The MetaDome track should be used by default for data exploration. In this track the raw data containing the MetaDome tolerance scores were converted into a signal ("wiggle") track. Since this data was computed on the proteome, there was a small amount of coordinate overlap, roughly 0.42%. In these regions the lowest possible score was chosen for display in the track to maintain sensitivity. For this reason, if a protein variant is being evaluated, the MetaDome All Data track can be used to validate the score. More information on this data can be found in the MetaDome FAQ. Interpretation: The authors suggest the following guidelines for evaluating intolerance. By default, the MetaDome track displays a horizontal line at 0.7 which signifies the first intolerant bin. For more information see the MetaDome publication. ClassificationMetaDome Tolerance Score Highly intolerant&le; 0.175 Intolerant&le; 0.525 Slightly intolerant&le; 0.7 MTR MTR data can be found on two tracks, MTR All data and MTR Scores. In the MTR Scores track the data has been converted into 4 separate signal tracks representing each base pair mutation, with the lowest possible score shown when multiple transcripts overlap at a position. Overlaps can happen since this score is derived from transcripts and multiple transcripts can overlap. A horizontal line is drawn on the 0.8 score line to roughly represent the 25th percentile, meaning the items below may be of particular interest. It is recommended that the data be explored using this version of the track, as it condenses the information substantially while retaining the magnitude of the data. Any specific point mutations of interest can then be researched in the MTR All data track. This track contains all of the information from MTRV2 including more than 3 possible scores per base when transcripts overlap. A mouse-over on this track shows the ref and alt allele, as well as the MTR score and the MTR score percentile. Filters are available for MTR score, False Discovery Rate (FDR), MTR percentile, and variant consequence. By default, only items in the bottom 25 percentile are shown. Items in the track are colored according to their MTR percentile: Green items MTR percentiles over 75 Black items MTR percentiles between 25 and 75 Red items MTR percentiles below 25 Blue items No MTR score Interpretation: Regions with low MTR scores were seen to be enriched with pathogenic variants. For example, ClinVar pathogenic variants were seen to have an average score of 0.77 whereas ClinVar benign variants had an average score of 0.92. Further validation using the FATHMM cancer-associated training dataset saw that scores less than 0.5 contained 8.6% of the pathogenic variants while only containing 0.9% of neutral variants. In summary, lower scores are more likely to represent pathogenic variants whereas higher scores could be pathogenic, but have a higher chance to be a false positive. For more information see the MTR-Viewer publication. Methods JARVIS Scores were downloaded and converted to a single bigWig file. See the hg19 makeDoc and the hg38 makeDoc for more info. HMC Scores were downloaded and converted to .bedGraph files with a custom Python script. The bedGraph files were then converted to bigWig files, as documented in our makeDoc hg19 build log. MetaDome The authors provided a bed file containing codon coordinates along with the scores. This file was parsed with a python script to create the two tracks. For the first track the scores were aggregated for each coordinate, then the lowest score chosen for any overlaps and the result written out to bedGraph format. The file was then converted to bigWig with the bedGraphToBigWig utility. For the second track the file was reorganized into a bed 4+3 and conveted to bigBed with the bedToBigBed utility. See the hg19 makeDoc for details including the build script. The raw MetaDome data can also be accessed via their Zenodo handle. MTR V2 file was downloaded and columns were reshuffled as well as itemRgb added for the MTR All data track. For the MTR Scores track the file was parsed with a python script to pull out the highest possible MTR score for each of the 3 possible mutations at each base pair and 4 tracks built out of these values representing each mutation. See the hg19 makeDoc entry on MTR for more info. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/hmc/hmc.bw stdout Please refer to our Data Access FAQ for more information. Credits Thanks to Jean-Madeleine Desainteagathe (APHP Paris, France) for suggesting the JARVIS, MTR, HMC tracks. Thanks to Xialei Zhang for providing the HMC data file and to Dimitrios Vitsios and Slave Petrovski for helping clean up the hg38 JARVIS files for providing guidance on interpretation. Additional thanks to Laurens van de Wiel for providing the MetaDome data as well as guidance on the track development and interpretation. References Vitsios D, Dhindsa RS, Middleton L, Gussow AB, Petrovski S. Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. Nat Commun. 2021 Mar 8;12(1):1504. PMID: 33686085; PMC: PMC7940646 Xiaolei Zhang, Pantazis I. Theotokis, Nicholas Li, the SHaRe Investigators, Caroline F. Wright, Kaitlin E. Samocha, Nicola Whiffin, James S. Ware Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery. Medrxiv 2022.02.16.22271023 Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat. 2019 Aug;40(8):1030-1038. PMID: 31116477; PMC: PMC6772141 Silk M, Petrovski S, Ascher DB. MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 2019 Jul 2;47(W1):W121-W126. PMID: 31170280; PMC: PMC6602522 Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO et al. The sequences of 150,119 genomes in the UK Biobank. Nature. 2022 Jul;607(7920):732-740. PMID: 35859178; PMC: PMC9329122 
polyASeqSites PolyA-Seq Poly(A)-sequencing from Merck Research Laboratories mRNA and EST Description This track displays the location of RNA polyadenylation (polyA) sites based on high-throughput RNA sequencing using the PolyA-seq protocol. PolyA-Seq data is strand-specific, therefore two tracks are provided for each tissue. PolyA site positions correspond to a single base, namely the ends of read alignments immediately upstream of the polyadenylation site. The data provided in this track consists of filtered polyA sites (see Methods). When multiple sites occurred within a 30-bp window on the same strand, the sum of the reads was attributed to the site with the most reads. Units are in reads per million (RPM) aligned. To obtain read counts, multiply RPM values by the total number of filtered reads for the corresponding experiment: Sample Filtered reads MAQC Universal Human Reference 1 5057048 MAQC Universal Human Reference 2 5030985 MAQC Brain 1 4086039 MAQC Brain 2 3921040 Brain 2980439 Kidney 4626843 Liver 5626271 Muscle 4920121 Testis 5098780 Display Conventions and Configuration These tracks may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page. For more information, see Configuring graph-based tracks. In the full and pack display modes, forward-strand tracks are shown in red and reverse-strand tracks are shown in black. In the squish and dense display modes, intensity is represented in grayscale (the darker the shading, the higher the intensity). To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Methods A detailed explanation of the experimental methods is provided at NCBI's Gene Expression Omnibus under accession GSE30198. Briefly, PolyA+ RNA was reverse-transcribed using a T(10)VN primer and strand-specific universal adapters, amplified, and sequenced on an Illumina GAIIx sequencer. Reads were reverse-complemented, aligned to the corresponding reference genome and splice junctions, and retained only if they aligned uniquely. 3' ends of alignments were considered polyA sites. Sites were then filtered using downstream base frequency matrices for true- and false-positive sites determined from a modified experiment based on a T(10) primer (i.e., excluding the 3' VN). When multiple filtered sites occurred within a 30-nt window on the same strand, read counts were summed and attributed to the most abundant peak. For each tissue, read counts were then divided by the total number of reads, in millions, from all filtered sites. Credits These data were generated at Merck Research Laboratories and submitted by Adnan Derti and Tomas Babak. Data Release Policy No restrictions. 
polyASeqSitesSignalView Signal Poly(A)-sequencing from Merck Research Laboratories mRNA and EST 
polyASeqSitesTestisRev PolyA-Seq Testis Poly(A)-tail sequencing of Testis from Merck (Rev strand) mRNA and EST 
polyASeqSitesTestisFwd PolyA-Seq Testis Poly(A)-tail sequencing of Testis from Merck (Fwd strand) mRNA and EST 
polyASeqSitesMuscleRev PolyA-Seq Muscle Poly(A)-tail sequencing of Muscle from Merck (Rev strand) mRNA and EST 
polyASeqSitesMuscleFwd PolyA-Seq Muscle Poly(A)-tail sequencing of Muscle from Merck (Fwd strand) mRNA and EST 
polyASeqSitesMaqcUhr2Rev PolyA-Seq MaqcUhr2 Poly(A)-tail sequencing of MAQC UHR (replicate 2) from Merck (Rev strand) mRNA and EST 
polyASeqSitesMaqcUhr2Fwd PolyA-Seq MaqcUhr2 Poly(A)-tail sequencing of MAQC UHR (replicate 2) from Merck (Fwd strand) mRNA and EST 
polyASeqSitesMaqcUhr1Rev PolyA-Seq MaqcUhr1 Poly(A)-tail sequencing of MAQC UHR (replicate 1) from Merck (Rev strand) mRNA and EST 
polyASeqSitesMaqcUhr1Fwd PolyA-Seq MaqcUhr1 Poly(A)-tail sequencing of MAQC UHR (replicate 1) from Merck (Fwd strand) mRNA and EST 
polyASeqSitesMaqcBrain2Rev PolyA-Seq MaqcBrain2 Poly(A)-tail sequencing of MAQC Brain (replicate 2) from Merck (Rev strand) mRNA and EST 
polyASeqSitesMaqcBrain2Fwd PolyA-Seq MaqcBrain2 Poly(A)-tail sequencing of MAQC Brain (replicate 2) from Merck (Fwd strand) mRNA and EST 
polyASeqSitesMaqcBrain1Rev PolyA-Seq MaqcBrain1 Poly(A)-tail sequencing of MAQC Brain (replicate 1) from Merck (Rev strand) mRNA and EST 
polyASeqSitesMaqcBrain1Fwd PolyA-Seq MaqcBrain1 Poly(A)-tail sequencing of MAQC Brain (replicate 1) from Merck (Fwd strand) mRNA and EST 
polyASeqSitesLiverRev PolyA-Seq Liver Poly(A)-tail sequencing of Liver from Merck (Rev strand) mRNA and EST 
polyASeqSitesLiverFwd PolyA-Seq Liver Poly(A)-tail sequencing of Liver from Merck (Fwd strand) mRNA and EST 
polyASeqSitesKidneyRev PolyA-Seq Kidney Poly(A)-tail sequencing of Kidney from Merck (Rev strand) mRNA and EST 
polyASeqSitesKidneyFwd PolyA-Seq Kidney Poly(A)-tail sequencing of Kidney from Merck (Fwd strand) mRNA and EST 
polyASeqSitesBrainRev PolyA-Seq Brain Poly(A)-tail sequencing of Brain from Merck (Rev strand) mRNA and EST 
polyASeqSitesBrainFwd PolyA-Seq Brain Poly(A)-tail sequencing of Brain from Merck (Fwd strand) mRNA and EST 
transMapEnsemblV5 TransMap Ensembl TransMap Ensembl and GENCODE Mappings Version 5 Genes and Gene Predictions Description This track contains GENCODE or Ensembl alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. GENCODE is Ensembl for human and mouse, for other Ensembl sources, only ones with full gene builds are used. Projection Ensembl gene annotations will not be used as sources. For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in human. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the human (hg19) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the human genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - hg19.ensembl.transMapV4.bigPsl TransMap RefGene - hg19.refseq.transMapV4.bigPsl TransMap RNA - hg19.rna.transMapV4.bigPsl TransMap ESTs - hg19.est.transMapV4.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/transMap/V4/hg19.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
transMapV5 TransMap V5 TransMap Alignments Version 5 Genes and Gene Predictions Description These tracks contain cDNA and gene alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered LASTZ or BLASTZ alignment chains, resulting in a prediction of the orthologous genes in human. For more distant organisms, reciprocal best alignments are used. TransMap maps genes and related annotations in one species to another using synteny-filtered pairwise genome alignments (chains and nets) to determine the most likely orthologs. For example, for the mRNA TransMap track on the human assembly, more than 400,000 mRNAs from 25 vertebrate species were aligned at high stringency to the native assembly using BLAT. The alignments were then mapped to the human assembly using the chain and net alignments produced using BLASTZ, which has higher sensitivity than BLAT for diverged organisms. Compared to translated BLAT, TransMap finds fewer paralogs and aligns more UTR bases. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the human (hg19) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the human genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - hg19.ensembl.transMapV5.bigPsl TransMap RefGene - hg19.refseq.transMapV5.bigPsl TransMap RNA - hg19.rna.transMapV5.bigPsl TransMap ESTs - hg19.est.transMapV5.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/transMap/V5/hg19.refseq.transMapV5.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
transMapRefSeqV5 TransMap RefGene TransMap RefSeq Gene Mappings Version 5 Genes and Gene Predictions Description This track contains RefSeq Gene alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in human. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the human (hg19) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the human genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - hg19.ensembl.transMapV4.bigPsl TransMap RefGene - hg19.refseq.transMapV4.bigPsl TransMap RNA - hg19.rna.transMapV4.bigPsl TransMap ESTs - hg19.est.transMapV4.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/transMap/V4/hg19.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
transMapRnaV5 TransMap RNA TransMap GenBank RNA Mappings Version 5 Genes and Gene Predictions Description This track contains GenBank mRNA alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in human. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the human (hg19) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the human genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - hg19.ensembl.transMapV4.bigPsl TransMap RefGene - hg19.refseq.transMapV4.bigPsl TransMap RNA - hg19.rna.transMapV4.bigPsl TransMap ESTs - hg19.est.transMapV4.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/transMap/V4/hg19.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
transMapEstV5 TransMap ESTs TransMap EST Mappings Version 5 Genes and Gene Predictions Description This track contains GenBank spliced EST alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered BLASTZ alignment chains, resulting in a prediction of the orthologous genes in human. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here. Methods Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. For all vertebrate assemblies that had BLASTZ alignment chains and nets to the human (hg19) genome, a subset of the alignment chains were selected as follows: For organisms whose branch distance was no more than 0.5 (as computed by phyloFit, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the netfilter -syn command. The chains corresponding to the selected nets were used for mapping. For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogous regions. The post-alignment filtering step removes some of the duplications. The pslMap program was used to do a base-level projection of the source transcript alignments via the selected chains to the human genome, resulting in pairwise alignments of the source transcripts to the genome. The resulting alignments were filtered with pslCDnaFilter with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: accession.version-srcUniq.destUniq Where srcUniq is a number added to make each source alignment unique, and destUniq is added to give the subsequent TransMap alignments unique identifiers. For example, in the cow genome, there are two alignments of mRNA BC149621.1. These are assigned the identifiers BC149621.1-1 and BC149621.1-2. When these are mapped to the human genome, BC149621.1-1 maps to a single location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. Data Access The raw data for these tracks can be accessed interactively through the Table Browser or the Data Integrator. For automated analysis, the annotations are stored in bigPsl files (containing a number of extra columns) and can be downloaded from our download server, or queried using our API. For more information on accessing track data see our Track Data Access FAQ. The files are associated with these tracks in the following way: TransMap Ensembl - hg19.ensembl.transMapV4.bigPsl TransMap RefGene - hg19.refseq.transMapV4.bigPsl TransMap RNA - hg19.rna.transMapV4.bigPsl TransMap ESTs - hg19.est.transMapV4.bigPsl Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/transMap/V4/hg19.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout Credits This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects. References Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246; PMC: PMC2099585 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818; PMC: PMC2134963 
sibTxGraph SIB Alt-Splicing Alternative Splicing Graph from Swiss Institute of Bioinformatics mRNA and EST Description This track shows the graphs constructed by analyzing experimental RNA transcripts and serves as basis for the predicted alternative splicing transcripts shown in the SIB Genes track. The blocks represent exons; lines indicate introns. The graphical display is drawn such that no exons overlap, making alternative events easier to view when the track is in full display mode and the resolution is set to approximately gene-level. Further information on the graphs can be found on the Transcriptome Web interface. Methods The splicing graphs were generated using a multi-step pipeline: RefSeq and GenBank RNAs and ESTs are aligned to the genome with SIBsim4, keeping only the best alignments for each RNA. Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out. A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge. Graphs consisting solely of unspliced ESTs are discarded. Credits The SIB Alternative Splicing Graphs track was produced on the Vital-IT high-performance computing platform using a computational pipeline developed by Christian Iseli with help from colleagues at the Ludwig Institute for Cancer Research and the Swiss Institute of Bioinformatics. It is based on data from NCBI RefSeq and GenBank/EMBL. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them. 
intronEst Spliced ESTs Human ESTs That Have Been Spliced mRNA and EST Description This track shows alignments between human expressed sequence tags (ESTs) in GenBank and the genome that show signs of splicing when aligned against the genome. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. To be considered spliced, an EST must show evidence of at least one canonical intron (i.e., the genomic sequence between EST alignment blocks must be at least 32 bases in length and have GT/AG ends). By requiring splicing, the level of contamination in the EST databases is drastically reduced at the expense of eliminating many genuine 3' ESTs. For a display of all ESTs (including unspliced), see the human EST track. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, darker shading indicates a larger number of aligned ESTs. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the EST display. For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only ESTs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, ESTs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display ESTs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those ESTs that match the filter criteria. This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, go to the Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods To make an EST, RNA is isolated from cells and reverse transcribed into cDNA. Typically, the cDNA is cloned into a plasmid vector and a read is taken from the 5' and/or 3' primer. For most &mdash; but not all &mdash; ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. The reverse transcriptase may or may not make it to the 5' end of the mRNA, which may or may not be degraded. In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. Some of the newer cap-selected libraries cover transcription start reasonably well. Before the cap-selection techniques emerged, some projects used random rather than poly-A priming in an attempt to retrieve sequence distant from the 3' end. These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. Even outside of the random-primed projects, there is a degree of non-mRNA contamination. Because of this, a single unspliced EST should be viewed with considerable skepticism. To generate this track, human ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence are displayed in this track. Credits This track was produced at UCSC from EST sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
uniGene_3 UniGene UniGene Alignments mRNA and EST Description This track shows the UniGene genes from NCBI. Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. Coding exons are represented by blocks connected by horizontal lines representing introns. In full display mode, arrowheads on the connecting intron lines indicate the direction of transcription. Methods The UniGene sequence file, Hs.seq.uniq.gz, is downloaded from NCBI. Sequences are aligned to base genome using BLAT to create this track. When a single UniGene gene aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.2% of the best and at least 96.5% base identity with the genomic sequence were kept. Credits Thanks to UniGene for providing this annotation. 
epdNew EPDnew Promoters Promoters from EPDnew human version 006 Expression Description These tracks represent the experimentally validated promoters generated by the Eukaryotic Promoter Database. Display Conventions and Configuration Each item in the track is a representation of the promoter sequence identified by EPD. The &quot;thin&quot; part of the element represents the 49 bp upstream of the annotated transcription start site (TSS) whereas the &quot;thick&quot; part represents the TSS plus 10 bp downstream. The relative position of the thick and thin parts define the orientation of the promoter. Note that the EPD team has created a public track hub containing promoter and supporting annotations for human, mouse, and other vertebrate and model organism genomes. Methods Briefly, gene transcript coordinates were obtained from multiple sources (HGNC, GENCODE, Ensembl, RefSeq) and validated using data from CAGE and RAMPAGE experimental studies obtained from FANTOM 5, UCSC, and ENCODE. Peak calling, clustering and filtering based on relative expression were applied to identify the most expressed promoters and those present in the largest number of samples. For the methodology and principles used by EPD to predict TSSs, refer to Dreos et al. (2013) in the References section below. A more detailed description of how this data was generated can be found at the following links: Human promoter pipelines: coding, non-coding Mouse promoter pipelines: coding, non-coding Credits Data was generated by the EPD team at the Swiss Institute of Bioinformatics. For inquiries, contact the EPD team using this on-line form or email &#112;&#104;&#105;&#108;&#105;&#112;&#112;. &#98;u&#99;h&#101;r&#64;&#101;&#112;fl. &#99;&#104; . References Dreos R, Ambrosini G, Perier RC, Bucher P. EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res. 2013 Jan 1;41(D1):D157-64. PMID: 23193273. 
wgEncodeGencodeV47lift37 GENCODE V47lift37 GENCODE lifted annotations from V47lift37 (Ensembl 113) Genes and Gene Predictions Description The GENCODE Genes track (version 47lift37, Oct 2024) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V47 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 47lift37 site. Release Notes GENCODE version 47lift37 corresponds to Ensembl 113. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeSuper GENCODE Versions Container of all new and previous GENCODE releases Genes and Gene Predictions Description The aim of the GENCODE Genes project (Harrow et al., 2006) is to produce a set of highly accurate annotations of evidence-based gene features on the human reference genome. This includes the identification of all protein-coding loci with associated alternative splice variants, non-coding with transcript evidence in the public databases (NCBI/EMBL/DDBJ) and pseudogenes. A high quality set of gene structures is necessary for many research studies such as comparative or evolutionary analyses, or for experimental design and interpretation of the results. The GENCODE Genes tracks display the high-quality manual annotations merged with evidence-based automated annotations across the entire human genome. The GENCODE gene set presents a full merge between HAVANA manual annotation and Ensembl automatic annotation. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. With each release, there is an increase in the number of annotations that have undergone manual curation. This annotation was carried out on the GRCh37 (hg19) genome assembly. Experimental verification details are given in each descriptions for each track. Transcript Support Levels were determined for version 10 onwards based on evidence provided by GenBank mRNA and EST sequences. Versions 7 and 10 are being used in data analysis by the ENCODE consortium. NOTE: Due to the UCSC Genome Browser using the NC_001807 mitochondrial genome sequence (chrM) and GENCODE annotating the NC_012920 mitochondrial sequence, the GENCODE mitochondrial sequences are not available in the UCSC Genome Browser. These annotations are available for download in the GENCODE GTF files. For more information on the different gene tracks, see our Genes FAQ. Display Conventions These are multi-view composite tracks that contain differing data sets (views). Instructions for configuring multi-view tracks are here. Only some subtracks are shown by default. The user can select which subtracks are displayed via the display controls on the track details pages. Further details on display conventions and data interpretation are available in the track descriptions. Data access GENCODE Genes and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. The GENCODE data files for hg19 are available in our downloads directory as wgEncodeGencode* in genePred format. All the tables can also be queried directly from our public MySQL servers, with instructions on this method available on our MySQL help page and on our blog. Release Notes GENCODE version 47lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 113. GENCODE version 46lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 112. GENCODE version 45lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 111. GENCODE version 43lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 109. GENCODE version 42lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 108. GENCODE version 41lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 107. GENCODE version 40lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 106. GENCODE version 39lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 105. GENCODE version 38lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 104. GENCODE version 37lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 103. GENCODE version 36lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 102. GENCODE version 35lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 101. GENCODE version 34lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 100. GENCODE version 33lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 99. GENCODE version 30lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 96. GENCODE version 29lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 94. GENCODE version 28lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 92. GENCODE version 27lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 90. GENCODE version 24lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 83. GENCODE version 19 corresponds to Ensembl 74 and Vega 54. GENCODE version 17 corresponds to Ensembl 72 and Vega 52. GENCODE version 14 corresponds to Ensembl 69 and Vega 49 GENCODE version 7 corresponds to Ensembl 62 and Vega 42 and is used in ENCODE analysis. See also: The GENCODE Project Release History. Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV47lift37ViewGenes Genes GENCODE lifted annotations from V47lift37 (Ensembl 113) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV47lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 47lift37 (Ensembl 113) Genes and Gene Predictions 
wgEncodeGencodeCompV47lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 47lift37 (Ensembl 113) Genes and Gene Predictions 
wgEncodeGencodeBasicV47lift37 Basic Basic Gene Annotation Set from GENCODE Version 47lift37 (Ensembl 113) Genes and Gene Predictions 
wgEncodeGencodeV46lift37 GENCODE V46lift37 GENCODE lifted annotations from V46lift37 (Ensembl 112) Genes and Gene Predictions Description The GENCODE Genes track (version 46lift37, May 2024) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V46 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 46lift37 site. Release Notes GENCODE version 46lift37 corresponds to Ensembl 112. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV46lift37ViewGenes Genes GENCODE lifted annotations from V46lift37 (Ensembl 112) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV46lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 46lift37 (Ensembl 112) Genes and Gene Predictions 
wgEncodeGencodeCompV46lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 46lift37 (Ensembl 112) Genes and Gene Predictions 
wgEncodeGencodeBasicV46lift37 Basic Basic Gene Annotation Set from GENCODE Version 46lift37 (Ensembl 112) Genes and Gene Predictions 
wgEncodeGencodeV45lift37 GENCODE V45lift37 GENCODE lifted annotations from V45lift37 (Ensembl 111) Genes and Gene Predictions Description The GENCODE Genes track (version 45lift37, Jan 2024) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V45 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 45lift37 site. Release Notes GENCODE version 45lift37 corresponds to Ensembl 111. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV45lift37ViewGenes Genes GENCODE lifted annotations from V45lift37 (Ensembl 111) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV45lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 45lift37 (Ensembl 111) Genes and Gene Predictions 
wgEncodeGencodeCompV45lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 45lift37 (Ensembl 111) Genes and Gene Predictions 
wgEncodeGencodeBasicV45lift37 Basic Basic Gene Annotation Set from GENCODE Version 45lift37 (Ensembl 111) Genes and Gene Predictions 
wgEncodeGencodeV44lift37 GENCODE V44lift37 GENCODE lifted annotations from V44lift37 (Ensembl 110) Genes and Gene Predictions Description The GENCODE Genes track (version 44lift37, July 2023) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V44 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 44lift37 site. Release Notes GENCODE version 44lift37 corresponds to Ensembl 110. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV44lift37ViewGenes Genes GENCODE lifted annotations from V44lift37 (Ensembl 110) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV44lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 44lift37 (Ensembl 110) Genes and Gene Predictions 
wgEncodeGencodeCompV44lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 44lift37 (Ensembl 110) Genes and Gene Predictions 
wgEncodeGencodeBasicV44lift37 Basic Basic Gene Annotation Set from GENCODE Version 44lift37 (Ensembl 110) Genes and Gene Predictions 
wgEncodeGencodeV43lift37 GENCODE V43lift37 GENCODE lifted annotations from V43lift37 (Ensembl 109) Genes and Gene Predictions Description The GENCODE Genes track (version 43lift37, Feb 2023) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V43 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 43lift37 site. Release Notes GENCODE version 43lift37 corresponds to Ensembl 109. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV43lift37ViewGenes Genes GENCODE lifted annotations from V43lift37 (Ensembl 109) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV43lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 43lift37 (Ensembl 109) Genes and Gene Predictions 
wgEncodeGencodeCompV43lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 43lift37 (Ensembl 109) Genes and Gene Predictions 
wgEncodeGencodeBasicV43lift37 Basic Basic Gene Annotation Set from GENCODE Version 43lift37 (Ensembl 109) Genes and Gene Predictions 
wgEncodeGencodeV42lift37 GENCODE V42lift37 GENCODE lifted annotations from V42lift37 (Ensembl 108) Genes and Gene Predictions Description The GENCODE Genes track (version 42lift37, Oct 2022) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V42 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 42lift37 site. Release Notes GENCODE version 42lift37 corresponds to Ensembl 108. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV42lift37ViewGenes Genes GENCODE lifted annotations from V42lift37 (Ensembl 108) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV42lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 42lift37 (Ensembl 108) Genes and Gene Predictions 
wgEncodeGencodeCompV42lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 42lift37 (Ensembl 108) Genes and Gene Predictions 
wgEncodeGencodeBasicV42lift37 Basic Basic Gene Annotation Set from GENCODE Version 42lift37 (Ensembl 108) Genes and Gene Predictions 
wgEncodeGencodeV41lift37 GENCODE V41lift37 GENCODE lifted annotations from V41lift37 (Ensembl 107) Genes and Gene Predictions Description The GENCODE Genes track (version 41lift37, July 2022) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V41 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 41lift37 site. Release Notes GENCODE version 41lift37 corresponds to Ensembl 107. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV41lift37ViewGenes Genes GENCODE lifted annotations from V41lift37 (Ensembl 107) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV41lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 41lift37 (Ensembl 107) Genes and Gene Predictions 
wgEncodeGencodeCompV41lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 41lift37 (Ensembl 107) Genes and Gene Predictions 
wgEncodeGencodeBasicV41lift37 Basic Basic Gene Annotation Set from GENCODE Version 41lift37 (Ensembl 107) Genes and Gene Predictions 
wgEncodeGencodeV40lift37 GENCODE V40lift37 GENCODE lifted annotations from V40lift37 (Ensembl 106) Genes and Gene Predictions Description The GENCODE Genes track (version 40lift37, Feb 2022) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V40 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 40lift37 site. Release Notes GENCODE version 40lift37 corresponds to Ensembl 106. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV40lift37ViewGenes Genes GENCODE lifted annotations from V40lift37 (Ensembl 106) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV40lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 40lift37 (Ensembl 106) Genes and Gene Predictions 
wgEncodeGencodeCompV40lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 40lift37 (Ensembl 106) Genes and Gene Predictions 
wgEncodeGencodeBasicV40lift37 Basic Basic Gene Annotation Set from GENCODE Version 40lift37 (Ensembl 106) Genes and Gene Predictions 
wgEncodeGencodeV39lift37 GENCODE V39lift37 GENCODE lifted annotations from V39lift37 (Ensembl 105) Genes and Gene Predictions Description The GENCODE Genes track (version 39lift37, Oct 2021) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V39 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 39lift37 site. Release Notes GENCODE version 39lift37 corresponds to Ensembl 105. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV39lift37ViewGenes Genes GENCODE lifted annotations from V39lift37 (Ensembl 105) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV39lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 39lift37 (Ensembl 105) Genes and Gene Predictions 
wgEncodeGencodeCompV39lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 39lift37 (Ensembl 105) Genes and Gene Predictions 
wgEncodeGencodeBasicV39lift37 Basic Basic Gene Annotation Set from GENCODE Version 39lift37 (Ensembl 105) Genes and Gene Predictions 
wgEncodeGencodeV38lift37 GENCODE V38lift37 GENCODE lifted annotations from V38lift37 (Ensembl 104) Genes and Gene Predictions Description The GENCODE Genes track (version 38lift37, May 2021) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V38 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 38lift37 site. Release Notes GENCODE version 38lift37 corresponds to Ensembl 104. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV38lift37ViewGenes Genes GENCODE lifted annotations from V38lift37 (Ensembl 104) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV38lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 38lift37 (Ensembl 104) Genes and Gene Predictions 
wgEncodeGencodeCompV38lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 38lift37 (Ensembl 104) Genes and Gene Predictions 
wgEncodeGencodeBasicV38lift37 Basic Basic Gene Annotation Set from GENCODE Version 38lift37 (Ensembl 104) Genes and Gene Predictions 
wgEncodeGencodeV37lift37 GENCODE V37lift37 GENCODE lifted annotations from V37lift37 (Ensembl 103) Genes and Gene Predictions Description The GENCODE Genes track (version 37lift37, Feb 2021) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V37 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 37lift37 site. Release Notes GENCODE version 37lift37 corresponds to Ensembl 103. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV37lift37ViewGenes Genes GENCODE lifted annotations from V37lift37 (Ensembl 103) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV37lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 37lift37 (Ensembl 103) Genes and Gene Predictions 
wgEncodeGencodeCompV37lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 37lift37 (Ensembl 103) Genes and Gene Predictions 
wgEncodeGencodeBasicV37lift37 Basic Basic Gene Annotation Set from GENCODE Version 37lift37 (Ensembl 103) Genes and Gene Predictions 
wgEncodeGencodeV36lift37 GENCODE V36lift37 GENCODE lifted annotations from V36lift37 (Ensembl 102) Genes and Gene Predictions Description The GENCODE Genes track (version 36lift37, Nov 2020) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V36 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 36lift37 site. Release Notes GENCODE version 36lift37 corresponds to Ensembl 102. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV36lift37ViewGenes Genes GENCODE lifted annotations from V36lift37 (Ensembl 102) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV36lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 36lift37 (Ensembl 102) Genes and Gene Predictions 
wgEncodeGencodeCompV36lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 36lift37 (Ensembl 102) Genes and Gene Predictions 
wgEncodeGencodeBasicV36lift37 Basic Basic Gene Annotation Set from GENCODE Version 36lift37 (Ensembl 102) Genes and Gene Predictions 
wgEncodeGencodeV35lift37 GENCODE V35lift37 GENCODE lifted annotations from V35lift37 (Ensembl 101) Genes and Gene Predictions Description The GENCODE Genes track (version 35lift37, June 2020) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V35 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 35lift37 site. Release Notes GENCODE version 35lift37 corresponds to Ensembl 101. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV35lift37ViewGenes Genes GENCODE lifted annotations from V35lift37 (Ensembl 101) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV35lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 35lift37 (Ensembl 101) Genes and Gene Predictions 
wgEncodeGencodeCompV35lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 35lift37 (Ensembl 101) Genes and Gene Predictions 
wgEncodeGencodeBasicV35lift37 Basic Basic Gene Annotation Set from GENCODE Version 35lift37 (Ensembl 101) Genes and Gene Predictions 
wgEncodeGencodeV34lift37 GENCODE V34lift37 GENCODE lifted annotations from V34lift37 (Ensembl 100) Genes and Gene Predictions Description The GENCODE Genes track (version 34lift37, April 2020) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V34 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 34lift37 site. Release Notes GENCODE version 34lift37 corresponds to Ensembl 100. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV34lift37ViewGenes Genes GENCODE lifted annotations from V34lift37 (Ensembl 100) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV34lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 34lift37 (Ensembl 100) Genes and Gene Predictions 
wgEncodeGencodeCompV34lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 34lift37 (Ensembl 100) Genes and Gene Predictions 
wgEncodeGencodeBasicV34lift37 Basic Basic Gene Annotation Set from GENCODE Version 34lift37 (Ensembl 100) Genes and Gene Predictions 
wgEncodeGencodeV33lift37 GENCODE V33lift37 GENCODE lifted annotations from V33lift37 (Ensembl 99) Genes and Gene Predictions Description The GENCODE Genes track (version 33lift37, Jan 2020) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V33 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 33lift37 site. Release Notes GENCODE version 33lift37 corresponds to Ensembl 99. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV33lift37ViewGenes Genes GENCODE lifted annotations from V33lift37 (Ensembl 99) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV33lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 33lift37 (Ensembl 99) Genes and Gene Predictions 
wgEncodeGencodeCompV33lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 33lift37 (Ensembl 99) Genes and Gene Predictions 
wgEncodeGencodeBasicV33lift37 Basic Basic Gene Annotation Set from GENCODE Version 33lift37 (Ensembl 99) Genes and Gene Predictions 
wgEncodeGencodeV31lift37 GENCODE V31lift37 GENCODE lifted annotations from V31lift37 (Ensembl 97) Genes and Gene Predictions Description The GENCODE Genes track (version 31lift37, June 2019) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V31 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 31lift37 site. Release Notes GENCODE version 31lift37 corresponds to Ensembl 97. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV31lift37ViewGenes Genes GENCODE lifted annotations from V31lift37 (Ensembl 97) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV31lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 31lift37 (Ensembl 97) Genes and Gene Predictions 
wgEncodeGencodeCompV31lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 31lift37 (Ensembl 97) Genes and Gene Predictions 
wgEncodeGencodeBasicV31lift37 Basic Basic Gene Annotation Set from GENCODE Version 31lift37 (Ensembl 97) Genes and Gene Predictions 
wgEncodeGencodeV28lift37 GENCODE V28lift37 GENCODE lifted annotations from V28lift37 (Ensembl 92) Genes and Gene Predictions Description The GENCODE Genes track (version 28lift37, Apr 2018) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V28 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 28lift37 site. Release Notes GENCODE version 28lift37 corresponds to Ensembl 92. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV28lift37ViewGenes Genes GENCODE lifted annotations from V28lift37 (Ensembl 92) Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV28lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 28lift37 (Ensembl 92) Genes and Gene Predictions 
wgEncodeGencodeCompV28lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 28lift37 (Ensembl 92) Genes and Gene Predictions 
wgEncodeGencodeBasicV28lift37 Basic Basic Gene Annotation Set from GENCODE Version 28lift37 (Ensembl 92) Genes and Gene Predictions 
wgEncodeGencodeV27lift37 GENCODE Gene V27lift37 Gene Annotations from GENCODE Version 27lift37 Genes and Gene Predictions Description The GENCODE Genes track (version 27lift37, August 2017) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The GENCODE V27 annotations on the GRCh38 (hg38) primary assembly were mapped to GRCh37 (hg19) using the process documented here. The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the corresponding release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem Methods The GENCODE project aims to annotate all evidence-based gene features on the human and mouse reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) was included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). If no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 27lift37 site. Release Notes GENCODE version 27lift37 corresponds to Ensembl 90. See also: The GENCODE Project Credits The GENCODE project is an international collaboration funded by NIH/NHGRI grant U41HG007234. More information is available at www.gencodegenes.org, Participating GENCODE institutions and personnel can be found here. References Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I et al. GENCODE 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. PMID: 33270111; PMC: PMC7778937; DOI: 10.1093/nar/gkaa1087 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV27lift37ViewGenes Genes Gene Annotations from GENCODE Version 27lift37 Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV27lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 27lift37 (Ensembl 90) Genes and Gene Predictions 
wgEncodeGencodeCompV27lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 27lift37 (Ensembl 90) Genes and Gene Predictions 
wgEncodeGencodeBasicV27lift37 Basic Basic Gene Annotation Set from GENCODE Version 27lift37 (Ensembl 90) Genes and Gene Predictions 
wgEncodeGencodeV24lift37 GENCODE Gene V24lift37 Gene Annotations from GENCODE Version 24lift37 Genes and Gene Predictions Description The GENCODE Genes track (version 24lift37, December 2015) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project and mapped from GRCh38 to GRCh37. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The annotation was carried out on genome assembly GRCh38 (hg38) and then the primary assembly was mapped to GRCh37 (hg19) using the process described documented here. As of GENCODE Version 11, Ensembl and GENCODE have converged. The gene annotations in the GENCODE comprehensive set are the same as the corresponding Ensembl release. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem all 2-way pseudogenes all polyA annotations --> Methods The GENCODE project aims to annotate all evidence-based gene features on the human reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) were included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). It no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in humans. Human transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes human leukocyte antigen (HLA) transcript immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable. PRINCIPAL:1 - Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. PRINCIPAL:2 - Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant. PRINCIPAL:3 - Where the APPRIS core modules are unable to choose a clear principal variant and there more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. PRINCIPAL:4 - Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with a distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. PRINCIPAL:5 - Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant. For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way: ALTERNATIVE:1 - Candidate transcript(s) models that are conserved in at least three tested species. ALTERNATIVE:2 - Candidate transcript(s) models that appear to be conserved in fewer than three tested species. Non-candidate transcripts are not tagged and are considered as "Minor" transcripts. Further information and additional web services can be found at the APPRIS website. Downloads GENCODE GFF3 and GTF files are available from the GENCODE release 24 (mapped to GRCh37) site. Verification Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. Those experiments can be found at GEO: GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes). GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009. GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human. --> GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010). GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010). GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data. See Harrow et al. (2006) for information on verification techniques. Release Notes GENCODE version 23 corresponds to Ensembl 83. See also: The GENCODE Project Credits This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: GENCODE at the Sanger Institute) Lab/Institution Contributors GENCODE Principal Investigator Jennifer Harrow GENCODE Co-Principal Investigator Tim Hubbard HAVANA manual annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Timothy Cutts, Bronwen Aken, James Gilbert, Jyoti Choudhary, Ed Griffiths, Jose Manuel Gonzalez, Electra Tapanari, Daniel Barrell, Adam Frankish, Andrew Berry, Alexandra Bignell, Veronika Boychenko, Claire Davidson, Gloria Despacio-Reyes, Mike Kay, Deepa Manthravadi, Gaurab Mukherjee, Catherine Snow, Gemma Barson, Matt Hardy, Joanne Howes Centre de Regulaci&oacute; Gen&ograve;mica (CRG), Barcelona, Spain Roderic Guig&oacute;, Julien Lagarde, Barbara Uszczy&#324;ska Genome Bioinformatics, University of California Santa Cruz (UCSC), USA David Haussler, Mark Diekhans, Benedict Paten, Joel Armstrong Computer Science and Artificial Intelligence Lab,Broad Institute of MIT and Harvard, USA Manolis Kellis, Irwin Jungreis Computational Biology and Bioinformatics, Yale University (Yale), USA Mark Gerstein, Suganthi Balasubramanian, Ekta Khurana, Cristina Sisu, Baikang Pei, Yan Zhang, Mihali Felipe Center for Integrative Genomics,University of Lausanne, Switzerland Alexandre Reymond, Cedric Howald, Anne-Maud Ferreira, Jacqueline Chrast Structural Computational Biology Group, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain Alfonso Valencia, Michael Tress, Jos&eacute; Manuel Rodr&iacute;guez, Victor de la Torre Former members of the GENCODE project Felix Kokocinski, Toby Hunt, Gary Saunders, Sarah Grubb, Thomas Derrien, Andrea Tanzer, Gang Fang, Mihali Felipe, Michael Brent, Randall Brown, Jeltje van Baren, Stephen Searle, Rachel Harte References Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012 Sep;22(9):1760-74. PMID: 22955987; PMC: PMC3431492 Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9. PMID: 16925838; PMC: PMC1810553 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV24lift37ViewGenes Genes Gene Annotations from GENCODE Version 24lift37 Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV24lift37 Pseudogenes Pseudogene Annotation Set from GENCODE Version 24lift37 (Ensembl 83) Genes and Gene Predictions 
wgEncodeGencodeCompV24lift37 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 24lift37 (Ensembl 83) Genes and Gene Predictions 
wgEncodeGencodeBasicV24lift37 Basic Basic Gene Annotation Set from GENCODE Version 24lift37 (Ensembl 83) Genes and Gene Predictions 
wgEncodeGencodeV19 GENCODE Genes V19 Gene Annotations from GENCODE Version 19 Genes and Gene Predictions Description The GENCODE Genes track (version 19, December 2013) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The annotation was carried out on genome assembly GRCh37 (hg19). As of GENCODE Version 11, Ensembl and GENCODE have converged. The gene annotations in the GENCODE comprehensive set are the same as the corresponding Ensembl release. UCSC will continue to provide a separate Ensembl track on Human in the same format as the Ensembl tracks on other organisms. NOTE: Due to the UCSC Genome Browser using the NC_001807 mitochondrial genome sequence (chrM) and GENCODE annotating the NC_012920 mitochondrial sequence, the GENCODE mitochondrial annotations have been lifted to NC_001807 coordinates in the UCSC Genome Browser. The original annotations with NC_012920 coordinates are available for download in the GENCODE GTF files. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. 2-way GENCODE 2-way Pseudogenes contains pseudogenes predicted by both the Yale Pseudopipe and UCSC Retrofinder pipelines. The set was derived by looking for 50 base pairs of overlap between pseudogenes derived from both sets based on their chromosomal coordinates. When multiple Pseudopipe predictions map to a single Retrofinder prediction, only one match is kept for the 2-way consensus set. PolyA GENCODE PolyA contains polyA signals and sites manually annotated on the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching the genome. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem all 2-way pseudogenes all polyA annotations Methods The GENCODE project aims to annotate all evidence-based gene features on the human reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) were included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). It no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in humans. Human transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes human leukocyte antigen (HLA) transcript immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) Downloads GENCODE GTF files are available from the GENCODE release 19 site. Verification Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. Those experiments can be found at GEO: GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes). GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009. GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human. --> GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010). GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010). GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data. See Harrow et al. (2006) for information on verification techniques. Release Notes GENCODE version 19 corresponds to Ensembl 74 and Vega 54. See also: The GENCODE Project Credits This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: GENCODE at the Sanger Institute) Lab/Institution Contributors GENCODE Principal Investigator Tim Hubbard HAVANA manual annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Jennifer Harrow, Timothy Cutts, Bronwen Aken, James Gilbert, Jyoti Choudhary, Ed Griffiths, Jose Manuel Gonzalez, Electra Tapanari, Daniel Barrell, Adam Frankish, Andrew Berry, Alexandra Bignell, Veronika Boychenko, Claire Davidson, Gloria Despacio-Reyes, Mike Kay, Deepa Manthravadi, Gaurab Mukherjee, Catherine Snow, Gemma Barson, Matt Hardy, Joanne Howes Centre de Regulaci&oacute; Gen&ograve;mica (CRG), Barcelona, Spain Roderic Guig&oacute;, Julien Lagarde, Barbara Uszczy&#324;ska Genome Bioinformatics, University of California Santa Cruz (UCSC), USA David Haussler, Rachel Harte, Mark Diekhans, Benedict Paten, Joel Armstrong Computer Science and Artificial Intelligence Lab,Broad Institute of MIT and Harvard, USA Manolis Kellis, Irwin Jungreis Computational Biology and Bioinformatics, Yale University (Yale), USA Mark Gerstein, Suganthi Balasubramanian, Ekta Khurana, Cristina Sisu, Baikang Pei, Yan Zhang, Mihali Felipe Center for Integrative Genomics,University of Lausanne, Switzerland Alexandre Reymond, Cedric Howald, Anne-Maud Ferreira, Jacqueline Chrast Structural Computational Biology Group, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain Alfonso Valencia, Michael Tress, Jos&eacute; Manuel Rodr&iacute;guez, Victor de la Torre Former members of the GENCODE project Felix Kokocinski, Toby Hunt, Gary Saunders, Sarah Grubb, Thomas Derrien, Andrea Tanzer, Gang Fang, Mihali Felipe, Michael Brent, Randall Brown, Jeltje van Baren, Stephen Searle References Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012 Sep;22(9):1760-74. PMID: 22955987; PMC: PMC3431492 Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9. PMID: 16925838; PMC: PMC1810553 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV19ViewPolya PolyA Gene Annotations from GENCODE Version 19 Genes and Gene Predictions 
wgEncodeGencodePolyaV19 PolyA PolyA Transcript Annotation Set from GENCODE Version 19 Genes and Gene Predictions 
wgEncodeGencodeV19ViewGenes Genes Gene Annotations from GENCODE Version 19 Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV19 Pseudogenes Pseudogene Annotation Set from GENCODE Version 19 Genes and Gene Predictions 
wgEncodeGencodeCompV19 Comprehensive Comprehensive Gene Annotation Set from GENCODE Version 19 Genes and Gene Predictions 
wgEncodeGencodeBasicV19 Basic Basic Gene Annotation Set from GENCODE Version 19 Genes and Gene Predictions 
wgEncodeGencodeV19View2Way 2-Way Gene Annotations from GENCODE Version 19 Genes and Gene Predictions 
wgEncodeGencode2wayConsPseudoV19 2-way Pseudogenes 2-way Pseudogene Annotation Set from GENCODE Version 19 Genes and Gene Predictions 
wgEncodeGencodeV17 GENCODE Genes V17 Gene Annotations from ENCODE/GENCODE Version 17 Genes and Gene Predictions Description The GENCODE Genes track (version 17, June 2013) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The annotation was carried out on genome assembly GRCh37 (hg19). As of GENCODE Version 11, Ensembl and GENCODE have converged. The gene annotations in the GENCODE comprehensive set are the same as the corresponding Ensembl release. UCSC will continue to provide a separate Ensembl track on Human in the same format as the Ensembl tracks on other organisms. NOTE: Due to the UCSC Genome Browser using the NC_001807 mitochondrial genome sequence (chrM) and GENCODE annotating the NC_012920 mitochondrial sequence, the GENCODE mitochondrial annotations have been lifted to NC_001807 coordinates in the UCSC Genome Browser. The original annotations with NC_012920 coordinates are available for download in the GENCODE GTF files. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. 2-way GENCODE 2-way Pseudogenes contains pseudogenes predicted by both the Yale Pseudopipe and UCSC Retrofinder pipelines. The set was derived by looking for 50 base pairs of overlap between pseudogenes derived from both sets based on their chromosomal coordinates. When multiple Pseudopipe predictions map to a single Retrofinder prediction, only one match is kept for the 2-way consensus set. PolyA GENCODE PolyA contains polyA signals and sites manually annotated on the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching the genome. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Support Level: filter transcripts by transcription support level Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem all 2-way pseudogenes all polyA annotations Methods The GENCODE project aims to annotate all evidence-based gene features on the human reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) were included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). It no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in humans. Human transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes human leukocyte antigen (HLA) transcript immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) Downloads GENCODE GTF files are available from the GENCODE release 17 site. Verification Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. Those experiments can be found at GEO: GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes). GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009. GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human. --> GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010). GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010). GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data. See Harrow et al. (2006) for information on verification techniques. Release Notes GENCODE version 17 corresponds to Ensembl 72 from June 2013 and Vega 52 from May 2013. See also: The GENCODE Project Credits This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: GENCODE at the Sanger Institute) Lab/Institution Contributors GENCODE Principal Investigator Tim Hubbard HAVANA manual annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Adam Frankish, Jose Manuel Gonzalez, Mike Kay, Alexandra Bignell, Gloria Despacio-Reyes, Garaub Mukherjee, Gary Sanders, Veronika Boychenko, Jennifer Harrow Genome Bioinformatics Lab (CRG), Barcelona, Spain Thomas Derrien, Tyler Alioto, Andrea Tanzer, Roderic Guig&oacute; Genome Bioinformatics, University of California Santa Cruz (UCSC), USA Rachel Harte, Mark Diekhans, Robert Baertsch, David Haussler Computational Genomics Lab, Washington University St. Louis (WUSTL), USA Jeltje van Baren, Charlie Comstock, David Lu, Michael Brent Computer Science and Artificial Intelligence Lab, Broad Institute of MIT and Harvard, USA Mike Lin, Manolis Kellis Computational Biology and Bioinformatics, Yale University (Yale), USA Philip Cayting, Suganthi Balasubramanian, Baikang Pei, Cristina Sisu, Mark Gerstein Center for Integrative Genomics, University of Lausanne, Switzerland Cedric Howald, Alexandre Reymond Ensembl Genebuild group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Steve Searle, Bronwen Aken, Amonida Zadissa, Daniel Barrell Structural Computational Biology Group, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain Jos&eacute; Manuel Rodr&iacute;guez, Michael Tress, Alfonso Valencia References Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012 Sep;22(9):1760-74. PMID: 22955987; PMC: PMC3431492 Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9. PMID: 16925838; PMC: PMC1810553 A full list of GENCODE publications are available at The GENCODE Project web site. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV17ViewPolya PolyA Gene Annotations from ENCODE/GENCODE Version 17 Genes and Gene Predictions 
wgEncodeGencodePolyaV17 PolyA PolyA Transcript Annotation Set from ENCODE/GENCODE Version 17 Genes and Gene Predictions 
wgEncodeGencodeV17ViewGenes Genes Gene Annotations from ENCODE/GENCODE Version 17 Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV17 Pseudogenes Pseudogene Annotation Set from ENCODE/GENCODE Version 17 Genes and Gene Predictions 
wgEncodeGencodeCompV17 Comprehensive Comprehensive Gene Annotation Set from ENCODE/GENCODE Version 17 Genes and Gene Predictions 
wgEncodeGencodeBasicV17 Basic Basic Gene Annotation Set from ENCODE/GENCODE Version 17 Genes and Gene Predictions 
wgEncodeGencodeV17View2Way 2-Way Gene Annotations from ENCODE/GENCODE Version 17 Genes and Gene Predictions 
wgEncodeGencode2wayConsPseudoV17 2-way Pseudogenes 2-way Pseudogene Annotation Set from ENCODE/GENCODE Version 17 Genes and Gene Predictions 
wgEncodeGencodeV14 GENCODE Genes V14 Gene Annotations from ENCODE/GENCODE Version 14 Genes and Gene Predictions Description The GENCODE Genes track (version 14, October 2012) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation process and Ensembl automatic annotation pipeline. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. The annotation was carried out on genome assembly GRCh37 (hg19). As of GENCODE Version 11, Ensembl and GENCODE have converged. The gene annotations in the GENCODE comprehensive set are the same as the corresponding Ensembl release. UCSC will continue to provide a separate Ensembl track on Human in the same format as the Ensembl tracks on other organisms. NOTE: Due to the UCSC Genome Browser using the NC_001807 mitochondrial genome sequence (chrM) and GENCODE annotating the NC_012920 mitochondrial sequence, the GENCODE mitochondrial annotations have been lifted to NC_001807 coordinates in the UCSC Genome Browser. The original annotations with NC_012920 coordinates are available for download in the GENCODE GTF files. Display Conventions and Configuration This track is a multi-view composite track that contains differing data sets (views). Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Views available on this track are: Genes The gene annotations in this view are divided into three subtracks: GENCODE Basic set is a subset of the Comprehensive set. The selection criteria are described in the methods section. GENCODE Comprehensive set contains all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. This is a super-set of the Basic set. GENCODE Pseudogenes include all annotations except polymorphic pseudogenes. 2-way GENCODE 2-way Pseudogenes contains pseudogenes predicted by both the Yale Pseudopipe and UCSC Retrofinder pipelines. The set was derived by looking for 50 base pairs of overlap between pseudogenes derived from both sets based on their chromosomal coordinates. When multiple Pseudopipe predictions map to a single Retrofinder prediction, only one match is kept for the 2-way consensus set. PolyA GENCODE PolyA contains polyA signals and sites manually annotated on the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching the genome. Filtering is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks using the following criteria: Transcript class: filter by the basic biological function of a transcript annotation All - don't filter by transcript class coding - display protein coding transcripts, including polymorphic pseudogenes nonCoding - display non-protein coding transcripts pseudo - display pseudogene transcript annotations problem - display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain) Transcript Annotation Method: filter by the method used to create the annotation All - don't filter by transcript class manual - display manually created annotations, including those that are also created automatically automatic - display automatically created annotations, including those that are also created manually manual_only - display manually created annotations that were not annotated by the automatic method automatic_only - display automatically created annotations that were not annotated by the manual method Transcript Biotype: filter transcripts by biotype Coloring for the gene annotations is based on the annotation type: coding non-coding pseudogene problem all 2-way pseudogenes all polyA annotations Methods The GENCODE project aims to annotate all evidence-based gene features on the human reference sequence with high accuracy by integrating computational approaches (including comparative methods), manual annotation and targeted experimental verification. This goal includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. For a detailed description of the methods and references used, see Harrow et al. (2006). GENCODE Basic Set selection: The GENCODE Basic Set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. The goal was to have a high-quality basic set that also covered all loci. Selection of GENCODE annotations for inclusion in the basic set was determined independently for the coding and non-coding transcripts at each gene locus. Criteria for selection of coding transcripts (including polymorphic pseudogenes) at a given locus: All full-length coding transcripts (except problem transcripts or transcripts that are nonsense-mediated decay) were included in the basic set. If there were no transcripts meeting the above criteria, then the partial coding transcript with the largest CDS was included in the basic set (excluding problem transcripts). Criteria for selection of non-coding transcripts at a given locus: All full-length non-coding transcripts (except problem transcripts) with a well characterized biotype (see below) were included in the basic set. If there were no transcripts meeting the above criteria, then the largest non-coding transcript was included in the basic set (excluding problem transcripts). It no transcripts were included by either the above criteria, the longest problem transcript is included. Non-coding transcript categorization: Non-coding transcripts are categorized using their biotype and the following criteria: well characterized: antisense, Mt_rRNA, Mt_tRNA, miRNA, rRNA, snRNA, snoRNA poorly characterized: 3prime_overlapping_ncrna, lincRNA, misc_RNA, non_coding, processed_transcript, sense_intronic, sense_overlapping Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in humans. Human transcript sequences from the International Nucleotide Sequence Database Collaboration (GenBank, ENA, and DDBJ) are used as the evidence for this analysis. Exonerate RNA alignments from Ensembl, BLAT RNA and EST alignments from the UCSC Genome Browser Database are used in the analysis. Erroneous transcripts and libraries identified in lists maintained by the Ensembl, UCSC, HAVANA and RefSeq groups are flagged as suspect. GENCODE annotations for protein-coding and non-protein-coding transcripts are compared with the evidence alignments. Annotations in the MHC region and other immunological genes are not evaluated, as automatic alignments tend to be very problematic. Methods for evaluating single-exon genes are still being developed and they are not included in the current analysis. Multi-exon GENCODE annotations are evaluated using the criteria that all introns are supported by an evidence alignment and the evidence alignment does not indicate that there are unannotated exons. Small insertions and deletions in evidence alignments are assumed to be due to polymorphisms and not considered as differing from the annotations. All intron boundaries must match exactly. The transcript start and end locations are allowed to differ. The following categories are assigned to each of the evaluated annotations: tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs tsl3 - the only support is from a single EST tsl4 - the best supporting EST is flagged as suspect tsl5 - no single transcript supports the model structure tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes human leukocyte antigen (HLA) transcript immunoglobin gene transcript T-cell receptor transcript single-exon transcript (will be included in a future version) Downloads GENCODE GTF files are available from the GENCODE release 14 site. Verification Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. Those experiments can be found at GEO: GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes). GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009. GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human. --> GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010). GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010). GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data. See Harrow et al. (2006) for information on verification techniques. Release Notes This GENCODE version 14 corresponds to Ensembl 69 from October 2012 and Vega 49 from September 2012. See also: The GENCODE Project Credits This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: GENCODE at the Sanger Institute) Lab/Institution Contributors GENCODE Principal Investigator Tim Hubbard HAVANA manual annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Adam Frankish, Jose Manuel Gonzalez, Mike Kay, Alexandra Bignell, Gloria Despacio-Reyes, Garaub Mukherjee, Gary Sanders, Veronika Boychenko, Jennifer Harrow Genome Bioinformatics Lab (CRG), Barcelona, Spain Thomas Derrien, Tyler Alioto, Andrea Tanzer, Roderic Guig&oacute; Genome Bioinformatics, University of California Santa Cruz (UCSC), USA Rachel Harte, Mark Diekhans, Robert Baertsch, David Haussler Computational Genomics Lab, Washington University St. Louis (WUSTL), USA Jeltje van Baren, Charlie Comstock, David Lu, Michael Brent Computer Science and Artificial Intelligence Lab, Broad Institute of MIT and Harvard, USA Mike Lin, Manolis Kellis Computational Biology and Bioinformatics, Yale University (Yale), USA Philip Cayting, Suganthi Balasubramanian, Baikang Pei, Cristina Sisu, Mark Gerstein Center for Integrative Genomics, University of Lausanne, Switzerland Cedric Howald, Alexandre Reymond Ensembl Genebuild group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Steve Searle, Bronwen Aken, Amonida Zadissa, Daniel Barrell Structural Computational Biology Group, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain Jos&eacute; Manuel Rodr&iacute;guez, Michael Tress, Alfonso Valencia References Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S et al. Ensembl 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D800-6. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9. Data Release Policy GENCODE data are available for use without restrictions. 
wgEncodeGencodeV14ViewPolya PolyA Gene Annotations from ENCODE/GENCODE Version 14 Genes and Gene Predictions 
wgEncodeGencodePolyaV14 PolyA PolyA Transcript Annotation Set from ENCODE/GENCODE Version 14 Genes and Gene Predictions 
wgEncodeGencodeV14ViewGenes Genes Gene Annotations from ENCODE/GENCODE Version 14 Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV14 Pseudogenes Pseudogene Annotation Set from ENCODE/GENCODE Version 14 Genes and Gene Predictions 
wgEncodeGencodeCompV14 Comprehensive Comprehensive Gene Annotation Set from ENCODE/GENCODE Version 14 Genes and Gene Predictions 
wgEncodeGencodeBasicV14 Basic Basic Gene Annotation Set from ENCODE/GENCODE Version 14 Genes and Gene Predictions 
wgEncodeGencodeV14View2Way 2-Way Gene Annotations from ENCODE/GENCODE Version 14 Genes and Gene Predictions 
wgEncodeGencode2wayConsPseudoV14 2-way Pseudogenes 2-way Pseudogene Annotation Set from ENCODE/GENCODE Version 14 Genes and Gene Predictions 
wgEncodeGencodeV7 GENCODE Genes V7 Gene Annotations from ENCODE/GENCODE Version 7 Genes and Gene Predictions Description The GENCODE Genes track (version 7, May 2011) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The GENCODE gene set presents a full merge between HAVANA manual annotation and ENSEMBL automatic annotation. Priority is given to the manually curated HAVANA annotation, using predicted ENSEMBL annotations when there are no corresponding manual annotations. The annotation was carried out on genome assembly GRCh37 (hg19). NOTE: Due to UCSC Genome Browser using the NC_001807 mitochondrial genome sequence (chrM) and GENCODE annotating the NC_012920 mitochondrial sequence, the GENCODE mitochondrial sequences are not available in the UCSC Genome Browser. These annotations are available for download in the GENCODE GTF files. NOTE: We try and synchronize the release cycles for GENCODE, Havana and Ensembl. This GENCODE version 7 corresponds to Ensembl 62 from 13 April 2011 and Vega 23-03-2011. Also see: GENCODE project. Display Conventions and Configuration The annotations are divided into separate tracks based on type of annotation. The basic set of coding and non-coding transcripts is a subset of the comprehensive set selected to provide a simplified view of the transcript set designed to suit the needs of a majority of users. The selection algorithm is described in the next section. The available tracks are: GENCODE Basic set - subset of the GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations. The selection criteria is described in the next section. This is subset of the comprehensive set. GENCODE Comprehensive set - all GENCODE coding and non-code transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations, except pseudogenes. This is super-set of the basic set. GENCODE Pseudogenes - all pseudogene annotations except polymorphic pseudogenes GENCODE 2-way Pseudogenes - Pseudogenes predicted by the Yale Pseudopipe and UCSC Retrofinder pipelines. The set was derived by looking for a 50 base pairs of overlap between pseudogenes derived from both sets based on their genomic locations i.e. chromosomal coordinates. When multiple Pseudopipe predictions map to a single Retrofinder prediction, only one match is kept for the 2-way consensus set. GENCODE PolyA - This track contains polyA signals and sites manually annotated on the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching to the genome. GENCODE basic set selection The GENCODE basic set is intended to provide a simplified subset of the GENCODE transcript annotations that will be useful to the majority of users. Selection for the GENCODE annotations to include in the basic set is done on a per-locus basis and then for coding and non-coding transcripts within that locus. The goal is to use the better quality transcript annotations while still having some annotation present for each locus. The selection criteria for a given locus is: Coding transcripts (including polymorphic pseudogenes): If there are any full length coding transcripts that are not nonsense-mediated decay or problem transcripts, then only they are included in the basic set. Otherwise, use the coding transcript with the largest CDS. Non-coding transcripts: If there are any full length non-coding transcripts and they have a well characterized BioType (see below), then only they are included in the basic set. Otherwise, use the largest non-coding transcript. Non-coding transcript categories Non-coding transcripts are categorized using their BioType and the following criteria: well characterized: antisense, lincRNA, miRNA, Mt_rRNA, Mt_tRNA, rRNA, snoRNA, snRNA poorly characterized: non_coding, processed_transcript, retrotransposed, misc_RNA Filtering Items in the GENCODE Basic, Comprehensive and Pseudogene tracks can be filter using the following criteria: Transcript class: Filter by the basic biological function of a transcript annotation. All - Don't filter by transcript class. coding - Display protein coding transcripts, including polymorphic pseudogenes. nonCoding - Display non-protein coding transcripts. pseudo - Display pseudogene transcript annotations. problem - Display problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain). Annotation Method: Filter by the method used to create the annotation. All - Don't filter by transcript class. manual - display manually created annotations, including those that are also created automatically. automatic - display automatically created annotations, including those that are also created manually. manual_only - display manually created annotations there were not annotated by the automatic method. automatic_only - display automatically created annotations there were not annotated by the manual method. Transcript Type: filter transcripts by BioType. Coloring The gene annotations are colored based on the annotation type: Manual and automatic coding non-coding pseudogene problem 2-way pseudogene all PolyA annotations all Methods We aim to annotate all evidence-based gene features at high accuracy on the human reference sequence. This includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. We integrate computational approaches (including comparative methods), manual annotation and targeted experimental verification. For a detailed description of the methods and references used, see Harrow et al (2006). Verification See Harrow et al. (2006) for information on verification techniques. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. Those experiments can be found at GEO: GSE30619:[E-MTAB-612] - Batch I is based on annotation from July 2008 (without pseudogenes). GSE25711:[E-MTAB-407] - Batch II is based on annotation from April 2009. GSE30612:[E-MTAB-533] - Batch III is verifying RGASP models for c.elegans and human. --> GSE34797:[E-MTAB-684] - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010). GSE34820:[E-MTAB-737] - Batch V is based on annotations from GENCODE 6 (November 2010). GSE34821:[E-MTAB-831] - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data. Credits This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: GENCODE at the Sanger Institute. ) Lab/Institution Contributors GENCODE Principal Investigator Tim Hubbard HAVANA manual annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Adam Frankish, Jose Manuel Gonzalez, Mike Kay, Alexandra Bignell, Gloria Despacio-Reyes, Garaub Mukherjee, Gary Sanders, Veronika Boychenko, Jennifer Harrow Genome Bioinformatics Lab (CRG), Barcelona, Spain Thomas Derrien, Tyler Alioto, Andrea Tanzer, Roderic Guig&oacute; Genome Bioinformatics, University of California Santa Cruz (UCSC), USA Rachel Harte, Mark Diekhans, Robert Baertsch, David Haussler Comp. Genomics Lab, Washington University St. Louis (WUSTL), USA Jeltje van Baren, Charlie Comstock, David Lu, Michael Brent Computer Science and Artificial Intelligence Lab, Broad Institute of MIT and Harvard, USA Mike Lin, Manolis Kellis Computational Biology and Bioinformatics, Yale University (Yale), USA Philip Cayting, Suganthi Balasubramanian, Baikang Pei, Cristina Sisu, Mark Gerstein Center for Integrative Genomics, University of Lausanne, Switzerland Cedric Howald, Alexandre Reymond ENSEMBL genebuild group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Steve Searle, Bronwen Aken, Amonida Zadissa, Daniel Barrell Structural Computational Biology Group, Centro Natcional de Investigaciones Oncologicas (CNIO), Madrid, Spain Jos&eacute; Manuel Rodr&iacute;guez, Michael Tress, Alfonso Valencia References Flicek et al. Ensembl 2011. Nucleic Acids Research. 2011;39 Database issue:D800-D806 Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9. Data Release Policy GENCODE data are available for use without restrictions. The full data release policy for ENCODE is available here. 
wgEncodeGencodeV7ViewPolya PolyA Gene Annotations from ENCODE/GENCODE Version 7 Genes and Gene Predictions 
wgEncodeGencodePolyaV7 PolyA Gencode 2011-05-01 wgEncodeEH001881 1881 Hubbard Sanger V7 PolyA Transcript Annotation Set wgEncodeGencodePolyaV7 GENCODE Hubbard Hubbard - GENCODE at Sanger Institute PolyA Transcript Annotation Set from ENCODE/GENCODE Version 7 Genes and Gene Predictions 
wgEncodeGencodeV7ViewGenes Genes Gene Annotations from ENCODE/GENCODE Version 7 Genes and Gene Predictions 
wgEncodeGencodePseudoGeneV7 Pseudogenes Gencode 2011-05-01 wgEncodeEH001881 1881 Hubbard Sanger V7 Pseudogene Annotation Set wgEncodeGencodePseudoGeneV7 GENCODE Hubbard Hubbard - GENCODE at Sanger Institute Pseudogene Annotation Set from ENCODE/GENCODE Version 7 Genes and Gene Predictions 
wgEncodeGencodeCompV7 Comprehensive Gencode 2011-05-01 wgEncodeEH001881 1881 Hubbard Sanger V7 Comprehensive Gene Annotation Set wgEncodeGencodeCompV7 GENCODE Hubbard Hubbard - GENCODE at Sanger Institute Comprehensive Gene Annotation Set from ENCODE/GENCODE Version 7 Genes and Gene Predictions 
wgEncodeGencodeBasicV7 Basic Gencode 2011-05-01 wgEncodeEH001881 1881 Hubbard Sanger V7 Basic Gene Annotation Set wgEncodeGencodeBasicV7 GENCODE Hubbard Hubbard - GENCODE at Sanger Institute Basic Gene Annotation Set from ENCODE/GENCODE Version 7 Genes and Gene Predictions 
wgEncodeGencodeV7View2Way 2-Way Gene Annotations from ENCODE/GENCODE Version 7 Genes and Gene Predictions 
wgEncodeGencode2wayConsPseudoV7 2-way Pseudogenes Gencode 2011-05-01 wgEncodeEH001881 1881 Hubbard Sanger V7 2-way Pseudogene Annotation Set wgEncodeGencode2wayConsPseudoV7 GENCODE Hubbard Hubbard - GENCODE at Sanger Institute 2-way Pseudogene Annotation Set from ENCODE/GENCODE Version 7 Genes and Gene Predictions 
tgpPhase1Accessibility 1000G Ph1 Accsbl 1000 Genomes Project Phase 1 Paired-end Accessible Regions Variation 
tgpArchive 1000G Archive 1000 Genomes Archive Variation Description This supertrack is a collection of tracks from the 1000 Genomes Project showing paired-end accessible regions and integrated variant calls. More information about display conventions, methods, credits, and references can be found on each subtrack's description page. For more details, see: 1000 Genomes Frequently Asked Questions (FAQ) 1000 Genomes Project - Analysis overview Credits Thanks to the International Genome Sample Resource (IGSR) for making these variant calls freely available. 
tgpPhase1AccessibilityStrictCriteria 1000G Accs Strict 1000 Genomes Project Phase 1 Paired-end Accessible Regions - Strict Criteria Variation 
tgpPhase1AccessibilityPilotCriteria 1000G Accs Pilot 1000 Genomes Project Phase 1 Paired-end Accessible Regions - Pilot Criteria Variation 
tgpPhase1 1000G Ph1 Vars 1000 Genomes Phase 1 Integrated Variant Calls: SNVs, Indels, SVs Variation Description This track shows ~38,200,000 single nucleotide variants (SNVs), ~3,900,000 short insertion/deletion variants (indels), and ~14,000 large deletions (also called structural variants, or SVs) discovered by the 1000 Genomes Project through its Phase 1 sequencing of 1,092 genomes from 14 populations in Africa, Europe, East Asia and the Americas. The variant genotypes have been phased by the 1000 Genomes Project (i.e., the two alleles of each diploid genotype have been assigned to two haplotypes, one inherited from each parent). This extra information enables a clustering of independent haplotypes by local similarity for display. Display Conventions In &quot;dense&quot; mode, a vertical line is drawn at the position of each variant. In &quot;pack&quot; mode, since these variants have been phased, the display shows a clustering of haplotypes in the viewed range, sorted by similarity of alleles weighted by proximity to a central variant. The clustering view can highlight local patterns of linkage. In the clustering display, each sample's phased diploid genotype is split into two independent haplotypes. Each haplotype is placed in a horizontal row of pixels; when the number of haplotypes exceeds the number of vertical pixels for the track, multiple haplotypes fall in the same pixel row and pixels are averaged across haplotypes. Each variant is a vertical bar with white (invisible) representing the reference allele and black representing the non-reference allele(s). Tick marks are drawn at the top and bottom of each variant's vertical bar to make the bar more visible when most alleles are reference alleles. The vertical bar for the central variant used in clustering is outlined in purple. In order to avoid long compute times, the range of alleles used in clustering may be limited; alleles used in clustering have purple tick marks at the top and bottom. The clustering tree is displayed to the left of the main image. It does not represent relatedness of individuals; it simply shows the arrangement of local haplotypes by similarity. When a rightmost branch is purple, it means that all haplotypes in that branch are identical, at least within the range of variants used in clustering. Methods Single-nucleotide variants, short insertions/deletions, and larger deletions were called from alignments of 1,092 individuals' low-coverage genomes and high-coverage exomes. For each type of variant, the results of multiple variant-calling methods were merged and filtered in order to provide high-confidence variant calls. For more details, see: 1000 Genomes Project - Analysis overview the Phase 1 integrated release version 3 README file the final Phase 1 integrated call set (adding chromosome Y and the mitochondrion) README file supplemental materials of the Phase 1 publication (1000 Genomes Consortium, 2012) Credits Thanks to the 1000 Genomes Project for making these data available in advance of publication. References 1000 Genomes Pilot Project: 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73. Phase 1 of the 1000 Genomes Project: 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65. 1000 Genomes Frequently Asked Questions (FAQ) 
tgpPhase3Accessibility 1000G Ph3 Accsbl 1000 Genomes Project Phase 3 Paired-end Accessible Regions Variation Description This track shows which genome regions are more or less accessible to next generation sequencing methods that use short, paired-end reads. It summarizes whole genome sequencing data from Phase 3 of the 1000 Genomes Project and shows two levels of stringency: &quot;pilot&quot; stringency regions (see below) cover 94.5% of non-N bases in the genome (excluding alternate haplotype sequences and unplaced contigs; 95.9% on autosomes) and &quot;strict&quot; regions cover 75.5% (76.9% on autosomes). Each site which meets &quot;strict&quot; criteria also passes the &quot;pilot&quot; criteria. This track does not show a mask of regions in which variant calls can or cannot be made. Some 1000 Genomes Phase 3 variant calls are in regions that do not meet the &quot;strict&quot; criteria. Phase 3 variant calls are filtered using various tools such as the Variant Quality Score Recalibrator (VQSR) method (implemented in the Genome Analysis Toolkit (GATK)) without regard to the thresholds applied here. VQSR and similar tools assess the evidence for variation at sites where a variant is called, but say nothing about the remaining sites. The 1000 Genomes Project Phase 3 variant calls combine information from low coverage sequencing, exome sequencing and array genotyping for improved sensitivity and specificity. The coverage masks are based on low coverage sequencing only. These regions will be useful for (a) comparing accessibility using current technologies to accessibility in the 1000 Genomes Pilot Project, and (b) population genetic analyses (such as estimates of mutation rate) that must focus on genomic regions with very low false positive and false negative rates. Methods The total depth of mapped sequence reads, the average mapping quality score and the fraction of reads with mapping quality zero (meaning that this read maps equally well to more than one location in the genome) are tabulated from 1000 Genomes Project Phase 3 .bam files. This combines whole genome sequence data from 2,504 individuals, giving a genome wide average depth of coverage of 17,920 reads. Both &quot;pilot&quot; and &quot;strict&quot; tracks are .bed file conversions of the &quot;pass&quot; regions from .fasta mask files. See the README file in that directory and Supplementary Information (section 9.2) of 1000 Genomes Project Consortium, et al. (2015) for more details. The &quot;pilot&quot; criteria require a depth of coverage between 8,960 and 35,840 inclusive (between one-half and twice the average depth) and that no more than 20% of covering reads have mapping quality zero. These are equivalent to the criteria used for analyses in the 1000 Genomes Pilot paper (2010). The &quot;strict&quot; criteria require a depth of coverage between 8,960 and 26,880 inclusive, no more than 0.1% of reads with mapping quality zero, and an average mapping quality of 56 or greater. This definition is quite stringent and focuses on the most unique regions of the genome. Since approximately one-half of 1000 Genomes Project individuals are males, the depth of coverage is generally lower on the X chromosome. Coverage thresholds on the X chromosome were adjusted by a factor of 3/4 and on the Y chromosome by a factor of 1/2. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server. The underlying data files for this track are called 20141020.pilot_mask.whole_genome.bb and 20141020.strict_mask.whole_genome.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/1000Genomes/phase3/20141020.strict_mask.whole_genome.bb -chrom=chr6 -start=0 -end=1000000 stdout Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Credits Thank you to Mary Kate Wing at the University of Michigan Center for Statistical Genetics for providing the track data files. Thank you to Tom Blackwell and Mary Kate Wing at UM for editing the description and methods. References 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73. PMID: 20981092; PMC: PMC3042601 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA et al. A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. PMID: 26432245 
tgpPhase3AccessibilityStrictCriteria 1000G Accs Strict 1000 Genomes Project Phase 3 Paired-end Accessible Regions - Strict Criteria Variation 
tgpPhase3AccessibilityPilotCriteria 1000G Accs Pilot 1000 Genomes Project Phase 3 Paired-end Accessible Regions - Pilot Criteria Variation 
tgpPhase3 1000G Ph3 Vars 1000 Genomes Phase 3 Integrated Variant Calls: SNVs, Indels, SVs Variation Description This track shows 84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants discovered by the 1000 Genomes Project through its Phase 3 sequencing of 2,504 genomes from 16 populations worldwide. The variant genotypes have been phased by the 1000 Genomes Project (i.e., the two alleles of each diploid genotype have been assigned to two haplotypes, one inherited from each parent). This extra information enables a clustering of independent haplotypes by local similarity for display. Display Conventions In &quot;dense&quot; mode, a vertical line is drawn at the position of each variant. In &quot;pack&quot; mode, since these variants have been phased, the display shows a clustering of haplotypes in the viewed range, sorted by similarity of alleles weighted by proximity to a central variant. The clustering view can highlight local patterns of linkage. In the clustering display, each sample's phased diploid genotype is split into two independent haplotypes. Each haplotype is placed in a horizontal row of pixels; when the number of haplotypes exceeds the number of vertical pixels for the track, multiple haplotypes fall in the same pixel row and pixels are averaged across haplotypes. Each variant is a vertical bar with white (invisible) representing the reference allele and black representing the non-reference allele(s). Tick marks are drawn at the top and bottom of each variant's vertical bar to make the bar more visible when most alleles are reference alleles. The vertical bar for the central variant used in clustering is outlined in purple. In order to avoid long compute times, the range of alleles used in clustering may be limited; alleles used in clustering have purple tick marks at the top and bottom. The clustering tree is displayed to the left of the main image. It does not represent relatedness of individuals; it simply shows the arrangement of local haplotypes by similarity. When a rightmost branch is purple, it means that all haplotypes in that branch are identical, at least within the range of variants used in clustering. Methods The genomes of 2,504 individuals were sequenced using both whole-genome sequencing (mean depth = 7.4x) and targeted exome sequencing (mean depth = 65.7x). Quoting the Phase 3 publication (1000 Genomes Project Consortium, 2015): In contrast to earlier phases of the project, we expanded analysis beyond bi-allelic events to include multi-allelic SNPs, indels, and a diverse set of structural variants (SVs). An overview of the sample collection, data generation, data processing, and analysis is given in Extended Data Fig. 1. Variant discovery used an ensemble of 24 sequence analysis tools (Supplementary Table 2), and machine-learning classifiers to separate high-quality variants from potential false positives, balancing sensitivity and specificity. Construction of haplotypes started with estimation of long-range phased haplotypes using array genotypes for project participants and, where available, their first degree relatives; continued with the addition of high confidence bi-allelic variants that were analysed jointly to improve these haplotypes; and concluded with the placement of multi-allelic and structural variants onto the haplotype scaffold one at a time. See also: 1000 Genomes Project - Analysis overview The Phase 3 integrated release README file Supplemental Information for 1000 Genomes Project Consortium, et al. (2015) 1000 Genomes Frequently Asked Questions (FAQ) Credits Thanks to the 1000 Genomes Project for making these data freely available. References 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA et al. A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. PMID: 26432245 
ntSssTop5p 5% Lowest S Selective Sweep Scan (S): 5% Smallest S scores Neandertal Assembly and Analysis Description This track shows regions of the human genome with a strong signal for depletion of Neandertal-derived alleles (regions from the Sel Swp Scan (S) track with S scores in the lowest 5%), which may indicate an episode of positive selection in early humans. Display Conventions and Configuration Grayscale shading is used as a rough indicator of the strength of the score; the darker the item, the stronger its negative score. The strongest negative score (-8.7011) is shaded black, and the shading lightens from dark to light gray as the negative score weakens (weakest score is -4.3202). Methods Green et al. identified single-base sites that are polymorphic among five modern human genomes of diverse ancestry (in the Modern Human Seq track) plus the human reference genome, and determined ancestral or derived state of each single nucleotide polymorphism (SNP) by comparison with the chimpanzee genome. The SNPs are displayed in the S SNPs track. The human allele states were used to estimate an expected number of derived alleles in Neandertal in the 100,000-base window around each SNP, and a measure called the S score was developed, displayed in the Sel Swp Scan (S) track, to compare the observed number of Neandertal alleles in each window to the expected number. An S score significantly less than zero indicates a reduction of Neandertal-derived alleles (or an increase of human-derived alleles not found in Neandertal), consistent with the scenario of positive selection in the human lineage since divergence from Neandertals. Genomic regions of 25,000 or more bases in which all polymorphic sites were at least 2 standard deviations below the expected value were identified, and S was recomputed on each such region. Regions with S scores in the lowest 5% (strongest negative scores) were prioritized for further analysis as described in Green et al.. Credits This track was produced at UCSC using data generated by Ed Green. References Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. PMID: 20448178 </p 
abSplice AbSplice Scores Aberrant Splicing Prediction Scores Phenotype and Literature Description AbSplice is a method that predicts aberrant splicing across human tissues, as described in Wagner, &Ccedil;elik et al., 2023. This track displays precomputed AbSplice scores for all possible single-nucleotide variants genome-wide. The scores represent the probability that a given variant causes aberrant splicing in a given tissue. AbSplice scores can be computed from VCF files and are based on quantitative tissue-specific splice site annotations (SpliceMaps). While SpliceMaps can be generated for any tissue of interest from a cohort of RNA-seq samples, this track includes 49 tissues available from the Genotype-Tissue Expression (GTEx) dataset. Display Conventions The AbSplice score is a probability estimate of how likely aberrant splicing of some sort takes place in a given tissue. The authors suggest three cutoffs which are represented by color in the track. High (red) - An AbSplice score over 0.2 indicates a high likelihood of aberrant splicing in at least one tissue. Medium (orange) - A score between 0.05 and 0.2 indicates a medium likelihood. Low (blue) - A score between 0.01 and 0.05 indicates a low likelihood. Scores below 0.01 are not displayed. Mouseover on items shows the gene name, maximum score, and tissues that had this score. Clicking on any item brings up a table with scores for all 49 GTEX tissues. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Precomputed AbSplice-DNA scores in all 49 GTEx tissues are available at Zenodo. Methods Data was converted from the files (AbSplice_DNA_ hg19 _snvs_high_scores.zip) provided by the authors at zenodo.org. Files in the score_cutoff=0.01 directory were concatenated. To convert the data to bigBed format, scores and their tissues were selected from the AbSplice_DNA fields and maximum scores, and then calculated using a custom Python script, which can be found in the makeDoc from our GitHub repository. Credits Thanks to Nils Wagner for helpful comments and suggestions. References Wagner N, &#199;elik MH, H&#246;lzlwimmer FR, Mertes C, Prokisch H, Y&#233;pez VA, Gagneur J. Aberrant splicing prediction across human tissues. Nat Genet. 2023 May;55(5):861-870. PMID: 37142848 
acembly AceView Genes AceView Gene Models With Alt-Splicing Genes and Gene Predictions Description This track shows AceView gene models constructed from cDNA and genomic evidence by Danielle and Jean Thierry-Mieg using the Acembly program. AceView is the only database that defines the genes genome-wide by using only, but exhaustively, the public experimental cDNA sequences from the same species. The analysis relies on the quality of the genome sequence and exploits sophisticated cDNA-to-genome co-alignment algorithms to provide a comprehensive and non-redundant representation of the GenBank, dbEST, GSS, Trace and RefSeq cDNA sequences. In a way, the AceView transcripts represent a fully annotated non-redundant &lsquo;nr&rsquo; view of the public RNAs, minus cloning artefacts, contaminations and bad quality sequences. AceView transcripts represent a 10 times compaction relative to the raw data, with minimal loss of sequence information. 87% of the public RNA sequences are coalesced into AceView alternative transcripts and genes, thereby identifying close to twice as many main genes as there are &quot;known genes&quot; in both human and mouse. 18% to 25% of the spliced genes appear non-coding, in mouse and human respectively. Alternative transcripts are prominent in both species. The typical human gene produces on average eight distinct alternatively spliced forms from three promoters and with three non-overlapping terminal exons. It has on average three cassette exons and four internal donor or acceptor sites. The AceView site further proposes a thorough biological annotation of the reconstructed genes, including association to diseases and tissue specificity of the alternative transcripts. AceView combines respect for the experimental data with extensive quality control. Evaluated in the ENCODE regions, AceView transcripts are close to indistinguishable from the manually curated Gencode reference genes (see Thierry-Mieg, 2006, or compare the two tracks in the Genome Browser), but over the entire genome the number of transcripts exceeds Havana/Vega by a factor of three and RefSeq by a factor of six. Display Conventions and Configuration This track follows the display conventions for gene tracks. Gene models that fall into the &quot;main&quot; class are displayed in purple; &quot;putative&quot; genes are displayed in pink. The main genes include at least one transcript which is spliced or putatively protein coding. Spliced genes contain at least one well-defined standard intron, i.e., an intron with a GT-AG or GC-AG boundary, supported by at least one clone matching exactly, with no ambiguous bases, 8 bases of the genome on each side of the intron. The putative genes have no standard intron and do not encode good proteins, yet are supported by more than six cDNA clones. The track description page offers the following filter and configuration options: Gene Class filter: Select the main or putative option to filter the display. Color track by codons: Select the genomic codons option to color and label each codon in a zoomed-in display to facilitate validation and comparison to gene predictions. Click the Codon coloring help link on the track description page for more information about this feature. Methods The millions of cDNA sequences available from the public databases (GenBank, dbEST, GSS, Traces, etc.) are aligned cooperatively on the genome sequence, taking care to keep the paired 5' and 3' reads from single clones associated in the same transcript. Useful information about tissue, stage, publications, isolation procedure and so on is gathered. AceView alignments on the genome use knowledge on sequencing errors gained from analyzing sequencing traces and cooperative refinements. They are usually obtained over the entire length of the EST or mRNA, (average 98.8% aligned, 0.2% mismatches in mRNAs or 95.5% aligned, 1.4% mismatches in ESTs). Multiple alignments are evaluated and the sequences are stringently kept only in their best position genome-wide. Less than 1% of the mRNAs and less than 2% of the ESTs will ultimately be aligned in more than one gene, usually in the ~1% closely repeated genes. The cDNA sequences are then processed and cleaned: the vectors and polyA are clipped, the reads submitted on the wrong strand are flipped, and the small insertion or deletion polymorphisms are identified. Eventual cDNA clone rearrangements or anomalous alignments are flagged and filtered (akin to manually) so as not to lose unique valuable information while avoiding pollution of the database with poorly supported anomalous data. Unfortunately, cDNA libraries are still far from saturation, so after 20% of the suspicious entries have been removed, a single good-quality cDNA sequence, aligned with standard introns on the genome, is considered sufficient evidence for a given mRNA structure. That is because cDNA sequences are difficult to obtain, but they remain the cleanest and most reliable information to best define the molecular genes. Unspliced non-coding genes are however reported (in the putative class) only if they are supported by six or more accessions. Others belong to what is termed &lsquo;the cloud&rsquo; (not displayed on the UCSC Genome Browser). The cDNA sequences are clustered into a minimal number of alternative transcript variants, preferring partial transcripts to artificially extended ones. Sequences are concatenated by simple contact, but the combinatorics are voided by allowing each cDNA accession to contribute to a single alternative variant, preferably one where it merges silently without bringing any new sequence information. As a result, for instance, all shorter reads compatible with a full-length mRNA will be absorbed in that transcript and will not be available to allow for extensions on other incompatible transcripts. About 70% of the variants, clearly identified on the Acembly site, have their entire coding region supported by a single cDNA; the others may be illicit concatenations that could be split when more data become available. For each transcript, the consensus sequence of the cDNAs most compatible to the genome sequence is generated. Single base insertion, deletion, transition or transversion is shown graphically in the mRNA view, where frequent SNPs become evident. The main sequence of the transcript used in the annotation is that of the footprint of the transcript on the genome, which is of better quality than the mRNAs: this procedure corrects up to 2% sequencing errors. Putative protein-coding regions are predicted from the mRNA sequence and annotated using BlastP, PFAM, Psort2, and comparison to AceView proteins from other species. Best proteins are scored (see the FAQ on the Acembly site) and transcripts are putatively proposed to be protein-coding or non-coding. Expression, cDNA support, tissue specificity, sequences of alternative transcripts, introns and exons, alternative promoters, alternative exons and alternative polyadenylation sites are evaluated and annotated on the Acembly web site. The reconstructed alternative transcripts are then grouped into genes if they share at least one exact intron boundary or if they have substantial sequence overlap. Coding and non-coding genes are defined, and genes in antisense are flagged. AceView genes are matched molecularly to Entrez genes and named according to the official nomenclature or the Entrez Gene nomenclature. For novel genes not in Entrez, AceView creates new gene names that are maintained from release to release until the genes receive an official or Entrez gene name. Each gene is annotated in depth, with the intention of AceView serving as a one-stop knowledgebase for systems biology. Selected functional annotations are gathered from various sources, including expression data, protein interactions and GO annotations. In particular, possible disease associations are extracted directly from PubMed, in addition to OMIM and GAD, and the users can help refine those annotations. Finally, lists of the most closely related genes by function, pathway, protein complex, GO annotation, disease, cellular localization or all criteria taken together are proposed, to stimulate research and development. Click the &quot;AceView Gene Summary&quot; on an individual transcript's details page to access the gene on the NCBI AceView website. Credits Thanks to Danielle and Jean Thierry-Mieg at NCBI for providing this track for human, worm and mouse. References Thierry-Mieg D, Thierry-Mieg J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 2006;7 Suppl 1:S12.1-14. PMID: 16925834; PMC: PMC1810549 AceView web site: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly 
genePredArchive Prediction Archive Gene Prediction Archive Genes and Gene Predictions Description This supertrack is a collection of gene prediction tracks and is composed of the following tracks: AUGUSTUS shows ab initio predictions from the program AUGUSTUS (version 3.1). The predictions are based on the genome sequence alone. Geneid Genes shows gene predictions from the geneid program. Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. Genscan Genes shows predictions from the Genscan program. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. SGP Genes shows gene predictions from the SGP2 homology-based gene prediction program. To predict genes in a genomic query, SGP2 combines geneid predictions with tblastx comparisons of the genome of the target species against genomic sequences of other species (reference genomes) deemed to be at an appropriate evolutionary distance from the target. SIB Genes a transcript-based set of gene predictions based on data from RefSeq and EMBL/GenBank. The track includes both protein-coding and non-coding transcripts. The coding regions are predicted using ESTScan. More information about display conventions, methods, credits, and references can be found on each subtrack's description page. 
altSeqLiftOverPsl Alt Haplotypes Reference Assembly Alternate Haplotype Sequence Alignments Mapping and Sequencing Description This track shows alignments of alternate locus (also known as &quot;alternate haplotype&quot;) reference sequences to main chromosome sequences in the reference genome assembly. Some loci in the genome are highly variable, with sets of variants that tend to segregate into distinct haplotypes. Only one haplotype can be included in a reference assembly chromosome sequence. Instead of providing a separate complete chromosome sequence for each haplotype, which could cause confusion with divergent chromosome coordinates and ambiguity about which sequence is the official reference, the Genome Reference Consortium (GRC) adds alternate locus sequences, ranging from tens of thousands of bases up to low millions of bases in size, to represent the distinct haplotypes. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. Mismatching bases are highlighted in red. Several types of alignment gap may also be colored; for more information, see Alignment Insertion/Deletion Display Options. Credits The alignments were provided by NCBI as GFF files and translated into the PSL representation for browser display by UCSC. 
genotypeArrays Array Probesets Microarray Probesets Variation Affymetrix Arrays Affymetrix Genome-Wide Human SNP Array 6.0 and SV The SNP Array 6.0 includes more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNPs include the 482,000 SNPs from the 5.0 Array (unbiased selection). In addition, 424,000 new SNPs were chosen in the following areas: Tag SNPs SNPs from chromosomes X and Y Mitochondrial SNPs New SNPs added to dbSNP SNPs in recombination hotspots The structural variation copy number (SV) probes include 202,000 probes targeting 5,677 known CNV regions from the Toronto Database of Genomic Variants. The additional 744,000 probes are evenly spaced throughout the genome. Affymetrix Genome-Wide Human SNP Array 5.0 The SNP Array 5.0 is a single microarray featuring all single nucleotide polymorphisms (SNPs) from the original two-chip Mapping 500K Array Set, as well as 420,000 additional non-polymorphic probes that can measure other genetic differences, such as copy number variation. Affymetrix 500K (250K Nsp and 250K Sty) This annotation displays the SNPs available for genotyping with the GeneChip Human Mapping 500K Array Set from Affymetrix. It is comprised of two arrays: Nsp and Sty, which contain approximately 262,000 and 238,000 SNPs, respectively. Affymetrix CytoScan HD The CytoScan High-Density (HD) Array provides whole-genome coverage with enriched coverage of all constitutional and cancer-related genes on a single array. The complete CytoScan array includes: Genome build hg19 Total number of copy-number markers 2,696,550 Total number of non-polymorphic markers 1,953,246 Number of SNP markers 743,304 SNP markers with &gt;99% genotype accuracy 749,157 Autosomal markers 2,491,915 Pseudoautosomal markers 4,624 Intragenic markers 1,410,535 Intergenic markers 1,286,015 Probes are colored green for CNV probesets and purple for SNP probesets. Some SNP probesets are also considered informative for CNV detection. Agilent Arrays Non-SNP subtracks are colored in alternating shades of green and orange to highlight track boundaries. SNP subtracks are colored blue with SNP probes colored dark blue and CGH probes colored light blue. The track consists of the following subtracks: The arrays listed in this track are probes from the Agilent Catalog Oligonucleotide Microarrays. The following table summarizes the different Agilent arrays: Description AMADID Samples per Slide Biological Features Median Probe Spacing Gene-biased SNPs SurePrint G3 Human CGH Microarray 1x1M 021529 1 969,033 2.1 kb Yes 0 SurePrint G3 Human High-Resolution Microarray 1x1M 023642 1 989,214 2.6 kb No (evenly tiled) 0 SurePrint G3 Human CGH+SNP Microarray 2x400K 028081 2 411,434 7 kb Yes 65,000 SurePrint G3 Human CGH Microarray 2x400K 021850 2 415,914 5.3 kb Yes 0 SurePrint G3 Human Cancer CGH+SNP Microarray 4x180K 030587 4 172,595 25 kb Yes (cancer genes) 65,000 SurePrint G3 Human CGH+SNP Microarray 4x180K 029830 4 172,595 25 kb No (ISCA regions) 65,000 SurePrint G3 Human CGH Microarray 4x180K 022060 4 174,675 13 kb Yes 0 SurePrint G3 Human CGH Microarray 8x60K 021924 8 59,175 41 kb Yes 0 SurePrint HD Human CGH Microarray 1x244K 014693 1 238,331 8.9 kb Yes 0 SurePrint HD Human CGH Microarray 2x105K 014698 2 100,034 22 kb Yes 0 SurePrint HD Human CGH Microarray 4x44K 014950 4 43,143 43 kb Yes 0 GenetiSure Cyto CGH+SNP 4x180K 085591 GenetiSure Cyto CGH 4x180K 085589 GenetiSure Cyto CGH 8x60k 085590 Illumina Arrays Illumina HumanHap650Y This annotation displays the SNPs available for genotyping with Illumina's HumanHap650Y Genotyping BeadChip. The HumanHap650Y contains over 650,000 markers, extending the HumanHap550 by adding 100,000 additional Yoruba-specific tag SNPs. On average, there is 1 SNP every 5.3 kb, 6.2 kb and 5.4 kb across the genome in the CEU, CHB+JPT and YRI populations, respectively. The HumanHap650Y was derived from release 21 of the International HapMap Project. Illumina HumanHap550 This annotation displays the SNPs available for genotyping with Illumina's HumanHap550 Genotyping BeadChip. The HumanHap550 contains over 550,000 markers, the majority of which are tag SNPs derived from release 20 of the International HapMap Project. In addition, approximately 7800 non-synonymous SNPs, a higher density of tag SNPs in the MHC region, over 150 mitochondrial SNPs and over 4000 SNPs from regions with copy number polymorphism were included. In the CEU population, an r-squared threshold of 0.8 was used for common SNPs in genes, within 10 kb of genes or in evolutionarily conserved regions. For all other regions, an r-squared threshold of 0.7 was used. On average, there is 1 SNP every 5.5 kb, 6.5 kb and 6.2 kb across the genome in the CEU, CHB+JPT and YRI populations, respectively. Illumina HumanHap300 This annotation displays the SNPs available for genotyping with Illumina's HumanHap300 Genotyping BeadChip. The HumanHap300 contains over 317,000 tagSNP markers derived from Phase I of the International HapMap Project. In addition, approximately 7300 non-synonymous SNPs and a higher density of tag SNPs in the MHC region were included. On average, there is 1 SNP every 9 kb across the genome and median spacing is 5 kb. Illumina Human1M-Duo This annotation displays the SNPs available for genotyping with Illumina's Human1M-Duo Genotyping BeadChip. The Human1M-Duo contains more than 1,100,000 tagSNP markers and a set of ~60,000 additional CNV-targeted markers. The median spacing is 1.5kb (mean - 2.4 kb). Illumina HumanOmni1-Quad v1 The HumanOmni1-Quad BeadChip consists of 1,140,419 markers in a 4-sample format. The whole-genome content provides high genomic coverage rates of 93%, 92%, and 76% at r2 &gt; 0.8 for the CEU, CHB+JPT, and YRI populations, respectively. High density markers with a median spacing of 1.2 kb ensure the highest level of resolution for CNV and breakpoint identification. The content has been derived from the 1,000 Genomes Project, all three HapMap phases, and recently published studies, including new coding variants identified by the 1000 Genomes Project and markers chosen in high-value regions of the genome: ABO blood typing SNPs, cSNPs, disease-associated SNPs, eSNPs, SNPs in mRNA splice sites, ADME genes, AIMs, HLA complexes, indels, introns, MHC regions, miRNA binding sites, mitochondrial DNA, PAR, promoter regions, and Y-chromosome. Illumina Human660W-Quad v1 The Human660W-Quad BeadChip consists of 657,366 markers in a 4-sample format. The Human660W-Quad BeadChip provides 87%, 85%, and 56% coverage of CEU, CHB+JPT, and YRI populations at r2 &gt; 0.8. For CNV and cytogenetic analysis, the dense backbone content is combined with an additional ~100,000 markers that target observed common CNVs. HumanCytoSNP-12 v2.1 The 301,232 markers on the HumanCytoSNP-12 represents a complete 12-sample panel of genome-wide SNPs for a uniform backbone and additional markers targeting all regions of known cytogenetic importance. Backbone markers provide genome-wide marker spacing of 10kb. This is supplemented with dense coverage (at 6 kb spacing average) of ~250 genomic regions commonly studied in cytogenetics labs and targeted coverage in ~400 additional genes, subtelomeric regions, pericentromeric regions, and sex chromosomes. An efficiency-optimized tagging strategy provides a panel for GWAS (70% coverage in CEU at r2 &gt; 0.8) in the highest throughput and most cost-effective whole-genome DNA Analysis BeadChip. Illumina Global Diversity Array The Global Diversity Array-8 v1.0 BeadChip includes coverage of the ACMG 59-gene clinical research variants and multi-ethnic, genome-wide content. The GDA is the commercial version of the array chosen by the All of Us Research Program and is designed to capture a wider range of the world's populationsthan traditional microarrays. Illumina 450k and 850k Methylation Arrays With the Infinium MethylationEPIC BeadChip Kit, researchers can interrogate over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution. Multiple samples, including FFPE, can be analyzed in parallel to deliver high-throughput power while minimizing the cost per sample. These tracks show positions being measured on the Illumina 450k and 850k (EPIC) microarray tracks. More information about the arrays can be found on the Infinium MethylationEPIC Kit website. Illumina CytoSNP 850K Probe Array The Infinium CytoSNP-850K v1.2 BeadChip provides comprehensive coverage of cytogenetically relevant genes on a proven platform, helping researchers find valuable information that may be missed by other technologies. It contains approximately 850,000 empirically selected single nucleotide polymorphisms (SNPs) spanning the entire genome with enriched coverage for 3,262 genes of known cytogenetics relevance in both constitutional and cancer applications. Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Position, strand, and polymorphism data were obtained from Affymetrix and supplemented with links to corresponding dbSNP rsIDs based on a positional lookup into dbSNP. The Affy 6.0 Array is based on dbSNP build 127; the Affy 5.0 Array is based on dbSNP build 126. The Affy 500K Array is based on dbSNP build 125 and was translated from hg17 by UCSC using rsID lookup. In fewer than 2% of the cases, a dbSNP rsID was not present in dbSNP at the Affymetrix array position. Reference allele information was retrieved from the UCSC database based on dbSNP position and strand data. Illumina data were supplied as rsIDs and position based on dbSNP build 126. Strand, polymorphism and reference allele information was retrieved from the UCSC database based on rsID and position. The Illumina arrays are comprised of probes for 4 of the possible single-base substitutions: A/C, A/G, C/T and G/T. A/T and C/G probes will be available in future arrays. For Illumina Human1M-Duo, the position, strand, polymorphism and reference allele information was retrieved from the snp129 table of UCSC database if the marker ID can be found in dbSNP 129, otherwise the information is retrieved from the data provided by Illumina. For Illumina HumanOmni1-Quad, Human660W-Quad, and HumanCytoSNP-12, the position, strand, polymorphism and reference allele information was retrieved from the snp130 table of UCSC database if the marker ID can be found in dbSNP 130, otherwise the information is retrieved from the data provided by Illumina. Agilent's oligonucleotide CGH (Comparative Genomic Hybridization) platform enables the study of genome-wide DNA copy number changes at a high resolution. The CGH probes on Agilent aCGH microarrays are 60-mer oligonucleotides synthesized in situ using Agilent's inkjet SurePrint technology. The probes represented on the Agilent CGH microarrays have been selected using algorithms developed specifically for the CGH application, assuring optimal performance of these probes in detecting DNA copy number changes. The Agilent SurePrint G3 CGH+SNP microarrays are designed for high quality human DNA copy-number profiling combined with the simultaneous detection of copy-neutral aberrations, such as lack or loss of heterozygosity (LOH) and uniparental disomy (UPD). Identification of LOH/UPD is enabled by the presence of a set of SNP probes on the CGH+SNP microarrays resulting in ~5-10 Mb resolution for copy neutral LOH/UPD detection across the entire genome. The Agilent catalog CGH and CGH+SNP microarrays are printed on 1 in. x 3 in. glass slides and are available in several formats. The human catalog SurePrint G3 microarrays formats are the 1x1M (gene-biased or evenly tiled), 2x400K (CGH-only or CGH+SNP), 4x180K (CGH-only or CGH+SNP), and 8x60K. The legacy human catalog SurePrint HD microarrays are the 1x244K, 2x105K, and 4x44K. Non-SNP subtracks are colored in alternating shades of green and orange to highlight track boundaries. SNP subtracks are colored blue with SNP probes colored dark blue and CGH probes colored light blue. The track consists of the following subtracks: The Illumina 450k track was created using a custom track by Brooke Rhead ( &#98;&#114;&#104;e&#97;d&#64;&#103;&#109;&#97;&#105;l. &#99;o&#109;) and then converted into a bigBed. The Illumina 850k (EPIC) track was created using a few columns from the Infinium MethylationEPIC v1.0 B5 Manifest File (CSV Format) and was then converted into a bigBed. The Illumina CytoSNP-850K track was created by downloading the CytoSNP-850K v1.2 Manifest File (CSV Format) file and then converted into a bigBed file using the hg19 coordinates. Data Access The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API or downloaded from our Downloads site. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. References More information on Agilent Oligonucleotide Microarrays can be found on Agilent's website. Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17765-70. PMID: 15591353; PMC: PMC535426 More information on the Affymetrix arrays is available at these sites: Genome-Wide Human SNP Array 6.0. Genome-Wide Human SNP Array 5.0. Mapping 500K Array Set. More information on the Illumina arrays is available at these sites: Human1M-Duo Genotyping BeadChip. HumanOmni1-Quad v1 Genotyping BeadChip. Human660W-Quad v1 Genotyping BeadChip. HumanCytoSNP-12 v2 Genotyping BeadChip. Credits Thanks to Shane Giles, Peter Webb, and Anniek De Witte from Agilent Technologies, Venu Valmeekam from Affymetrix, and Luana Galver and Jennifer L. Stone from Illumina for providing these data. 
snpArrayCytoSnp850k CytoSNP 850k Illumina 850k CytoSNP Array Variation Affymetrix Arrays Affymetrix Genome-Wide Human SNP Array 6.0 and SV The SNP Array 6.0 includes more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNPs include the 482,000 SNPs from the 5.0 Array (unbiased selection). In addition, 424,000 new SNPs were chosen in the following areas: Tag SNPs SNPs from chromosomes X and Y Mitochondrial SNPs New SNPs added to dbSNP SNPs in recombination hotspots The structural variation copy number (SV) probes include 202,000 probes targeting 5,677 known CNV regions from the Toronto Database of Genomic Variants. The additional 744,000 probes are evenly spaced throughout the genome. Affymetrix Genome-Wide Human SNP Array 5.0 The SNP Array 5.0 is a single microarray featuring all single nucleotide polymorphisms (SNPs) from the original two-chip Mapping 500K Array Set, as well as 420,000 additional non-polymorphic probes that can measure other genetic differences, such as copy number variation. Affymetrix 500K (250K Nsp and 250K Sty) This annotation displays the SNPs available for genotyping with the GeneChip Human Mapping 500K Array Set from Affymetrix. It is comprised of two arrays: Nsp and Sty, which contain approximately 262,000 and 238,000 SNPs, respectively. Affymetrix CytoScan HD The CytoScan High-Density (HD) Array provides whole-genome coverage with enriched coverage of all constitutional and cancer-related genes on a single array. The complete CytoScan array includes: Genome build hg19 Total number of copy-number markers 2,696,550 Total number of non-polymorphic markers 1,953,246 Number of SNP markers 743,304 SNP markers with &gt;99% genotype accuracy 749,157 Autosomal markers 2,491,915 Pseudoautosomal markers 4,624 Intragenic markers 1,410,535 Intergenic markers 1,286,015 Probes are colored green for CNV probesets and purple for SNP probesets. Some SNP probesets are also considered informative for CNV detection. Agilent Arrays Non-SNP subtracks are colored in alternating shades of green and orange to highlight track boundaries. SNP subtracks are colored blue with SNP probes colored dark blue and CGH probes colored light blue. The track consists of the following subtracks: The arrays listed in this track are probes from the Agilent Catalog Oligonucleotide Microarrays. The following table summarizes the different Agilent arrays: Description AMADID Samples per Slide Biological Features Median Probe Spacing Gene-biased SNPs SurePrint G3 Human CGH Microarray 1x1M 021529 1 969,033 2.1 kb Yes 0 SurePrint G3 Human High-Resolution Microarray 1x1M 023642 1 989,214 2.6 kb No (evenly tiled) 0 SurePrint G3 Human CGH+SNP Microarray 2x400K 028081 2 411,434 7 kb Yes 65,000 SurePrint G3 Human CGH Microarray 2x400K 021850 2 415,914 5.3 kb Yes 0 SurePrint G3 Human Cancer CGH+SNP Microarray 4x180K 030587 4 172,595 25 kb Yes (cancer genes) 65,000 SurePrint G3 Human CGH+SNP Microarray 4x180K 029830 4 172,595 25 kb No (ISCA regions) 65,000 SurePrint G3 Human CGH Microarray 4x180K 022060 4 174,675 13 kb Yes 0 SurePrint G3 Human CGH Microarray 8x60K 021924 8 59,175 41 kb Yes 0 SurePrint HD Human CGH Microarray 1x244K 014693 1 238,331 8.9 kb Yes 0 SurePrint HD Human CGH Microarray 2x105K 014698 2 100,034 22 kb Yes 0 SurePrint HD Human CGH Microarray 4x44K 014950 4 43,143 43 kb Yes 0 GenetiSure Cyto CGH+SNP 4x180K 085591 GenetiSure Cyto CGH 4x180K 085589 GenetiSure Cyto CGH 8x60k 085590 Illumina Arrays Illumina HumanHap650Y This annotation displays the SNPs available for genotyping with Illumina's HumanHap650Y Genotyping BeadChip. The HumanHap650Y contains over 650,000 markers, extending the HumanHap550 by adding 100,000 additional Yoruba-specific tag SNPs. On average, there is 1 SNP every 5.3 kb, 6.2 kb and 5.4 kb across the genome in the CEU, CHB+JPT and YRI populations, respectively. The HumanHap650Y was derived from release 21 of the International HapMap Project. Illumina HumanHap550 This annotation displays the SNPs available for genotyping with Illumina's HumanHap550 Genotyping BeadChip. The HumanHap550 contains over 550,000 markers, the majority of which are tag SNPs derived from release 20 of the International HapMap Project. In addition, approximately 7800 non-synonymous SNPs, a higher density of tag SNPs in the MHC region, over 150 mitochondrial SNPs and over 4000 SNPs from regions with copy number polymorphism were included. In the CEU population, an r-squared threshold of 0.8 was used for common SNPs in genes, within 10 kb of genes or in evolutionarily conserved regions. For all other regions, an r-squared threshold of 0.7 was used. On average, there is 1 SNP every 5.5 kb, 6.5 kb and 6.2 kb across the genome in the CEU, CHB+JPT and YRI populations, respectively. Illumina HumanHap300 This annotation displays the SNPs available for genotyping with Illumina's HumanHap300 Genotyping BeadChip. The HumanHap300 contains over 317,000 tagSNP markers derived from Phase I of the International HapMap Project. In addition, approximately 7300 non-synonymous SNPs and a higher density of tag SNPs in the MHC region were included. On average, there is 1 SNP every 9 kb across the genome and median spacing is 5 kb. Illumina Human1M-Duo This annotation displays the SNPs available for genotyping with Illumina's Human1M-Duo Genotyping BeadChip. The Human1M-Duo contains more than 1,100,000 tagSNP markers and a set of ~60,000 additional CNV-targeted markers. The median spacing is 1.5kb (mean - 2.4 kb). Illumina HumanOmni1-Quad v1 The HumanOmni1-Quad BeadChip consists of 1,140,419 markers in a 4-sample format. The whole-genome content provides high genomic coverage rates of 93%, 92%, and 76% at r2 &gt; 0.8 for the CEU, CHB+JPT, and YRI populations, respectively. High density markers with a median spacing of 1.2 kb ensure the highest level of resolution for CNV and breakpoint identification. The content has been derived from the 1,000 Genomes Project, all three HapMap phases, and recently published studies, including new coding variants identified by the 1000 Genomes Project and markers chosen in high-value regions of the genome: ABO blood typing SNPs, cSNPs, disease-associated SNPs, eSNPs, SNPs in mRNA splice sites, ADME genes, AIMs, HLA complexes, indels, introns, MHC regions, miRNA binding sites, mitochondrial DNA, PAR, promoter regions, and Y-chromosome. Illumina Human660W-Quad v1 The Human660W-Quad BeadChip consists of 657,366 markers in a 4-sample format. The Human660W-Quad BeadChip provides 87%, 85%, and 56% coverage of CEU, CHB+JPT, and YRI populations at r2 &gt; 0.8. For CNV and cytogenetic analysis, the dense backbone content is combined with an additional ~100,000 markers that target observed common CNVs. HumanCytoSNP-12 v2.1 The 301,232 markers on the HumanCytoSNP-12 represents a complete 12-sample panel of genome-wide SNPs for a uniform backbone and additional markers targeting all regions of known cytogenetic importance. Backbone markers provide genome-wide marker spacing of 10kb. This is supplemented with dense coverage (at 6 kb spacing average) of ~250 genomic regions commonly studied in cytogenetics labs and targeted coverage in ~400 additional genes, subtelomeric regions, pericentromeric regions, and sex chromosomes. An efficiency-optimized tagging strategy provides a panel for GWAS (70% coverage in CEU at r2 &gt; 0.8) in the highest throughput and most cost-effective whole-genome DNA Analysis BeadChip. Illumina Global Diversity Array The Global Diversity Array-8 v1.0 BeadChip includes coverage of the ACMG 59-gene clinical research variants and multi-ethnic, genome-wide content. The GDA is the commercial version of the array chosen by the All of Us Research Program and is designed to capture a wider range of the world's populationsthan traditional microarrays. Illumina 450k and 850k Methylation Arrays With the Infinium MethylationEPIC BeadChip Kit, researchers can interrogate over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution. Multiple samples, including FFPE, can be analyzed in parallel to deliver high-throughput power while minimizing the cost per sample. These tracks show positions being measured on the Illumina 450k and 850k (EPIC) microarray tracks. More information about the arrays can be found on the Infinium MethylationEPIC Kit website. Illumina CytoSNP 850K Probe Array The Infinium CytoSNP-850K v1.2 BeadChip provides comprehensive coverage of cytogenetically relevant genes on a proven platform, helping researchers find valuable information that may be missed by other technologies. It contains approximately 850,000 empirically selected single nucleotide polymorphisms (SNPs) spanning the entire genome with enriched coverage for 3,262 genes of known cytogenetics relevance in both constitutional and cancer applications. Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand. Methods Position, strand, and polymorphism data were obtained from Affymetrix and supplemented with links to corresponding dbSNP rsIDs based on a positional lookup into dbSNP. The Affy 6.0 Array is based on dbSNP build 127; the Affy 5.0 Array is based on dbSNP build 126. The Affy 500K Array is based on dbSNP build 125 and was translated from hg17 by UCSC using rsID lookup. In fewer than 2% of the cases, a dbSNP rsID was not present in dbSNP at the Affymetrix array position. Reference allele information was retrieved from the UCSC database based on dbSNP position and strand data. Illumina data were supplied as rsIDs and position based on dbSNP build 126. Strand, polymorphism and reference allele information was retrieved from the UCSC database based on rsID and position. The Illumina arrays are comprised of probes for 4 of the possible single-base substitutions: A/C, A/G, C/T and G/T. A/T and C/G probes will be available in future arrays. For Illumina Human1M-Duo, the position, strand, polymorphism and reference allele information was retrieved from the snp129 table of UCSC database if the marker ID can be found in dbSNP 129, otherwise the information is retrieved from the data provided by Illumina. For Illumina HumanOmni1-Quad, Human660W-Quad, and HumanCytoSNP-12, the position, strand, polymorphism and reference allele information was retrieved from the snp130 table of UCSC database if the marker ID can be found in dbSNP 130, otherwise the information is retrieved from the data provided by Illumina. Agilent's oligonucleotide CGH (Comparative Genomic Hybridization) platform enables the study of genome-wide DNA copy number changes at a high resolution. The CGH probes on Agilent aCGH microarrays are 60-mer oligonucleotides synthesized in situ using Agilent's inkjet SurePrint technology. The probes represented on the Agilent CGH microarrays have been selected using algorithms developed specifically for the CGH application, assuring optimal performance of these probes in detecting DNA copy number changes. The Agilent SurePrint G3 CGH+SNP microarrays are designed for high quality human DNA copy-number profiling combined with the simultaneous detection of copy-neutral aberrations, such as lack or loss of heterozygosity (LOH) and uniparental disomy (UPD). Identification of LOH/UPD is enabled by the presence of a set of SNP probes on the CGH+SNP microarrays resulting in ~5-10 Mb resolution for copy neutral LOH/UPD detection across the entire genome. The Agilent catalog CGH and CGH+SNP microarrays are printed on 1 in. x 3 in. glass slides and are available in several formats. The human catalog SurePrint G3 microarrays formats are the 1x1M (gene-biased or evenly tiled), 2x400K (CGH-only or CGH+SNP), 4x180K (CGH-only or CGH+SNP), and 8x60K. The legacy human catalog SurePrint HD microarrays are the 1x244K, 2x105K, and 4x44K. Non-SNP subtracks are colored in alternating shades of green and orange to highlight track boundaries. SNP subtracks are colored blue with SNP probes colored dark blue and CGH probes colored light blue. The track consists of the following subtracks: The Illumina 450k track was created using a custom track by Brooke Rhead ( &#98;&#114;&#104;e&#97;d&#64;&#103;&#109;&#97;&#105;l. &#99;o&#109;) and then converted into a bigBed. The Illumina 850k (EPIC) track was created using a few columns from the Infinium MethylationEPIC v1.0 B5 Manifest File (CSV Format) and was then converted into a bigBed. The Illumina CytoSNP-850K track was created by downloading the CytoSNP-850K v1.2 Manifest File (CSV Format) file and then converted into a bigBed file using the hg19 coordinates. Data Access The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API or downloaded from our Downloads site. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. References More information on Agilent Oligonucleotide Microarrays can be found on Agilent's website. Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17765-70. PMID: 15591353; PMC: PMC535426 More information on the Affymetrix arrays is available at these sites: Genome-Wide Human SNP Array 6.0. Genome-Wide Human SNP Array 5.0. Mapping 500K Array Set. More information on the Illumina arrays is available at these sites: Human1M-Duo Genotyping BeadChip. HumanOmni1-Quad v1 Genotyping BeadChip. Human660W-Quad v1 Genotyping BeadChip. HumanCytoSNP-12 v2 Genotyping BeadChip. Credits Thanks to Shane Giles, Peter Webb, and Anniek De Witte from Agilent Technologies, Venu Valmeekam from Affymetrix, and Luana Galver and Jennifer L. Stone from Illumina for providing these data. 
snpArrayIllumina850k Illumina 850k Illumina 850k EPIC Methylation Array Variation 
snpArrayIllumina450k Illumina 450k Illumina 450k Methylation Array Variation 
snpArrayIlluminaGDA Illumina GDA Illumina GDA Variation 
snpArrayIlluminaHumanOmni1_Quad Illumina Omni1-Q Illumina Human Omni1-Quad Variation 
snpArrayIlluminaHuman660W_Quad Illumina 660W-Q Illumina Human 660W-Quad Variation 
snpArrayIlluminaHumanCytoSNP_12 Illumina Cyto-12 Illumina Human CytoSNP-12 Variation 
snpArrayIllumina1M Illumina 1M-Duo Illumina Human1M-Duo Variation 
snpArrayIllumina300 Illumina 300 Illumina Human Hap 300v3 Variation 
snpArrayIllumina650 Illumina 650 Illumina Human Hap 650v3 Variation 
snpArrayIllumina550 Illumina 550 Illumina Human Hap 550v3 Variation 
agilentCgh4x44k Ag CGH 4x44k Agilent SurePrint HD Human CGH Microarray 4x44K AMADID 014950 Variation 
agilentCgh2x105k Ag CGH 2x105k Agilent SurePrint HD Human CGH Microarray 2x105K AMADID 014698 Variation 
agilentCgh1x244k Ag CGH 1x244k Agilent SurePrint HD Human CGH Microarray 1x244K AMADID 014693 Variation 
agilentCgh8x60k Ag CGH 8x60k Agilent SurePrint G3 Human CGH Microarray 8x60K AMADID 021924 Variation 
agilentCgh4x180k Ag CGH 4x180k Agilent SurePrint G3 Human CGH Microarray 4x180K AMADID 022060 Variation 
agilentCghSnp4x180k Ag SNP 4x180k Agilent SurePrint G3 Human CGH+SNP Microarray 4x180K AMADID 029830 Variation 
agilentCghSnpCancer4x180k Ag Can 4x180k Agilent SurePrint G3 Human CGH+SNP Cancer Microarray 4x180K AMADID 030587 Variation 
agilentCgh2x400k Ag CGH 2x400k Agilent SurePrint G3 Human CGH Microarray 2x400K AMADID 021850 Variation 
agilentCghSnp2x400k Ag SNP 2x400k Agilent SurePrint G3 Human CGH+SNP Microarray 2x400K AMADID 028081 Variation 
agilentHrd1x1m Ag HRD 1x1m Agilent SurePrint G3 Human High-Resolution Microarray 1x1M AMADID 023642 Variation 
agilentCgh1x1m Ag CGH 1x1m Agilent SurePrint G3 Human CGH Microarray 1x1M AMADID 021529 Variation 
affyCytoScan Affy CytoScan Affymetrix Cytoscan CNV and SNP Array Probeset Variation 
snpArrayAffy250Sty Affy 250KSty Affymetrix GeneChip Human Mapping 250K Sty Variation 
snpArrayAffy250Nsp Affy 250KNsp Affymetrix GeneChip Human Mapping 250K Nsp Variation 
snpArrayAffy5 Affy SNP 5.0 Affymetrix SNP 5.0 Variation 
snpArrayAffy6SV Affy SNP 6.0 SV Affymetrix SNP 6.0 Structural Variation Variation 
snpArrayAffy6 Affy SNP 6.0 Affymetrix SNP 6.0 Variation 
gold Assembly Assembly from Fragments Mapping and Sequencing Description This track shows the finished assembly of the human genome. This assembly merges contigs from overlapping drafts and finished clones into longer sequence contigs. The sequence contigs are ordered and oriented when possible by mRNA, EST, paired plasmid reads (from the SNP Consortium) and BAC end sequence pairs. In dense mode, this track depicts the path through the draft and finished clones (aka the golden path) used to create the assembled sequence. Clone boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist in the path, spaces are shown between the gold and brown blocks. If the relative order and orientation of the contigs between the two blocks is known, a line is drawn to bridge the blocks. Clone Type Key: F - Finished (HTGS phase 3) O - Other sequence (typically means no HTG keyword) P - Pre draft W - WGS contig See also NCBI discussion of genome assembly procedures. Credits The Feb. 2009 human reference sequence (GRCh37) was produced by the Genome Reference Consortium. 
augustusGene AUGUSTUS AUGUSTUS ab initio gene predictions v3.1 Genes and Gene Predictions Description This track shows ab initio predictions from the program AUGUSTUS (version 3.1). The predictions are based on the genome sequence alone. For more information on the different gene tracks, see our Genes FAQ. Methods Statistical signal models were built for splice sites, branch-point patterns, translation start sites, and the poly-A signal. Furthermore, models were built for the sequence content of protein-coding and non-coding regions as well as for the length distributions of different exon and intron types. Detailed descriptions of most of these different models can be found in Mario Stanke's dissertation. This track shows the most likely gene structure according to a Semi-Markov Conditional Random Field model. Alternative splicing transcripts were obtained with a sampling algorithm (--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2 --minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2). The different models used by Augustus were trained on a number of different species-specific gene sets, which included 1000-2000 training gene structures. The --species option allows one to choose the species used for training the models. Different training species were used for the --species option when generating these predictions for different groups of assemblies. Assembly Group Training Species Fish zebrafish Birds chicken Human and all other vertebrates human Nematodes caenorhabditis Drosophila fly A. mellifera honeybee1 A. gambiae culex S. cerevisiae saccharomyces This table describes which training species was used for a particular group of assemblies. When available, the closest related training species was used. Credits Thanks to the Stanke lab for providing the AUGUSTUS program. The training for the chicken version was done by Stefanie K&ouml;nig and the training for the human and zebrafish versions was done by Mario Stanke. References Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25. PMID: 14534192 
avada Avada Variants Avada Variants extracted from full text publications Phenotype and Literature Description This track shows the genomic positions of variants in the AVADA database. AVADA is a database of variants built by a machine learning software that analyzes full text research articles to find the gene mentions in the text that look like they are most relevant for monogenic (non-cancer) genetic diagnosis, finds variant descriptions and uses the genes to map the variants to the genome. For details see the AVADA paper. As the data is automatically extracted from full-text publications, it includes some false positives. In the original study, out of 200 randomly selected articles, only 99 were considered relevant after manual curation. However, this share is very high compared to the Genomenom track. Ideally, the track is used in combination with variants found in human patients, to find relevant literature, or with Genome Browser tracks of variant databases that curated a single study for each variant, like our tracks for HGMD or LOVD. Display Conventions and Configuration Genomic locations of a variants are labeled with the variant description in the original text. This is not a normalized HGVS string, but the original text as the authors of the study described it. The Pubmed ID, gene and transcript for each variant are shown on the variant's details page, as well as the PubMed title, authors, and abstract. Mouse over the variants to show the gene, variant, first author, year, and title. The data has been lifted from hg19 to hg38. Data access The raw data can be explored interactively with the Table Browser, for download, intersection or correlations with other tracks. To join this track with others based on the chromosome positions, use the Data Integrator. For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called avada.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/avada.bb -chrom=chr21 -start=0 -end=100000000 stdout For automated access, this track like all others, is also available via our API. However, for bulk processing in pipelines, downloading the data and/or using bigBed files as described above is usually faster. Methods The AVADA VCF file was reformatted at UCSC to the bigBed format. The program that performs the conversion is available on Github. The paper reference information was added from MEDLINE and is used Courtesy of the U.S. National Library of Medicine, according to its Terms and Conditions. Credits Thanks to Gill Bejerano and Johannes Birgmeier for making the data available. References Johannes Birgmeier, Cole A. Deisseroth, Laura E. Hayward, Luisa M. T. Galhardo, Andrew P. Tierno, Karthik A. Jagadeesh, Peter D. Stenson, David N. Cooper, Jonathan A. Bernstein, Maximilian Haeussler, and Gill Bejerano. AVADA: Towards Automated Pathogenic Variant Evidence Retrieval Directly from the Full Text Literature. . Genetics in Medicine. 2019. PMID: 31467448 
varsInPubs Variants in Papers Genetic Variants mentioned in scientific publications Phenotype and Literature Description The tracks that are listed here contain genetic variants and links to scientific publications that mention them. The Mastermind track was created by Genomenom, a company that analyzes fulltext of publications with their own proprietary software with an unknown false positive rate. The AVADA track was created in the Bejerano lab at Stanford by J. Birgmeier also on fulltext papers, using sophisticated machine learning methods and was evaluated to have a false positive rate of around 50% in their study. The PubTator rsIDs track was created using PubTator 3 data. For additional information please click on the hyperlink of the respective track above. Display conventions By default, each variant is labeled with the nucleotide change. Hover over the feature to see more information, explained on the track details page of the particular track or when clicking onto the feature. Credits For data provenance, access and descriptions, please click the documentation via the link above. 
bacEndPairs BAC End Pairs BAC End Pairs Mapping and Sequencing Description Bacterial artificial chromosomes (BACs) are a key part of many large-scale sequencing projects. A BAC typically consists of 25 - 350 kb of DNA. During the early phase of a sequencing project, it is common to sequence a single read (approximately 500 bases) off each end of a large number of BACs. Later on in the project, these BAC end reads can be mapped to the genome sequence. This track shows these mappings in cases where both ends could be mapped. These BAC end pairs can be useful for validating the assembly over relatively long ranges. In some cases, the BACs are useful biological reagents. This track can also be used for determining which BAC contains a given gene, useful information for certain wet lab experiments. A valid pair of BAC end sequences must be at least 25 kb but no more than 350 kb away from each other. The orientation of the first BAC end sequence must be &quot;+&quot; and the orientation of the second BAC end sequence must be &quot;-&quot;. The scoring scheme used for this annotation assigns 1000 to an alignment when the BAC end pair aligns to only one location in the genome (after filtering). When a BAC end pair or clone aligns to multiple locations, the score is calculated as 1500/(number of alignments). Methods BAC end sequences are placed on the assembled sequence using Jim Kent's blat program. Credits Additional information about the clone, including how it can be obtained, may be found at the NCBI Clone Registry. To view the registry entry for a specific clone, open the details page for the clone and click on its name at the top of the page. Some BAC library clones (RPCI-11, and others) can be ordered from BACPAC Genomics, RIKEN, or from Thermofisher and possibly other companies. 
bayesDel BayesDel BayesDel - deleteriousness meta-score Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
predictionScoresSuper Prediction Scores Human Prediction Scores Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
noAFmutT No MaxAF Mutation: T BayesDel v1 Score (without MaxAF): Mutation is T Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
noAFmutG No MaxAF Mutation: G BayesDel v1 Score (without MaxAF): Mutation is G Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
noAFmutC No MaxAF Mutation: C BayesDel v1 Score (without MaxAF): Mutation is C Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
noAFmutA No MaxAF Mutation: A BayesDel v1 Score (without MaxAF): Mutation is A Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
MaxAFmutT MaxAF Mutation: T BayesDel v1 Score (MaxAF): Mutation is T Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
MaxAFmutG MaxAF Mutation: G BayesDel v1 Score (MaxAF): Mutation is G Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
MaxAFmutC MaxAF Mutation: C BayesDel v1 Score (MaxAF): Mutation is C Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
maxAFmutA MaxAF Mutation: A BayesDel v1 Score (MaxAF): Mutation is A Phenotype and Literature Description The "Prediction Scores" container track includes subtracks showing the results of prediction scores. BayesDel BayesDel is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. MaxAF stands for maximum allele frequency. The old ACMG (American College of Medical Genetics and Genomics) rules utilize allele frequency to classify variants, so the "BayesDel without MaxAF" tracks were created to avoid double-dipping. However, new ACMG rules will not include allele frequency, so it is okay to use the "BayesDel with MaxAF" for variant classification in the future. For gene discovery research, it is better to use BayesDel with MaxAF. For gene discovery research, a universal cutoff value (0.0692655 with MaxAF, -0.0570105 without MaxAF) was obtained by maximizing sensitivity and specificity in classifying ClinVar variants; Version 1 (build date 2017-08-24). For clinical variant classification, Bayesdel thresholds have been calculated for a variant to reach various levels of evidence; please refer to Pejaver et al. 2022 for general application of these scores in clinical applications. Display Conventions and Configuration BayesDel There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated. For SNVs, at each genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, (e.g. A to A) is always set to zero. Note: There are cases in which a genomic position will have one value missing. When using this track, zoom in until you can see every base pair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Data Access BayesDel scores are available at the BayesDel website. Methods BayesDel data was converted from the files provided on the BayesDel_170824 Database. The number 170824 is the date (2017-08-24) the scores were created. Both sets of BayesDel scores are available in this database, one integrated MaxAF (named BayesDel_170824_addAF) and one without (named BayesDel_170824_noAF). Data conversion was performed using custom Python scripts. Credits Thanks to the BayesDel team for providing precomputed data, and to Tiana Pereira, Christopher Lee, Gerardo Perez, and Anna Benet-Pages of the Genome Browser team. References Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat. 2017 Mar;38(3):243-251. PMID: 27995669; PMC: PMC5299048 Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS et al. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. PMID: 36413997; PMC: PMC9748256 Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D. REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification. Sci Rep. 2019 Sep 4;9(1):12752. PMID: 31484976; PMC: PMC6726608 
wgEncodeBuOrchid BU ORChID ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius lab) Mapping and Sequencing Description This set of tracks displays the predicted hydroxyl radical cleavage intensity on naked DNA for each nucleotide in the genome. Because the hydroxyl radical cleavage intensity is proportional to the solvent accessible surface area of the deoxyribose hydrogen atoms (Balasubramanian et al., 1998), these tracks represent a structural profile of the DNA in the genome. For additional details, please visit the Tullius lab website. Display Conventions and Configuration These tracks may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page. For more information, click the Graph configuration help link. In the full and pack display modes, positive intensity values are shown in red and negative intensity values are shown in tan. In the squish and dense display modes, intensity is represented in grayscale (the darker the shading, the higher the intensity). To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Recommended Track Settings Because the ORChID tracks are single nucleotide resolution and different viewing scales result in different levels of smoothing, the default data view scale parameter (auto-scale to data view) is not always ideal for visualizing the variability in the data. As a result, we recommend the following data view scale parameters for different scales: Viewing scale Data view scaling Vertical viewing range:&nbsp;min Vertical viewing range:&nbsp;max less than 10 Kb auto-scale to data view NA NA 10 Kb use vertical viewing range setting 0 0.75 100 Kb use vertical viewing range setting 0.1 0.5 1 Mb or larger use vertical viewing range setting 0.2 0.4 Note that these settings are only recommendations and may not be ideal for all viewing circumstances. Methods Hydroxyl radical cleavage intensity predictions were performed using an in-house sliding tetramer window (STW) algorithm on the hg19 version of the human genome. This algorithm draws data from the &middot;OH Radical Cleavage Intensity Database (ORChID), which contains more than 150 experimentally determined cleavage patterns. The ORChID Version 1 predictions are performed on the + strand of the DNA sequence. These predictions are fairly accurate, with a Pearson coefficient of 0.88 between the predicted and experimentally determined cleavage intensities. For ORChID Version 2, two predictions are performed, one on the + strand and the other on the - strand, and then the average of the predicted cleavage intensity for nucleotides in close proximity across the minor groove is presented. For more details on the hydroxyl radical cleavage method, see below for reference (Greenbaum et al. 2007). The hydroxyl radical cleavage pattern for any DNA sequence can be predicted, either using a web-based server or via a Perl script. For details please see the ORChID website. Verification The STW algorithm has been cross-validated by removing each test sequence from the training set and performing a prediction. The mean correlation coefficient (between predicted and experimental cleavage patterns) from this study was 0.88. Credits These data were generated at Boston University and NHGRI. Contact: Tom Tullius These data are the result of the combined efforts of Bo Pang (now at MIT), Jason Greenbaum (now at The La Jolla Institute for Allergy and Immunology), Steve Parker and Elliott Margulies at The National Human Genome Research Institute, National Institutes of Health, and Eric Bishop and Tom Tullius at Boston University. References Balasubramanian B, Pogozelski WK, and Tullius TD. DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. USA. 1998 Aug 18;95(17):9738-43. Greenbaum JA, Pang B, and Tullius TD. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res. 2007 Jun;17(6):947-53. Price MA, and Tullius TD. Using the Hydroxyl Radical to Probe DNA Structure. Meth. Enzymol. 1992;212:194-219. Tullius TD. Probing DNA Structure with Hydroxyl Radicals. Curr Protoc Nucleic Acid Chem. 2002 Feb;Chapter 6:Unit 6.7. Review. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeBuOrchidSignalView Signal ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius lab) Mapping and Sequencing 
wgEncodeBuOrchidV2 ORChID V2 Orchid ENCODE Jan 2011 Freeze 2011-01-03 2010-01-24 2010-10-24 wgEncodeEH000001 1 Tullius BU hg18 wgEncodeBuOrchidV2 Signal ORChID DNA Cleavage Tullius Tullius - Boston University Signal OH Radical Cleavage Intensity Database (ORChID) V2 from ENCODE/Boston Univ Mapping and Sequencing 
wgEncodeBuOrchidV1 ORChID V1 Orchid ENCODE Jan 2011 Freeze 2011-01-03 2010-01-24 2010-10-24 wgEncodeEH000001 1 Tullius BU hg18 wgEncodeBuOrchidV1 Signal ORChID DNA Cleavage Tullius Tullius - Boston University Signal OH Radical Cleavage Intensity Database (ORChID) V1 from ENCODE/Boston Univ Mapping and Sequencing 
cadd CADD 1.6 CADD 1.6 Score for all possible single-basepair mutations (zoom in for scores) Phenotype and Literature Description This track collection shows Combined Annotation Dependent Depletion scores. CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion variants in the human genome. Some mutation annotations tend to exploit a single information type (e.g., phastCons or phyloP for conservation) and/or are restricted in scope (e.g., to missense changes). Thus, a broadly applicable metric that objectively weights and integrates diverse information is needed. Combined Annotation Dependent Depletion (CADD) is a framework that integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS. A CADD score represents a ranking not a prediction, and no threshold is defined for a specific purpose. Higher scores are more likely to be deleterious: Scores are 10 * -log of the rank so that variants with scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in the human genome. We recommend thinking carefully about what threshold is appropriate for your application. Display Conventions and Configuration There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0. PHRED-scaled scores are normalized to all potential &#126;9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw score in the top 1%, regardless of the details of the annotation set, model parameters, etc. The four single-nucleotide mutation tracks have a default viewing range of score 10 to 50. As explained in the paragraph above, that results in slightly less than 10% of the data displayed. The deletion and insertion tracks have a default filter of 10-100, because they display discrete items and not graphical data. Single nucleotide variants (SNV): For SNVs, at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, e.g., A to A, is always set to zero. When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Averages of scores are not useful for any application of CADD. Insertions and deletions: Scores are also shown on mouseover for a set of insertions and deletions. On hg38, the set has been obtained from gnomAD3. On hg19, the set of indels has been obtained from various sources (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest is not in the track, you will need to use CADD's online scoring tool to obtain them. Data access CADD scores are freely available for all non-commercial applications from the CADD website. For commercial applications, see the license instructions there. The CADD data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd/a.bw stdout or bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd/ins.bb stdout Methods Data were converted from the files provided on the CADD Downloads website, provided by the Kircher lab, using custom Python scripts, documented in our makeDoc files. Credits Thanks to the CADD development team for providing precomputed data as simple tab-separated files. References Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Mar;46(3):310-5. PMID: 24487276; PMC: PMC3992975 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. PMID: 30371827; PMC: PMC6323892 
caddSuper CADD 1.6 CADD 1.6 Score for all single-basepair mutations and selected insertions/deletions Phenotype and Literature Description This track collection shows Combined Annotation Dependent Depletion scores. CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion variants in the human genome. Some mutation annotations tend to exploit a single information type (e.g., phastCons or phyloP for conservation) and/or are restricted in scope (e.g., to missense changes). Thus, a broadly applicable metric that objectively weights and integrates diverse information is needed. Combined Annotation Dependent Depletion (CADD) is a framework that integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS. A CADD score represents a ranking not a prediction, and no threshold is defined for a specific purpose. Higher scores are more likely to be deleterious: Scores are 10 * -log of the rank so that variants with scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in the human genome. We recommend thinking carefully about what threshold is appropriate for your application. Display Conventions and Configuration There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0. PHRED-scaled scores are normalized to all potential &#126;9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw score in the top 1%, regardless of the details of the annotation set, model parameters, etc. The four single-nucleotide mutation tracks have a default viewing range of score 10 to 50. As explained in the paragraph above, that results in slightly less than 10% of the data displayed. The deletion and insertion tracks have a default filter of 10-100, because they display discrete items and not graphical data. Single nucleotide variants (SNV): For SNVs, at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, e.g., A to A, is always set to zero. When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Averages of scores are not useful for any application of CADD. Insertions and deletions: Scores are also shown on mouseover for a set of insertions and deletions. On hg38, the set has been obtained from gnomAD3. On hg19, the set of indels has been obtained from various sources (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest is not in the track, you will need to use CADD's online scoring tool to obtain them. Data access CADD scores are freely available for all non-commercial applications from the CADD website. For commercial applications, see the license instructions there. The CADD data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd/a.bw stdout or bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd/ins.bb stdout Methods Data were converted from the files provided on the CADD Downloads website, provided by the Kircher lab, using custom Python scripts, documented in our makeDoc files. Credits Thanks to the CADD development team for providing precomputed data as simple tab-separated files. References Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Mar;46(3):310-5. PMID: 24487276; PMC: PMC3992975 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. PMID: 30371827; PMC: PMC6323892 
caddT Mutation: T CADD 1.6 Score: Mutation is T Phenotype and Literature 
caddG Mutation: G CADD 1.6 Score: Mutation is G Phenotype and Literature 
caddC Mutation: C CADD 1.6 Score: Mutation is C Phenotype and Literature 
caddA Mutation: A CADD 1.6 Score: Mutation is A Phenotype and Literature 
caddDel CADD 1.6 Del CADD 1.6 Score: Deletions - label is length of deletion Phenotype and Literature Description This track collection shows Combined Annotation Dependent Depletion scores. CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion variants in the human genome. Some mutation annotations tend to exploit a single information type (e.g., phastCons or phyloP for conservation) and/or are restricted in scope (e.g., to missense changes). Thus, a broadly applicable metric that objectively weights and integrates diverse information is needed. Combined Annotation Dependent Depletion (CADD) is a framework that integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS. A CADD score represents a ranking not a prediction, and no threshold is defined for a specific purpose. Higher scores are more likely to be deleterious: Scores are 10 * -log of the rank so that variants with scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in the human genome. We recommend thinking carefully about what threshold is appropriate for your application. Display Conventions and Configuration There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0. PHRED-scaled scores are normalized to all potential &#126;9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw score in the top 1%, regardless of the details of the annotation set, model parameters, etc. The four single-nucleotide mutation tracks have a default viewing range of score 10 to 50. As explained in the paragraph above, that results in slightly less than 10% of the data displayed. The deletion and insertion tracks have a default filter of 10-100, because they display discrete items and not graphical data. Single nucleotide variants (SNV): For SNVs, at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, e.g., A to A, is always set to zero. When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Averages of scores are not useful for any application of CADD. Insertions and deletions: Scores are also shown on mouseover for a set of insertions and deletions. On hg38, the set has been obtained from gnomAD3. On hg19, the set of indels has been obtained from various sources (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest is not in the track, you will need to use CADD's online scoring tool to obtain them. Data access CADD scores are freely available for all non-commercial applications from the CADD website. For commercial applications, see the license instructions there. The CADD data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd/a.bw stdout or bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd/ins.bb stdout Methods Data were converted from the files provided on the CADD Downloads website, provided by the Kircher lab, using custom Python scripts, documented in our makeDoc files. Credits Thanks to the CADD development team for providing precomputed data as simple tab-separated files. References Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Mar;46(3):310-5. PMID: 24487276; PMC: PMC3992975 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. PMID: 30371827; PMC: PMC6323892 
caddIns CADD 1.6 Ins CADD 1.6 Score: Insertions - label is length of insertion Phenotype and Literature Description This track collection shows Combined Annotation Dependent Depletion scores. CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion variants in the human genome. Some mutation annotations tend to exploit a single information type (e.g., phastCons or phyloP for conservation) and/or are restricted in scope (e.g., to missense changes). Thus, a broadly applicable metric that objectively weights and integrates diverse information is needed. Combined Annotation Dependent Depletion (CADD) is a framework that integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS. A CADD score represents a ranking not a prediction, and no threshold is defined for a specific purpose. Higher scores are more likely to be deleterious: Scores are 10 * -log of the rank so that variants with scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in the human genome. We recommend thinking carefully about what threshold is appropriate for your application. Display Conventions and Configuration There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0. PHRED-scaled scores are normalized to all potential &#126;9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw score in the top 1%, regardless of the details of the annotation set, model parameters, etc. The four single-nucleotide mutation tracks have a default viewing range of score 10 to 50. As explained in the paragraph above, that results in slightly less than 10% of the data displayed. The deletion and insertion tracks have a default filter of 10-100, because they display discrete items and not graphical data. Single nucleotide variants (SNV): For SNVs, at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, e.g., A to A, is always set to zero. When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Averages of scores are not useful for any application of CADD. Insertions and deletions: Scores are also shown on mouseover for a set of insertions and deletions. On hg38, the set has been obtained from gnomAD3. On hg19, the set of indels has been obtained from various sources (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest is not in the track, you will need to use CADD's online scoring tool to obtain them. Data access CADD scores are freely available for all non-commercial applications from the CADD website. For commercial applications, see the license instructions there. The CADD data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd/a.bw stdout or bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd/ins.bb stdout Methods Data were converted from the files provided on the CADD Downloads website, provided by the Kircher lab, using custom Python scripts, documented in our makeDoc files. Credits Thanks to the CADD development team for providing precomputed data as simple tab-separated files. References Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Mar;46(3):310-5. PMID: 24487276; PMC: PMC3992975 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. PMID: 30371827; PMC: PMC6323892 
cadd1_7 CADD 1.7 CADD 1.7 Score for all possible single-basepair mutations (zoom in for scores) Phenotype and Literature Description This track collection shows Combined Annotation Dependent Depletion scores. CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion variants in the human genome. Some mutation annotations tend to exploit a single information type (e.g., phastCons or phyloP for conservation) and/or are restricted in scope (e.g., to missense changes). Thus, a broadly applicable metric that objectively weights and integrates diverse information is needed. Combined Annotation Dependent Depletion (CADD) is a framework that integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS. A CADD score represents a ranking not a prediction, and no threshold is defined for a specific purpose. Higher scores are more likely to be deleterious: Scores are 10 * -log of the rank so that variants with scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in the human genome. We recommend thinking carefully about what threshold is appropriate for your application. Display Conventions and Configuration There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0. PHRED-scaled scores are normalized to all potential &#126;9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw score in the top 1%, regardless of the details of the annotation set, model parameters, etc. The four single-nucleotide mutation tracks have a default viewing range of score 10 to 50. As explained in the paragraph above, that results in slightly less than 10% of the data displayed. The deletion and insertion tracks have a default filter of 10-100, because they display discrete items and not graphical data. Single nucleotide variants (SNV): For SNVs, at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, e.g., A to A, is always set to zero. When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Averages of scores are not useful for any application of CADD. Insertions and deletions: Scores are also shown on mouseover for a set of insertions and deletions. On hg38, the set has been obtained from gnomAD3. On hg19, the set of indels has been obtained from various sources (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest is not in the track, you will need to use CADD's online scoring tool to obtain them. Methods In CADD version 1.7, new features have been added to improve CADD scores for certain variant effects, boosting the overall performance of CADD and bringing new developments to the community. CADD v1.7 integrates annotations from recent efforts to assess variant effects, along with new conservation and mutation scores. CADD v1.7 supports only the major chromosomes of the hg38/GRCh38 reference genome (chromosomes 1-22, X, and Y) and may be the last version to support the hg19/GRCh37 human reference genome. This version includes scores derived from Evolutionary Scale Modeling (ESM) for assessing variants in protein-coding regions, along with scores from a convolutional neural network (CNN) trained on open chromatin sequences, used as a proxy for regulatory regions in the genome. The previously included conservation scores have been updated with data from the Zoonomia project. New annotations have also been added for 3' Untranslated Regions (3' UTRs), along with models of genome-wide mutational rates. The gene and transcript models have been updated by advancing from Ensembl version 95 to version 110, and the Ensembl Variant Effect Predictor (VEP) has been upgraded accordingly. The models in CADD v1.7 have been trained similarly to the version 1.6 release. The logistic regression uses an L2 penalty with C = 1, and training was completed after thirteen L-BFGS iterations using the sklearn library The new models exhibit a high degree of similarity to the previous release, with a Spearman correlation of 0.946 for CADD scores calculated for 100,000 randomly selected variants between CADD GRCh38-v1.6 and CADD GRCh38-v1.7. The v1.7 models perform comparably to earlier versions in distinguishing known pathogenic variants (ClinVar) from common variants (gnomAD) across the genome. Improvements in CADD v1.7 are particularly evident when focusing on specific variant categories, such as missense or 3' UTR variants, where the latest release includes updated annotations. More information can be found at the CADD site and the Schubach et al., Nucleic Acids Res, 2024 publication. Data were converted from the files provided on the CADD Downloads website, provided by the Kircher lab, using custom Python scripts, documented in our makeDoc files. Data access CADD scores are freely available for all non-commercial applications from the CADD website. For commercial applications, see the license instructions there. The CADD data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd1.7/a.bw stdout or bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd1.7/ins.bb stdout Credits Thanks to the CADD development team for providing precomputed data as simple tab-separated files. References Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Mar;46(3):310-5. PMID: 24487276; PMC: PMC3992975 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. PMID: 30371827; PMC: PMC6323892 Schubach M, Maass T, Nazaretyan L, R&#246;ner S, Kircher M. CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions. Nucleic Acids Res. 2024 Jan 5;52(D1):D1143-D1154. PMID: 38183205; PMC: PMC10767851 
caddSuper1_7 CADD 1.7 CADD 1.7 Score for all single-basepair mutations and selected insertions/deletions Phenotype and Literature Description This track collection shows Combined Annotation Dependent Depletion scores. CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion variants in the human genome. Some mutation annotations tend to exploit a single information type (e.g., phastCons or phyloP for conservation) and/or are restricted in scope (e.g., to missense changes). Thus, a broadly applicable metric that objectively weights and integrates diverse information is needed. Combined Annotation Dependent Depletion (CADD) is a framework that integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS. A CADD score represents a ranking not a prediction, and no threshold is defined for a specific purpose. Higher scores are more likely to be deleterious: Scores are 10 * -log of the rank so that variants with scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in the human genome. We recommend thinking carefully about what threshold is appropriate for your application. Display Conventions and Configuration There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0. PHRED-scaled scores are normalized to all potential &#126;9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw score in the top 1%, regardless of the details of the annotation set, model parameters, etc. The four single-nucleotide mutation tracks have a default viewing range of score 10 to 50. As explained in the paragraph above, that results in slightly less than 10% of the data displayed. The deletion and insertion tracks have a default filter of 10-100, because they display discrete items and not graphical data. Single nucleotide variants (SNV): For SNVs, at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, e.g., A to A, is always set to zero. When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Averages of scores are not useful for any application of CADD. Insertions and deletions: Scores are also shown on mouseover for a set of insertions and deletions. On hg38, the set has been obtained from gnomAD3. On hg19, the set of indels has been obtained from various sources (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest is not in the track, you will need to use CADD's online scoring tool to obtain them. Methods In CADD version 1.7, new features have been added to improve CADD scores for certain variant effects, boosting the overall performance of CADD and bringing new developments to the community. CADD v1.7 integrates annotations from recent efforts to assess variant effects, along with new conservation and mutation scores. CADD v1.7 supports only the major chromosomes of the hg38/GRCh38 reference genome (chromosomes 1-22, X, and Y) and may be the last version to support the hg19/GRCh37 human reference genome. This version includes scores derived from Evolutionary Scale Modeling (ESM) for assessing variants in protein-coding regions, along with scores from a convolutional neural network (CNN) trained on open chromatin sequences, used as a proxy for regulatory regions in the genome. The previously included conservation scores have been updated with data from the Zoonomia project. New annotations have also been added for 3' Untranslated Regions (3' UTRs), along with models of genome-wide mutational rates. The gene and transcript models have been updated by advancing from Ensembl version 95 to version 110, and the Ensembl Variant Effect Predictor (VEP) has been upgraded accordingly. The models in CADD v1.7 have been trained similarly to the version 1.6 release. The logistic regression uses an L2 penalty with C = 1, and training was completed after thirteen L-BFGS iterations using the sklearn library The new models exhibit a high degree of similarity to the previous release, with a Spearman correlation of 0.946 for CADD scores calculated for 100,000 randomly selected variants between CADD GRCh38-v1.6 and CADD GRCh38-v1.7. The v1.7 models perform comparably to earlier versions in distinguishing known pathogenic variants (ClinVar) from common variants (gnomAD) across the genome. Improvements in CADD v1.7 are particularly evident when focusing on specific variant categories, such as missense or 3' UTR variants, where the latest release includes updated annotations. More information can be found at the CADD site and the Schubach et al., Nucleic Acids Res, 2024 publication. Data were converted from the files provided on the CADD Downloads website, provided by the Kircher lab, using custom Python scripts, documented in our makeDoc files. Data access CADD scores are freely available for all non-commercial applications from the CADD website. For commercial applications, see the license instructions there. The CADD data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd1.7/a.bw stdout or bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd1.7/ins.bb stdout Credits Thanks to the CADD development team for providing precomputed data as simple tab-separated files. References Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Mar;46(3):310-5. PMID: 24487276; PMC: PMC3992975 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. PMID: 30371827; PMC: PMC6323892 Schubach M, Maass T, Nazaretyan L, R&#246;ner S, Kircher M. CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions. Nucleic Acids Res. 2024 Jan 5;52(D1):D1143-D1154. PMID: 38183205; PMC: PMC10767851 
cadd1_7_T Mutation: T CADD 1.7 Score: Mutation is T Phenotype and Literature 
cadd1_7_G Mutation: G CADD 1.7 Score: Mutation is G Phenotype and Literature 
cadd1_7_C Mutation: C CADD 1.7 Score: Mutation is C Phenotype and Literature 
cadd1_7_A Mutation: A CADD 1.7 Score: Mutation is A Phenotype and Literature 
cadd1_7_Del CADD 1.7 Del CADD 1.7 Score: Deletions - label is length of deletion Phenotype and Literature Description This track collection shows Combined Annotation Dependent Depletion scores. CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion variants in the human genome. Some mutation annotations tend to exploit a single information type (e.g., phastCons or phyloP for conservation) and/or are restricted in scope (e.g., to missense changes). Thus, a broadly applicable metric that objectively weights and integrates diverse information is needed. Combined Annotation Dependent Depletion (CADD) is a framework that integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS. A CADD score represents a ranking not a prediction, and no threshold is defined for a specific purpose. Higher scores are more likely to be deleterious: Scores are 10 * -log of the rank so that variants with scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in the human genome. We recommend thinking carefully about what threshold is appropriate for your application. Display Conventions and Configuration There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0. PHRED-scaled scores are normalized to all potential &#126;9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw score in the top 1%, regardless of the details of the annotation set, model parameters, etc. The four single-nucleotide mutation tracks have a default viewing range of score 10 to 50. As explained in the paragraph above, that results in slightly less than 10% of the data displayed. The deletion and insertion tracks have a default filter of 10-100, because they display discrete items and not graphical data. Single nucleotide variants (SNV): For SNVs, at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, e.g., A to A, is always set to zero. When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Averages of scores are not useful for any application of CADD. Insertions and deletions: Scores are also shown on mouseover for a set of insertions and deletions. On hg38, the set has been obtained from gnomAD3. On hg19, the set of indels has been obtained from various sources (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest is not in the track, you will need to use CADD's online scoring tool to obtain them. Methods In CADD version 1.7, new features have been added to improve CADD scores for certain variant effects, boosting the overall performance of CADD and bringing new developments to the community. CADD v1.7 integrates annotations from recent efforts to assess variant effects, along with new conservation and mutation scores. CADD v1.7 supports only the major chromosomes of the hg38/GRCh38 reference genome (chromosomes 1-22, X, and Y) and may be the last version to support the hg19/GRCh37 human reference genome. This version includes scores derived from Evolutionary Scale Modeling (ESM) for assessing variants in protein-coding regions, along with scores from a convolutional neural network (CNN) trained on open chromatin sequences, used as a proxy for regulatory regions in the genome. The previously included conservation scores have been updated with data from the Zoonomia project. New annotations have also been added for 3' Untranslated Regions (3' UTRs), along with models of genome-wide mutational rates. The gene and transcript models have been updated by advancing from Ensembl version 95 to version 110, and the Ensembl Variant Effect Predictor (VEP) has been upgraded accordingly. The models in CADD v1.7 have been trained similarly to the version 1.6 release. The logistic regression uses an L2 penalty with C = 1, and training was completed after thirteen L-BFGS iterations using the sklearn library The new models exhibit a high degree of similarity to the previous release, with a Spearman correlation of 0.946 for CADD scores calculated for 100,000 randomly selected variants between CADD GRCh38-v1.6 and CADD GRCh38-v1.7. The v1.7 models perform comparably to earlier versions in distinguishing known pathogenic variants (ClinVar) from common variants (gnomAD) across the genome. Improvements in CADD v1.7 are particularly evident when focusing on specific variant categories, such as missense or 3' UTR variants, where the latest release includes updated annotations. More information can be found at the CADD site and the Schubach et al., Nucleic Acids Res, 2024 publication. Data were converted from the files provided on the CADD Downloads website, provided by the Kircher lab, using custom Python scripts, documented in our makeDoc files. Data access CADD scores are freely available for all non-commercial applications from the CADD website. For commercial applications, see the license instructions there. The CADD data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd1.7/a.bw stdout or bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd1.7/ins.bb stdout Credits Thanks to the CADD development team for providing precomputed data as simple tab-separated files. References Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Mar;46(3):310-5. PMID: 24487276; PMC: PMC3992975 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. PMID: 30371827; PMC: PMC6323892 Schubach M, Maass T, Nazaretyan L, R&#246;ner S, Kircher M. CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions. Nucleic Acids Res. 2024 Jan 5;52(D1):D1143-D1154. PMID: 38183205; PMC: PMC10767851 
cadd1_7_Ins CADD 1.7 Ins CADD 1.7 Score: Insertions - label is length of insertion Phenotype and Literature Description This track collection shows Combined Annotation Dependent Depletion scores. CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion variants in the human genome. Some mutation annotations tend to exploit a single information type (e.g., phastCons or phyloP for conservation) and/or are restricted in scope (e.g., to missense changes). Thus, a broadly applicable metric that objectively weights and integrates diverse information is needed. Combined Annotation Dependent Depletion (CADD) is a framework that integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS. A CADD score represents a ranking not a prediction, and no threshold is defined for a specific purpose. Higher scores are more likely to be deleterious: Scores are 10 * -log of the rank so that variants with scores above 20 are predicted to be among the 1.0% most deleterious possible substitutions in the human genome. We recommend thinking carefully about what threshold is appropriate for your application. Display Conventions and Configuration There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0. PHRED-scaled scores are normalized to all potential &#126;9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw score in the top 1%, regardless of the details of the annotation set, model parameters, etc. The four single-nucleotide mutation tracks have a default viewing range of score 10 to 50. As explained in the paragraph above, that results in slightly less than 10% of the data displayed. The deletion and insertion tracks have a default filter of 10-100, because they display discrete items and not graphical data. Single nucleotide variants (SNV): For SNVs, at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, e.g., A to A, is always set to zero. When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and instead of an actual score, the tooltip text will show the average score of all nucleotides under the cursor. This is indicated by the prefix &quot;~&quot; in the mouseover. Averages of scores are not useful for any application of CADD. Insertions and deletions: Scores are also shown on mouseover for a set of insertions and deletions. On hg38, the set has been obtained from gnomAD3. On hg19, the set of indels has been obtained from various sources (gnomAD2, ExAC, 1000 Genomes, ESP). If your insertion or deleletion of interest is not in the track, you will need to use CADD's online scoring tool to obtain them. Methods In CADD version 1.7, new features have been added to improve CADD scores for certain variant effects, boosting the overall performance of CADD and bringing new developments to the community. CADD v1.7 integrates annotations from recent efforts to assess variant effects, along with new conservation and mutation scores. CADD v1.7 supports only the major chromosomes of the hg38/GRCh38 reference genome (chromosomes 1-22, X, and Y) and may be the last version to support the hg19/GRCh37 human reference genome. This version includes scores derived from Evolutionary Scale Modeling (ESM) for assessing variants in protein-coding regions, along with scores from a convolutional neural network (CNN) trained on open chromatin sequences, used as a proxy for regulatory regions in the genome. The previously included conservation scores have been updated with data from the Zoonomia project. New annotations have also been added for 3' Untranslated Regions (3' UTRs), along with models of genome-wide mutational rates. The gene and transcript models have been updated by advancing from Ensembl version 95 to version 110, and the Ensembl Variant Effect Predictor (VEP) has been upgraded accordingly. The models in CADD v1.7 have been trained similarly to the version 1.6 release. The logistic regression uses an L2 penalty with C = 1, and training was completed after thirteen L-BFGS iterations using the sklearn library The new models exhibit a high degree of similarity to the previous release, with a Spearman correlation of 0.946 for CADD scores calculated for 100,000 randomly selected variants between CADD GRCh38-v1.6 and CADD GRCh38-v1.7. The v1.7 models perform comparably to earlier versions in distinguishing known pathogenic variants (ClinVar) from common variants (gnomAD) across the genome. Improvements in CADD v1.7 are particularly evident when focusing on specific variant categories, such as missense or 3' UTR variants, where the latest release includes updated annotations. More information can be found at the CADD site and the Schubach et al., Nucleic Acids Res, 2024 publication. Data were converted from the files provided on the CADD Downloads website, provided by the Kircher lab, using custom Python scripts, documented in our makeDoc files. Data access CADD scores are freely available for all non-commercial applications from the CADD website. For commercial applications, see the license instructions there. The CADD data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server. The files for this track are called a.bw, c.bw, g.bw, t.bw, ins.bb and del.bb. Individual regions or the whole genome annotation can be obtained using our tools bigWigToWig or bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd1.7/a.bw stdout or bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/cadd1.7/ins.bb stdout Credits Thanks to the CADD development team for providing precomputed data as simple tab-separated files. References Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Mar;46(3):310-5. PMID: 24487276; PMC: PMC3992975 Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. PMID: 30371827; PMC: PMC6323892 Schubach M, Maass T, Nazaretyan L, R&#246;ner S, Kircher M. CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions. Nucleic Acids Res. 2024 Jan 5;52(D1):D1143-D1154. PMID: 38183205; PMC: PMC10767851 
ntOoaHaplo Cand. Gene Flow Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans Neandertal Assembly and Analysis Description This track shows 13 regions of the human genome in which there is considerably more haplotype diversity among non-African genomes than within African genomes. A prediction of Neandertal-to-modern human gene flow is that these deeply divergent haplotypes which exist only in non-African populations entered the human gene pool from Neandertals. Of the 12 candidate gene flow regions with tag SNP data, there are 10 regions in which Neandertals match the deep haplotype clade unique to non-Africans (out of Africa, OOA) instead of the cosmopolitan haplotype clade shared by Africans and non-Africans (cosmopolitan, COS). The table below was copied from Table 5, &quot;Non-African haplotypes match Neandertal at an unexpected rate&quot;, from Green et al.: RegionGenomic SizeST AverageFrequencyin OOAAMDMANDN QualitativeAssessment chr1:168,110,001-168,220,000110,0002.96.3%51010OOA chr1:223,760,001-223,910,000150,0002.86.3%1400OOA chr4:171,180,001-171,280,000100,0001.95.2%1200OOA chr5:28,950,001-29,070,000120,0003.83.1%161660OOA chr6:66,160,001-66,260,000100,0005.728.1%6600OOA chr9:32,940,001-33,040,000100,0002.84.2%71400OOA chr10:4,820,001-4,920,000100,0002.69.4%9500OOA chr10:38,000,001-38,160,000160,0003.58.3%5920OOA chr10:69,630,001-69,740,000110,0004.219.8%2201OOA chr15:45,250,001-45,350,000100,0002.51.1%5610OOA chr17:35,500,001-35,600,000100,0002.9(no tags)n/an/an/an/an/a chr20:20,030,001-20,140,000110,0005.164.6%00105COS chr22:30,690,001-30,820,000130,0003.54.2%0252COS ST = estimated ratio of OOA/African gene tree depth. Average Frequency in OOA = average (across tag SNPs in the region) of the population frequency in the 48 OOA individuals of the OOA-only allele for each tag SNP. AM = Neandertal has ancestral allele and matches OOA-specific clade. DM = Neandertal has derived allele and matches OOA-specific clade. AN = Neandertal has ancestral allele and does not match OOA-specific clade. DN = Neandertal has derived allele and does not match OOA-specific clade. Display Conventions and Configuration A region is colored green if its qualitative assessment is OOA, blue if COS, and gray if unknown (no tag SNPs in region). Methods Green et al. used 1,263,750 Perlegen Class A SNPs, identified in 71 individuals of diverse ancestry (see Hinds et al.), to identify 13 candidate gene flow regions (Supplemental Online Materials Text 17). 24 individuals of European ancestry and 24 individuals of Han Chinese ancestry were used to represent the non-African population, and the remaining 23 individuals, of African American ancestry, were used to represent the African population. From the 1,263,750 Perlegen Class A SNPs, they identified 166 tag SNPs that separate (see below) 12 of the haplotype clades in non-Africans (OOA) from the cosmopolitan haplotype clades shared between Africans and non-Africans (COS) and for which they had data from the Neandertals. Of the 13 regions, one had no tag SNPs so could not be assessed, two were COS, and 10 were OOA (see final column Table 1). Overall, the Neandertals match the deep clade unique to non-Africans (OOA) at 133 of the 166 tag SNPs. They assessed the rate at which Neandertal matches each of these clades by further subdividing the 133 tag SNPs based on their ancestral or derived status in Neandertal and whether they matched the OOA-specific clade or not. Candidate regions were qualitatively assessed to be OOA matches for Neandertal when the proportion of tag SNPs matching the OOA-specific clade is much more than 50%. Credits This track was produced at UCSC using data generated by Ed Green. References Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. PMID: 20448178 Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR. Whole-genome patterns of common DNA variation in three human populations. Science. 2005 Feb 18;307(5712):1072-9. PMID: 15718463 
ccdsGene CCDS Consensus CDS Genes and Gene Predictions Description This track shows human genome high-confidence gene annotations from the Consensus Coding Sequence (CCDS) project. This project is a collaborative effort to identify a core set of human protein-coding regions that are consistently annotated and of high quality. The long-term goal is to support convergence towards a standard set of gene annotations on the human genome. Collaborators include: European Bioinformatics Institute (EBI) National Center for Biotechnology Information (NCBI) University of California, Santa Cruz (UCSC) Wellcome Trust Sanger Institute (WTSI) For more information on the different gene tracks, see our Genes FAQ. Methods CDS annotations of the human genome were obtained from two sources: NCBI RefSeq and a union of the gene annotations from Ensembl and Vega, collectively known as Hinxton. Genes with identical CDS genomic coordinates in both sets become CCDS candidates. The genes undergo a quality evaluation, which must be approved by all collaborators. The following criteria are currently used to assess each gene: an initiating ATG (Exception: a non-ATG translation start codon is annotated if it has sufficient experimental support), a valid stop codon, and no in-frame stop codons (Exception: selenoproteins, which contain a TGA codon that is known to be translated to a selenocysteine instead of functioning as a stop codon) ability to be translated from the genome reference sequence without frameshifts recognizable splicing sites no intersection with putative pseudogene predictions supporting transcripts and protein homology conservation evidence with other species A unique CCDS ID is assigned to the CCDS, which links together all gene annotations with the same CDS. CCDS gene annotations are under continuous review, with periodic updates to this track. Credits This track was produced at UCSC from data downloaded from the CCDS project web site. References Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161 Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul;19(7):1316-23. PMID: 19498102; PMC: PMC2704439 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
eioJcviNAS CD34 DnaseI Eur. Inst. Oncology/J. C. Venter Inst. Nuclease Accessible Sites Regulation Description Genes in metazoa are controlled by a complex array of cis-regulatory elements that include core and distal promoters, enhancers, insulators, silencers, etc. (Levine and Tjian, 2003). In living cells, functionally active cis-regulatory elements bear a unifying feature, which is a chromatin-based epigenetic signature known as nuclease hypersensitivity (Elgin, 1988; Gross and Garrard, 1988; Wolffe, 1998). This track presents the results of a collaboration between J. Craig Venter Institute (JCVI, Rockville MD) and the European Institute of Oncology (Milan, Italy) to isolate nuclease accessible sites (NAS) from primary human CD34+ hematopoietic stem and progenitor cells, and from CD34- cells, maturating myeloid cells generated by in vitro differentiation of CD34+ cells (Gargiulo et al., submitted). This effort made use of a method (originally developed at Sangamo BioSciences, Richmond, CA) to isolate such NAS from living cells using restriction enzymes (RE), leading to minimal, if any, contamination from bulk DNA. High throughput 454 sequencing was then used to generate NAS libraries in CD34+ and CD34- cells: this technology has been named "NA-Seq" (Gargiulo et al., submitted). Display Conventions The track annotates the location of NAS in the genome of human CD34+ and CD34- cells in the form of tags, generated by NA-Seq and obtained by merging NAS within 600 bp. Note that the method identifies a specific position in chromatin that is sensitive to nucleases, but does not map the boundaries of a regulatory element per se. A conservative estimate of element size would be the space occupied by one nucleosome, i.e., 180 - 200 bp surrounding the tag, although there is precedent in the literature for nuclease hypersensitive sites that span more than the length of one nucleosome (Turner, 2001; Wolffe, 1998; Boyle, 2008). Methods CD34+ cells (enriched in hematopoietic stem and progenitor cells) were prepared from healthy donors following guidelines established by the Ethics Committee of the European Institute of Oncology (IEO), Milan. Mobilization of CD34+ cells to the peripheral blood was stimulated by G-CSF treatment according to standard procedures. After mobilization, donors were subjected to leukaphereses, and &lt;10% of the sample was used in the experiment. CD34+ cells were purified using a magnetic positive selection procedure ("EASYSEP"; Stemcell, Vancouver, Canada). Purity of separation was evaluated by FACS after staining with an anti-Human CD34 FITC-conjugate antibody (Stemcell). Upon purification, the cell cycle status of the CD34+ cells was monitored by propidium iodide staining and FACS analysis. G0/G1 cells varied from approximately 90% to &gt;95% of the total cells. Cells were immediately used for the isolation of NAS using the nuclease hypersensitive site isolation protocol (Gargiulo et al., submitted). Verification The method was initially validated on human tissue culture cells by examining the colocalization of DNA fragments isolated from cells with experimentally determined nuclease hypersensitive sites in chromatin as mapped by indirect end-labeling and Southern blotting (Nedospasov and Georgiev, 1980; Wu, 1980). Nineteen out of nineteen randomly chosen clones from those libraries represented bona fide DNAse I hypersensitive sites in chromatin (Fyodor Urnov, unpublished results). These data confirmed that the method yields very high-content libraries of active cis-regulatory DNA elements, supporting its application to human CD34+ cells. In collaboration with scientists at the J. Craig Venter Institute and the European Institute of Oncology, libraries of NAS were prepared using this method in HT 454 sequencing from CD34+ and CD34- cells, and showed that 41 out of 51 randomly chosen clones - &gt;80% - coincided with DNAse I hypersensitive sites (Gargiulo et al., submitted). Credits The library of Nuclease Accessible sites (NAS) from human CD34+/CD34- cells was prepared and validated by Saverio Minucci and colleagues at the European Institute of Oncology. Sequencing was performed by Sam Levy and colleagues (J. Craig Venter Institute). This method was initially developed and validated by Fyodor Urnov, Alan Wolffe, and colleagues at Sangamo BioSciences, Inc. References Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008 Jan 25;132(2):311-22. PMID: 18243105; PMC: PMC2669738 Elgin SC. The formation and function of DNase I hypersensitive sites in the process of gene activation. J Biol Chem. 1988 Dec 25;263(36):19259-62. PMID: 3198625 Gargiulo G, Levy S, et al. A Global Analysis of chromatin Accessibility and Dynamics during Hematopoietic Differentiation. Submitted. Gross DS, Garrard WT. Nuclease hypersensitive sites in chromatin. Annu Rev Biochem. 1988;57:159-97. PMID: 3052270 Levine M, Tjian R. Transcription regulation and animal diversity. Nature. 2003 Jul 10;424(6945):147-51. PMID: 12853946 Nedospasov SA, Georgiev GP. Non-random cleavage of SV40 DNA in the compact minichromosome and free in solution by micrococcal nuclease. Biochem Biophys Res Commun. 1980 Jan 29;92(2):532-9. PMID: 6243943 Turner BM. Chromatin and Gene Regulation: Mechanisms in Epigenetics. Blackwell Science Ltd., Oxford. 2001. Wolffe AP. Chromatin: Structure and Function. Academic Press, San Diego, CA. 1998. Wu C. The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature. 1980 Aug 28;286(5776):854-60. PMID: 6774262 
eioJcviNASNeg EIO/JCVI CD34- NAS CD34- cells Nuclease Accessible Sites Regulation 
eioJcviNASPos EIO/JCVI CD34+ NAS CD34+ cells Nuclease Accessible Sites Regulation 
chm13LiftOver CHM13 alignments CHM13 (GCA_009914755.4) v1_nfLO liftOver alignments Comparative Genomics Description These tracks show the one-to-one v1_nfLO alignments of the GRCh37/hg19 to the T2T-CHM13 v2.0 assembly. Display Conventions The track displays boxes joined together by either single or double lines, with the boxes represent aligning regions, single lines indicating gaps that are largely due to a deletion in the CHM13 v2.0 assembly or an insertion in the GRCh37/hg19, and double lines representing more complex gaps that involve substantial sequence in both assembly. Methods Alignment and Chain Creation For the minimap2-based pipeline, the initial chain file was generated using nf-LO v1.5.1 with minimap2 v2.24 alignments. These chains were then split at all locations that contained unaligned segments greater than 1 kbp or gaps greater than 10 kbp. Split chain files were then converted to PAF format with extended CIGAR strings using chaintools (v0.1), and alignments between nonhomologous chromosomes were removed. The trim-paf operation of rustybam (v0.1.29) was next used to remove overlapping alignments in the query sequence, and then the target sequence, to create 1:1 alignments. PAF alignments were converted back to the chain format with paf2chain commit f68eeca, and finally, chaintools was used to generate the inverted chain file. Full commands with parameters used were: nextflow run main.nf --source GRCh37.fa --target chm13v2.0.fasta --outdir dir -profile local --aligner minimap2 python chaintools/src/split.py -c input.chain -o input-split.chain python chaintools/src/to_paf.py -c input-split.chain -t target.fa -q query.fa -o input-split.paf awk '$1==$6' input-split.paf | rb break-paf --max-size 10000 | rb trim-paf -r | rb invert | rb trim-paf -r | rb invert > out.paf paf2chain -i out.paf > out.chain python chaintools/src/invert.py -c out.chain -o out_inverted.chain The above process does not add chain ids or scores. The UCSC utilities chainMergeSort and chainScore are used to update the chains: chainMergeSort out.chain | chainScore stdin chm13v2.0.2bit hg19.2bit chm13v2.0-hg19.chain chainMergeSort out_inverted.chain | chainScore stdin hg19.2bit chm13v2.0.2bit hg19-chm13v2.0.chain Rustybam trim-paf uses dynamic programming and the CIGAR string to find an optimal splitting point between overlapping alignments in the query sequence. It starts its trimming with the largest overlap and then recursively trims smaller overlaps. Results were validated by using chaintools to confirm that there were no overlapping sequences with respect to both CHM13v2.0 and GRCh37 in the released chain file. In addition, trimmed alignments were visually inspected with SafFire to confirm their quality. Chains were swapped to make GRCh37/hg19 the target. Credits The v1_nflo chains were generated by Nae-Chyun Chen&lt;naechyun.chen@gmail.com&gt; and Mitchell Vollger&lt;mvollger@uw.edu&gt; References Nurk S, Koren S, Rhie A, Rautiainen M, et al. The complete sequence of a human genome. bioRxiv, 2021. 
cytoBand Chromosome Band Chromosome Bands Localized by FISH Mapping Clones Mapping and Sequencing Description The chromosome band track represents the approximate location of bands seen on Giemsa-stained chromosomes. Chromosomes are displayed in the browser with the short arm first. Cytologically identified bands on the chromosome are numbered outward from the centromere on the short (p) and long (q) arms. At low resolution, bands are classified using the nomenclature [chromosome][arm][band], where band is a single digit. Examples of bands on chromosome 3 include 3p2, 3p1, cen, 3q1, and 3q2. At a finer resolution, some of the bands are subdivided into sub-bands, adding a second digit to the band number, e.g. 3p26. This resolution produces about 500 bands. A final subdivision into a total of 862 sub-bands is made by adding a period and another digit to the band, resulting in 3p26.3, 3p26.2, etc. Methods Chromosome band information was downloaded from NCBI using the ideogram.gz file for the respective assembly. These data were then transformed into our visualization format. See our assembly creation documentation for the organism of interest to see the specific steps taken to transform these data. Band lengths are typically estimated based on FISH or other molecular markers interpreted via microscopy. For some of our older assemblies, greater than 10 years old, the tracks were created as detailed below and in Furey and Haussler, 2003. Barbara Trask, Vivian Cheung, Norma Nowak and others in the BAC Resource Consortium used fluorescent in-situ hybridization (FISH) to determine a cytogenetic location for large genomic clones on the chromosomes. The results from these experiments are the primary source of information used in estimating the chromosome band locations. For more information about the process, see the paper, Cheung, et al., 2001. and the accompanying web site, Human BAC Resource. BAC clone placements in the human sequence are determined at UCSC using a combination of full BAC clone sequence, BAC end sequence, and STS marker information. Credits We would like to thank all the labs that have contributed to this resource: Fred Hutchinson Cancer Research Center (FHCRC) National Cancer Institute (NCI) Roswell Park Cancer Institute (RPCI) The Wellcome Trust Sanger Institute (SC) Cedars-Sinai Medical Center (CSMC) Los Alamos National Laboratory (LANL) UC San Francisco Cancer Center (UCSF) References Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001 Feb 15;409(6822):953-8. PMID: 11237021 Furey TS, Haussler D. Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet. 2003 May 1;12(9):1037-44. PMID: 12700172 
cytoBandIdeo Chromosome Band (Ideogram) Chromosome Bands Localized by FISH Mapping Clones (for Ideogram) Mapping and Sequencing 
clinGenComp ClinGen ClinGen curation activities (Dosage Sensitivity and Gene-Disease Validity) Phenotype and Literature Description NOTE: These data are for research purposes only. While the ClinGen data are open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal medical questions. UCSC presents these data for use by qualified professionals, and even such professionals should use caution in interpreting the significance of information found here. No single data point should be taken at face value and such data should always be used in conjunction with as much corroborating data as possible. No treatment protocols should be developed or patient advice given on the basis of these data without careful consideration of all possible sources of information. No attempt to identify individual patients should be undertaken. No one is authorized to attempt to identify patients by any means. The Clinical Genome Resource (ClinGen) tracks display data generated from several key curation activities related to gene-disease validity, dosage sensitivity, and variant pathogenicity. ClinGen is a National Institute of Health (NIH)-funded initiative dedicated to identifying clinically relevant genes and variants for use in precision medicine and research. This is accomplished by harnessing the data from both research efforts and clinical genetic testing and using it to propel expert and machine-driven curation activities. ClinGen works closely with the National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM) which distributes part of this information through its ClinVar database. The available data tracks are: ClinGen Dosage Sensitivity Map -Haploinsufficiency (ClinGen Haploinsufficiency) and -Triplosensitivity (ClinGen Triplosensitivity) - Shows evidence supporting or refuting haploinsufficiency (loss) and triplosensitivity (gain) as mechanisms for disease at gene-level and larger genomic regions. ClinGen Gene-Disease Validity Classification (ClinGen Validity) - Provides a semi-qualitative measurement for the strength of evidence of a gene-disease relationship. Clingen CSPEC variant interpretation VCEP specifications - Identifies loci that have ClinGen criteria Specification (CSpec) information. This is used and applied by ClinGen Variant Curation Expert Panels (VCEPs) and biocurators in the classification of variants. A rating system is used to classify the evidence supporting or refuting dosage sensitivity for individual genes and regions, which takes in consideration the following criteria: number of causative variants reported, patterns of inheritance, consistency of phenotype, evidence from large-scale case-control studies, mutational mechanisms, data from public genome variation databases, and expert consensus opinion. The system is intended to be of a &quot;dynamic nature&quot;, with regions being reevaluated periodically to incorporate emerging evidence. The evidence collected is displayed within a publicly available database. Evidence that haploinsufficiency or triplosensitivity of a gene is associated with a specific phenotype will aid in the interpretive assessment of CNVs including that gene or genomic region. Similarly, a qualitative classification system is used to correlate the evidence of a gene-disease relationship: &quot;Definitive&quot;, &quot;Strong&quot;, &quot;Moderate&quot;, &quot;Limited&quot;, &quot;Animal Model Only&quot;, &quot;No Known Disease Relationship&quot;, &quot;Disputed&quot;, or &quot;Refuted&quot;. Display Conventions Haploinsufficiency/Triplosensitivity tracks Items are shaded according to dosage sensitivity type, red for haploinsufficiency score 3, blue for triplosensitivity score 3, and grey for other evidence scores or not yet evaluated). Mouseover on items shows the supporting evidence of dosage sensitivity. Tracks can be filtered according to the supporting evidence of dosage sensitivity. Dosage Scores are used to classify the evidence of the supporting dosage sensitivity map: 0 - no evidence available 1 - little evidence for dosage pathogenicity 2 - some evidence for dosage pathogenicity 3 - sufficient evidence for dosage pathogenicity 30 - gene associated with autosomal recessive phenotype 40 - dosage sensitivity unlikely For more information on the use of the scores see the ClinGen FAQs. Gene-Disease Validity track The gene-disease validity classifications are labeled with the disease entity and hovering over the features shows the associated gene. Items are color coded based on the strength of their classification as provided below: Color Classifications Definitive: The role of this gene in this particular disease has been repeatedly demonstrated and has been upheld over time Strong: The role of this gene in disease has been independently demonstrated typically in at least two separate studies, including both strong variant-level evidence in unrelated probands and compelling gene-level evidence from experimental data Moderate: There is moderate evidence to support a causal role for this gene in this disease, typically including both several probands with variants and moderate experimental data supporting the gene-disease assertion Limited: There is limited evidence to support a causal role for this gene in this disease, such as few probands with variants and limited experimental data supporting the gene-disease assertion Animal Model Only: There are no published human probands with variants but there is animal model data supporting the gene-disease assertion No Known Disease Relationship: Evidence for a causal role in disease has not been reported Disputed: Conflicting evidence disputing a role for this gene in this disease has arisen since the initial report identifying an association between the gene and disease Refuted: Evidence refuting the role of the gene in the specified disease has been reported and significantly outweighs any evidence supporting the role The version of the ClinGen Standard Operating Procedures (SOPs) that each gene-disease classification was performed with is provided as well. An older or newer SOP version does not necessarily mean the classification is any more or less valid but is provided for clarity. Each details page also contains a direct link to an evidence summary detailing the rationale behind the specific classification and information such as a breakdown of the semi-qualitative framework, relevant PubMed IDs, the type of data (Genetic vs Experimental Evidence), and a detailed summary. These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. ClinGen VCEP Specifications track Item names correspond to the VCEP loci, usually the gene symbol. Mouseovers display the disease with a link to the CSpec, the VCEP panel with a link to the ClinGen VCEP page, and the current expert panel status. Data Updates Our programs check every day if ClinGen has an updated data file, and if so, update the track with the latest file. Click the "Data Format" on this track documentation page to see when the track was last updated. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Data is also freely available on the ClinGen website (gene-disease curation methods) and FTP (dosage curations). Credits Thank you to ClinGen and NCBI, especially Erin Rooney Riggs, Christa Lese Martin, Tristan Nelson, May Flowers, Scott Goehringer, and Phillip Weller for technical coordination and consultation, and to Christopher Lee, Luis Nassar, and Anna Benet-Pages of the Genome Browser team. References Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL et al. ClinGen--the Clinical Genome Resource. N Engl J Med. 2015 Jun 4;372(23):2235-42. PMID: 26014595; PMC: PMC4474187 Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-24. PMID: 25741868; PMC: PMC4544753 Riggs ER, Church DM, Hanson K, Horner VL, Kaminsky EB, Kuhn RM, Wain KE, Williams ES, Aradhya S, Kearney HM et al. Towards an evidence-based process for the clinical interpretation of copy number variation. Clin Genet. 2012 May;81(5):403-12. PMID: 22097934; PMC: PMC5008023 Strande NT, Riggs ER, Buchanan AH, Ceyhan-Birsoy O, DiStefano M, Dwight SS, Goldstein J, Ghosh R, Seifert BA, Sneddon TP et al. Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource. Am J Hum Genet. 2017 Jun 1;100(6):895-906. PMID: 28552198; PMC: PMC5473734 
clinGenCspec ClinGen VCEP Specifications Clingen CSpec Variant Interpretation VCEP Specifications Phenotype and Literature 
clinGenGeneDisease ClinGen Validity ClinGen Gene-Disease Validity Classification Phenotype and Literature 
clinGenTriplo ClinGen Triplosensitivity ClinGen Dosage Sensitivity Map - Triplosensitivity Phenotype and Literature 
clinGenHaplo ClinGen Haploinsufficiency ClinGen Dosage Sensitivity Map - Haploinsufficiency Phenotype and Literature 
iscaComposite ClinGen CNVs Clinical Genome Resource (ClinGen) CNVs Phenotype and Literature The ClinGen CNVs track is no longer being updated. These data, along with updates, can be found in the ClinVar Copy Number Variants (ClinVar CNVs) track. See our news archive for more information. Description NOTE: These data are for research purposes only. While the ClinGen data are open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal medical questions. UCSC presents these data for use by qualified professionals, and even such professionals should use caution in interpreting the significance of information found here. No single data point should be taken at face value and such data should always be used in conjunction with as much corroborating data as possible. No treatment protocols should be developed or patient advice given on the basis of these data without careful consideration of all possible sources of information. No attempt to identify individual patients should be undertaken. No one is authorized to attempt to identify patients by any means. The Clinical Genome Resource (ClinGen) is a National Institutes of Health (NIH)-funded program dedicated to building a genomic knowledge base to improve patient care. This will be accomplished by harnessing the data from both research efforts and clinical genetic testing, and using it to propel expert and machine-driven curation activities. By facilitating collaboration within the genomics community, we will all better understand the relationship between genomic variation and human health. ClinGen will work closely with the National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM), which will distribute this information through its ClinVar database. The ClinGen dataset displays clinical microarray data submitted to dbGaP/dbVar at NCBI by ClinGen member laboratories (dbVar study nstd37), as well as clinical data reported in Kaminsky et al., 2011 (dbVar study ntsd101) (see reference below). This track shows copy number variants (CNVs) found in patients referred for genetic testing for indications such as intellectual disability, developmental delay, autism and congenital anomalies. Additionally, the ClinGen &quot;Curated Pathogenic&quot; and &quot;Curated Benign&quot; tracks represent genes/genomic regions reviewed for dosage sensitivity in an evidence-based manner by the ClinGen Structural Variation Working Group (dbVar study nstd45). The CNVs in this study have been reviewed for their clinical significance by the submitting ClinGen laboratory. Some of the deletions and duplications in the track have been reported as causative for a phenotype by the submitting clinical laboratory; this information was based on current knowledge at the time of submission. However, it should be noted that phenotype information is often vague and imprecise and should be used with caution. While all samples were submitted because of a phenotype in a patient, only 15% of patients had variants determined to be causal, and most patients will have additional variants that are not causal. CNVs are separated into subtracks and are labeled as: Pathogenic Uncertain: Likely Pathogenic Uncertain Uncertain: Likely Benign Benign The user should be aware that some of the data were submitted using a 3-class system, with the two &quot;Likely&quot; categories omitted. Two subtracks, &quot;Path Gain&quot; and &quot;Path Loss&quot;, are aggregate tracks showing graphically the accumulated level of gains and losses in the Pathogenic subtrack across the genome. Similarly, &quot;Benign Gain&quot; and &quot;Benign Loss&quot; show the accumulated level of gains and losses in the Benign subtrack. These tracks are collectively called &quot;Coverage&quot; tracks. Many samples have multiple variants, not all of which are causative of the phenotype. The CNVs in these samples have been decoupled, so it is not possible to connect multiple imbalances as coming from a single patient. It is therefore not possible to identify individuals via their genotype. Methods and Color Convention The samples were analyzed by arrays from patients referred for cytogenetic testing due to clinical phenotypes. Samples were analyzed with a probe spacing of 20-75 kb. The minimum CNV breakpoints are shown; if available, the maximum CNV breakpoints are provided in the details page, but are not shown graphically on the Browser image. Data were submitted to dbGaP at NCBI and thence decoupled as described into dbVar for unrestricted release. The entries are colored red for loss and blue for gain. The names of items use the ClinVar convention of appending "_inheritance" indicating the mechanism of inheritance, if known: "_pat, _mat, _dnovo, _unk" as paternal, maternal, de novo and unknown, respectively. Verification Most data were validated by the submitting laboratory using various methods, including FISH, G-banded karyotype, MLPA and qPCR. Credits Thank you to ClinGen and NCBI for technical coordination and consultation, and to the UCSC Genome Browser staff for engineering the track display. References Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010 May 14;86(5):749-64. PMID: 20466091; PMC: PMC2869000 Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST et al. An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities. Genet Med. 2011 Sep;13(9):777-84. PMID: 21844811; PMC: PMC3661946 
iscaViewTotal Coverage (Graphical) Clinical Genome Resource (ClinGen) CNVs Phenotype and Literature 
iscaPathLossCum Path Loss ClinGen CNVs: Pathogenic Loss Coverage Phenotype and Literature 
iscaPathGainCum Path Gain ClinGen CNVs: Pathogenic Gain Coverage Phenotype and Literature 
iscaBenignLossCum Benign Loss ClinGen CNVs: Benign Loss Coverage Phenotype and Literature 
iscaBenignGainCum Benign Gain ClinGen CNVs: Benign Gain Coverage Phenotype and Literature 
iscaViewDetail CNVs Clinical Genome Resource (ClinGen) CNVs Phenotype and Literature 
iscaUncertain Uncertain ClinGen CNVs: Uncertain Phenotype and Literature 
iscaPathogenic Pathogenic ClinGen CNVs: Pathogenic Phenotype and Literature 
iscaCuratedPathogenic Curated Path ClinGen CNVs: Curated Pathogenic Phenotype and Literature 
iscaLikelyPathogenic Uncert Path ClinGen CNVs: Uncertain: Likely Pathogenic Phenotype and Literature 
iscaLikelyBenign Uncert Ben ClinGen CNVs: Uncertain: Likely Benign Phenotype and Literature 
iscaBenign Benign ClinGen CNVs: Benign Phenotype and Literature 
iscaCuratedBenign Curated Ben ClinGen CNVs: Curated Benign Phenotype and Literature 
clinvar ClinVar Variants ClinVar Variants Phenotype and Literature Description NOTE: ClinVar is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the ClinVar database is open to all academic users, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. These tracks show the genomic positions of variants in the ClinVar database. ClinVar is a free, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. The ClinVar SNVs track displays substitutions and indels shorter than 50 bp and the ClinVar CNVs track displays copy number variants (CNVs) equal or larger than 50 bp. Until October 2017, all variants with the ClinVar types copy number gain/loss and DbVar "nsv" accessions were assigned in the CNV category. Because the ClinVar type no longer captures this information, any variation equal to or larger than 50 bp is now considered a CNV. The ClinVar Interpretations track displays the genomic positions of individual variant submissions and interpretations of the clinical significance and their relationship to disease in the ClinVar database. Note: The data in the track are obtained directly from ClinVar's FTP site. We display the data obtained from ClinVar as-is to avoid discrepancies between UCSC and NCBI. However, be aware that the ClinVar conventions are different from the VCF standard. Variants may be right-aligned or may contain additional context, e.g. for inserts. ExAC/gnomAD make available a converter to make ClinVar more comparable to VCF files. Display Conventions and Configuration Items can be filtered according to the size of the variant, variant type, clinical significance, allele origin, and molecular consequence, using the track Configure options. Each subtrack has separate display controls, as described here. Mouseover on the genomic locations of ClinVar variants shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant. ClinVar is an archive for assertions of clinical significance made by the submitters. The level of review supporting the assertion of clinical significance for the variation is reported as the review status. Stars (0 to 4) provide a graphical representation of the aggregate review status. Entries in the ClinVar CNVs track are colored by type of variant, among others: red for loss blue for gain purple for inversion orange for insertion A light-to-dark color gradient indicates the clinical significance of each variant, with the lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the CNV color code is described here. Entries in the ClinVar SNVs and ClinVar Interpretations tracks are colored by clinical significance: red for pathogenic dark blue for variant of uncertain significance green for benign dark grey for not provided light blue for conflicting The variants in the ClinVar Interpretations track are sorted by the variant classification of each submission: P: Pathogenic LP: Likely Pathogenic VUS: Variant of Unknown Significance LB: Likely Benign B: Benign OTH: Others The size of the bead represents the number of submissions at that genomic position. For track display clarity, these submission numbers are binned into three categories: Small-sized beads: 1-2 submissions Medium-sized beads: 3-7 submissions Large-sized beads: 8 or more submissions Hovering on the track items shows the genomic variations which start at that position and the number of individual submissions with that classification. The details page lists all rated submissions from ClinVar, with specific details to the interpretation of the clinical or functional significance of each variant in relation to a condition. Interpretation is at variant-level, not at case (or patient-specific) level. More information about using and understanding the ClinVar data can be found here. For the human genome version hg19: the hg19 genome released by UCSC in 2009 had a mitochondrial genome "chrM" that was not the same as the one later used for most databases like ClinVar. As a result, we added the official mitochondrial genome in 2020 as "chrMT" and all mitochondrial annotations of ClinVar and most other databases are shown on the mitochondrial genome called "chrMT". For full description of the issue of the mitochondrial genome in hg19, please see the README file on our download site. Data updates ClinVar publishes a new release on the first Thursday every month. This track is then updated automatically at most six days later. The exact date of our last update is shown when you click onto any variant. You can find the previous versions of the track organized by month on our downloads server in the archive directory. To display one of these previous versions, paste the URL to one of the older files into the custom track text input field under "My Data &gt; Custom Tracks". Data access The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can be accessed from scripts through our API, the track names are "clinVarMain and "clinVarCnv". For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called clinVarMain.bb and clinVarCnv.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/clinvarMain.bb -chrom=chr21 -start=0 -end=100000000 stdout Methods ClinVar files were reformatted at UCSC to the bigBed format. The data is updated every month, one week after the ClinVar release date. The program that performs the update is available on Github. Credits Thanks to NCBI for making the ClinVar data available on their FTP site as a tab-separated file. References Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016 Jan 4;44(D1):D862-8. PMID: 26582918; PMC: PMC4702865 Azzariti DR, Riggs ER, Niehaus A, Rodriguez LL, Ramos EM, Kattman B, Landrum MJ, Martin CL, Rehm HL. Points to consider for sharing variant-level information from clinical genetic testing with ClinVar. Cold Spring Harb Mol Case Stud. 2018 Feb;4(1). PMID: 29437798; PMC: PMC5793773 
clinvarSubLolly ClinVar interp ClinVar SNVs submitted interpretations and evidence Phenotype and Literature 
clinvarCnv ClinVar CNVs ClinVar Copy Number Variants >= 50bp Phenotype and Literature 
clinvarMain ClinVar SNVs ClinVar Short Variants < 50bp Phenotype and Literature 
coriellDelDup Coriell CNVs Coriell Cell Line Copy Number Variants Phenotype and Literature Description The Coriell Cell Line Copy Number Variants track displays copy-number variants (CNVs) in chromosomal aberration and inherited disorder cell lines in the NIGMS Human Genetic Cell Repository. The Repository, sponsored by the National Institute of General Medical Sciences, provides scientists around the world with resources for cell and genetic research. The samples include highly characterized cell lines and high quality DNA. NIGMS Repository samples represent a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. Approximately 1000 samples from the Chromosomal Aberrations and Heritable Diseases collections of the NIGMS Repository were genotyped on the Affymetrix Genome-Wide Human SNP 6.0 Array and analyzed for CNVs at the Coriell Institute for Medical Research. Genotyping data for many of these samples is available through dbGaP. The genotyped samples represent a diverse set of copy-number variants. The selection was weighted to over-sample commonly manifested types of aberrations. Karyotyping was performed on all NIGMS Repository cell lines that were submitted with reported chromosome abnormalities. When available, the ISCN description of the sample, based on G-banding and FISH analysis, is included in the phenotypic data. Karyotypes for these cells can be viewed in the online Repository catalog. Field definitions for an item description: CN State: Copy Number of the imbalance. Note that all CNVs with a copy number of 2 are colored neutral (black) and occur on the sex chromosomes, where a CN State of 2 should not be interpreted as normal, as it would be on an autosome. Cell Type: Type of cell culture; one of the following: B Lymphocyte, Fibroblast, Amniotic fluid-derived cell line or Chorionic villus-derived cell line. Description (Diagnosis): May be a medical diagnosis, such as "albinism" or a chromosomal phenotype, such as "translocation" or other description. ISCN nomenclature: A description of the chromosomal karyotype in formal ISCN nomenclature. CN State item coloring: CN State 0 == score 0 CN State 1 == score 100 CN State 2 == score 200 CN State 3 == score 300 CN State 4 == score 400 Use the score filter limits on the configuration page to select desired CN States. Credits We thank Dorit Berlin and Zhenya Tang of the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research for these data. References NCBI dbGaP: Genotyping NIGMS Chromosomal Aberration and Inherited Disorder Samples. NIGMS Human Genetic Cell Repository online catalog at the Coriell Institute for Medical Research. 
cosmicRegions COSMIC Regions Catalogue of Somatic Mutations in Cancer V82 Phenotype and Literature Description COSMIC, the "Catalogue Of Somatic Mutations In Cancer," is an online database of somatic mutations found in human cancer. Focused exclusively on non-inherited acquired mutations, COSMIC combines information from a range of sources, curating the described relationships between cancer phenotypes and gene (and genomic) mutations. These data are then made available in a number of ways including here in the UCSC genome browser, on the COSMIC website with custom analytical tools, or via the COSMIC sftp server. Publications using COSMIC as a data source may cite our reference below. Methods The data in COSMIC are curated from a number of high-quality sources and combined into a single resource. The sources include: Peer-reviewed journal articles CGP laboratories at the Sanger Institute, UK TCGA data portal The ICGC data portal IARC p53 database Information on known cancer genes, selected from the Cancer Gene Census is curated manually to maximize its descriptive content. The data was downloaded from the COSMIC sftp server. It was first converted to a bed file using the UCSC utility cosmicToBed, then converted into a bigBed file using the UCSC utility bedToBigBed. The bigBed file is used to generate the track. Display Dense - Indicate the positions where COSMIC mutations have been annotated in a single horizontal track. Squish - Indicate each mutation, in vertical pileups where appropriate, while minimizing screen space used. Pack - Indicate each mutation with COSMIC identifier (COSMnnnnn). Full - Show each mutation in detail, one per line, with COSM identifier (COSMnnnnn). Data Access Due to licensed material, we do not allow downloads or Table Browser access for the bigBed data. The raw data underlying this track can be explored and downloaded via the COSMIC website. The CosmicMutantExport.tsv.gz file was converted to a BED file using the cosmicToBed utility, and then converted into a bigBed file using the bedToBigBed utility. You can download these tools from the utilities directory. Contacts For further information on COSMIC, or for help with the information provided, please contact &#99;&#111;sm&#105;&#99;&#64;&#115;a&#110;g&#101;&#114;. &#97;&#99;. &#117;&#107;. References Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, Cole CG, Ward S, Dawson E, Ponting L et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 2017 Jan 4;45(D1):D777-D783. PMID: 27899578; PMC: PMC5210583 
crisprAllTargets CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome Genes and Gene Predictions Description This track shows the DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (PAM: NGG) over the entire human (hg19) genome. CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool CRISPOR. Sp-Cas9 usually cuts double-stranded DNA three or four base pairs 5' of the PAM site. Display Conventions and Configuration The track &quot;CRISPR Targets&quot; shows all potential -NGG target sites across the genome. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. Guides are colored to reflect both predicted specificity and efficiency. Specificity reflects the &quot;uniqueness&quot; of a 20mer sequence in the genome; the less unique a sequence is, the more likely it is to cleave other locations of the genome (off-target effects). Efficiency is the frequency of cleavage at the target site (on-target efficiency). Shades of gray stand for sites that are hard to target specifically, as the 20mer is not very unique in the genome: impossible to target: target site has at least one identical copy in the genome and was not scored hard to target: many similar sequences in the genome that alignment stopped, repeat? hard to target: target site was aligned but results in a low specificity score &lt;= 50 (see below) Colors highlight targets that are specific in the genome (MIT specificity &gt; 50) but have different predicted efficiencies: unable to calculate Doench/Fusi 2016 efficiency score low predicted cleavage: Doench/Fusi 2016 Efficiency percentile &lt;= 30 medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile &gt; 30 and &lt; 55 high predicted cleavage: Doench/Fusi 2016 Efficiency &gt; 55 Mouse-over a target site to show predicted specificity and efficiency scores: The MIT Specificity score summarizes all off-targets into a single number from 0-100. The higher the number, the fewer off-target effects are expected. We recommend guides with an MIT specificity &gt; 50. The efficiency score tries to predict if a guide leads to rather strong or weak cleavage. According to (Haeussler et al. 2016), the Doench 2016 Efficiency score should be used to select the guide with the highest cleavage efficiency when expressing guides from RNA PolIII Promoters such as U6. Scores are given as percentiles, e.g. &quot;70%&quot; means that 70% of mammalian guides have a score equal or lower than this guide. The raw score number is also shown in parentheses after the percentile. The Moreno-Mateos 2015 Efficiency score should be used instead of the Doench 2016 score when transcribing the guide in vitro with a T7 promoter, e.g. for injections in mouse, zebrafish or Xenopus embryos. The Moreno-Mateos score is given in percentiles and the raw value in parentheses, see the note above. Click onto features to show all scores and predicted off-targets with up to four mismatches. The Out-of-Frame score by Bae et al. 2014 is correlated with the probability that mutations induced by the guide RNA will disrupt the open reading frame. The authors recommend out-of-frame scores &gt; 66 to create knock-outs with a single guide efficiently. Off-target sites are sorted by the CFD (Cutting Frequency Determination) score (Doench et al. 2016). The higher the CFD score, the more likely there is off-target cleavage at that site. Off-targets with a CFD score &lt; 0.023 are not shown on this page, but are available when following the link to the external CRISPOR tool. When compared against experimentally validated off-targets by Haeussler et al. 2016, the large majority of predicted off-targets with CFD scores &lt; 0.023 were false-positives. For storage and performance reasons, on the level of individual off-targets, only CFD scores are available. Methods Relationship between predictions and experimental data Like most algorithms, the MIT specificity score is not always a perfect predictor of off-target effects. Despite low scores, many tested guides caused few and/or weak off-target cleavage when tested with whole-genome assays (Figure 2 from Haeussler et al. 2016), as shown below, and the published data contains few data points with high specificity scores. Overall though, the assays showed that the higher the specificity score, the lower the off-target effects. Similarly, efficiency scoring is not very accurate: guides with low scores can be efficient and vice versa. As a general rule, however, the higher the score, the less likely that a guide is very inefficient. The following histograms illustrate, for each type of score, how the share of inefficient guides drops with increasing efficiency scores: When reading this plot, keep in mind that both scores were evaluated on their own training data. Especially for the Moreno-Mateos score, the results are too optimistic, due to overfitting. When evaluated on independent datasets, the correlation of the prediction with other assays was around 25% lower, see Haeussler et al. 2016. At the time of writing, there is no independent dataset available yet to determine the Moreno-Mateos accuracy for each score percentile range. Track methods The entire human (hg19) genome was scanned for the -NGG motif. Flanking 20mer guide sequences were aligned to the genome with BWA and scored with MIT Specificity scores using the command-line version of crispor.org. Non-unique guide sequences were skipped. Flanking sequences were extracted from the genome and input for Crispor efficiency scoring, available from the Crispor downloads page, which includes the Doench 2016, Moreno-Mateos 2015 and Bae 2014 algorithms, among others. Note that the Doench 2016 scores were updated by the Broad institute in 2017 (&quot;Azimuth&quot; update). As a result, earlier versions of the track show the old Doench 2016 scores and this version of the track shows new Doench 2016 scores. Old and new scores are almost identical, they are correlated to 0.99 and for more than 80% of the guides the difference is below 0.02. However, for very few guides, the difference can be bigger. In case of doubt, we recommend the new scores. Crispor.org can display both scores and many more with the &quot;Show all scores&quot; link. Data Access Positional data can be explored interactively with the Table Browser or the Data Integrator. For small programmatic positional queries, the track can be accessed using our REST API. For genome-wide data or automated analysis, CRISPR genome annotations can be downloaded from our download server as a bigBedFile. The files for this track are called crispr.bb, which lists positions and scores, and crisprDetails.tab, which has information about off-target matches. Individual regions or whole genome annotations can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a pre-compiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/crisprAllTargets/crispr.bb -chrom=chr21 -start=0 -end=1000000 stdout Credits Track created by Maximilian Haeussler, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU). References Haeussler M, Sch&#246;nig K, Eckert H, Eschstruth A, Miann&#233; J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016 Jul 5;17(1):148. PMID: 27380939; PMC: PMC4934014 Bae S, Kweon J, Kim HS, Kim JS. Microhomology-based choice of Cas9 nuclease target sites. Nat Methods. 2014 Jul;11(7):705-6. PMID: 24972169 Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016 Feb;34(2):184-91. PMID: 26780180; PMC: PMC4744125 Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013 Sep;31(9):827-32. PMID: 23873081; PMC: PMC3969858 Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods. 2015 Oct;12(10):982-8. PMID: 26322839; PMC: PMC4589495 
dbVar_common dbVar Common SV NCBI dbVar Curated Common Structural Variants Variation Description This track displays common copy number genomic variations from nstd186 (NCBI Curated Common Structural Variants), divided into subtracks according to population and source of original submission. This curated dataset of all structural variants in dbVar includes variants from gnomAD, 1000 Genomes Phase 3, and DECIPHER (dbVar studies nstd166, estd219, and nstd183, respectively). It only includes copy number gain, copy number loss, copy number variation, duplications, and deletions (including mobile element deletions), that are part of a study with at least 100 samples, include allele frequency data, and have an allele frequency of &gt;=0.01 in at least one population. For more information on the number of variant calls and latest statistics for nstd186 see Summary of nstd186 (NCBI Curated Common Structural Variants). There are six subtracks in this track set: NCBI Curated Common SVs: African - Variants with AF &gt;= 0.01 for African Population. NCBI Curated Common SVs: European - Variants with AF &gt;= 0.01 for European Population. NCBI Curated Common SVs: all populations - Variants with AF &gt;= 0.01 for Global Population. NCBI Curated Common SVs: all populations from gnomAD - Variants with AF &gt;= 0.01 from gnomAD Structural Variants. NCBI Curated Common SVs: all populations from 1000 Genomes - Variants with AF &gt;= 0.01 from 1000 Genomes Consortium Phase 3 Integrated SV. NCBI Curated Common SVs: all populations from DECIPHER - Variants with AF &gt;= 0.01 from DECIPHER Consensus CNVs. Display Conventions and Configuration Items in all subtracks follow the same conventions: items are colored by variant type, and are based on the dbVar colors described in the dbVar Overview page. Red for copy number loss or deletion, blue for copy number gain or duplication, and violet for copy number variation. Mouseover on items indicates genes affected, size, variant type, and allele frequencies (AF). All tracks can be filtered according to the Variant Size and Variant Type. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. The data can also be found directly from the dbVar nstd186 data access, as well as in the dbVar Track Hub, where additional subtracks are included. For questions about dbVar track data, please contact &#100;&#98;&#118;&#97;r&#64;&#110;&#99;&#98;&#105;.n&#108;&#109;.&#110;&#105;&#104;.&#103;&#111;v . Credits Thanks to the dbVAR team at NCBI, especially John Lopez and Timothy Hefferon for technical coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter, of the Genome Browser team for engineering the track display. References Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G et al. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41. PMID: 23193291; PMC: PMC3531204 
dbVarSv dbVar Common Struct Var NCBI Curated Common Structural Variants from dbVar Variation Description The tracks listed here contain data from the nstd186 (NCBI Curated Common Structural Variants) study. This is a collection of structural variants (SV) originally submitted to dbVar which are part of a study with at least 100 samples and have an allele frequency of &gt;=0.01 in at least one population. The complete dataset is imported from these common-population studies: gnomAD Structural Variants (nstd166): Catalog of SVs detected from the sequencing of the complete genome of 10,847 unrelated individuals from the GnomAD v2.1 release. 1000 Genomes Consortium Phase 3 Integrated SV (estd219): Structural variants of the 1000 Genomes project Phase 3 as reported in a separate article specifically dedicated to the analysis of SVs. Many of these data are identical to those reported in the estd214 study. DECIPHER Common CNVs (nstd183): Consensus set of common population CNVs selected from high-resolution controls sets where frequency information is available. There are two tracks in this collection: NCBI dbVar Curated Common Structural Variants (dbVar Common SV): Shows copy number variants calls (variants &gt;=50 nucleotides) from the nstd186 study. NCBI dbVar Curated Conflict Variants (dbVar Conflict SV): Shows copy number variants from nstd186 (NCBI Curated Common Structural Variants) that overlap with nstd102 (Clinical Structural Variants). Display Conventions These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Some dbVar tracks contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details page. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. The data can also be found directly from the dbVar nstd186 data access, as well as in the dbVar Track Hub, where additional subtracks are included. For questions about dbVar track data, please contact &#100;&#98;&#118;&#97;r&#64;&#110;&#99;&#98;&#105;. n&#108;&#109;. &#110;&#105;&#104;. &#103;&#111;v. Credits Thanks to the dbVAR team at NCBI, especially John Lopez and Timothy Hefferon for technical coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter of the Genome Browser team for engineering the track display. References Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G et al. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41. PMID: 23193291; PMC: PMC3531204 
dbVar_common_gnomad dbVar Curated gnomAD SVs NCBI dbVar Curated Common SVs: all populations from gnomAD Variation 
dbVar_common_european dbVar Curated European SVs NCBI dbVar Curated Common SVs: European Variation 
dbVar_common_decipher dbVar Curated DECIPHER SVs NCBI dbVar Curated Common SVs: all populations from DECIPHER Variation 
dbVar_common_global dbVar Curated All Populations NCBI dbVar Curated Common SVs: all populations Variation 
dbVar_common_african dbVar Curated African SVs NCBI dbVar Curated Common SVs: African Variation 
dbVar_common_1000g dbVar Curated 1000 Genomes SVs NCBI dbVar Curated Common SVs: all populations from 1000 Genomes Variation 
dbVar_conflict dbVar Conflict SV NCBI dbVar Curated Conflict Variants Variation Description The track NCBI dbVar Curated Common SVs: Conflicts with Pathogenic highlights loci where common copy number variants from nstd186 (NCBI Curated Common Structural Variants) overlap with structural Variants with clinical assertions, submitted to ClinVar by external labs (Clinical Structural Variants - nstd102). Overlap in the track refers to reciprocal overlap between variants in the common (NCBI Curated Common Structural Variants) versus clinical (ClinVar Long Variants) tracks. Reciprocal overlap values can be anywhere from 10% to 100%. For more information on the number of variant calls and latest statistics for nstd186 see Summary of nstd186 (NCBI Curated Common Structural Variants). Display Conventions and Configuration Items in all subtracks follow the same conventions: items are colored by variant type, and are based on the dbVar colors described in the dbVar Overview page. Red for copy number loss or deletion, blue for copy number gain or duplication, and violet for copy number variation. Mouseover on items indicates genes affected, size, variant type, and allele frequencies (AF). All tracks can be filtered according to the variant length, variant type and variant overlap. This last filter defines four bins within that range from which the user can choose. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. The data can also be found directly from the dbVar nstd186 data access, as well as in the dbVar Track Hub, where additional subtracks are included. For questions about dbVar track data, please contact &#100;&#98;&#118;&#97;r&#64;&#110;&#99;&#98;&#105;. n&#108;&#109;. &#110;&#105;&#104;. &#103;&#111;v. Thanks to the dbVAR team at NCBI, especially John Lopez and Timothy Hefferon for technical coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter of the Genome Browser team for engineering the track display. References Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G et al. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41. PMID: 23193291; PMC: PMC3531204 
dbVar_conflict_pathogenic dbVar Curated Conflict SVs NCBI dbVar Curated Common SVs: Conflicts with Pathogenic Variation 
decipher DECIPHER CNVs DECIPHER CNVs (not updated anymore - use the hg38 track) Phenotype and Literature Description NOTE: Decipher is not updating hg19 anymore. This data is outdated. New Decipher data will not appear on hg19. Please use the hg38 track ! To go to the corresponding location in hg38 now, go back to the chromosome view, click in the menu bar "View &gt; In other Genomes" and select the hg38 assembly. Data Display Agreement Notice These data are only available for display in the Browser, and not for bulk download. Access to bulk data may be obtained directly from DECIPHER (https://www.deciphergenomics.org/about/data-sharing) and is subject to a Data Access Agreement, in which the user certifies that no attempt to identify individual patients will be undertaken. The same restrictions apply to the public data displayed at UCSC in the UCSC Genome Browser; no one is authorized to attempt to identify patients by any means. These data are made available as soon as possible and may be a pre-publication release. For information on the proper use of DECIPHER data, please see https://www.deciphergenomics.org/about/data-sharing. The DECIPHER consortium provides these data in good faith as a research tool, but without verifying the accuracy, clinical validity, or utility of the data. The DECIPHER consortium makes no warranty, express or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used. The DECIPHER database of submicroscopic chromosomal imbalance collects clinical information about chromosomal microdeletions/duplications/insertions, translocations and inversions, and displays this information on the human genome map. This track shows genomic regions of reported cases and their associated phenotype information. All data have passed the strict consent requirements of the DECIPHER project and are approved for unrestricted public release. Clicking the Patient View ID link brings up a more detailed informational page on the patient at the DECIPHER web site. Display Conventions and Configuration The genomic locations of DECIPHER variants are labeled with the DECIPHER variant descriptions. Mouseover on items shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant. For the CNVs track, the entries are colored by the type of variant: red for loss blue for gain grey for amplification A light-to-dark color gradient indicates the clinical significance of each variant, with the lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the CNV color code is described here. Items can be filtered according to the size of the variant, variant type, and clinical significance using the track Configure options. For the SNVs track, the entries are colored according to the estimated clinical significance of the variant: black for likely or definitely pathogenic dark grey for uncertain or unknown light grey for likely or definitely benign Method Data provided by the DECIPHER project group are imported and processed to create a simple BED track to annotate the genomic regions associated with individual patients. Contact For more information on DECIPHER, please contact &#99;&#111;n&#116;&#97;c&#116;&#64;&#100;&#101;&#99;&#105;p&#104;&#101;&#114;&#103;&#101;&#110;&#111;&#109;&#105;c&#115;. &#111;&#114;g References Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet. 2009 Apr;84(4):524-33. PMID: 19344873; PMC: PMC2667985 
decipherSnvs DECIPHER SNVs DECIPHER SNVs (not updated anymore - use the hg38 track) Phenotype and Literature Description NOTE: Decipher is not updating hg19 anymore. This data is outdated. New Decipher data will not appear on hg19. Please use the hg38 track ! To go to the corresponding location in hg38 now, go back to the chromosome view, click in the menu bar "View &gt; In other Genomes" and select the hg38 assembly. Data Display Agreement Notice These data are only available for display in the Browser, and not for bulk download. Access to bulk data may be obtained directly from DECIPHER (https://www.deciphergenomics.org/about/data-sharing) and is subject to a Data Access Agreement, in which the user certifies that no attempt to identify individual patients will be undertaken. The same restrictions apply to the public data displayed at UCSC in the UCSC Genome Browser; no one is authorized to attempt to identify patients by any means. These data are made available as soon as possible and may be a pre-publication release. For information on the proper use of DECIPHER data, please see https://www.deciphergenomics.org/about/data-sharing. The DECIPHER consortium provides these data in good faith as a research tool, but without verifying the accuracy, clinical validity, or utility of the data. The DECIPHER consortium makes no warranty, express or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used. The DECIPHER database of submicroscopic chromosomal imbalance collects clinical information about chromosomal microdeletions/duplications/insertions, translocations and inversions, and displays this information on the human genome map. This track shows genomic regions of reported cases and their associated phenotype information. All data have passed the strict consent requirements of the DECIPHER project and are approved for unrestricted public release. Clicking the Patient View ID link brings up a more detailed informational page on the patient at the DECIPHER web site. Display Conventions and Configuration The genomic locations of DECIPHER variants are labeled with the DECIPHER variant descriptions. Mouseover on items shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant. For the CNVs track, the entries are colored by the type of variant: red for loss blue for gain grey for amplification A light-to-dark color gradient indicates the clinical significance of each variant, with the lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the CNV color code is described here. Items can be filtered according to the size of the variant, variant type, and clinical significance using the track Configure options. For the SNVs track, the entries are colored according to the estimated clinical significance of the variant: black for likely or definitely pathogenic dark grey for uncertain or unknown light grey for likely or definitely benign Method Data provided by the DECIPHER project group are imported and processed to create a simple BED track to annotate the genomic regions associated with individual patients. Contact For more information on DECIPHER, please contact &#99;&#111;n&#116;&#97;c&#116;&#64;&#100;&#101;&#99;&#105;p&#104;&#101;&#114;&#103;&#101;&#110;&#111;&#109;&#105;c&#115;. &#111;&#114;g References Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet. 2009 Apr;84(4):524-33. PMID: 19344873; PMC: PMC2667985 
decodeRmap deCODE Recomb deCODE Recombination maps, 10Kb bin size, October 2010 Mapping and Sequencing Description The deCODE recombination rate track represents calculated rates of recombination based on the deCODE recombination maps in 10 Kb bins from October 2010. Sex averaged-, female- and male-specific recombination rates can be displayed by choosing the appropriate options on the track visibility controls. Corresponding to each of these tracks are separate tracks for carriers and non-carriers of the PRDM9 14/15 composite allele which can be displayed as well. There are also tracks depicting the difference between male and female recombination rates, and a track showing recombination hotspots (i.e., bins with standardized recombination rates higher than 10). In addition to the deCODE display, three data tracks from the HapMap project are included. CEU, YRI and combined maps from release #24 can be turned on with the track visibility controls. Methods The deCODE genetic map was created at deCODE Genetics and is based on 289,658 and 8,411 SNPs on the autosomal and X chromosomes, respectively, for 15,257 parent-offspring pairs. For more information on this map, see Kong, et al., 2010. Each base is assigned the recombination rate calculated by assuming a linear genetic distance across the immediately flanking genetic markers. The recombination rate assigned to each 10 Kb window is the average recombination rate of the bases contained within the window. The recombination rates are standardized, bringing the average to 1 for all bins used for the standardization. Credits This track was produced at UCSC using data that are freely available for the deCODE genetic maps. Thanks to all who played a part in the creation of these maps. References Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G et al. A high-resolution recombination map of the human genome. Nat Genet. 2002 Jul;31(3):241-7. PMID: 12053178 Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, Jonasdottir A, Walters GB, Jonasdottir A, Gylfason A, Kristinsson KT et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature. 2010 Oct 28;467(7319):1099-103. PMID: 20981099 
avgView Sex Avg deCODE Recombination maps, 10Kb bin size, October 2010 Mapping and Sequencing 
decodeSexAveragedNonCarrier Sex Avg Non-carry deCODE recombination map, sex-average non-carrier Mapping and Sequencing 
decodeSexAveragedCarrier Sex Avg Carry deCODE recombination map, sex-average carrier Mapping and Sequencing 
decodeSexAveraged Sex Avg deCODE recombination map, sex-average Mapping and Sequencing 
diffView Male-Female deCODE Recombination maps, 10Kb bin size, October 2010 Mapping and Sequencing 
decodeMaleFemaleDifference Sex Difference deCODE recombination map, male minus female difference Mapping and Sequencing 
maleView Male deCODE Recombination maps, 10Kb bin size, October 2010 Mapping and Sequencing 
decodeMaleNonCarrier Male Non-carry deCODE recombination map, male non-carrier Mapping and Sequencing 
decodeMaleCarrier Male Carry deCODE recombination map, male carrier Mapping and Sequencing 
decodeMale Male deCODE recombination map, male Mapping and Sequencing 
hotView Hot Spots deCODE recombination map, Female and Male hot spots, >= 10.0 Mapping and Sequencing 
decodeHotSpotFemale Hot Spot Female deCODE recombination map, female >= 10.0 Mapping and Sequencing 
decodeHotSpotMale Hot Spot Male deCODE recombination map, male >= 10.0 Mapping and Sequencing 
otherMaps HapMap HapMap Release 24 recombination maps Mapping and Sequencing 
hapMapRelease24YRIRecombMap HapMap YRI HapMap Release 24 YRI recombination map Mapping and Sequencing 
hapMapRelease24CEURecombMap HapMap CEU HapMap Release 24 CEU recombination map Mapping and Sequencing 
hapMapRelease24CombinedRecombMap HapMap HapMap Release 24 combined recombination map Mapping and Sequencing 
femaleView Female deCODE Recombination maps, 10Kb bin size, October 2010 Mapping and Sequencing 
decodeFemaleNonCarrier Female Non-carry deCODE recombination map, female non-carrier Mapping and Sequencing 
decodeFemaleCarrier Female Carry deCODE recombination map, female carrier Mapping and Sequencing 
decodeFemale Female deCODE recombination map, female Mapping and Sequencing 
denisovaMethylation Denisova Methyl Denisova Reconstructed DNA Methylation Map Denisova Assembly and Analysis Description This track shows the reconstructed DNA methylation map of the Denisova genome, derived from bone tissues. Display conventions and configuration Green to red scaling is used as a rough indicator of methylation. Values range from 0% (green, unmethylated) to 100% (red, methylated). Data are displayed for CpG positions across the genome. Methods Gokhman et al. reconstructed the DNA methylation maps of two archaic humans, the Neandertal and the Denisovan, based on the natural deamination of cytosines in ancient DNA. With time, cytosines (C's) in post-mortem DNA lose their amine group (deamination). However, deamination of methylated vs. unmethylated C's results in different products - Methylated C's are deaminated with time to T's, whereas unmethylated C's are deaminated to U's. The U's are later removed during ancient DNA library preparation and as a result, a distinct pattern is observed: methylated regions in the genome display high C--&gt;T conversion rate, whereas unmethylated regions display a low C--&gt;T conversion rate. These patterns were used to reconstruct the full DNA methylation maps of the archaic humans. Credits This track was produced at UCSC using data generated by Gokhman et al., 2014. References Gokhman D, Lavi E, Pr&#252;fer K, Fraga MF, Riancho JA, Kelso J, P&#228;&#228;bo S, Meshorer E, Carmel L. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science. 2014 May 2;344(6183):523-7. PMID: 24786081 
dhcBamDenisova Denisova Seq Denisova High-Coverage Sequence Reads Denisova Assembly and Analysis Denisova cave entrance in the Altai Mountains of Siberia, Russia where the bones were found from which DNA was sequenced (Copyright (C) 2010, Johannes Krause) Description The Denisova Sequence track shows high-coverage sequence reads from an archaic Denisovan individual mapped to the human genome reference assembly. The Denisova DNA was extracted from a phalanx bone excavated from Denisova Cave in the Altai Mountains in southern Siberia. Methods A novel single-stranded DNA library preparation method (Note 2, supplementary online materials of Meyer, 2012) was applied to DNA previously extracted from 40mg of bone (Reich, 2010). Using single-stranded DNA greatly increased the genomic coverage to 30X compared to an earlier 1.9X sequence (Reich, 2010). Sequence reads were aligned to human sequence Feb. 2009 (GRCh37/hg19) (downloaded from the 1000 Genomes Project) using the Burrows-Wheeler Aligner. Credits Thanks to the Max Planck Institute for Evolutionary Anthropology for providing the BAM files used for this track. References Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Pr&#252;fer K, de Filippo C et al. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012 Oct 12;338(6104):222-6. PMID: 22936568; PMC: PMC3617501; supplementary online materials, Note 2 Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010 Dec 23;468(7327):1053-60. PMID: 21179161 
dhcVcfDenisovaPinky Denisova Variants Variant Calls from High-Coverage Genome Sequence of an Archaic Denisovan Individual Denisova Assembly and Analysis Denisova cave entrance in the Altai Mountains of Siberia, Russia where the bones were found from which DNA was sequenced (Copyright (C) 2010, Johannes Krause) Description The Denisova Variants track shows variant calls made using high-coverage sequence reads from an archaic Denisovan individual mapped to the human genome reference assembly. The Denisova DNA was extracted from a phalanx bone excavated from Denisova Cave in the Altai Mountains in southern Siberia. Methods A novel single-stranded DNA library preparation method (Meyer, 2012) was applied to DNA previously extracted from 40mg of bone (Reich, 2010). Using single-stranded DNA greatly increased the genomic coverage to 30X compared to an earlier 1.9X sequence (Reich, 2010). Sequence reads were aligned to human sequence Feb. 2009 (GRCh37/hg19) (downloaded from the 1000 Genomes Project) using the Burrows-Wheeler Aligner. Genotype calls for single nucleotide variants and small insertions and deletions were made using the Unified Genotyper from the Genome Analysis Toolkit (GATK), with an additional iteration using a modified reference genome in order to reduce reference bias (Note 6, supplementary online materials of Meyer, 2012). Variant Call Format (VCF) files were enhanced by adding information from Ensembl Compara EPO alignments of 6 primates and of 35 Eutherian mammals, phastCons conservation scores generated using EPO alignments, 1000 Genomes Project integrated variant call files, University of Washington background selection scores, ENCODE/Duke Uniqueness of 20mers (see the Mappability track), segmental duplications from the Eichler lab (see the Segmental Dups track), and samtools mpileup summaries of mapped reads. Comprehensive VCF files that include information for homozygous-reference bases and uncovered bases are available. This track uses VCF files that were filtered to retain only those locations that clearly differ from the human reference genome. Reference genome bases without variant calls may indicate either matching Denisova sequence or insufficient data. Credits Thanks to the Max Planck Institute for Evolutionary Anthropology for providing the variant-only VCF files used for this track. References Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Pr&#252;fer K, de Filippo C et al. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012 Oct 12;338(6104):222-6. PMID: 22936568; PMC: PMC3617501; supplementary online materials, Note 2 Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010 Dec 23;468(7327):1053-60. PMID: 21179161 
cnvDevDelay Development Delay Copy Number Variation Morbidity Map of Developmental Delay Phenotype and Literature Description Enrichment of large copy number variants (CNVs) has been linked to severe pediatric disease including developmental delay, intellectual disability and autism spectrum disorder. The association of individual loci with specific disorders, however, has still been problematic. This track shows CNVs from cases of developmental delay along with healthy control sets from two separate studies. The study by Cooper et al. (2011) analyzed samples from 15,767 children with various developmental disabilities and compared them with samples from 8,329 adult controls to produce a detailed genome-wide morbidity map of developmental delay and congenital birth defects. The study by Coe et al. (2014) further expanded the morbidity map by analyzing 13,318 new case samples along with 11,255 new controls. Display Conventions and Configuration This is a composite track consisting of a Case subtrack and a Control subtrack. To turn a subtrack on or off, toggle the checkbox to the left of the subtrack name in the track controls at the top of the track description page. Items in this track are colored red for copy number loss and blue for copy number gain. Methods The samples were analyzed using nine different CGH platforms with initial CNV calls filtered as described in Coe et al. (2014). Final CNV calls were decoupled from identifying information and submitted to dbVar as nstd54 and nstd100 for unrestricted release. The 15,767 case individuals from the Cooper study comprise nstd54 sampleset 1, while the 8,329 control individuals from the Cooper study comprise nstd54 samplesets 2-12. The 13,318 case individuals from the Coe study were combined with the Cooper case individuals to comprise nstd100 sampleset 1. The 11,255 control individuals from the Coe study comprise nsdt100 samplesets 2 and 3. The Case subtrack was constructed using nstd100 sampleset 1. The Control subtrack was constructed by combining nstd100 samplesets 2 and 3 with nstd54 samplesets 2-12. Credits We would like to thank Gregory Cooper, Brad Coe and the Eichler Lab at the University of Washington for providing the data for this track. References Coe BP, Witherspoon K, Rosenfeld JA, van Bon BW, Vulto-van Silfhout AT, Bosco P, Friend KL, Baker C, Buono S, Vissers LE et al. Refining analyses of copy number variation identifies specific genes associated with developmental delay. Nat Genet. 2014 Oct;46(10):1063-71. PMID: 25217958; PMC: PMC4177294 Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig V et al. A copy number variation morbidity map of developmental delay. Nat Genet. 2011 Aug 14;43(9):838-46. PMID: 21841781; PMC: PMC3171215 
cnvDevDelayControl Control Copy Number Variation Morbidity Map of Developmental Delay - Control Phenotype and Literature 
cnvDevDelayCase Case Copy Number Variation Morbidity Map of Developmental Delay - Case Phenotype and Literature 
dgvPlus DGV Struct Var Database of Genomic Variants: Structural Variation (CNV, Inversion, In/del) Variation Description This track displays copy number variants (CNVs), insertions/deletions (InDels), inversions and inversion breakpoints annotated by the Database of Genomic Variants (DGV), which contains genomic variations observed in healthy individuals. DGV focuses on structural variation, defined as genomic alterations that involve segments of DNA that are larger than 1000 bp. Insertions/deletions of 50 bp or larger are also included. Display Conventions This track contains three subtracks: Structural Variant Regions: annotations that have been generated from one or more reported structural variants at the same location. Supporting Structural Variants: the sample-level reported structural variants. Gold Standard Variants: curated variants from a selected number of studies in DGV. Color is used in these subtracks to indicate the type of variation: Inversions and inversion breakpoints are purple. CNVs and InDels are blue if there is a gain in size relative to the reference. CNVs and InDels are red if there is a loss in size relative to the reference. CNVs and InDels are brown if there are reports of both a loss and a gain in size relative to the reference. The DGV Gold Standard subtrack utilizes a boxplot-like display to represent the merging of records as explained in the Methods section below. In this track, the middle box (where applicable), represents the high confidence location of the CNV, while the thin lines and end boxes represent the possible range of the CNV. Clicking on a variant leads to a page with detailed information about the variant, such as the study reference and PubMed abstract link, the study's method and any genes overlapping the variant. Also listed, if available, are the sequencing or array platform used for the study, a sample cohort description, sample size, sample ID(s) in which the variant was observed, observed gains and observed losses. If the particular variant is a merged variant, links to genome browser views of the supporting variants are listed. If the particular variant is a supporting variant, a link to the genome browser view of its merged variant is displayed. A link to DGV's Variant Details page for each variant is also provided. For most variants, DGV uses accessions from peer archives of structural variation (dbVar at NCBI or DGVa at EBI). These accessions begin with either &quot;essv&quot;, &quot;esv&quot;, &quot;nssv&quot;, or &quot;nsv&quot;, followed by a number. Variant submissions processed by EBI begin with &quot;e&quot; and those processed by NCBI begin with &quot;n&quot;. Accessions with ssv are for variant calls on a particular sample, and if they are copy number variants, they generally indicate whether the change is a gain or loss. In a few studies the ssv represents the variant called by a single algorithm. If multiple algorithms were used, overlapping ssv's from the same individual would be combined to generate a sample level sv. If there are many samples analyzed in a study, and if there are many samples which have the same variant, there will be multiple ssv's with the same start and end coordinates. These sample level variants are then merged and combined to form a representative variant that highlights the common variant found in that study. The result is called a structural variant (sv) record. Accessions with sv are for regions asserted by submitters to contain structural variants, and often span ssv elements for both losses and gains. dbVar and DGVa do not record numbers of losses and gains encompassed within sv regions. DGV merges clusters of variants that share at least 70% reciprocal overlap in size/location, and assigns an accession beginning with &quot;dgv&quot;, followed by an internal variant serial number, followed by an abbreviated study id. For example, the first merged variant from the Shaikh et al. 2009 study (study accession=nstd21) would be dgv1n21. The second merged variant would be dgv2n21 and so forth. Since in this case there is an additional level of clustering, it is possible for an &quot;sv&quot; variant to be both a merged variant and a supporting variant. For most sv and dgv variants, DGV displays the total number of sample-level gains and/or losses at the bottom of their variant detail page. Since each ssv variant is for one sample, its total is 1. Methods Published structural variants are imported from peer archives dbVar and DGVa. DGV then applies quality filters and merges overlapping variants. For data sets where the variation calls are reported at a sample-by-sample level, DGV merges calls with similar boundaries across the sample set. Only variants of the same type (i.e. CNVs, Indels, inversions) are merged, and gains and losses are merged separately. Sample level calls that overlap by &ge; 70% are merged in this process. The initial criteria for the Gold Standard set require that a variant is found in at least two different studies and found in at least two different samples. After filtering out low-quality variants, the remaining variants are clustered according to 50% minimum overlap, and then merged into a single record. Gains and losses are merged separately. The highest ranking variant in the cluster defines the inner box, while the outer lines define the maximum possible start and stop coordinates of the CNV. In this way, the inner box forms a high-confidence CNV location and the thin connecting lines indicate confidence intervals for the location of CNV. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed file that can be downloaded from the download server. The exact filenames can be found in the track configuration file. Annotations can be converted to ASCII text by our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/dgv/dgvMerged.bb -chrom=chr6 -start=0 -end=1000000 stdout Credits Thanks to the Database of Genomic Variants for providing these data. In citing the Database of Genomic Variants please refer to MacDonald et al. References Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. Detection of large-scale variation in the human genome. Nat Genet. 2004 Sep;36(9):949-51. PMID: 15286789 MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 2014 Jan;42(Database issue):D986-92. PMID: 24174537; PMC: PMC3965079 Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res. 2006;115(3-4):205-14. PMID: 17124402 
dgvGold DGV Gold Standard Database of Genomic Variants: Gold Standard Variants Variation 
dgvSupporting DGV Supp Var Database of Genomic Variants: Supporting Structural Var (CNV, Inversion, In/del) Variation 
dgvMerged DGV Struct Var Database of Genomic Variants: Structural Var Regions (CNV, Inversion, In/del) Variation 
dosageSensitivity Dosage Sensitivity pHaplo and pTriplo dosage sensitivity map from Collins et al 2022 Phenotype and Literature Description This container track represents dosage sensitivity map data from Collins et al 2022. There are two tracks, one corresponding to the probability of haploinsufficiency (pHaplo) and one to the probability of triplosensitivity (pTriplo). Rare copy-number variants (rCNVs) include deletions and duplications that occur infrequently in the global human population and can confer substantial risk for disease. Collins et al aimed to quantify the properties of haploinsufficiency (i.e., deletion intolerance) and triplosensitivity (i.e., duplication intolerance) throughout the human genome by analyzing rCNVs from nearly one million individuals to construct a genome-wide catalog of dosage sensitivity across 54 disorders, which defined 163 dosage sensitive segments associated with at least one disorder. These segments were typically gene-dense and often harbored dominant dosage sensitive driver genes. An ensemble machine learning model was built to predict dosage sensitivity probabilities (pHaplo &amp; pTriplo) for all autosomal genes, which identified 2,987 haploinsufficient and 1,559 triplosensitive genes, including 648 that were uniquely triplosensitive. Display Conventions and Configuration Each of the tracks is displayed with a distinct item (bed track) covering the entire gene locus wherever a score was available. Clicking on an item provides a link to DECIPHER which contains the sensitivity scores as well as additional information. Mousing over the items will display the gene symbol, the ESNG ID for that gene, and the respective sensitivity score for the track rounded to two decimal places. Filters are also available to specify specific score thresholds to display for each of the tracks. Coloring and Interpretation Each of the tracks is colored based on standardized cutoffs for pHaplo and pTriplo as described by the authors: pHaplo scores &ge;0.86 indicate that the average effect sizes of deletions are as strong as the loss-of-function of genes known to be constrained against protein truncating variants (average OR&ge;2.7) (Karczewski et al., 2020). pHaplo scores &ge;0.55 indicate an odds ratio &ge;2. pTriplo scores &ge;0.94 indicate that the average effect sizes of deletions are as strong as the loss-of-function of genes known to be constrained against protein truncating variants (average OR&ge;2.7) (Karczewski et al., 2020). pHaplo scores &ge;0.68 indicate an odds ratio &ge;2. Applying these cutoffs defined 2,987 haploinsufficient (pHaplo&ge;0.86) and 1,559 triplosensitive (pTriplo&ge;0.94) genes with rCNV effect sizes comparable to loss-of-function of gold-standard PTV-constrained genes. See below for a summary of the color scheme: Dark red items - pHaplo &ge; 0.86 Bright red items - pHaplo &lt; 0.86 Dark blue items - pTriplo &ge; 0.94 Bright blue items - pTriplo &lt; 0.94 Methods The data were downloaded from Zenodo which consisted of a 3-column file with gene symbols, pHaplo, and pTriplo scores. Since the data were created using GENCODEv19 models, the hg19 data was mapped using those coordinates by picking the earliest transcription start site of all of the respective gene transcripts and the furthest transcription end site. This leads to some gene boundaries that are not representative of a real transcript, but since the data are for gene loci annotations this maximum coverage was used. Finally, both scores were rounded to two decimal points for easier interpretation. For hg38, we attempted to use updated gene positions using a few different datasets since gene symbols have been updated many times since GENCODEv19. A summary of the workflow can be seen below, with each subsequent step being used only for genes where mapping failed: Gene symbols were mapped using MANE1.0. &lt; 2000 items failed mapping here. Mapping with GENCODEv45 was attempted. Mapping with GENCODEv20 was attempted. At this point, 448 items were not mapped. Finally, any missing items were lifted using the hg19 track. 19/448 items failed mapping due to their regions having been split from hg19 to hg38. In summary, the hg19 track was mapped using the original GENCODEv19 mappings, and a series of steps were taken to map the hg38 gene symbols with updated coordinates. 19/18641 items could not be mapped and are missing from the hg38 tracks. The complete makeDoc can be found online. This includes all of the track creation steps. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. For automated download and analysis, the genome annotation is stored at UCSC in bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/dosageSensitivityCollins2022/pHaploDosageSensitivity.bb stdout Please refer to our Data Access FAQ for more information. Credits Thanks to DECIPHER for their support and assistance with the data. We would also like to thank Anna Benet-Pagès for suggesting and assisting in track development and interpretation. References Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, Han L, Morley T, Niestroj LM, Ulirsch J et al. A cross-disorder dosage sensitivity map of the human genome. Cell. 2022 Aug 4;185(16):3041-3055.e25. PMID: 35917817; PMC: PMC9742861 
pTriplo pTriplosensitivity Probability of triplosensitivity Phenotype and Literature 
pHaplo pHaploinsufficiency Probability of haploinsufficiency Phenotype and Literature 
wgEncodeOpenChromDnase Duke DNaseI HS GSE32970 Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) Regulation Description These tracks display DNaseI hypersensitivity (HS) evidence as part of the four Open Chromatin track sets. DNaseI is an enzyme that has long been used to map general chromatin accessibility and DNaseI "hypersensitivity" is a feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions, and novel elements. DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome. Together with FAIRE and ChIP-seq experiments, these tracks display the locations of active regulatory elements identified as open chromatin in multiple cell types from the Duke, UNC-Chapel Hill, UT-Austin, and EBI ENCODE group. Within this project, open chromatin was identified using two independent and complementary methods: these DNaseI HS assays and Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE), combined with chromatin immunoprecipitation (ChIP) for select regulatory factors. DNaseI HS and FAIRE provide assay cross-validation with commonly identified regions delineating the highest confidence areas of open chromatin. ChIP assays provide functional validation and preliminary annotation of a subset of open chromatin sites. Each method employed Illumina (formerly Solexa) sequencing by synthesis as the detection platform. The Tier 1 and Tier 2 cell types were additionally verified using high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen. Other Open Chromatin track sets: Data for the FAIRE experiments can be found in UNC FAIRE. Data for the ChIP experiments can be found in UTA TFBS. A synthesis of all the open chromatin assays for select cell lines can be previewed in Open Chrom Synth. Display Conventions and Configuration This track is a multi-view composite track that contains a single data type with multiple levels of annotation (views). For each view, there are multiple subtracks representing different cell types that display individually on the browser. Instructions for configuring multi-view tracks are here. Chromatin data displayed here represents a continuum of signal intensities. The Crawford lab recommends setting the &quot;Data view scaling: auto-scale&quot; option when viewing signal data in full mode to see the full dynamic range of the data. Note that in regions that do not have open chromatin sites, autoscale will rescale the data and inflate the background signal, making the regions appear noisy. Changing back to fixed scale will alleviate this issue. In general, for each experiment in each of the cell types, the Duke DNaseI HS tracks contain the following views: Peaks Regions of enriched signal in DNaseI HS experiments. Peaks were called based on signals created using F-Seq, a software program developed at Duke (Boyle et al., 2008b). Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. The solid vertical line in the peak represents the point with the highest signal. F-Seq Density Signal Density graph (wiggle) of signal enrichment calculated using F-Seq for the combined set of sequences from all replicates. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). This method does not look at fixed-length windows, but rather weights contributions of nearby sequences in proportion to their distance from that base. It only considers sequences aligned 4 or less times in the genome and uses an alignability background model to try to correct for regions where sequences cannot be aligned. For each cell type (especially important for those with an abnormal karyotype), a model to try to correct for amplifications and deletions that is based on control input data was also used. Base Overlap Signal An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Peaks and signals displayed in this track are the results of pooled replicates. The raw sequence and alignment files for each replicate are available for download. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. DNaseI hypersensitive sites were isolated using methods called DNase-seq or DNase-chip (Song and Crawford, 2010; Boyle et al., 2008a; Crawford et al., 2006). Briefly, cells were lysed with NP40, and intact nuclei were digested with optimal levels of DNaseI enzyme. DNaseI-digested ends were captured from three different DNase concentrations, and material was sequenced using Illumina (Solexa) sequencing. DNase-seq data for Tier 1 and Tier 2 cell lines were verified by comparing multiple independent growths (replicates) and determining the reproducibility of the data. In general, cell lines were verified if 80% of the top 50,000 peaks in one replicate were detected in the top 100,000 peaks of a second replicate. For some cell types, additional verification was performed using similar material hybridized to NimbleGen Human ENCODE tiling arrays (1% of the genome) along with the input DNA as reference (DNase-chip). A more detailed protocol is available here. The read length for sequences from DNase-seq was 20 bases long due to a MmeI cutting step of the approximately 50 kb DNA fragments extracted after DNaseI digestion. Sequences from each experiment were aligned to the genome using BWA (Li et al., 2008) for the GRCh37 (hg19) assembly. The command used for these alignments was: &gt; bwa aln -t 8 genome.fa s_1.sequence.txt.bfq &gt; s_1.sequence.txt.sai where genome.fa is the whole genome sequence and s_1.sequence.txt.bfq is one lane of sequences converted into the required bfq format. Sequences from multiple lanes were combined for a single replicate using the bwa samse command and converted to the sam/bam format using SAMtools. Only those sequences that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes - see supplemental materials). The mappings of these short reads to the genome are available for download. Using F-seq, the resulting digital signal was converted to a continuous wiggle track that employs a Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Input data was generated for several cell lines. These were used directly to create a control/background model used for F-Seq when generating signal annotations for these cell lines. These models were meant to correct for sequencing biases, alignment artifacts, and copy number changes in these cell lines. Input data was not generated directly for other cell lines. For cell lines for which there is no input experiment available, the peaks were generated using the control of generic_male or generic_female, as an attempt to create a general background based on input data from several cell types. These files are in &quot;iff&quot; format, which is used when calling peaks with F-seq software, and can be downloaded from the production lab directly from under the section titled &quot;Copy number / karyotype correction.&quot; Using a general background model derived from the available Input data sets provided corrections for sequencing biases and alignment artifacts, but did not correct for cell type-specific copy number changes. The exact command used for this step was: &gt; fseq -l 600 -v -f 0 -b &lt;bff files&gt; -p &lt;iff files&gt; aligments.bed where the bff files are the background files based on alignability, the iff files are the background files based on the Input experiments, and alignments.bed is a bed file of filtered sequence alignments. Discrete DNaseI HS sites (peaks) were identified from DNase-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. Data from the high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen were normalized using the Tukey biweight normalization and peaks were called using ChIPOTle (Buck et al., 2005) at multiple levels of significance. Regions matched on size to these peaks that were devoid of any significant signal were also created as a null model. These data were used for additional verification of Tier 1 and Tier 2 cell lines by ROC analysis. Files containing this data can be found in the Downloads directory, labeled 'Validation' in the View column. Release Notes This is Release 3 (August 2012) of the track. It includes 27 new experiments including 18 new cell lines. A synthesis of open chromatin evidence from the three assay types was compiled for Tier 1 and 2 cell lines and can be viewed in Open Chromatin Synthesis. Enhancer and Insulator Functional assays: A subset of DNase and FAIRE regions were cloned into functional tissue culture reporter assays to test for enhancer and insulator activity. Coordinates and results from these experiments can be found in the supplemental materials. Credits These data and annotations were created by a collaboration of multiple institutions (contact: Terry Furey) Duke University's Institute for Genome Sciences & Policy (IGSP): Alan Boyle, Lingyun Song, and Greg Crawford University of North Carolina at Chapel Hill: Paul Giresi, Jason Lieb, and Terry Furey Universty of Texas at Austin: Zheng Liu, Ryan McDaniell, Bum-Kyu Lee, and Vishy Iyer European Bioinformatics Insitute: Paul Flicek, Damian Keefe, and Ewan Birney University of Cambridge, Department of Oncology and CR-UK Cambridge Research Institute (CRI): Stefan Graf We thank NHGRI for ENCODE funding support. References Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res. 2007 Jun;17(6):910-6. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008 Jan 25;132(2):311-22. Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8. Buck MJ, Nobel AB, Lieb JD. ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 2005;6(11):R97. Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods. 2006 Jul;3(7):503-9. Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123-31. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guig&#243; R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007 Jun;17(6):877-85. Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods. 2009 Jul;48(3):233-9. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Nov;18(11):1851-8. Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeOpenChromDnaseViewSignal Duke DNaseI HS Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) Regulation 
wgEncodeOpenChromDnaseUrothelSigV2 Urothel DS Urothelia DnaseSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH001113 1113 GSM1008605 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseUrothelSigV2 Signal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene DNaseI HS Sequencing Crawford Crawford - Duke University Signal Urothelia DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseUrothelUt189SigV2 Urothel UT189 DS Urothelia DnaseSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH001114 1114 GSM1008606 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseUrothelUt189SigV2 UT189 Signal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene DNaseI HS Sequencing Crawford Crawford - Duke University UT189 E.Coli treatment 1 hour, followed by 24 hour incubation Signal Urothelia UT189 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseT47dSig T-47D DS T-47D DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001109 1109 GSM816673 Crawford Duke fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromDnaseT47dSig Signal epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Crawford Crawford - Duke University Signal T-47D DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseT47dEst10nm30mSig T-47D Estr 30m DS T-47D DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002566 2566 GSM1008576 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseT47dEst10nm30mSig Estradiol_10nM_30m Signal epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Crawford Crawford - Duke University 30 min with 10nM 7b-Estradiol (Crawford) Signal T-47D Estradiol 10 nM 30 m DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseStellateSig Stellate DS Stellate DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001108 1108 GSM816672 Crawford Duke fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromDnaseStellateSig Signal hepatic stellate cells, liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient DNaseI HS Sequencing Crawford Crawford - Duke University Signal Stellate DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseRwpe1Sig RWPE1 DS RWPE1 DnaseSeq ENCODE Mar 2012 Freeze 2011-10-03 2012-07-03 wgEncodeEH002553 2553 GSM1008595 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseRwpe1Sig Signal prostate epithelial DNaseI HS Sequencing Crawford Crawford - Duke University Signal RWPE1 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePsoasmuscleocSig Psoas muscle DS Psoas_muscle_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003491 3491 GSM1008560 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnasePsoasmuscleocSig Signal Primary frozen psoas muscle tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1540 (Rep B1), 1863 (Rep B2 FAIRE) DNaseI HS Sequencing Crawford Crawford - Duke University Signal Psoas muscle OC DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseProgfibSig ProgFib DS ProgFib DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-17 2010-09-17 wgEncodeEH000576 576 GSM816661 Crawford Duke private-noSequence fseq v 1.84, iff_FB0167P hg18 wgEncodeOpenChromDnaseProgfibSig Signal fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNaseI HS Sequencing Crawford Crawford - Duke University Signal ProgFib DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePhteSig pHTE DS pHTE DnaseSeq ENCODE Jan 2011 Freeze 2010-10-18 2011-07-18 wgEncodeEH001099 1099 GSM816647 Crawford Duke private-noSequence fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromDnasePhteSig Signal primary tracheal epithelial cells DNaseI HS Sequencing Crawford Crawford - Duke University Signal pHTE DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePanisletsSig PanIslets DS PanIslets DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-17 2010-09-17 wgEncodeEH000575 575 GSM816660 Crawford Duke private-noSequence fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnasePanisletsSig Signal pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) DNaseI HS Sequencing Crawford Crawford - Duke University Signal PanIslets DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePanisdSig PanIsletD DS PanIsletD DnaseSeq ENCODE Jan 2011 Freeze 2010-10-29 2011-07-29 wgEncodeEH001102 1102 GSM816666 Crawford Duke private-noSequence fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnasePanisdSig Signal dedifferentiated human pancreatic islets from the National Disease Research Interchange (NDRI), same source as PanIslets DNaseI HS Sequencing Crawford Crawford - Duke University Signal PanIsletD DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseOsteoblSig Osteoblasts DS Osteobl DnaseSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001098 1098 GSM816654 Crawford Duke fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromDnaseOsteoblSig Signal osteoblasts (NHOst) DNaseI HS Sequencing Crawford Crawford - Duke University Signal Osteoblasts DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseOlfneurosphereSig Olfact neuro DS Olf_neurosphere DnaseSeq ENCODE Jul 2012 Freeze 2012-07-02 2013-04-02 wgEncodeEH003475 3475 GSM1008584 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseOlfneurosphereSig Signal Human olfactory neurosphere-derived cells from mucosal biopsies DNaseI HS Sequencing Crawford Crawford - Duke University Signal Olf neurosphere DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseNhekSig NHEK DS NHEK DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-29 2010-06-29 wgEncodeEH000553 553 GSM816635 Crawford Duke fseq v 1.84, iff_generic_female hg18 wgEncodeOpenChromDnaseNhekSig Signal epidermal keratinocytes DNaseI HS Sequencing Crawford Crawford - Duke University Signal NHEK DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseNaivebcellSig Naive B cell DS Naive_B_cell DnaseSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-02 wgEncodeEH003478 3478 GSM1008557 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseNaivebcellSig Signal Naive B cells (IgD+) isolated from de-identified tonsillectomy DNaseI HS Sequencing Crawford Crawford - Duke University Signal Naive B cell DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMyometrSig Myometr DS Myometr DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-09 2010-10-08 wgEncodeEH000603 603 GSM816630 Crawford Duke private-noSequence fseq v 1.84, iff_generic_female hg18 wgEncodeOpenChromDnaseMyometrSig Signal myometrial cells DNaseI HS Sequencing Crawford Crawford - Duke University Signal Myometr DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMelanoSig Melano DS Melano DnaseSeq ENCODE Jan 2011 Freeze 2010-08-11 2011-05-11 wgEncodeEH000602 602 GSM816631 Crawford Duke fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnaseMelanoSig Signal epidermal melanocytes DNaseI HS Sequencing Crawford Crawford - Duke University Signal Melano DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMel2183Sig Mel 2183 DS Mel_2183 DnaseSeq ENCODE Mar 2012 Freeze 2012-01-31 2012-10-31 wgEncodeEH002557 2557 GSM1008599 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseMel2183Sig Signal Melanoma Cell line DNaseI HS Sequencing Crawford Crawford - Duke University Signal Mel 2183 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMedullod341Sig Medullo D341 DS Medullo_D341 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH002688 2688 GSM1008577 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseMedullod341Sig Signal Medulloblastoma cell line of neuron or neuron precurosr origin DNaseI HS Sequencing Crawford Crawford - Duke University Signal Medullo D341 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMedulloSig Medullo DS Medullo DnaseSeq ENCODE June 2010 Freeze 2010-06-15 2009-12-16 2010-09-16 wgEncodeEH000574 574 GSM816636 Crawford Duke fseq v 1.84, iff_generic_female (should have been male) hg18 wgEncodeOpenChromDnaseMedulloSig Signal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) DNaseI HS Sequencing Crawford Crawford - Duke University Signal Medullo DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseLncapSig LNCaP DS LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001097 1097 GSM816637 Crawford Duke fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromDnaseLncapSig Signal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Crawford Crawford - Duke University Signal LNCaP DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseLncapAndroSig LNCaP Methyl DS LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001096 1096 GSM816634 Crawford Duke fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromDnaseLncapAndroSig androgen Signal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Crawford Crawford - Duke University 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Signal LNCaP Methyltrienolone DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIshikawaEst10nm30mSig Ishi Estr 30m DS Ishikawa DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002551 2551 GSM1008593 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseIshikawaEst10nm30mSig Estradiol_10nM_30m Signal endometrial adenocarcinoma DNaseI HS Sequencing Crawford Crawford - Duke University 30 min with 10nM 7b-Estradiol (Crawford) Signal Ishikawa Estradiol 10 nM 30 m DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIshikawaTam10030Sig Ishi OHTAM DS Ishikawa DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002552 2552 GSM1008594 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseIshikawaTam10030Sig 4OHTAM_100nM_30m Signal endometrial adenocarcinoma DNaseI HS Sequencing Crawford Crawford - Duke University 30 minutes with 100 nM 4-hydroxytamoxifen (Crawford) Signal Ishikawa 4-OHTAM 100 nM 30 m DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIpsnihi11Sig iPS NIHi11 DS iPS_NIHi11 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH002561 2561 GSM1008569 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseIpsnihi11Sig Signal iPS cells derived from AG20443 fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Signal iPS NIHi11 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIpsnihi7Sig iPS NIHi7 DS iPS_NIHi7 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEH002558 2558 GSM1008600 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseIpsnihi7Sig Signal iPS cells derived from AG08395 fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Signal iPS NIHi7 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIpscwru1Sig iPS CWRU1 DS iPS_CWRU1 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH002560 2560 GSM1008570 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseIpscwru1Sig Signal iPS cells derived from MSC658 fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Signal iPS CWRU1 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHuh75Sig Huh-7.5 DS Huh-7.5 DnaseSeq ENCODE Jan 2011 Freeze 2010-12-07 2011-09-07 wgEncodeEH001112 1112 GSM816671 Crawford Duke fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromDnaseHuh75Sig Signal hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication DNaseI HS Sequencing Crawford Crawford - Duke University Signal Huh-7.5 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHuh7Sig Huh-7 DS Huh-7 DnaseSeq ENCODE Jan 2011 Freeze 2010-12-07 2011-09-07 wgEncodeEH001111 1111 GSM816641 Crawford Duke fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromDnaseHuh7Sig Signal hepatocellular carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University Signal Huh-7 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHtr8Sig HTR8svn DS HTR8svn DnaseSeq ENCODE Jan 2011 Freeze 2010-11-02 2011-08-02 wgEncodeEH001105 1105 GSM816644 Crawford Duke fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromDnaseHtr8Sig Signal trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo DNaseI HS Sequencing Crawford Crawford - Duke University Signal HTR8svn DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmtSig HSMMtube DS HSMMtube DnaseSeq ENCODE June 2010 Freeze 2010-06-20 2009-12-20 2010-09-19 wgEncodeEH000585 585 GSM816651 Crawford Duke private-noSequence fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnaseHsmmtSig Signal skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing Crawford Crawford - Duke University Signal HSMMtube DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmfshdSig HSMM FSHD DS HSMM_FSHD DnaseSeq ENCODE Mar 2012 Freeze 2012-01-31 2012-10-31 wgEncodeEH002556 2556 GSM1008598 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseHsmmfshdSig Signal primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies DNaseI HS Sequencing Crawford Crawford - Duke University Signal HSMM FSHD DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmembSig HSMM emb DS HSMM_emb DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002550 2550 GSM1008592 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseHsmmembSig Signal embryonic myoblast DNaseI HS Sequencing Crawford Crawford - Duke University Signal HSMM emb DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmSig HSMM DS HSMM DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-20 2010-09-19 wgEncodeEH000584 584 GSM816650 Crawford Duke private-noSequence fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnaseHsmmSig Signal skeletal muscle myoblasts DNaseI HS Sequencing Crawford Crawford - Duke University Signal HSMM DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHpde6e6e7Sig HPDE6-E6E7 DS HPDE6-E6E7 DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001106 1106 GSM816639 Crawford Duke fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromDnaseHpde6e6e7Sig Signal pancreatic duct cells immortalized with E6E7 gene of HPV DNaseI HS Sequencing Crawford Crawford - Duke University Signal HPDE6-E6E7 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHmecSig HMEC DS HMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001101 1101 GSM816669 Crawford Duke private-noSequence fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromDnaseHmecSig Signal mammary epithelial cells DNaseI HS Sequencing Crawford Crawford - Duke University Signal HMEC DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHepatocytesSig Hepatocytes DS Hepatocytes DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001107 1107 GSM816663 Crawford Duke fseq v 1.84, iff_generic_female (should have been male) hg19 wgEncodeOpenChromDnaseHepatocytesSig Signal primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNaseI HS Sequencing Crawford Crawford - Duke University Signal Hepatocytes DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHek293tSig HEK293T DS HEK293T DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002565 2565 GSM1008573 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseHek293tSig Signal embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line DNaseI HS Sequencing Crawford Crawford - Duke University Signal HEK293T DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHeartocSig Heart DS Heart_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-05 2013-04-05 wgEncodeEH003479 3479 GSM1008559 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseHeartocSig Signal Primary frozen heart tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B1 FAIRE), 4548 (Rep B2 FAIRE) DNaseI HS Sequencing Crawford Crawford - Duke University Signal Heart OC DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseH9esSig H9ES DS H9ES DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-24 2010-09-23 wgEncodeEH000594 594 GSM816629 Crawford Duke fseq v 1.84, iff_generic_female hg18 wgEncodeOpenChromDnaseH9esSig Signal embryonic stem cell (hESC) H9 DNaseI HS Sequencing Crawford Crawford - Duke University Signal H9ES DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseH7esSig H7hESC DS H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-29 2012-09-29 wgEncodeEH002554 2554 GSM1008596 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseH7esSig Signal undifferentiated embryonic stem cells DNaseI HS Sequencing Crawford Crawford - Duke University Signal H7-hESC DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm20000Sig GM20000 DS GM20000 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-15 wgEncodeEH003485 3485 GSM1008587 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseGm20000Sig Signal lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM20000 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm19240Sig GM19240 DS GM19240 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000568 568 GSM816648 Crawford Duke fseq v 1.84, iff_generic_female hg18 wgEncodeOpenChromDnaseGm19240Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM19240 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm19239Sig GM19239 DS GM19239 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000567 567 GSM816659 Crawford Duke fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnaseGm19239Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM19239 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm19238Sig GM19238 DS GM19238 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000566 566 GSM816658 Crawford Duke fseq v 1.84, iff_generic_female hg18 wgEncodeOpenChromDnaseGm19238Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM19238 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm18507Sig GM18507 DS GM18507 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-19 2010-09-18 wgEncodeEH000581 581 GSM816653 Crawford Duke fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnaseGm18507Sig Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM18507 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm13977Sig GM13977 DS GM13977 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003488 3488 GSM1008556 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseGm13977Sig Signal lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM13977 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm13976Sig GM13976 DS GM13976 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-16 wgEncodeEH003486 3486 GSM1008591 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseGm13976Sig Signal lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM13976 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm12892Sig GM12892 DS GM12892 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000565 565 GSM816657 Crawford Duke fseq v 1.84, iff_generic_female hg18 wgEncodeOpenChromDnaseGm12892Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM12892 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm12891Sig GM12891 DS GM12891 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-03 2010-07-03 wgEncodeEH000564 564 GSM816656 Crawford Duke fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnaseGm12891Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM12891 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm10266Sig GM10266 DS GM10266 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-15 wgEncodeEH003484 3484 GSM1008590 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseGm10266Sig Signal lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM10266 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm10248Sig GM10248 DS GM10248 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003487 3487 GSM1008589 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseGm10248Sig Signal lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM10248 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGlioblaSig Gliobla DS Gliobla DnaseSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001100 1100 GSM816668 Crawford Duke fseq v 1.84, iff_H54 hg19 wgEncodeOpenChromDnaseGlioblaSig Signal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) DNaseI HS Sequencing Crawford Crawford - Duke University Signal Gliobla DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGcbcellSig GC B cell DS GC_B_cell DnaseSeq ENCODE Jul 2012 Freeze 2012-07-02 2013-04-02 wgEncodeEH003474 3474 GSM1008579 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseGcbcellSig Signal Germinal center B cells (CD77+) isolated from de-identified tonsillectomy DNaseI HS Sequencing Crawford Crawford - Duke University Signal GC B cell DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFrontalcortexocSig Front crtx DS Frontal_cortex_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-06-27 2013-03-27 wgEncodeEH003471 3471 GSM1008566 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseFrontalcortexocSig Signal Primary ventromedial prefrontal cortex, from KPBBB donor IDs 673 (Rep B1) and 913 (Rep B2) DNaseI HS Sequencing Crawford Crawford - Duke University Signal Frontal cortex OC DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibropag20443Sig FibroP DS FibroP_AG20443 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002569 2569 GSM1008561 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseFibropag20443Sig Signal fibroblasts taken from individuals with Parkinson's disease DNaseI HS Sequencing Crawford Crawford - Duke University Signal FibroP AG20443 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibropag08396Sig FibroP DS FibroP_AG08396 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002568 2568 GSM1008562 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseFibropag08396Sig Signal fibroblasts taken from individuals with Parkinson's disease DNaseI HS Sequencing Crawford Crawford - Duke University Signal FibroP AG08396 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibropag08395Sig FibroP DS FibroP_AG08395 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002567 2567 GSM1008575 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseFibropag08395Sig Signal fibroblasts taken from individuals with Parkinson's disease DNaseI HS Sequencing Crawford Crawford - Duke University Signal FibroP AG08395 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblgm03348Sig FibroB DS Fibrobl_GM03348 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-02 wgEncodeEH003476 3476 GSM1008563 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseFibroblgm03348Sig Signal skin fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Signal Fibrobl GM03348 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblgm03348LentimyodSig FibroB Lenti-M DS Fibrobl_GM03348 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-02 2013-04-02 wgEncodeEH003473 3473 GSM1008568 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseFibroblgm03348LentimyodSig lenti-MyoD Signal skin fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were induced for MYOD expression for 10 days with doxycycline and at concentration of 3ug per ml. Standard media was used (and replaced every 2 days) during induction: DMEM, 1% Pen Strep, and 10% FBS. (Crawford) Signal Fibrobl GM03348 Lenti-MyoD DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblgm03348LenticonSig FibroB Lenti-C DS Fibrobl_GM03348 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-02 wgEncodeEH003477 3477 GSM1008564 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseFibroblgm03348LenticonSig lenti-control Signal skin fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were cultured for 10 days (NO DOXYCYCLINE) (Crawford) Signal Fibrobl GM03348 Lenti-Control DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblSig Fibrob DS Fibrobl DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-20 2010-09-20 wgEncodeEH000583 583 GSM816652 Crawford Duke private-noSequence fseq v 1.84, iff_FB8470 hg18 wgEncodeOpenChromDnaseFibroblSig Signal child fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Signal Fibrobl DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseEcc1Est10nm30mSig ECC-1 Estr 30m DS ECC-1 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002564 2564 GSM1008574 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseEcc1Est10nm30mSig Estradiol_10nM_30m Signal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNaseI HS Sequencing Crawford Crawford - Duke University 30 min with 10nM 7b-Estradiol (Crawford) Signal ECC-1 Estradiol 10 nM 30 m DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseEcc1Dm002p1hSig ECC-1 DMSO DS ECC-1 DnaseSeq ENCODE Mar 2012 Freeze 2012-01-31 2012-10-31 wgEncodeEH002555 2555 GSM1008597 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseEcc1Dm002p1hSig DMSO_0.02pct Signal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNaseI HS Sequencing Crawford Crawford - Duke University 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Signal ECC-1 DMSO 0.02% DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseColo829Sig Colo829 DS Colo829 DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002549 2549 GSM1008571 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseColo829Sig Signal malignant melanoma DNaseI HS Sequencing Crawford Crawford - Duke University Signal Colo829 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCllSig CLL DS CLL DnaseSeq ENCODE Jan 2011 Freeze 2010-11-01 2011-08-01 wgEncodeEH001104 1104 GSM816664 Crawford Duke private-noSequence fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromDnaseCllSig Signal chronic lymphocytic leukemia cell, T-cell lymphocyte DNaseI HS Sequencing Crawford Crawford - Duke University Signal CLL DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseChorionSig Chorion DS Chorion DnaseSeq ENCODE June 2010 Freeze 2010-06-14 2009-12-28 2010-09-27 wgEncodeEH000595 595 GSM816628 Crawford Duke fseq v 1.84, iff_generic_female hg18 wgEncodeOpenChromDnaseChorionSig Signal chorion cells (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes. DNaseI HS Sequencing Crawford Crawford - Duke University Signal Chorion DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCerebrumfrontalocSig Cerbrm frnt DS Cerebrum_frontal_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-08 2013-04-07 wgEncodeEH003480 3480 GSM1008578 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseCerebrumfrontalocSig Signal Primary frozen frontal cerebrum tissue from NICHD donor IDs 1104 (Rep B1), 602 (Rep B2), 1442 (Rep B3), all Caucasian DNaseI HS Sequencing Crawford Crawford - Duke University Signal Cerebrum frontal OC DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCerebellumocSig Cerbllm DS Cerebellum_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-09 2013-04-09 wgEncodeEH003481 3481 GSM1008583 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseCerebellumocSig Signal Primary frozen cerebellum tissue from NICHD donor IDs 1104 (Rep B1), 602 (Rep B2), 1442 (Rep B3), all Caucasian DNaseI HS Sequencing Crawford Crawford - Duke University Signal Cerebellum OC DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseAosmcSerumfreeSig AoSMC Srm Free DS AoSMC DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-09 2010-10-08 wgEncodeEH000601 601 GSM816638 Crawford Duke private-noSequence fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnaseAosmcSerumfreeSig serum_free_media Signal aortic smooth muscle cells DNaseI HS Sequencing Crawford Crawford - Duke University Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford) Signal AoSMC Serum Free Media DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseAdultcd4th1Sig CD4+ Th1 DS Adult_CD4_Th1 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002563 2563 GSM1008604 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseAdultcd4th1Sig Signal CD4+ cells isolated from human blood and enriched for Th1 populations DNaseI HS Sequencing Crawford Crawford - Duke University Signal Adult CD4+ Th1 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseAdultcd4th0Sig CD4+ Th0 DS Adult_CD4_Th0 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002562 2562 GSM1008572 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseAdultcd4th0Sig Signal CD4+ cells isolated from human blood and enriched for Th0 populations DNaseI HS Sequencing Crawford Crawford - Duke University Signal Adult CD4+ Th0 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnase8988tSig 8988T DS 8988T DnaseSeq ENCODE Jan 2011 Freeze 2010-11-01 2011-08-01 wgEncodeEH001103 1103 GSM816667 Crawford Duke fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromDnase8988tSig Signal pancreas adenocarcinoma (PA-TU-8988T), "established in 1985 from the liver metastasis of a primary pancreatic adenocarcinoma from a 64-year-old woman" - DSMZ DNaseI HS Sequencing Crawford Crawford - Duke University Signal 8988T DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseSknshSig SK-N-SH DS SK-N-SH DnaseSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEH003483 3483 GSM1008585 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseSknshSig Signal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. DNaseI HS Sequencing Crawford Crawford - Duke University Signal SK-N-SH DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMonocd14Sig CD14 DS Monocytes-CD14+ DnaseSeq ENCODE Jul 2012 Freeze 2012-04-25 2013-01-25 wgEncodeEH003466 3466 GSM1008582 Crawford Duke fseq v 1.84, iff_CD14_monocytes wgEncodeOpenChromDnaseMonocd14Sig Signal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Signal Monocytes CD14+ DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7Sig MCF7 DS MCF-7 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-18 2010-09-18 wgEncodeEH000579 579 GSM816627 Crawford Duke fseq v 1.84, iff_MCF7 hg18 wgEncodeOpenChromDnaseMcf7Sig Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Signal MCF-7 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7RandshrnaSig MCF7 shRNACtrl DS MCF-7 DnaseSeq ENCODE Jul 2012 Freeze 2012-05-02 2013-02-02 wgEncodeEH003468 3468 GSM1008603 Crawford Duke fseq v 1.84, iff_MCF7 wgEncodeOpenChromDnaseMcf7RandshrnaSig Randomized_shRNA_control Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Signal MCF-7 Randomized shRNA Control DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7HypoxlacconSig MCF7 HypxCtrl DS MCF-7 DnaseSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003470 3470 GSM1008565 Crawford Duke fseq v 1.84, iff_MCF7 wgEncodeOpenChromDnaseMcf7HypoxlacconSig Hypoxia_LacAcid_ctrl Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Untreated cells grown along side Hypoxia LacAcid treated cells (Crawford) Signal MCF-7 Hypoxia LacAcid Control DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7HypoxlacSig MCF7 HypxLacA DS MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-17 2012-02-17 wgEncodeEH001745 1745 GSM816670 Crawford Duke fseq v 1.84, iff_MCF7 wgEncodeOpenChromDnaseMcf7HypoxlacSig Hypoxia_LacAcid Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) Signal MCF-7 Hypoxia LacAcid DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7CtcfshrnaSig MCF7 CTCFshRNA DS MCF-7 DnaseSeq ENCODE Jul 2012 Freeze 2012-05-02 2013-02-02 wgEncodeEH003467 3467 GSM1008581 Crawford Duke fseq v 1.84, iff_MCF7 wgEncodeOpenChromDnaseMcf7CtcfshrnaSig CTCF_shRNA_knockdown Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Signal MCF-7 CTCF shRNA knockdown DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseImr90Sig IMR90 DS IMR90 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEH003482 3482 GSM1008586 Crawford Duke fseq v 1.84, iff_generic_female wgEncodeOpenChromDnaseImr90Sig Signal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Signal IMR90 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHuvecSig HUVEC DS HUVEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-24 2010-06-24 wgEncodeEH000548 548 GSM816646 Crawford Duke fseq v 1.84, iff_HUVEC hg18 wgEncodeOpenChromDnaseHuvecSig Signal umbilical vein endothelial cells DNaseI HS Sequencing Crawford Crawford - Duke University Signal HUVEC DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHepg2Sig HepG2 DS HepG2 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-11 2009-12-11 wgEncodeEH000537 537 GSM816662 Crawford Duke fseq v 1.84, iff_HepG2 hg18 wgEncodeOpenChromDnaseHepg2Sig Signal hepatocellular carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University Signal HepG2 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHelas3Sig HeLaS3 DS HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000540 540 GSM816643 Crawford Duke fseq v 1.84, iff_HelaS3 hg18 wgEncodeOpenChromDnaseHelas3Sig Signal cervical carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University Signal HeLa-S3 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHelas3Ifna4hSig HeLaS3 IFNa 4h DS HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-03-21 2009-12-21 wgEncodeEH000577 577 GSM816633 Crawford Duke fseq v 1.84, iff_HelaS3 hg18 wgEncodeOpenChromDnaseHelas3Ifna4hSig IFNa4h Signal cervical carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University 4 hours of 500 U/ml Interferon alpha (Crawford) Signal HeLa-S3 IFN-a 4 h DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCd20ro01794Sig CD20 DS CD20+_RO01794 DnaseSeq ENCODE Jul 2012 Freeze 2012-04-25 2013-01-25 wgEncodeEH003465 3465 GSM1008588 Crawford Duke fseq v 1.84, iff_generic_male wgEncodeOpenChromDnaseCd20ro01794Sig Signal B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Signal B-cells CD20+ RO01794 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseA549Sig A549 DS A549 DnaseSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001095 1095 GSM816649 Crawford Duke fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromDnaseA549Sig Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Signal A549 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562SigV2 K562 DS K562 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH000530 530 GSM816655 Crawford Duke fseq v 1.84, iff_K562 wgEncodeOpenChromDnaseK562SigV2 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Signal K562 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562SahactrlSig K562 SAHA Ctrl DS K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003489 3489 GSM1008580 Crawford Duke fseq v 1.84, iff_K562 wgEncodeOpenChromDnaseK562SahactrlSig SAHA_ctrl Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells grown with DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (DMSO volume is ~ .05% of the total media volume). This is an untreated control. Signal K562 SAHA Control DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562Saha1u72hrSig K562 SAHA 72h DS K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003490 3490 GSM1008558 Crawford Duke fseq v 1.84, iff_K562 wgEncodeOpenChromDnaseK562Saha1u72hrSig SAHA_1uM_72hr Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells grown with 1 uM suberoylanilide hydroxamic acid (SAHA) dissolved in DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (SAHA vehicle volume is ~ .05% of the total media volume). SAHA was provided by Cayman Chemical, item # 10009929. Signal K562 SAHA 1 uM 72 h DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562NabutSig K562 NaBut DS K562 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH002559 2559 GSM1008601 Crawford Duke fseq v 1.84, iff_K562 wgEncodeOpenChromDnaseK562NabutSig NaBut Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Signal K562 NaBut DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562G2mphaseSig K562 G2-M DS K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-06-27 2013-03-27 wgEncodeEH003472 3472 GSM1008567 Crawford Duke fseq v 1.84, iff_K562 wgEncodeOpenChromDnaseK562G2mphaseSig G2-M_phase Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of double DNA content taken as G2 and M cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford) Signal K562 G2-M phase DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562G1phaseSig K562 G1 DS K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003469 3469 GSM1008602 Crawford Duke fseq v 1.84, iff_K562 wgEncodeOpenChromDnaseK562G1phaseSig G1_phase Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of the single DNA content peak taken as G1 cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford) Signal K562 G1 phase DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseH1hescSig H1hESC DS H1-hESC DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-30 2010-06-30 wgEncodeEH000556 556 GSM816632 Crawford Duke fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromDnaseH1hescSig Signal embryonic stem cells DNaseI HS Sequencing Crawford Crawford - Duke University Signal H1-hESC DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm12878Sig GM12878 DS GM12878 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-02-27 2009-11-27 wgEncodeEH000534 534 GSM816665 Crawford Duke fseq v 1.84, iff_GM12878 hg18 wgEncodeOpenChromDnaseGm12878Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing Crawford Crawford - Duke University Signal GM12878 DNaseI HS Density Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseViewSigBo Duke DNaseI HS Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) Regulation 
wgEncodeOpenChromDnaseUrothelBaseOverlapSignalV2 Urothel OS Urothelia DnaseSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH001113 1113 GSM1008605 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseUrothelBaseOverlapSignalV2 Base_Overlap_Signal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Urothelia DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseUrothelUt189BaseOverlapSignalV2 Urothel UT189 OS Urothelia DnaseSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH001114 1114 GSM1008606 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseUrothelUt189BaseOverlapSignalV2 UT189 Base_Overlap_Signal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene DNaseI HS Sequencing Crawford Crawford - Duke University UT189 E.Coli treatment 1 hour, followed by 24 hour incubation An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Urothelia UT189 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseT47dBaseOverlapSignal T-47D OS T-47D DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001109 1109 GSM816673 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseT47dBaseOverlapSignal Base_Overlap_Signal epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. T-47D DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseT47dEst10nm30mBaseOverlapSignal T-47D Estr 30m OS T-47D DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002566 2566 GSM1008576 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseT47dEst10nm30mBaseOverlapSignal Estradiol_10nM_30m Base_Overlap_Signal epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Crawford Crawford - Duke University 30 min with 10nM 7b-Estradiol (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. T-47D Estradiol 10 nM 30 m DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseStellateBaseOverlapSignal Stellate OS Stellate DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001108 1108 GSM816672 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseStellateBaseOverlapSignal Base_Overlap_Signal hepatic stellate cells, liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Stellate DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseRwpe1BaseOverlapSignal RWPE1 OS RWPE1 DnaseSeq ENCODE Mar 2012 Freeze 2011-10-03 2012-07-03 wgEncodeEH002553 2553 GSM1008595 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseRwpe1BaseOverlapSignal Base_Overlap_Signal prostate epithelial DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. RWPE1 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePsoasmuscleocBaseOverlapSignal Psoas muscle OS Psoas_muscle_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003491 3491 GSM1008560 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnasePsoasmuscleocBaseOverlapSignal Base_Overlap_Signal Primary frozen psoas muscle tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1540 (Rep B1), 1863 (Rep B2 FAIRE) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Psoas muscle OC DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseProgfibBaseOverlapSignal ProgFib OS ProgFib DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-17 2010-09-17 wgEncodeEH000576 576 GSM816661 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseProgfibBaseOverlapSignal Base_Overlap_Signal fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. ProgFib DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePhteBaseOverlapSignal pHTE OS pHTE DnaseSeq ENCODE Jan 2011 Freeze 2010-10-18 2011-07-18 wgEncodeEH001099 1099 GSM816647 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnasePhteBaseOverlapSignal Base_Overlap_Signal primary tracheal epithelial cells DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. pHTE DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePanisletsBaseOverlapSignal PanIslets OS PanIslets DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-17 2010-09-17 wgEncodeEH000575 575 GSM816660 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnasePanisletsBaseOverlapSignal Base_Overlap_Signal pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. PanIslets DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePanisdBaseOverlapSignal PanIsletD OS PanIsletD DnaseSeq ENCODE Jan 2011 Freeze 2010-10-29 2011-07-29 wgEncodeEH001102 1102 GSM816666 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnasePanisdBaseOverlapSignal Base_Overlap_Signal dedifferentiated human pancreatic islets from the National Disease Research Interchange (NDRI), same source as PanIslets DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. PanIsletD DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseOsteoblBaseOverlapSignal Osteoblasts OS Osteobl DnaseSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001098 1098 GSM816654 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseOsteoblBaseOverlapSignal Base_Overlap_Signal osteoblasts (NHOst) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Osteoblasts DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseOlfneurosphereBaseOverlapSignal Olfact neuro OS Olf_neurosphere DnaseSeq ENCODE Jul 2012 Freeze 2012-07-02 2013-04-02 wgEncodeEH003475 3475 GSM1008584 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseOlfneurosphereBaseOverlapSignal Base_Overlap_Signal Human olfactory neurosphere-derived cells from mucosal biopsies DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Olf neurosphere DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseNhekBaseOverlapSignal NHEK OS NHEK DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-29 2010-06-29 wgEncodeEH000553 553 GSM816635 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseNhekBaseOverlapSignal Base_Overlap_Signal epidermal keratinocytes DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. NHEK DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseNaivebcellBaseOverlapSignal Naive B cell OS Naive_B_cell DnaseSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-02 wgEncodeEH003478 3478 GSM1008557 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseNaivebcellBaseOverlapSignal Base_Overlap_Signal Naive B cells (IgD+) isolated from de-identified tonsillectomy DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Naive B cell DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMyometrBaseOverlapSignalV2 Myometr OS Myometr DnaseSeq ENCODE June 2010 Freeze 2012-08-24 2010-01-09 2010-10-08 wgEncodeEH000603 603 GSM816630 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseMyometrBaseOverlapSignalV2 Base_Overlap_Signal myometrial cells DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Myometr DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMelanoBaseOverlapSignal Melano OS Melano DnaseSeq ENCODE Jan 2011 Freeze 2010-08-11 2011-05-11 wgEncodeEH000602 602 GSM816631 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseMelanoBaseOverlapSignal Base_Overlap_Signal epidermal melanocytes DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Melano DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMel2183BaseOverlapSignal Mel 2183 OS Mel_2183 DnaseSeq ENCODE Mar 2012 Freeze 2012-01-31 2012-10-31 wgEncodeEH002557 2557 GSM1008599 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseMel2183BaseOverlapSignal Base_Overlap_Signal Melanoma Cell line DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Mel 2183 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMedullod341BaseOverlapSignal Medullo D341 OS Medullo_D341 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH002688 2688 GSM1008577 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseMedullod341BaseOverlapSignal Base_Overlap_Signal Medulloblastoma cell line of neuron or neuron precurosr origin DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Medullo D341 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMedulloBaseOverlapSignal Medullo OS Medullo DnaseSeq ENCODE June 2010 Freeze 2010-06-15 2009-12-16 2010-09-16 wgEncodeEH000574 574 GSM816636 Crawford Duke baseAlignCounts.pl v 1, input was generic_female (should have been male) hg18 wgEncodeOpenChromDnaseMedulloBaseOverlapSignal Base_Overlap_Signal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Medullo DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseLncapBaseOverlapSignal LNCaP OS LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001097 1097 GSM816637 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseLncapBaseOverlapSignal Base_Overlap_Signal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. LNCaP DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseLncapAndroBaseOverlapSignal LNCaP Methyl OS LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001096 1096 GSM816634 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseLncapAndroBaseOverlapSignal androgen Base_Overlap_Signal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Crawford Crawford - Duke University 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. LNCaP Methyltrienolone DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIshikawaEst10nm30mBaseOverlapSignal Ishi Estr 30m OS Ishikawa DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002551 2551 GSM1008593 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseIshikawaEst10nm30mBaseOverlapSignal Estradiol_10nM_30m Base_Overlap_Signal endometrial adenocarcinoma DNaseI HS Sequencing Crawford Crawford - Duke University 30 min with 10nM 7b-Estradiol (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Ishikawa Estradiol 10 nM 30 m DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIshikawaTam10030BaseOverlapSignal Ishi OHTAM OS Ishikawa DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002552 2552 GSM1008594 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseIshikawaTam10030BaseOverlapSignal 4OHTAM_100nM_30m Base_Overlap_Signal endometrial adenocarcinoma DNaseI HS Sequencing Crawford Crawford - Duke University 30 minutes with 100 nM 4-hydroxytamoxifen (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Ishikawa 4-OHTAM 100 nM 30 m DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIpsnihi11BaseOverlapSignal iPS NIHi11 OS iPS_NIHi11 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH002561 2561 GSM1008569 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseIpsnihi11BaseOverlapSignal Base_Overlap_Signal iPS cells derived from AG20443 fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. iPS NIHi11 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIpsnihi7BaseOverlapSignal iPS NIHi7 OS iPS_NIHi7 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEH002558 2558 GSM1008600 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseIpsnihi7BaseOverlapSignal Base_Overlap_Signal iPS cells derived from AG08395 fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. iPS NIHi7 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIpscwru1BaseOverlapSignal iPS CWRU1 OS iPS_CWRU1 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH002560 2560 GSM1008570 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseIpscwru1BaseOverlapSignal Base_Overlap_Signal iPS cells derived from MSC658 fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. iPS CWRU1 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHuh75BaseOverlapSignal Huh-7.5 OS Huh-7.5 DnaseSeq ENCODE Jan 2011 Freeze 2010-12-07 2011-09-07 wgEncodeEH001112 1112 GSM816671 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseHuh75BaseOverlapSignal Base_Overlap_Signal hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Huh-7.5 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHuh7BaseOverlapSignal Huh-7 OS Huh-7 DnaseSeq ENCODE Jan 2011 Freeze 2010-12-07 2011-09-07 wgEncodeEH001111 1111 GSM816641 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseHuh7BaseOverlapSignal Base_Overlap_Signal hepatocellular carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Huh-7 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHtr8BaseOverlapSignal HTR8svn OS HTR8svn DnaseSeq ENCODE Jan 2011 Freeze 2010-11-02 2011-08-02 wgEncodeEH001105 1105 GSM816644 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseHtr8BaseOverlapSignal Base_Overlap_Signal trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HTR8svn DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmtBaseOverlapSignal HSMMtube OS HSMMtube DnaseSeq ENCODE June 2010 Freeze 2010-06-20 2009-12-20 2010-09-19 wgEncodeEH000585 585 GSM816651 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseHsmmtBaseOverlapSignal Base_Overlap_Signal skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HSMMtube DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmfshdBaseOverlapSignal HSMM FSHD OS HSMM_FSHD DnaseSeq ENCODE Mar 2012 Freeze 2012-01-31 2012-10-31 wgEncodeEH002556 2556 GSM1008598 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseHsmmfshdBaseOverlapSignal Base_Overlap_Signal primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HSMM FSHD DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmembBaseOverlapSignal HSMM emb OS HSMM_emb DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002550 2550 GSM1008592 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseHsmmembBaseOverlapSignal Base_Overlap_Signal embryonic myoblast DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HSMM emb DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmBaseOverlapSignal HSMM OS HSMM DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-20 2010-09-19 wgEncodeEH000584 584 GSM816650 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseHsmmBaseOverlapSignal Base_Overlap_Signal skeletal muscle myoblasts DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HSMM DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHpde6e6e7BaseOverlapSignal HPDE6-E6E7 OS HPDE6-E6E7 DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001106 1106 GSM816639 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseHpde6e6e7BaseOverlapSignal Base_Overlap_Signal pancreatic duct cells immortalized with E6E7 gene of HPV DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HPDE6-E6E7 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHmecBaseOverlapSignal HMEC OS HMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001101 1101 GSM816669 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseHmecBaseOverlapSignal Base_Overlap_Signal mammary epithelial cells DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HMEC DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHepatocytesBaseOverlapSignal Hepatocytes OS Hepatocytes DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001107 1107 GSM816663 Crawford Duke baseAlignCounts.pl v 1, input was generic_female (should have been male) hg19 wgEncodeOpenChromDnaseHepatocytesBaseOverlapSignal Base_Overlap_Signal primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Hepatocytes DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHek293tBaseOverlapSignal HEK293T OS HEK293T DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002565 2565 GSM1008573 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseHek293tBaseOverlapSignal Base_Overlap_Signal embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HEK293T DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHeartocBaseOverlapSignal Heart OS Heart_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-05 2013-04-05 wgEncodeEH003479 3479 GSM1008559 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseHeartocBaseOverlapSignal Base_Overlap_Signal Primary frozen heart tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B1 FAIRE), 4548 (Rep B2 FAIRE) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Heart OC DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseH9esBaseOverlapSignal H9ES OS H9ES DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-24 2010-09-23 wgEncodeEH000594 594 GSM816629 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseH9esBaseOverlapSignal Base_Overlap_Signal embryonic stem cell (hESC) H9 DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H9ES DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseH7esBaseOverlapSignal H7hESC OS H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-29 2012-09-29 wgEncodeEH002554 2554 GSM1008596 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseH7esBaseOverlapSignal Base_Overlap_Signal undifferentiated embryonic stem cells DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H7-hESC DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm20000BaseOverlapSignal GM20000 OS GM20000 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-15 wgEncodeEH003485 3485 GSM1008587 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseGm20000BaseOverlapSignal Base_Overlap_Signal lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM20000 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm19240BaseOverlapSignal GM19240 OS GM19240 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000568 568 GSM816648 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseGm19240BaseOverlapSignal Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19240 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm19239BaseOverlapSignalV2 GM19239 OS GM19239 DnaseSeq ENCODE June 2010 Freeze 2012-03-23 2009-10-06 2010-07-06 wgEncodeEH000567 567 GSM816659 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseGm19239BaseOverlapSignalV2 Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19239 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm19238BaseOverlapSignal GM19238 OS GM19238 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000566 566 GSM816658 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseGm19238BaseOverlapSignal Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19238 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm18507BaseOverlapSignal GM18507 OS GM18507 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-19 2010-09-18 wgEncodeEH000581 581 GSM816653 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseGm18507BaseOverlapSignal Base_Overlap_Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM18507 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm13977BaseOverlapSignal GM13977 OS GM13977 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003488 3488 GSM1008556 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseGm13977BaseOverlapSignal Base_Overlap_Signal lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM13977 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm13976BaseOverlapSignal GM13976 OS GM13976 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-16 wgEncodeEH003486 3486 GSM1008591 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseGm13976BaseOverlapSignal Base_Overlap_Signal lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM13976 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm12892BaseOverlapSignal GM12892 OS GM12892 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000565 565 GSM816657 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseGm12892BaseOverlapSignal Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12892 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm12891BaseOverlapSignal GM12891 OS GM12891 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-03 2010-07-03 wgEncodeEH000564 564 GSM816656 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseGm12891BaseOverlapSignal Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12891 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm10266BaseOverlapSignal GM10266 OS GM10266 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-15 wgEncodeEH003484 3484 GSM1008590 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseGm10266BaseOverlapSignal Base_Overlap_Signal lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM10266 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm10248BaseOverlapSignal GM10248 OS GM10248 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003487 3487 GSM1008589 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseGm10248BaseOverlapSignal Base_Overlap_Signal lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM10248 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGlioblaBaseOverlapSignal Gliobla OS Gliobla DnaseSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001100 1100 GSM816668 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseGlioblaBaseOverlapSignal Base_Overlap_Signal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Gliobla DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGcbcellBaseOverlapSignal GC B cell OS GC_B_cell DnaseSeq ENCODE Jul 2012 Freeze 2012-07-02 2013-04-02 wgEncodeEH003474 3474 GSM1008579 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseGcbcellBaseOverlapSignal Base_Overlap_Signal Germinal center B cells (CD77+) isolated from de-identified tonsillectomy DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GC B cell DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFrontalcortexocBaseOverlapSignal Front crtx OS Frontal_cortex_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-06-27 2013-03-27 wgEncodeEH003471 3471 GSM1008566 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseFrontalcortexocBaseOverlapSignal Base_Overlap_Signal Primary ventromedial prefrontal cortex, from KPBBB donor IDs 673 (Rep B1) and 913 (Rep B2) DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Frontal cortex OC DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibropag20443BaseOverlapSignal FibroP OS FibroP_AG20443 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002569 2569 GSM1008561 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseFibropag20443BaseOverlapSignal Base_Overlap_Signal fibroblasts taken from individuals with Parkinson's disease DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. FibroP AG20443 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibropag08396BaseOverlapSignal FibroP OS FibroP_AG08396 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002568 2568 GSM1008562 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseFibropag08396BaseOverlapSignal Base_Overlap_Signal fibroblasts taken from individuals with Parkinson's disease DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. FibroP AG08396 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibropag08395BaseOverlapSignal FibroP OS FibroP_AG08395 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002567 2567 GSM1008575 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseFibropag08395BaseOverlapSignal Base_Overlap_Signal fibroblasts taken from individuals with Parkinson's disease DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. FibroP AG08395 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblgm03348BaseOverlapSignal FibroB OS Fibrobl_GM03348 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-02 wgEncodeEH003476 3476 GSM1008563 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseFibroblgm03348BaseOverlapSignal Base_Overlap_Signal skin fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Fibrobl GM03348 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblgm03348LentimyodBaseOverlapSignal FibroB Lenti-M OS Fibrobl_GM03348 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-02 2013-04-02 wgEncodeEH003473 3473 GSM1008568 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseFibroblgm03348LentimyodBaseOverlapSignal lenti-MyoD Base_Overlap_Signal skin fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were induced for MYOD expression for 10 days with doxycycline and at concentration of 3ug per ml. Standard media was used (and replaced every 2 days) during induction: DMEM, 1% Pen Strep, and 10% FBS. (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Fibrobl GM03348 Lenti-MyoD DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblgm03348LenticonBaseOverlapSignal FibroB Lenti-C OS Fibrobl_GM03348 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-02 wgEncodeEH003477 3477 GSM1008564 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseFibroblgm03348LenticonBaseOverlapSignal lenti-control Base_Overlap_Signal skin fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were cultured for 10 days (NO DOXYCYCLINE) (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Fibrobl GM03348 Lenti-Control DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblBaseOverlapSignal Fibrob OS Fibrobl DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-20 2010-09-20 wgEncodeEH000583 583 GSM816652 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseFibroblBaseOverlapSignal Base_Overlap_Signal child fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Fibrobl DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseEcc1Est10nm30mBaseOverlapSignal ECC-1 Estr 30m OS ECC-1 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002564 2564 GSM1008574 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseEcc1Est10nm30mBaseOverlapSignal Estradiol_10nM_30m Base_Overlap_Signal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNaseI HS Sequencing Crawford Crawford - Duke University 30 min with 10nM 7b-Estradiol (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. ECC-1 Estradiol 10 nM 30 m DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseEcc1Dm002p1hBaseOverlapSignal ECC-1 DMSO OS ECC-1 DnaseSeq ENCODE Mar 2012 Freeze 2012-01-31 2012-10-31 wgEncodeEH002555 2555 GSM1008597 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseEcc1Dm002p1hBaseOverlapSignal DMSO_0.02pct Base_Overlap_Signal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNaseI HS Sequencing Crawford Crawford - Duke University 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. ECC-1 DMSO 0.02% DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseColo829BaseOverlapSignal Colo829 OS Colo829 DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002549 2549 GSM1008571 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseColo829BaseOverlapSignal Base_Overlap_Signal malignant melanoma DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Colo829 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCllBaseOverlapSignal CLL OS CLL DnaseSeq ENCODE Jan 2011 Freeze 2010-11-01 2011-08-01 wgEncodeEH001104 1104 GSM816664 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseCllBaseOverlapSignal Base_Overlap_Signal chronic lymphocytic leukemia cell, T-cell lymphocyte DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. CLL DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseChorionBaseOverlapSignal Chorion OS Chorion DnaseSeq ENCODE June 2010 Freeze 2010-06-14 2009-12-28 2010-09-27 wgEncodeEH000595 595 GSM816628 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseChorionBaseOverlapSignal Base_Overlap_Signal chorion cells (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes. DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Chorion DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCerebrumfrontalocBaseOverlapSignal Cerbrm frnt OS Cerebrum_frontal_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-08 2013-04-07 wgEncodeEH003480 3480 GSM1008578 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseCerebrumfrontalocBaseOverlapSignal Base_Overlap_Signal Primary frozen frontal cerebrum tissue from NICHD donor IDs 1104 (Rep B1), 602 (Rep B2), 1442 (Rep B3), all Caucasian DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Cerebrum frontal OC DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCerebellumocBaseOverlapSignal Cerbllm OS Cerebellum_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-09 2013-04-09 wgEncodeEH003481 3481 GSM1008583 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseCerebellumocBaseOverlapSignal Base_Overlap_Signal Primary frozen cerebellum tissue from NICHD donor IDs 1104 (Rep B1), 602 (Rep B2), 1442 (Rep B3), all Caucasian DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Cerebellum OC DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseAosmcSerumfreeBaseOverlapSignal AoSMC Srm Free OS AoSMC DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-09 2010-10-08 wgEncodeEH000601 601 GSM816638 Crawford Duke private-noSequence baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseAosmcSerumfreeBaseOverlapSignal serum_free_media Base_Overlap_Signal aortic smooth muscle cells DNaseI HS Sequencing Crawford Crawford - Duke University Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. AoSMC Serum Free Media DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseAdultcd4th1BaseOverlapSignal CD4+ Th1 OS Adult_CD4_Th1 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002563 2563 GSM1008604 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseAdultcd4th1BaseOverlapSignal Base_Overlap_Signal CD4+ cells isolated from human blood and enriched for Th1 populations DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Adult CD4+ Th1 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseAdultcd4th0BaseOverlapSignal CD4+ Th0 OS Adult_CD4_Th0 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002562 2562 GSM1008572 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseAdultcd4th0BaseOverlapSignal Base_Overlap_Signal CD4+ cells isolated from human blood and enriched for Th0 populations DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Adult CD4+ Th0 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnase8988tBaseOverlapSignal 8988T OS 8988T DnaseSeq ENCODE Jan 2011 Freeze 2010-11-01 2011-08-01 wgEncodeEH001103 1103 GSM816667 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnase8988tBaseOverlapSignal Base_Overlap_Signal pancreas adenocarcinoma (PA-TU-8988T), "established in 1985 from the liver metastasis of a primary pancreatic adenocarcinoma from a 64-year-old woman" - DSMZ DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. 8988T DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseSknshBaseOverlapSignal SK-N-SH OS SK-N-SH DnaseSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEH003483 3483 GSM1008585 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseSknshBaseOverlapSignal Base_Overlap_Signal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. SK-N-SH DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMonocd14BaseOverlapSignal CD14 OS Monocytes-CD14+ DnaseSeq ENCODE Jul 2012 Freeze 2012-04-25 2013-01-25 wgEncodeEH003466 3466 GSM1008582 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseMonocd14BaseOverlapSignal Base_Overlap_Signal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Monocytes CD14+ DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7BaseOverlapSignal MCF7 OS MCF-7 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-18 2010-09-18 wgEncodeEH000579 579 GSM816627 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseMcf7BaseOverlapSignal Base_Overlap_Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7RandshrnaBaseOverlapSignal MCF7 shRNACtrl OS MCF-7 DnaseSeq ENCODE Jul 2012 Freeze 2012-05-02 2013-02-02 wgEncodeEH003468 3468 GSM1008603 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseMcf7RandshrnaBaseOverlapSignal Randomized_shRNA_control Base_Overlap_Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 Randomized shRNA Control DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7HypoxlacconBaseOverlapSignal MCF7 HypxCtrl OS MCF-7 DnaseSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003470 3470 GSM1008565 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseMcf7HypoxlacconBaseOverlapSignal Hypoxia_LacAcid_ctrl Base_Overlap_Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Untreated cells grown along side Hypoxia LacAcid treated cells (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 Hypoxia LacAcid Control DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7HypoxlacBaseOverlapSignal MCF7 HypxLacA OS MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-17 2012-02-17 wgEncodeEH001745 1745 GSM816670 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseMcf7HypoxlacBaseOverlapSignal Hypoxia_LacAcid Base_Overlap_Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 Hypoxia LacAcid DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7CtcfshrnaBaseOverlapSignal MCF7 CTCFshRNA OS MCF-7 DnaseSeq ENCODE Jul 2012 Freeze 2012-05-02 2013-02-02 wgEncodeEH003467 3467 GSM1008581 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseMcf7CtcfshrnaBaseOverlapSignal CTCF_shRNA_knockdown Base_Overlap_Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 CTCF shRNA knockdown DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseImr90BaseOverlapSignal IMR90 OS IMR90 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEH003482 3482 GSM1008586 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseImr90BaseOverlapSignal Base_Overlap_Signal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. IMR90 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHuvecBaseOverlapSignal HUVEC OS HUVEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-24 2010-06-24 wgEncodeEH000548 548 GSM816646 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseHuvecBaseOverlapSignal Base_Overlap_Signal umbilical vein endothelial cells DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HUVEC DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHepg2BaseOverlapSignal HepG2 OS HepG2 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-11 2009-12-11 wgEncodeEH000537 537 GSM816662 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseHepg2BaseOverlapSignal Base_Overlap_Signal hepatocellular carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HepG2 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHelas3BaseOverlapSignal HeLaS3 OS HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000540 540 GSM816643 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseHelas3BaseOverlapSignal Base_Overlap_Signal cervical carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHelas3Ifna4hBaseOverlapSignal HeLaS3 IFNa 4h OS HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-03-21 2009-12-21 wgEncodeEH000577 577 GSM816633 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseHelas3Ifna4hBaseOverlapSignal IFNa4h Base_Overlap_Signal cervical carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University 4 hours of 500 U/ml Interferon alpha (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 IFN-a 4 h DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCd20ro01794BaseOverlapSignal CD20 OS CD20+_RO01794 DnaseSeq ENCODE Jul 2012 Freeze 2012-04-25 2013-01-25 wgEncodeEH003465 3465 GSM1008588 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseCd20ro01794BaseOverlapSignal Base_Overlap_Signal B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. B-cells CD20+ RO01794 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseA549BaseOverlapSignal A549 OS A549 DnaseSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001095 1095 GSM816649 Crawford Duke baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromDnaseA549BaseOverlapSignal Base_Overlap_Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. A549 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562BaseOverlapSignalV2 K562 OS K562 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH000530 530 GSM816655 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseK562BaseOverlapSignalV2 Base_Overlap_Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562SahactrlBaseOverlapSignal K562 SAHA Ctrl OS K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003489 3489 GSM1008580 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseK562SahactrlBaseOverlapSignal SAHA_ctrl Base_Overlap_Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells grown with DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (DMSO volume is ~ .05% of the total media volume). This is an untreated control. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 SAHA Control DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562Saha1u72hrBaseOverlapSignal K562 SAHA 72h OS K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003490 3490 GSM1008558 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseK562Saha1u72hrBaseOverlapSignal SAHA_1uM_72hr Base_Overlap_Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells grown with 1 uM suberoylanilide hydroxamic acid (SAHA) dissolved in DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (SAHA vehicle volume is ~ .05% of the total media volume). SAHA was provided by Cayman Chemical, item # 10009929. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 SAHA 1 uM 72 h DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562NabutBaseOverlapSignal K562 NaBut OS K562 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH002559 2559 GSM1008601 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseK562NabutBaseOverlapSignal NaBut Base_Overlap_Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 NaBut DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562G2mphaseBaseOverlapSignal K562 G2-M OS K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-06-27 2013-03-27 wgEncodeEH003472 3472 GSM1008567 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseK562G2mphaseBaseOverlapSignal G2-M_phase Base_Overlap_Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of double DNA content taken as G2 and M cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 G2-M phase DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562G1phaseBaseOverlapSignal K562 G1 OS K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003469 3469 GSM1008602 Crawford Duke baseAlignCounts.pl v 1 wgEncodeOpenChromDnaseK562G1phaseBaseOverlapSignal G1_phase Base_Overlap_Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of the single DNA content peak taken as G1 cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 G1 phase DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseH1hescBaseOverlapSignal H1hESC OS H1-hESC DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-30 2010-06-30 wgEncodeEH000556 556 GSM816632 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseH1hescBaseOverlapSignal Base_Overlap_Signal embryonic stem cells DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H1-hESC DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm12878BaseOverlapSignal GM12878 OS GM12878 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-02-27 2009-11-27 wgEncodeEH000534 534 GSM816665 Crawford Duke baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromDnaseGm12878BaseOverlapSignal Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing Crawford Crawford - Duke University An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12878 DNaseI HS Overlap Signal from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseViewPeaks Duke DNaseI HS Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) Regulation 
wgEncodeOpenChromDnaseUrothelPkV2 Urothel Pk Urothelia DnaseSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH001113 1113 GSM1008605 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseUrothelPkV2 Peaks primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Urothelia DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseUrothelUt189PkV2 Urothel UT189 Pk Urothelia DnaseSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH001114 1114 GSM1008606 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseUrothelUt189PkV2 UT189 Peaks primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene DNaseI HS Sequencing Crawford Crawford - Duke University UT189 E.Coli treatment 1 hour, followed by 24 hour incubation Regions of enriched signal in experiment Urothelia UT189 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseT47dPk T-47D Pk T-47D DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001109 1109 GSM816673 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseT47dPk Peaks epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment T-47D DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseT47dEst10nm30mPk T-47D Estr 30m Pk T-47D DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002566 2566 GSM1008576 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseT47dEst10nm30mPk Estradiol_10nM_30m Peaks epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Crawford Crawford - Duke University 30 min with 10nM 7b-Estradiol (Crawford) Regions of enriched signal in experiment T-47D Estradiol 10 nM 30 m DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseStellatePk Stellate Pk Stellate DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001108 1108 GSM816672 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseStellatePk Peaks hepatic stellate cells, liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Stellate DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseRwpe1Pk RWPE1 Pk RWPE1 DnaseSeq ENCODE Mar 2012 Freeze 2011-10-03 2012-07-03 wgEncodeEH002553 2553 GSM1008595 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseRwpe1Pk Peaks prostate epithelial DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment RWPE1 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePsoasmuscleocPk Psoas muscle Pk Psoas_muscle_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003491 3491 GSM1008560 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnasePsoasmuscleocPk Peaks Primary frozen psoas muscle tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1540 (Rep B1), 1863 (Rep B2 FAIRE) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Psoas muscle OC DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseProgfibPk ProgFib Pk ProgFib DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-17 2010-09-17 wgEncodeEH000576 576 GSM816661 Crawford Duke private-noSequence p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseProgfibPk Peaks fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment ProgFib DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePhtePk pHTE Pk pHTE DnaseSeq ENCODE Jan 2011 Freeze 2010-10-18 2011-07-18 wgEncodeEH001099 1099 GSM816647 Crawford Duke private-noSequence p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnasePhtePk Peaks primary tracheal epithelial cells DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment pHTE DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePanisletsPk PanIslets Pk PanIslets DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-17 2010-09-17 wgEncodeEH000575 575 GSM816660 Crawford Duke private-noSequence p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnasePanisletsPk Peaks pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment PanIslets DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnasePanisdPk PanIsletD Pk PanIsletD DnaseSeq ENCODE Jan 2011 Freeze 2010-10-29 2011-07-29 wgEncodeEH001102 1102 GSM816666 Crawford Duke private-noSequence p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnasePanisdPk Peaks dedifferentiated human pancreatic islets from the National Disease Research Interchange (NDRI), same source as PanIslets DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment PanIsletD DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseOsteoblPk Osteoblasts Pk Osteobl DnaseSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001098 1098 GSM816654 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseOsteoblPk Peaks osteoblasts (NHOst) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Osteoblasts DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseOlfneurospherePk Olfact neuro Pk Olf_neurosphere DnaseSeq ENCODE Jul 2012 Freeze 2012-07-02 2013-04-02 wgEncodeEH003475 3475 GSM1008584 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseOlfneurospherePk Peaks Human olfactory neurosphere-derived cells from mucosal biopsies DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Olf neurosphere DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseNhekPk NHEK Pk NHEK DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-29 2010-06-29 wgEncodeEH000553 553 GSM816635 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseNhekPk Peaks epidermal keratinocytes DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment NHEK DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseNaivebcellPk Naive B cell Pk Naive_B_cell DnaseSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-02 wgEncodeEH003478 3478 GSM1008557 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseNaivebcellPk Peaks Naive B cells (IgD+) isolated from de-identified tonsillectomy DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Naive B cell DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMyometrPk Myometr Pk Myometr DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-09 2010-10-08 wgEncodeEH000603 603 GSM816630 Crawford Duke private-noSequence p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseMyometrPk Peaks myometrial cells DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Myometr DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMelanoPk Melano Pk Melano DnaseSeq ENCODE Jan 2011 Freeze 2010-08-11 2011-05-11 wgEncodeEH000602 602 GSM816631 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseMelanoPk Peaks epidermal melanocytes DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Melano DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMel2183Pk Mel 2183 Pk Mel_2183 DnaseSeq ENCODE Mar 2012 Freeze 2012-01-31 2012-10-31 wgEncodeEH002557 2557 GSM1008599 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseMel2183Pk Peaks Melanoma Cell line DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Mel 2183 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMedullod341Pk Medullo D341 Pk Medullo_D341 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH002688 2688 GSM1008577 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseMedullod341Pk Peaks Medulloblastoma cell line of neuron or neuron precurosr origin DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Medullo D341 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMedulloPk Medullo Pk Medullo DnaseSeq ENCODE June 2010 Freeze 2010-06-15 2009-12-16 2010-09-16 wgEncodeEH000574 574 GSM816636 Crawford Duke p-value cutoff: 0.05, input was generic_female (should have been male) hg18 wgEncodeOpenChromDnaseMedulloPk Peaks medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Medullo DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseLncapPk LNCaP Pk LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001097 1097 GSM816637 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseLncapPk Peaks prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment LNCaP DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseLncapAndroPk LNCaP Methyl Pk LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001096 1096 GSM816634 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseLncapAndroPk androgen Peaks prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Crawford Crawford - Duke University 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Regions of enriched signal in experiment LNCaP Methyltrienolone DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIshikawaEst10nm30mPk Ishi Estr 30m Pk Ishikawa DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002551 2551 GSM1008593 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseIshikawaEst10nm30mPk Estradiol_10nM_30m Peaks endometrial adenocarcinoma DNaseI HS Sequencing Crawford Crawford - Duke University 30 min with 10nM 7b-Estradiol (Crawford) Regions of enriched signal in experiment Ishikawa Estradiol 10 nM 30 m DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIshikawaTam10030Pk Ishi OHTAM Pk Ishikawa DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002552 2552 GSM1008594 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseIshikawaTam10030Pk 4OHTAM_100nM_30m Peaks endometrial adenocarcinoma DNaseI HS Sequencing Crawford Crawford - Duke University 30 minutes with 100 nM 4-hydroxytamoxifen (Crawford) Regions of enriched signal in experiment Ishikawa 4-OHTAM 100 nM 30 m DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIpsnihi11Pk iPS NIHi11 Pk iPS_NIHi11 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH002561 2561 GSM1008569 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseIpsnihi11Pk Peaks iPS cells derived from AG20443 fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment iPS NIHi11 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIpsnihi7Pk iPS NIHi7 Pk iPS_NIHi7 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEH002558 2558 GSM1008600 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseIpsnihi7Pk Peaks iPS cells derived from AG08395 fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment iPS NIHi7 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseIpscwru1Pk iPS CWRU1 Pk iPS_CWRU1 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH002560 2560 GSM1008570 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseIpscwru1Pk Peaks iPS cells derived from MSC658 fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment iPS CWRU1 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHuh75Pk Huh-7.5 Pk Huh-7.5 DnaseSeq ENCODE Jan 2011 Freeze 2010-12-07 2011-09-07 wgEncodeEH001112 1112 GSM816671 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseHuh75Pk Peaks hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Huh-7.5 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHuh7Pk Huh-7 Pk Huh-7 DnaseSeq ENCODE Jan 2011 Freeze 2010-12-07 2011-09-07 wgEncodeEH001111 1111 GSM816641 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseHuh7Pk Peaks hepatocellular carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Huh-7 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHtr8Pk HTR8svn Pk HTR8svn DnaseSeq ENCODE Jan 2011 Freeze 2010-11-02 2011-08-02 wgEncodeEH001105 1105 GSM816644 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseHtr8Pk Peaks trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HTR8svn DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmtPk HSMMtube Pk HSMMtube DnaseSeq ENCODE June 2010 Freeze 2010-06-20 2009-12-20 2010-09-19 wgEncodeEH000585 585 GSM816651 Crawford Duke private-noSequence p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseHsmmtPk Peaks skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HSMMtube DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmfshdPk HSMM FSHD Pk HSMM_FSHD DnaseSeq ENCODE Mar 2012 Freeze 2012-01-31 2012-10-31 wgEncodeEH002556 2556 GSM1008598 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseHsmmfshdPk Peaks primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HSMM FSHD DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmembPk HSMM emb Pk HSMM_emb DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002550 2550 GSM1008592 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseHsmmembPk Peaks embryonic myoblast DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HSMM emb DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHsmmPk HSMM Pk HSMM DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-20 2010-09-19 wgEncodeEH000584 584 GSM816650 Crawford Duke private-noSequence p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseHsmmPk Peaks skeletal muscle myoblasts DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HSMM DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHpde6e6e7Pk HPDE6-E6E7 Pk HPDE6-E6E7 DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001106 1106 GSM816639 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseHpde6e6e7Pk Peaks pancreatic duct cells immortalized with E6E7 gene of HPV DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HPDE6-E6E7 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHmecPk HMEC Pk HMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001101 1101 GSM816669 Crawford Duke private-noSequence p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseHmecPk Peaks mammary epithelial cells DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HMEC DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHepatocytesPk Hepatocytes Pk Hepatocytes DnaseSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001107 1107 GSM816663 Crawford Duke p-value cutoff: 0.05, input was generic_female (should have been male) hg19 wgEncodeOpenChromDnaseHepatocytesPk Peaks primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Hepatocytes DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHek293tPk HEK293T Pk HEK293T DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002565 2565 GSM1008573 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseHek293tPk Peaks embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HEK293T DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHeartocPk Heart Pk Heart_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-05 2013-04-05 wgEncodeEH003479 3479 GSM1008559 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseHeartocPk Peaks Primary frozen heart tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B1 FAIRE), 4548 (Rep B2 FAIRE) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Heart OC DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseH9esPk H9ES Pk H9ES DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-24 2010-09-23 wgEncodeEH000594 594 GSM816629 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseH9esPk Peaks embryonic stem cell (hESC) H9 DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment H9ES DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseH7esPk H7hESC Pk H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-29 2012-09-29 wgEncodeEH002554 2554 GSM1008596 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseH7esPk Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment H7-hESC DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm20000Pk GM20000 Pk GM20000 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-15 wgEncodeEH003485 3485 GSM1008587 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseGm20000Pk Peaks lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM20000 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm19240Pk GM19240 Pk GM19240 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000568 568 GSM816648 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseGm19240Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM19240 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm19239Pk GM19239 Pk GM19239 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000567 567 GSM816659 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseGm19239Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM19239 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm19238Pk GM19238 Pk GM19238 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000566 566 GSM816658 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseGm19238Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM19238 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm18507Pk GM18507 Pk GM18507 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-19 2010-09-18 wgEncodeEH000581 581 GSM816653 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseGm18507Pk Peaks lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM18507 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm13977Pk GM13977 Pk GM13977 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003488 3488 GSM1008556 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseGm13977Pk Peaks lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM13977 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm13976Pk GM13976 Pk GM13976 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-16 wgEncodeEH003486 3486 GSM1008591 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseGm13976Pk Peaks lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM13976 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm12892Pk GM12892 Pk GM12892 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000565 565 GSM816657 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseGm12892Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM12892 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm12891Pk GM12891 Pk GM12891 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-03 2010-07-03 wgEncodeEH000564 564 GSM816656 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseGm12891Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM12891 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm10266Pk GM10266 Pk GM10266 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-15 wgEncodeEH003484 3484 GSM1008590 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseGm10266Pk Peaks lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM10266 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm10248Pk GM10248 Pk GM10248 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003487 3487 GSM1008589 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseGm10248Pk Peaks lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM10248 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGlioblaPk Gliobla Pk Gliobla DnaseSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001100 1100 GSM816668 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseGlioblaPk Peaks glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Gliobla DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGcbcellPk GC B cell Pk GC_B_cell DnaseSeq ENCODE Jul 2012 Freeze 2012-07-02 2013-04-02 wgEncodeEH003474 3474 GSM1008579 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseGcbcellPk Peaks Germinal center B cells (CD77+) isolated from de-identified tonsillectomy DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GC B cell DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFrontalcortexocPk Front crtx Pk Frontal_cortex_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-06-27 2013-03-27 wgEncodeEH003471 3471 GSM1008566 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseFrontalcortexocPk Peaks Primary ventromedial prefrontal cortex, from KPBBB donor IDs 673 (Rep B1) and 913 (Rep B2) DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Frontal cortex OC DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibropag20443Pk FibroP Pk FibroP_AG20443 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002569 2569 GSM1008561 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseFibropag20443Pk Peaks fibroblasts taken from individuals with Parkinson's disease DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment FibroP AG20443 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibropag08396Pk FibroP Pk FibroP_AG08396 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002568 2568 GSM1008562 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseFibropag08396Pk Peaks fibroblasts taken from individuals with Parkinson's disease DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment FibroP AG08396 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibropag08395Pk FibroP Pk FibroP_AG08395 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002567 2567 GSM1008575 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseFibropag08395Pk Peaks fibroblasts taken from individuals with Parkinson's disease DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment FibroP AG08395 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblgm03348Pk FibroB Pk Fibrobl_GM03348 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-02 wgEncodeEH003476 3476 GSM1008563 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseFibroblgm03348Pk Peaks skin fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Fibrobl GM03348 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblgm03348LentimyodPk FibroB Lenti-M Pk Fibrobl_GM03348 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-02 2013-04-02 wgEncodeEH003473 3473 GSM1008568 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseFibroblgm03348LentimyodPk lenti-MyoD Peaks skin fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were induced for MYOD expression for 10 days with doxycycline and at concentration of 3ug per ml. Standard media was used (and replaced every 2 days) during induction: DMEM, 1% Pen Strep, and 10% FBS. (Crawford) Regions of enriched signal in experiment Fibrobl GM03348 Lenti-MyoD DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblgm03348LenticonPk FibroB Lenti-C Pk Fibrobl_GM03348 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-02 wgEncodeEH003477 3477 GSM1008564 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseFibroblgm03348LenticonPk lenti-control Peaks skin fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University GM03348 skin fibroblasts (Coriell) were transduced with an induceable lentivirus (pAK111-TRE-3xflag hMyoD-T2A-dsRed) containing get inducible MyoD. Cells were selected in 1ug per ml puro (Sigma catalog P8833) to obtain a pure cell population. Cells were cultured for 10 days (NO DOXYCYCLINE) (Crawford) Regions of enriched signal in experiment Fibrobl GM03348 Lenti-Control DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseFibroblPk Fibrob Pk Fibrobl DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-12-20 2010-09-20 wgEncodeEH000583 583 GSM816652 Crawford Duke private-noSequence p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseFibroblPk Peaks child fibroblast DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Fibrobl DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseEcc1Est10nm30mPk ECC-1 Estr 30m Pk ECC-1 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002564 2564 GSM1008574 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseEcc1Est10nm30mPk Estradiol_10nM_30m Peaks epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNaseI HS Sequencing Crawford Crawford - Duke University 30 min with 10nM 7b-Estradiol (Crawford) Regions of enriched signal in experiment ECC-1 Estradiol 10 nM 30 m DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseEcc1Dm002p1hPk ECC-1 DMSO Pk ECC-1 DnaseSeq ENCODE Mar 2012 Freeze 2012-01-31 2012-10-31 wgEncodeEH002555 2555 GSM1008597 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseEcc1Dm002p1hPk DMSO_0.02pct Peaks epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNaseI HS Sequencing Crawford Crawford - Duke University 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 DMSO 0.02% DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseColo829Pk Colo829 Pk Colo829 DnaseSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002549 2549 GSM1008571 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseColo829Pk Peaks malignant melanoma DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Colo829 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCllPk CLL Pk CLL DnaseSeq ENCODE Jan 2011 Freeze 2010-11-01 2011-08-01 wgEncodeEH001104 1104 GSM816664 Crawford Duke private-noSequence p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseCllPk Peaks chronic lymphocytic leukemia cell, T-cell lymphocyte DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment CLL DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseChorionPk Chorion Pk Chorion DnaseSeq ENCODE June 2010 Freeze 2010-06-14 2009-12-28 2010-09-27 wgEncodeEH000595 595 GSM816628 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseChorionPk Peaks chorion cells (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes. DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Chorion DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCerebrumfrontalocPk Cerbrm frnt Pk Cerebrum_frontal_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-08 2013-04-07 wgEncodeEH003480 3480 GSM1008578 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseCerebrumfrontalocPk Peaks Primary frozen frontal cerebrum tissue from NICHD donor IDs 1104 (Rep B1), 602 (Rep B2), 1442 (Rep B3), all Caucasian DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Cerebrum frontal OC DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCerebellumocPk Cerbllm Pk Cerebellum_OC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-09 2013-04-09 wgEncodeEH003481 3481 GSM1008583 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseCerebellumocPk Peaks Primary frozen cerebellum tissue from NICHD donor IDs 1104 (Rep B1), 602 (Rep B2), 1442 (Rep B3), all Caucasian DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Cerebellum OC DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseAosmcSerumfreePk AoSMC Srm Free Pk AoSMC DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-09 2010-10-08 wgEncodeEH000601 601 GSM816638 Crawford Duke private-noSequence p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseAosmcSerumfreePk serum_free_media Peaks aortic smooth muscle cells DNaseI HS Sequencing Crawford Crawford - Duke University Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford) Regions of enriched signal in experiment AoSMC Serum Free Media DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseAdultcd4th1Pk CD4+ Th1 Pk Adult_CD4_Th1 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002563 2563 GSM1008604 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseAdultcd4th1Pk Peaks CD4+ cells isolated from human blood and enriched for Th1 populations DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Adult CD4+ Th1 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseAdultcd4th0Pk CD4+ Th0 Pk Adult_CD4_Th0 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-03 2012-11-03 wgEncodeEH002562 2562 GSM1008572 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseAdultcd4th0Pk Peaks CD4+ cells isolated from human blood and enriched for Th0 populations DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Adult CD4+ Th0 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnase8988tPk 8988T Pk 8988T DnaseSeq ENCODE Jan 2011 Freeze 2010-11-01 2011-08-01 wgEncodeEH001103 1103 GSM816667 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnase8988tPk Peaks pancreas adenocarcinoma (PA-TU-8988T), "established in 1985 from the liver metastasis of a primary pancreatic adenocarcinoma from a 64-year-old woman" - DSMZ DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment 8988T DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseSknshPk SK-N-SH Pk SK-N-SH DnaseSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEH003483 3483 GSM1008585 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseSknshPk Peaks neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment SK-N-SH DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMonocd14Pk CD14 Pk Monocytes-CD14+ DnaseSeq ENCODE Jul 2012 Freeze 2012-04-25 2013-01-25 wgEncodeEH003466 3466 GSM1008582 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseMonocd14Pk Peaks Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment Monocytes CD14+ DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7Pk MCF7 Pk MCF-7 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-18 2010-09-18 wgEncodeEH000579 579 GSM816627 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseMcf7Pk Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment MCF-7 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7RandshrnaPk MCF7 shRNACtrl Pk MCF-7 DnaseSeq ENCODE Jul 2012 Freeze 2012-05-02 2013-02-02 wgEncodeEH003468 3468 GSM1008603 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseMcf7RandshrnaPk Randomized_shRNA_control Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Regions of enriched signal in experiment MCF-7 Randomized shRNA Control DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7HypoxlacconPk MCF7 HypxCtrl Pk MCF-7 DnaseSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003470 3470 GSM1008565 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseMcf7HypoxlacconPk Hypoxia_LacAcid_ctrl Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Untreated cells grown along side Hypoxia LacAcid treated cells (Crawford) Regions of enriched signal in experiment MCF-7 Hypoxia LacAcid Control DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7HypoxlacPk MCF7 HypxLacA Pk MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-17 2012-02-17 wgEncodeEH001745 1745 GSM816670 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseMcf7HypoxlacPk Hypoxia_LacAcid Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) Regions of enriched signal in experiment MCF-7 Hypoxia LacAcid DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseMcf7CtcfshrnaPk MCF7 CTCFshRNA Pk MCF-7 DnaseSeq ENCODE Jul 2012 Freeze 2012-05-02 2013-02-02 wgEncodeEH003467 3467 GSM1008581 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseMcf7CtcfshrnaPk CTCF_shRNA_knockdown Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Regions of enriched signal in experiment MCF-7 CTCF shRNA knockdown DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseImr90Pk IMR90 Pk IMR90 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEH003482 3482 GSM1008586 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseImr90Pk Peaks fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment IMR90 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHuvecPk HUVEC Pk HUVEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-24 2010-06-24 wgEncodeEH000548 548 GSM816646 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseHuvecPk Peaks umbilical vein endothelial cells DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HUVEC DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHepg2Pk HepG2 Pk HepG2 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-20 2009-12-20 wgEncodeEH000537 537 GSM816662 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseHepg2Pk Peaks hepatocellular carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HepG2 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHelas3Pk HeLaS3 Pk HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000540 540 GSM816643 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseHelas3Pk Peaks cervical carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment HeLa-S3 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseHelas3Ifna4hPk HeLaS3 IFNa 4h Pk HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-18 2010-09-18 wgEncodeEH000577 577 GSM816633 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseHelas3Ifna4hPk IFNa4h Peaks cervical carcinoma DNaseI HS Sequencing Crawford Crawford - Duke University 4 hours of 500 U/ml Interferon alpha (Crawford) Regions of enriched signal in experiment HeLa-S3 IFN-a 4 h DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseCd20ro01794Pk CD20 Pk CD20+_RO01794 DnaseSeq ENCODE Jul 2012 Freeze 2012-04-25 2013-01-25 wgEncodeEH003465 3465 GSM1008588 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseCd20ro01794Pk Peaks B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment B-cells CD20+ RO01794 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseA549Pk A549 Pk A549 DnaseSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001095 1095 GSM816649 Crawford Duke p-value cutoff: 0.05 hg19 wgEncodeOpenChromDnaseA549Pk Peaks epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment A549 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562PkV2 K562 Pk K562 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH000530 530 GSM816655 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseK562PkV2 Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment K562 DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562SahactrlPk K562 SAHA Ctrl Pk K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003489 3489 GSM1008580 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseK562SahactrlPk SAHA_ctrl Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells grown with DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (DMSO volume is ~ .05% of the total media volume). This is an untreated control. Regions of enriched signal in experiment K562 SAHA Control DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562Saha1u72hrPk K562 SAHA 72h Pk K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003490 3490 GSM1008558 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseK562Saha1u72hrPk SAHA_1uM_72hr Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells grown with 1 uM suberoylanilide hydroxamic acid (SAHA) dissolved in DMSO supplementing RPMI1640 + 10% FBS media for 72 hours (SAHA vehicle volume is ~ .05% of the total media volume). SAHA was provided by Cayman Chemical, item # 10009929. Regions of enriched signal in experiment K562 SAHA 1 uM 72 h DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562NabutPk K562 NaBut Pk K562 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH002559 2559 GSM1008601 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseK562NabutPk NaBut Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Regions of enriched signal in experiment K562 NaBut DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562G2mphasePk K562 G2-M Pk K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-06-27 2013-03-27 wgEncodeEH003472 3472 GSM1008567 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseK562G2mphasePk G2-M_phase Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of double DNA content taken as G2 and M cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford) Regions of enriched signal in experiment K562 G2-M phase DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseK562G1phasePk K562 G1 Pk K562 DnaseSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003469 3469 GSM1008602 Crawford Duke p-value cutoff: 0.05 wgEncodeOpenChromDnaseK562G1phasePk G1_phase Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Crawford Crawford - Duke University Cells were synchronized and subjected to FACS sorting based on DNA content with the peak of the single DNA content peak taken as G1 cells. The intermediate DNA content cells between G2-M and G1 phases were excluded. (Crawford) Regions of enriched signal in experiment K562 G1 phase DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseH1hescPk H1hESC Pk H1-hESC DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-30 2010-06-30 wgEncodeEH000556 556 GSM816632 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseH1hescPk Peaks embryonic stem cells DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment H1-hESC DNaseI HS Peaks from ENCODE/Duke Regulation 
wgEncodeOpenChromDnaseGm12878Pk GM12878 Pk GM12878 DnaseSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-20 2009-12-20 wgEncodeEH000534 534 GSM816665 Crawford Duke p-value cutoff: 0.05 hg18 wgEncodeOpenChromDnaseGm12878Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing Crawford Crawford - Duke University Regions of enriched signal in experiment GM12878 DNaseI HS Peaks from ENCODE/Duke Regulation 
encodeRegions ENCODE Pilot Regions Used for ENCODE Pilot Project (1%) Mapping and Sequencing Description This track depicts target regions for the NHGRI ENCODE project. The long-term goal of this project is to identify all functional elements in the human genome sequence to facilitate a better understanding of human biology and disease. During the pilot phase, 44 regions comprising 30 Mb &mdash; approximately 1% of the human genome &mdash; have been selected for intensive study to identify, locate and analyze functional elements within the regions. These targets are being studied by a diverse public research consortium to test and evaluate the efficacy of various methods, technologies, and strategies for locating genomic features. The outcome of this initial phase will form the basis for a larger-scale effort to analyze the entire human genome. See the NHGRI target selection process web page for a description of how the target regions were selected. To open a UCSC Genome Browser with a menu for selecting ENCODE regions on the human genome, use ENCODE Regions in the UCSC Browser. The UCSC resources provided for the ENCODE project are described on the UCSC ENCODE Portal. Credits Thanks to the NHGRI ENCODE project for providing this initial set of data. 
ensGene Ensembl Genes Ensembl Genes Genes and Gene Predictions Description These gene predictions were generated by Ensembl. For more information on the different gene tracks, see our Genes FAQ. Methods For a description of the methods used in Ensembl gene predictions, please refer to Hubbard et al. (2002), also listed in the References section below. Data access Ensembl Gene data can be explored interactively using the Table Browser or the Data Integrator. For local downloads, the genePred format files for hg19 are available in our downloads directory as ensGene.txt.gz or in our genes download directory in GTF format. For programmatic access, the data can be queried from the REST API or directly from our public MySQL servers. Instructions on this method are available on our MySQL help page and on our blog. Previous versions of this track can be found on our archive download server. Credits We would like to thank Ensembl for providing these gene annotations. For more information, please see Ensembl&#39s genome annotation page. References Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161 
evofold EvoFold EvoFold Predictions of RNA Secondary Structure Genes and Gene Predictions Description This track shows RNA secondary structure predictions made with the EvoFold program, a comparative method that exploits the evolutionary signal of genomic multiple-sequence alignments for identifying conserved functional RNA structures. Display Conventions and Configuration Track elements are labeled using the convention ID_strand_score. When zoomed out beyond the base level, secondary structure prediction regions are indicated by blocks, with the stem-pairing regions shown in a darker shade than unpaired regions. Arrows indicate the predicted strand. When zoomed in to the base level, the specific secondary structure predictions are shown in parenthesis format. The confidence score for each position is indicated in grayscale, with darker shades corresponding to higher scores. The details page for each track element shows the predicted secondary structure (labeled SS anno), together with details of the multiple species alignments at that location. Substitutions relative to the human sequence are color-coded according to their compatibility with the predicted secondary structure (see the color legend on the details page). Each prediction is assigned an overall score and a sequence of position-specific scores. The overall score measures evidence for any functional RNA structures in the given region, while the position-specific scores (0 - 9) measure the confidence of the base-specific annotations. Base-pairing positions are annotated with the same pair symbol. The offsets are provided to ease visual navigation of the alignment in terms of the human sequence. The offset is calculated (in units of ten) from the start position of the element on the positive strand or from the end position when on the negative strand. The graphical display may be filtered to show only those track elements with scores that meet or exceed a certain threshhold. To set a threshhold, type the minimum score into the text box at the top of the description page. Methods Evofold makes use of phylogenetic stochastic context-free grammars (phylo-SCFGs), which are combined probabilistic models of RNA secondary structure and primary sequence evolution. The predictions consist of both a specific RNA secondary structure and an overall score. The overall score is essentially a log-odd score between a phylo-SCFG modeling the constrained evolution of stem-pairing regions and one which only models unpaired regions. The predictions for this track were based on the conserved elements of an 8-way vertebrate alignment of the human, chimpanzee, mouse, rat, dog, chicken, zebrafish, and Fugu assemblies. NOTE: These predictions were originally computed on the hg17 (May 2004) human assembly, from which the hg16 (July 2003), hg18 (May 2006), and hg19 (Feb 2009) predictions were lifted. As a result, the multiple alignments shown on the track details pages may differ from the 8-way alignments used for their prediction. Additionally, some weak predictions have been eliminated from the set displayed on hg18 and hg19. The hg17 prediction set corresponds exactly to the set analyzed in the EvoFold paper referenced below. Credits The EvoFold program and browser track were developed by Jakob Skou Pedersen of the UCSC Genome Bioinformatics Group, now at Aarhus University, Denmark. The RNA secondary structure is rendered using the VARNA Java applet. References EvoFold Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006 Apr;2(4):e33. PMID: 16628248; PMC: PMC1440920 Phylo-SCFGs Knudsen B, Hein J. RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics. 1999 Jun;15(6):446-54. PMID: 10383470 Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. 2004;32(16):4925-36. PMID: 15448187; PMC: PMC519121 PhastCons Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216 
evsEsp6500 EVS Variants NHLBI GO Exome Sequencing Project (ESP) - Variants from 6,503 Exomes Variation Description The goal of the NHLBI GO Exome Sequencing Project (ESP) is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders. The current data release (ESP6500SI-V2-SSA137) through the EVS website is taken from 6,503 samples drawn from multiple ESP cohorts and represents all of the ESP exome variant data. Data in this track were obtained from the EVS Release Version: v.0.0.25. (Feb. 7, 2014). Display Conventions In &quot;dense&quot; mode, a vertical line is drawn at the position of each variant. In &quot;pack&quot; and &quot;full&quot; modes, in addition to the vertical line, a label to the left shows the reference allele first and variant alleles below (A = red, C = blue, G = green, T = magenta, Indels = black). Hovering the pointer over any variant will prompt the display of the occurrences numbers for each allele in the Exome Sequencing Project's database. Clicking on any variant will result in full details of that variant being displayed as well as possible links to the ESP and dbSNP databases. Methods Sequences were aligned to NCBI build 37 human genome reference using BWA. PCR duplicates were removed using Picard. Alignments were recalibrated using GATK. Lane-level indel realignments and base alignment quality (BAQ) adjustments were applied. All data were simultaneously analyzed for exome SNP variants at the University of Michigan (by the Abecasis Laboratory). SNPs were called using a two-step approach. First, genotype likelihood files (GLFs) were generated using samtools pileup on individual BAM files. Next, we used glfMultiples, a multi-sample variant caller, to generate initial SNP calls. Details of the likelihood model implemented in glfMultiples are given in Li, et al., 2011 (in the section entitled "Identifying Potential Polymorphic Sites"). The Michigan SNP calling pipeline is available at: http://genome.sph.umich.edu/wiki/UMAKE. This pipeline makes diploid calls for pseudo-autosomal regions of male samples and haploid calls for the rest of the chromosome. Female samples have diploid calls for all regions on the X chromosome. SNPs were filtered by a machine-learning technique called support vector machine (SVM) classification (for a detailed description, see Filter Status). Small INDEL variants were analyzed at the Broad Institute (by the Genome Sequencing and Analysis group) using the GATK variation discovery pipeline following the guidelines in the GATK best practices v4. More specifically, each BAM was reduced to create a Reduced BAM, and then INDELs were discovered by analyzing all samples simultaneously with the GATK UnifiedGenotyper, and subsequently filtered by the GATK Variant Quality Score Recalibration (VQSR) filtering model, again following the V4 best practices. The INDEL genotypes for X and Y chromosomes were adjusted to be consistent with the samples' genders. Female samples have diploid calls for all regions on the X chromosome. Male samples have diploid calls for pseudo-autosomal regions on the X chromosome and haploid calls for the rest of the X chromosome and on the Y chromosome as well. However, the INDEL calls for the ESP data are preliminary and not as robust as the SNP calls at this point. Users are advised to keep this difference in mind when applying the ESP data to research studies. All SNPs and INDELs were further annotated by SeattleSeqAnnotation137, and the variant annotations at the coding-DNA and protein levels mostly follow HGVS notations. The SNP calls are included in the release of dbSNP build 138. The full dataset is described in Fu, et al., 2013, and a subset of the data (i.e., 2,500 exomes) was published by the ESP Population Genetics and Statistical Analysis Working Group in Tennessen, et al., 2012. Credits The authors would like to thank the NHLBI GO Exome Sequencing Project and its ongoing studies which produced and provided exome variant calls for comparison: the Lung GO Sequencing Project (HL-102923), the WHI Sequencing Project (HL-102924), the Broad GO Sequencing Project (HL-102925), the Seattle GO Sequencing Project (HL-102926), and the Heart GO Sequencing Project (HL-103010). Contact: &#101;&#118;&#115;&#115;&#101;&#114;&#118;&#101;&#114;&#064;&#117;&#119;&#046;&#101;&#100;&#117; References Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J et al. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 2013 Jan 10;493(7431):216-20. PMID: 23201682; PMC: PMC3676746 Li Y, Sidore C, Kang HM, Boehnke M, Abecasis GR. Low-coverage sequencing: implications for design of complex trait association studies. Genome Res. 2011 Jun;21(6):940-51. PMID: 21460063; PMC: PMC3106327 Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012 Jul 6;337(6090):64-9. PMID: 22604720; PMC: PMC3708544 
exac ExAC Exome Aggregation Consortium (ExAC) Variants and Calling Regions Variation Description This track shows over 8.75 million single nucleotide variants (SNVs) and over 600,000 insertions or deletions (indels) as well as exome variant calling regions in 60,706 unrelated individuals sequenced as part of various population genetic and disease-specific studies collected by the Exome Aggregation Consortium (ExAC), release 0.3. Raw data from all studies have been reprocessed through a unified pipeline and jointly variant-called to increase consistency across projects. For more information on the processing pipeline and population annotations, see the release files README.release0.3 and README.population_annotations respectively. Display Conventions For the variants subtrack, in &quot;dense&quot; mode, a vertical line is drawn at the position of each variant. In &quot;pack&quot; mode, ref and alt alleles are displayed to the left of a vertical line with colored portions corresponding to allele counts. Hovering the mouse pointer over a variant pops up a display of alleles and counts. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server. The underlying data files for this track are called ExAC.r0.3.sites.vep.hg19.vcf.gz and exacCallingRegions.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/ExAC/exacCallingRegions.bb -chrom=chr6 -start=0 -end=1000000 stdout Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Credits Thanks to the Exome Aggregation Consortium for making these data available in advance of publication. The data are released under a Fort Lauderdale Agreement; please email &#101;x&#111;&#109;&#101;&#99;&#111;&#110;&#115;o&#114;&#116;&#105;&#117;&#109;&#64;&#103;&#109;&#97;&#105;&#108;.c&#111;m with any further questions and please reference the 2016 paper. References Exome Aggregation Consortium (ExAC), Cambridge, MA (http://exac.broadinstitute.org), release 0.3, downloaded Mar. 30, 2015. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 17;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 
exacVariants ExAC Variants Exome Aggregation Consortium (ExAC) - Variants from 60,706 Exomes Variation 
exacRegions ExAC Regions ExAC Calling Regions Variation 
exomeProbesets Exome Probesets Exome Capture Probesets and Targeted Region Mapping and Sequencing Description This set of tracks shows the genomic positions of probes and targets from a full suite of in-solution-capture target enrichment exome kits for Next Generation Sequencing (NGS) applications. Also known as exome sequencing or whole exome sequencing (WES), this technique allows high-throughput parallel sequencing of all exons (e.g., coding regions of genes which affect protein function), constituting about 1% of the human genome, or approximately 30 million base pairs. The tracks are intended to show the major differences in target genomic regions between the different exome capture kits from the major players in the NGS sequencing market: Illumina Inc., Roche NimbleGen Inc., Agilent Technologies Inc., MGI Tech, Twist Bioscience, and Integrated DNA Technologies Inc.. Display Conventions and Configuration Items are shaded according to manufacturing company: IDT (Integrated DNA Technologies) Twist Biosciences MGI Tech (Beijing Genomics Institute) Roche NimbleGen Agilent Technologies Illumina Tracks labeled as Probes (P) indicate the footprint of the oligonucleotide probes mapped to the human genome. This is the technically relevant targeted region by the assay. However, the sequenced region will be bigger than this since flanking sequences are sequenced as well. Tracks labeled as Target Regions (T) indicate the genomic regions targeted by the assay. This is the biologically relevant target region. Not all targeted regions will necessarily be sequenced perfectly; there might be some capture bias at certain locations. The Target Regions are those normally used for coverage analysis. Note that most exome probesets are available on hg19 only. If you are working with hg38 and cannot find a particular probeset there, try to go to hg19, configure the same track, and see if it exists there. If you cannot find an array, do not hesitate to send us an email with the name of the manufacturer website with the probe file. If an array is available on hg19 but not on hg38 and you need it for your work, we can lift the locations. Our mailing list can be reached at genome@soe.ucsc.edu. Methods The capture of the genomic regions of interest using in-solution capture, is achieved through the hybridization of a set of probes (oligonucleotides) with a sample of fragmented genomic DNA in a solution environment. The probes hybridize selectively to the genomic regions of interest which, after a process of exclusion of the non-selective DNA material, can be pulled down and sequenced, enabling selective DNA sequencing of the genomic regions of interest (e.g., exons). In-solution capture sequencing is a sensitive method to detect single nucleotide variants, insertions and deletions, and copy number variations. #kit, #kit table, #kit th, #kit td { border: 1px solid black; border-collapse: collapse; padding: 2px; } Kit Targeted Region Databases Used for Design Year of Release IDT - xGen Exome Research Panel V1.0 39 Mb Coding sequences from RefSeq (19,396 genes) 2015 IDT - xGen Exome Research Panel V2.0 34 Mb Coding sequences from RefSeq 109 (19,433 genes) 2020 Twist - RefSeq Exome Panel 3.6 Mb Curated subset of protein coding genes from CCDS N/A Twist - Core Exome Panel 33 Mb Protein coding genes from CCDS N/A Twist - Comprehensive Exome Panel 36.8 Mb Protein coding genes from RefSeq, CCDS, and GENCODE 2020 Twist - Exome Panel 2.0 36.4 Mb Protein coding genes from RefSeq, CCDS, and GENCODE 2021 MGI - Easy Exome Capture V4 59 Mb CCDS, GENCODE, RefSeq, and miRBase N/A MGI - Easy Exome Capture V5 69 Mb CCDS, GENCODE, RefSeq, miRBase, and MGI Clinical Database N/A Agilent - SureSelect Clinical Research Exome 54 Mb Disease-associated regions from OMIM, HGMD, and ClinVar 2014 Agilent - SureSelect Clinical Research Exome V2 63.7 Mb Disease-associated regions from OMIM, HGMD, ClinVar, and ACMG 2017 Agilent - SureSelect Focused Exome 12 Mb Disease-associated regions from HGMD, OMIM and ClinVar 2016 Agilent - SureSelect All Exon V4 51 Mb Coding regions from CCDS, RefSeq, and GENCODE v6, miRBase v17, TCGA v6, and UCSC known genes 2011 Agilent - SureSelect All Exon V4 + UTRs 71 Mb Coding regions and 5' and 3' UTR sequences from CCDS, RefSeq, and GENCODE v6, regions from miRBase v17, TCGA v6, and UCSC known genes 2011 Agilent - SureSelect All Exon V5 50 Mb Coding regions from Refseq, GENCODE, UCSC, TCGA, CCDS, and miRBase (21.522 genes) 2012 Agilent - SureSelect All Exon V5 + UTRs 74 Mb Coding regions and 5' and 3' UTR sequences from Refseq, GENCODE, UCSC, TCGA, CCDS, and miRBase (21.522 genes) 2012 Agilent - SureSelect All Exon V6 r2 60 Mb Coding regions from RefSeq, CCDS, GENCODE, HGMD, and OMIM 2016 Agilent - SureSelect All Exon V6 + COSMIC r2 66 Mb Coding regions from RefSeq, CCDS, GENCODE, HGMD, and OMIM, and targets from both TCGA and COSMIC 2016 Agilent - SureSelect All Exon V6 + UTR r2 75 Mb Coding regions and 5' and 3' UTR sequences from RefSeq, GENCODE, CCDS, and UCSC known genes,and miRNAs and lncRNA sequences 2016 Agilent - SureSelect All Exon V7 35.7 Mb Coding regions from RefSeq, CCDS, GENCODE, and UCSC known genes 2018 Roche - KAPA HyperExome 43Mb Coding regions from CCDS, RefSeq, Ensembl, GENCODE,and variants from ClinVar 2020 Roche - SeqCap EZ Exome V3 64 Mb Coding regions from RefSeq RefGene CDS, CCDS, and miRBase v14 databases, plus coverage of 97% Vega, 97% Gencode, and 99% Ensembl 2018 Roche - SeqCap EZ Exome V3 + UTR 92 Mb Coding sequences from RefSeq RefGene, CCDS, and miRBase v14, plus coverage of 97% Vega, 97% Gencode, and 99% Ensembl and UTRs from RefSeq RefGene table from UCSC GRCh37/hg19 March 2012 and Ensembl (GRCh37 v64) 2018 Roche - SeqCap EZ MedExome 47 Mb Coding sequences from CCDS 17, RefSeq, Ensembl 76, VEGA 56, GENCODE 20, miRBase 21, and disease-associated regions from GeneTests, ClinVar, and based on customer input 2014 Roche - SeqCap EZ MedExome + Mito 47 Mb Coding sequences and mitochondrial genes from CCDS 17, RefSeq, Ensembl 76, VEGA 56, GENCODE 20 and miRBase 21, disease-associated regions from GeneTests, ClinVar, and based on customer input 2014 Illumina - Nextera DNA Exome V1.2 45 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENCODE v19 2015 Illumina - Nextera Rapid Capture Exome 37 Mb 212,158 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19 2013 Illumina - Nextera Rapid Capture Exome V1.2 37 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENCODE v12 2014 Illumina - Nextera Rapid Capture Expanded Exome 66 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENCODE v12 2013 Illumina - TruSeq DNA Exome V1.2 45 Mb Coding regions from RefSeq, CCDS, and Ensembl 2017 Illumina - TruSeq Rapid Exome V1.2 45 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENECODE v19 2015 Illumina - TruSight ONE V1.1 12 Mb Coding regions of 6700 genes from HGMD, OMIM, and GeneTest 2017 Illumina - TruSight Exome 7 Mb Disease-causing mutations as curated by HGMD 2017 Illumina - AmpliSeq Exome Panel N/A CCDS coding regions 2019 Data Access The raw data can be explored interactively with the Table Browser or cross-referenced with Data Integrator. The data can be accessed from scripts through our API, with track names found in the Table Schema page for each subtrack after "Primary Table:". For downloading the data, the annotations are stored in bigBed files that can be accessed at our download directory. Regional or the whole genome text annotations can be obtained using our utility bigBedToBed. Instructions for downloading utilities can be found here. Credits Thanks to Illumina (U.S.), Roche NimbleGen, Inc. (U.S.), Agilent Technologies (U.S.), MGI Tech (Beijing Genomics Institute, China), Twist Bioscience (U.S.), and Integrated DNA Technologies (IDT), Inc. (U.S.) for making these data available and to Tiana Pereira, Pranav Muthuraman, Began Nguy and Anna Benet-Pages for enginering these tracks. 
Twist_Exome_RefSeq_Targets Twist RefSeq T Twist - RefSeq Exome Panel Target Regions Mapping and Sequencing 
Twist_Exome_Target2 Twist Exome 2.0 Twist - Exome 2.0 Panel Target Regions Mapping and Sequencing 
Twist_Exome_Target Twist Core T Twist - Core Exome Panel Target Regions Mapping and Sequencing 
Twist_Comp_Exome_Target Twist Compr. T Twist - Comprehensive Exome Panel Target Regions Mapping and Sequencing 
trusight_exome_manifest_a TruSight Target Illumina - TruSight Exome Target Regions Mapping and Sequencing 
TruSight_One_v1 TruSight One V1.1 T Illumina - TruSight ONE V1.1 Target Regions Mapping and Sequencing 
TSOne_Expanded_BED_v2 TruSight One Exp. V2.0 T Illumina - TruSight ONE Expanded V2.0 Target Regions Mapping and Sequencing 
truseq-rapid-exome-targeted-regions-manifest-v1-2 TruSeq Rapid v1.2 T Illumina - TruSeq Rapid Exome V1.2 Target Regions Regions Mapping and Sequencing 
truseq-dna-exome-targeted-manifest-v1-2 TruSeq DNA V1.2 T Illumina - TruSeq DNA Exome V1.2 Target Regions Mapping and Sequencing 
Agilent_Human_Exon_V6_UTRs_Regions SureSelect SureSel. V6+UTR T Agilent - SureSelect All Exon V6 + UTR r2 Target Regions Mapping and Sequencing 
Agilent_Human_Exon_V7_Regions SureSel. V7 T Agilent - SureSelect All Exon V7 Target Regions Mapping and Sequencing 
Agilent_Human_Exon_V7_Covered SureSel. V7 P Agilent - SureSelect All Exon V7 Covered by Probes Mapping and Sequencing 
Agilent_Human_Exon_V6_UTRs_Covered SureSel. V6+UTR P Agilent - SureSelect All Exon V6 + UTR r2 Covered by Probes Mapping and Sequencing 
Agilent_Human_Exon_V6_COSMIC_Regions SureSel. V6+COSMIC T Agilent - SureSelect All Exon V6 + COSMIC r2 Target Regions Mapping and Sequencing 
Agilent_Human_Exon_V6_COSMIC_Covered SureSel. V6+COSMIC P Agilent - SureSelect All Exon V6 + COSMIC r2 Covered by Probes Mapping and Sequencing 
Agilent_Human_Exon_V6_Regions SureSel. V6 T Agilent - SureSelect All Exon V6 r2 Target Regions Mapping and Sequencing 
Agilent_Human_Exon_V6_Covered SureSel. V6 P Agilent - SureSelect All Exon V6 r2 Covered by Probes Mapping and Sequencing 
Agilent_Human_Exon_V5_UTRs_Regions SureSel. V5+UTR T Agilent - SureSelect All Exon V5 + UTRs Target Regions Mapping and Sequencing 
Agilent_Human_Exon_V5_UTRs_Covered SureSel. V5+UTR P Agilent - SureSelect All Exon V5 + UTRs Covered by Probes Mapping and Sequencing 
Agilent_Human_Exon_V5_Regions SureSel. V5 T Agilent - SureSelect All Exon V5 Target Regions Mapping and Sequencing 
Agilent_Human_Exon_V5_Covered SureSel. V5 P Agilent - SureSelect All Exon V5 Covered by Probes Mapping and Sequencing 
Agilent_Human_Exon_V4_UTRs_Regions SureSel. V4+UTR T Agilent - SureSelect All Exon V4 + UTRs Target Regions Mapping and Sequencing 
Agilent_Human_Exon_V4_UTRs_Covered SureSel. V4+UTR P Agilent - SureSelect All Exon V4 + UTRs Covered by Probe Mapping and Sequencing 
Agilent_Human_Exon_V4_Regions SureSel. V4 T Agilent - SureSelect All Exon V4 Target Regions Mapping and Sequencing 
Agilent_Human_Exon_V4_Covered SureSel. V4 P Agilent - SureSelect All Exon V4 Covered by Probes Mapping and Sequencing 
Agilent_Human_Exon_Focused_Regions SureSel. Focused T Agilent - SureSelect Focused Exome Target Regions Mapping and Sequencing 
Agilent_Human_Exon_Focused_Covered SureSel. Focused P Agilent - SureSelect Focused Exome Covered by Probes Mapping and Sequencing 
Agilent_Human_Exon_Clinical_Research_V2_Regions SureSel. Clinical V2 T Agilent - SureSelect Clinical Research Exome V2 Target Mapping and Sequencing 
Agilent_Human_Exon_Clinical_Research_V2_Covered SureSel. Clinical V2 P Agilent - SureSelect Clinical Research Exome V2 Covered by Probes Mapping and Sequencing 
Agilent_Human_Exon_Clinical_Research_Regions SureSel. Clinical T Agilent - SureSelect Clinical Research Exome Target Regions Mapping and Sequencing 
Agilent_Human_Exon_Clinical_Research_Covered SureSel. Clinical P Agilent - SureSelect Clinical Research Exome Covered by Probes Mapping and Sequencing 
SeqCap_EZ_ExomeV3_Plus_UTR_hg19_primary_annotated SeqCap EZ V3 UTR T Roche - SeqCap EZ Exome V3 + UTR Primary Target Regions Mapping and Sequencing 
SeqCap_EZ_ExomeV3_Plus_UTR_hg19_capture_annotated SeqCap EZ V3 UTR P Roche - SeqCap EZ Exome V3 + UTR Capture Probe Footprint Mapping and Sequencing 
SeqCap_EZ_Exome_v3_hg19_primary SeqCap EZ V3 T Roche - SeqCap EZ Exome V3 Primary Target Regions Mapping and Sequencing 
SeqCap_EZ_Exome_v3_hg19_capture SeqCap EZ V3 P Roche - SeqCap EZ Exome V3 Capture Probe Footprint Mapping and Sequencing 
SeqCap-EZ_MedExomePlusMito_hg19_empirical_targets SeqCap EZ Med+Mito T Roche - SeqCap EZ MedExome + Mito Empirical Target Regions Mapping and Sequencing 
SeqCap-EZ_MedExomePlusMito_hg19_capture SeqCap EZ Med+Mito P Roche - SeqCap EZ MedExome + Mito Capture Probe Footprint Mapping and Sequencing 
SeqCap-EZ_MedExome_hg19_empirical_targets SeqCap EZ Med T Roche - SeqCap EZ MedExome Empirical Target Regions Mapping and Sequencing 
SeqCap-EZ_MedExome_hg19_capture_targets SeqCap EZ Med P Roche - SeqCap EZ MedExome Capture Probe Footprint Mapping and Sequencing 
nexterarapidcapture_exome_targetedregions_v1 Nextera Rapid V1.2 T Illumina - Nextera Rapid Capture Exome V1.2 Target Regions Mapping and Sequencing 
nexterarapidcapture_exome_targetedregions Nextera Rapid T Illumina - Nextera Rapid Capture Exome Target Regions Mapping and Sequencing 
nexterarapidcapture_expandexome_targetedregions Nextera Rapid Exp. T Illumina - Nextera Rapid Capture Expanded Exome Target Regions Mapping and Sequencing 
nextera-dna-exome-targeted-regions-manifest-v1-2 Nextera DNA V1.2 T Illumina - Nextera DNA Exome V1.2 Target Regions Mapping and Sequencing 
MGI_Exome_Capture_V5 MGI Easy V5 T MGI - Easy Exome Capture V5 Target Regions Mapping and Sequencing 
MGI_Exome_Capture_V4 MGI Easy V4 T MGI - Easy Exome Capture V4 Target Regions Mapping and Sequencing 
KAPA_HyperExome_hg19_primary_targets KAPA Hyper T Roche - KAPA HyperExome Primary Target Regions Mapping and Sequencing 
KAPA_HyperExome_hg19_capture_targets KAPA Hyper P Roche - KAPA HyperExome Capture Probe Footprint Mapping and Sequencing 
xGen_research_Targets_V2 IDT xGen V2.0 T IDT - xGen Exome Research Panel V2.0 Target Regions Mapping and Sequencing 
xGen_Research_Probes_V2 IDT xGen V2.0 P IDT -  xGen Exome Research Panel V2.0 Probes Mapping and Sequencing 
xGen_Research_Targets IDT xGen V1.0 T IDT - xGen Exome Research Panel V1.0 Target Regions Mapping and Sequencing 
xGen_Research_Probes IDT xGen v1.0 P IDT -  xGen Exome Research Panel V1.0 Probes Mapping and Sequencing 
AmpliSeq-Target AmpliSeq Target Illumina - AmpliSeq Exome Panel Target Regions Mapping and Sequencing 
exoniphy Exoniphy Exoniphy Human/Mouse/Rat/Dog Genes and Gene Predictions Description The exoniphy program identifies evolutionarily conserved protein-coding exons in a multiple alignment using a phylogenetic hidden Markov model (phylo-HMM), a statistical model that simultaneously describes exon structure and exon evolution. This track shows exoniphy predictions for the human Feb. 2009 (GRCh37), mouse Jul. 2007 (mm9), rat Nov. 2004 (rn4), and dog May 2005 (canFam2) genomes, as aligned by the multiz program. For this track, only alignments on the &quot;syntenic net&quot; between human and each other species were considered. Methods For a description of exoniphy, see Siepel et al., 2004. Multiz is described in Blanchette et al., 2004. The alignment chaining methods behind the &quot;syntenic net&quot; are described in Kent et al., 2003. Acknowledgments Thanks to Melissa Hubisz of the Siepel lab at Cornell University for producing these predictions. References Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Siepel A, Haussler D. Computational identification of evolutionarily conserved exons. RECOMB '04. 2004. 
fishClones FISH Clones Clones Placed on Cytogenetic Map Using FISH Mapping and Sequencing Description This track shows the location of fluorescent in situ hybridization (FISH)-mapped clones along the assembly sequence. The locations of these clones were obtained from the NCBI Human BAC Resource here. Earlier versions of this track obtained this information directly from the paper Cheung, et al. (2001). More information about the BAC clones, including how they may be obtained, can be found at the Human BAC Resource and the Clone Registry web sites hosted by NCBI. To view Clone Registry information for a clone, click on the clone name at the top of the details page for that item. Using the Filter This track has a filter that can be used to change the color or include/exclude the display of a dataset from an individual lab. This is helpful when many items are shown in the track display, especially when only some are relevant to the current task. The filter is located at the top of the track description page, which is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu. To use the filter: In the pulldown menu, select the lab whose data you would like to highlight or exclude in the display. Choose the color or display characteristic that will be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display clones from the lab selected in the pulldown list. If &quot;include&quot; is selected, the browser will display clones only from the selected lab. When you have finished configuring the filter, click the Submit button. Credits We would like to thank all of the labs that have contributed to this resource: Fred Hutchinson Cancer Research Center (FHCRC) National Cancer Institute (NCI) Roswell Park Cancer Institute (RPCI) The Wellcome Trust Sanger Institute (SC) Cedars-Sinai Medical Center (CSMC) Los Alamos National Laboratory (LANL) UC San Francisco Cancer Center (UCSF) References Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001 Feb 15;409(6822):953-8. PMID: 11237021 
fosEndPairs Fosmid End Pairs Fosmid End Pairs Mapping and Sequencing Description A valid pair of fosmid end sequences must be at least 30 kb but no more than 50 kb away from each other. The orientation of the first fosmid end sequence must be &quot;+&quot; and the orientation of the second fosmid end sequence must be &quot;-&quot;. Note: For hg19 and hg18 assemblies, the Fosmid End Pairs track is a main track under the &quot;Mapping and Sequencing&quot; track category. On the hg38 assembly, the FOSMID End Pairs track is a subtrack within the Clone Ends track under the &quot;Mapping and Sequencing&quot; track category. Under the list of subtracks on the Clone Ends Track Settings page, the FOSMID End Pairs track is now named &quot;WIBR-2 Fosmid library.&quot; With the WIBR-2 Fosmid library track setting on full, individual clone end mapping items are listed in the browser; click into any item to see details from NCBI. Methods End sequences were trimmed at the NCBI using ssahaCLIP written by Jim Mullikin. Trimmed fosmid end sequences were placed on the assembled sequence using Jim Kent's blat program. Credits Sequencing of the fosmid ends was done at the Eli & Edythe L. Broad Institute of MIT and Harvard University. Clones are available through the BACPAC Resources Center at Children's Hospital Oakland Research Institute (CHORI). 
wgEncodeFsuRepliChip FSU Repli-chip Replication Timing by Repli-chip from ENCODE/FSU Regulation Description This track displays replication timing and was produced as part of the ENCODE Project. Replication timing refers to the order in which DNA is duplicated during the synthesis phase of the cell cycle and is correlated with the expression of genes and the structure of chromosomes. This track shows genome-wide assessment of DNA replication timing in cell lines using NimbleGen tiling CGH microarrays. Each experiment represents the relative enrichment of early versus late S-phase nascent strands in a given cell line, with data represented as a loess-smoothed function of individual timing values at probes spaced at even intervals across the genome. Regions with high values indicate domains of early replication where initiation occurs earlier in S-phase. Display Conventions and Configuration The graph displays a wavelet-smoothed signal of mean early/late S-phase ratios. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Experimental Procedures Cells were grown according to the approved ENCODE cell culture protocols. Methods for replication timing profile creation and analysis are described in detail in Hiratani et al. (2008) and Ryba et al. (June 2011). Methods for individual stages of extraction, hybridization, scanning and processing are summarized below. For the extraction protocol, replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays. Replication intermediates were prepared from cells that were first pulse-labeled with 5'-bromo-2'-deoxyuridine (BrdU) and then sorted into early and late stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates newly synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). The hybridization set used the NimbleGen standard hybridization protocol. Cy3- and Cy5-labeled DNA samples (6 &micro;g each) were co-hybridized to Nimblegen CGH arrays containing evenly-spaced oligonucleotide probes across the human genome, with a median probe spacing of 1.1-5.8 kb. No differences in smoothed data have been detected with probe densities from 100 bp to 5.8 kb. The NimbleGen MS 200 2 &micro;m resolution scanner and GenePix software were used per NimbleGen's standard scanning protocol. Data Processing NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates, in which early- and late-replicating DNA were labeled reciprocally, were loess-normalized to remove signal intensity-dependent bias. The data were then scaled to a reference data set to have the same median absolute deviation and then averaged (limma package, R/Bioconductor). The mean early/late ratios were used to generate a final smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300 kb span) for each chromosome using basic functions in the statistical language R. Verification Technical data quality was assessed by verifying high autocorrelation between neighboring timing values. Biological identity was confirmed by verifying consistent early or late replication by PCR at individual loci, as well as uniformity in replication profiles between replicate experiments. Release Notes This is Release 2 (July 2012) of this track. It adds 6 more data sets including additional replicates for H1-hESC and H7-hESC and all new data for the iPS skin fibroblast bio samples. Credits These data were generated by the Florida State University ENCODE group. Contact: David M. Gilbert References Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S et al. Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res. 2010 Feb;20(2):155-69. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Sch&#252;beler D, Gilbert DM. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 Oct 7;6(10):e245. Pope BD, Tsumagari K, Battaglia D, Ryba T, Hiratani I, Ehrlich M, Gilbert DM. DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy. PLoS One. 2011;6(11):e27413. Ryba T, Battaglia D, Pope BD, Hiratani I, Gilbert DM. Genome-scale analysis of replication timing: from bench to bioinformatics. Nat Protoc. 2011 Jun;6(6):870-95. Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 2010 Jun;20(6):761-70. Ryba T, Hiratani I, Sasaki T, Battaglia D, Kulik M, Zhang J, Dalton S, Gilbert DM. Replication timing: a fingerprint for cell identity and pluripotency. PLoS Comput Biol. 2011 Oct;7(10):e1002225. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeFsuRepliChipIpshfib2ips5WaveSignalRep2 iPS_hFib2_iPS5 2 iPS_hFib2_iPS5 RepliChip ENCODE Jul 2012 Freeze 2012-07-28 2012-07-28 wgEncodeEH003045 3045 Gilbert FSU hFib-iPS5_R2_294709 Cell line from GQ. Daley lab, Cell. 2008 Sep 5.134(5):877-86 GPL13190 2 wgEncodeFsuRepliChipIpshfib2ips5WaveSignalRep2 WaveSignal induced pluripotent stem cell line 5 derived from skin fibroblast of a 30 year old donor, same donor as iPS_hFib2_iPS4 Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases iPS hFib2 iPS5 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipIpshfib2ips5WaveSignalRep1 iPS_hFib2_iPS5 1 iPS_hFib2_iPS5 RepliChip ENCODE Jul 2012 Freeze 2012-07-28 2012-07-28 wgEncodeEH003045 3045 Gilbert FSU hFib-iPS5_R1_294988 Cell line from GQ. Daley lab, Cell. 2008 Sep 5.134(5):877-86 GPL13190 1 wgEncodeFsuRepliChipIpshfib2ips5WaveSignalRep1 WaveSignal induced pluripotent stem cell line 5 derived from skin fibroblast of a 30 year old donor, same donor as iPS_hFib2_iPS4 Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases iPS hFib2 iPS5 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipIpshfib2ips4WaveSignalRep2 iPS_hFib2_iPS4 2 iPS_hFib2_iPS4 RepliChip ENCODE Jul 2012 Freeze 2012-07-28 2012-07-28 wgEncodeEH003044 3044 Gilbert FSU hFib-iPS4_R2_293676 Cell line from GQ. Daley lab, Cell. 2008 Sep 5.134(5):877-86 GPL13190 2 wgEncodeFsuRepliChipIpshfib2ips4WaveSignalRep2 WaveSignal induced pluripotent stem cell line 4 derived from skin fibroblast of a 30 year old donor, same donor as iPS_hFib2_iPS5 Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases iPS hFib2 iPS4 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipIpshfib2ips4WaveSignalRep1 iPS_hFib2_iPS4 1 iPS_hFib2_iPS4 RepliChip ENCODE Jul 2012 Freeze 2012-07-28 2012-07-28 wgEncodeEH003044 3044 Gilbert FSU hFib-iPS4_R1_294988 Cell line from GQ. Daley lab, Cell. 2008 Sep 5.134(5):877-86 GPL13190 1 wgEncodeFsuRepliChipIpshfib2ips4WaveSignalRep1 WaveSignal induced pluripotent stem cell line 4 derived from skin fibroblast of a 30 year old donor, same donor as iPS_hFib2_iPS5 Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases iPS hFib2 iPS4 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipH9esWaveSignalRep1 H9ES 1 H9ES RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002772 2772 Gilbert FSU H9hESC_R1_294986 GPL13190 1 wgEncodeFsuRepliChipH9esWaveSignalRep1 WaveSignal embryonic stem cell (hESC) H9 Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases H9ES Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipH7esWaveSignalRep2 H7-hESC 2 H7-hESC RepliChip ENCODE Jul 2012 Freeze 2012-07-28 2012-07-28 wgEncodeEH002771 2771 Gilbert FSU H7-hESC_R2_15470902 GPL13190 2 wgEncodeFsuRepliChipH7esWaveSignalRep2 WaveSignal undifferentiated embryonic stem cells Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases H7-hESC Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipH7esWaveSignalRep1 H7-hESC 1 H7-hESC RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002771 2771 Gilbert FSU H7hESC_R1_294986 GPL13190 1 wgEncodeFsuRepliChipH7esWaveSignalRep1 WaveSignal undifferentiated embryonic stem cells Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases H7-hESC Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipGm06990WaveSignalRep2 GM06990 2 GM06990 RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002769 2769 Gilbert FSU GM06990_R2_434444_A02_62510 GPL14965 2 wgEncodeFsuRepliChipGm06990WaveSignalRep2 WaveSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human 3x720k Whole Genome CGH Shows smoothed wavelet over all phases GM06990 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipGm06990WaveSignalRep1 GM06990 1 GM06990 RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002769 2769 Gilbert FSU GM06990_R1_434444_A01_62510 GPL14965 1 wgEncodeFsuRepliChipGm06990WaveSignalRep1 WaveSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human 3x720k Whole Genome CGH Shows smoothed wavelet over all phases GM06990 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipBg02esWaveSignalRep2 BG02ES 2 BG02ES RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002768 2768 Gilbert FSU BG02hESC_R2_294988 GPL13190 2 wgEncodeFsuRepliChipBg02esWaveSignalRep2 WaveSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases BG02ES Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipBg02esWaveSignalRep1 BG02ES 1 BG02ES RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002768 2768 Gilbert FSU BG02hESC_R1_293676 GPL13190 1 wgEncodeFsuRepliChipBg02esWaveSignalRep1 WaveSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases BG02ES Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipImr90WaveSignalRep1 IMR90 1 IMR90 RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002774 2774 Gilbert FSU IMR90_R1_369858-3A01 GPL14965 1 wgEncodeFsuRepliChipImr90WaveSignalRep1 WaveSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human 3x720k Whole Genome CGH Shows smoothed wavelet over all phases IMR90 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipHelas3WaveSignalRep1 HeLa-S3 1 HeLa-S3 RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002773 2773 Gilbert FSU HeLaS3_R1_369858A02_2 GPL14965 1 wgEncodeFsuRepliChipHelas3WaveSignalRep1 WaveSignal cervical carcinoma Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human 3x720k Whole Genome CGH Shows smoothed wavelet over all phases HeLa-S3 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipH1hescWaveSignalRep3 H1-hESC 3 H1-hESC RepliChip ENCODE Jul 2012 Freeze 2012-07-28 2012-07-28 wgEncodeEH002770 2770 Gilbert FSU H1-hESC_R3_294986 GPL13190 3 wgEncodeFsuRepliChipH1hescWaveSignalRep3 WaveSignal embryonic stem cells Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases H1-hESC Repli-chip Wavelet-smoothed Signal Rep 3 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipH1hescWaveSignalRep2 H1-hESC 2 H1-hESC RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002770 2770 Gilbert FSU H1hESC_R2_293676 GPL13190 2 wgEncodeFsuRepliChipH1hescWaveSignalRep2 WaveSignal embryonic stem cells Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases H1-hESC Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Regulation 
wgEncodeFsuRepliChipH1hescWaveSignalRep1 H1-hESC 1 H1-hESC RepliChip ENCODE Mar 2012 Freeze 2012-03-02 2012-03-02 wgEncodeEH002770 2770 Gilbert FSU H1hESC_R1_15470602 GPL13190 1 wgEncodeFsuRepliChipH1hescWaveSignalRep1 WaveSignal embryonic stem cells Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University Human CGH 2.1M Whole-Genome Tiling v2.0D Array Shows smoothed wavelet over all phases H1-hESC Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Regulation 
gad GAD View Genetic Association Studies of Complex Diseases and Disorders Phenotype and Literature Disclaimer The Genetic Association Database (GAD) is intended for use primarily by medical scientists and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the GAD database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. These data are provided by the GAD and do not represent any additional curation by UCSC. Description After serving the scientific community for more than 10 years, the Genetic Association Database (GAD) has been retired and all data is "frozen" as of 09/01/2014. The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The goal of the database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature. If the track is displayed in &quot;pack&quot; or &quot;full&quot; mode, mousing over an entry of this track will show a pop-up message listing all associated diseases. In &quot;full&quot; mode, each feature is labeled with the associated disease class code (as defined below). Disease Class Disease Class Code AGING AGE CANCER CAN CARDIOVASCULAR CARD CHEMICAL DEPENDENCY CHEM DEVELOPMENTAL DEV HEMATOLOGICAL HEM IMMUNE IMM INFECTION INF METABOLIC MET MITOCHONDRIAL MITO NEUROLOGICAL NEUR NORMAL VARIATION NV OTHER OTH PHARMACOGENOMICS PHARM PSYCHIATRIC PSY RENAL REN REPRODUCTION REP UNKNOWN UNK VISION VIS Methods Study data are recorded in the context of official human gene nomenclature with additional molecular reference numbers and links. The data are gene-centered; that is, each record is based on a gene or marker. For example, if a study investigated six genes for a particular disorder, there will be six records. Gene information is standardized and annotated with molecular information, enabling integration with other molecular and genomic data resources. Data Data are added to GAD on a periodic basis by the curator or investigators. A majority of the records in GAD are extracted from the online HuGE Navigator database, which is sponsored by the Centers for Disease Control and Prevention. HuGE Navigator provides access to a continuously updated, curated knowledge base of gene-disease associations, meta-analyses, and related information on genes and diseases extracted from NCBI PubMed. A gene-centered view is available via Genopedia. Contacts For more information on this dataset, contact Kevin G. Becker, PhD, Yongqing Zhang, PhD, and John Garner, MS, from the DNA Array Unit, NIA, NIH. References Becker KG, Barnes KC, Bright TJ, Wang AS. The Genetic Association Database. Nature Genetics 2004 May; 36(5):431-432. 
gap Gap Gap Locations Mapping and Sequencing Description This track depicts gaps in the assembly. These gaps &mdash; with the exception of intractable heterochromatic gaps &mdash; will be closed during the finishing process. Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is known, it is a bridged gap and a white line is drawn through the black box representing the gap. This assembly contains the following principal types of gaps: Clone &mdash; gaps between clones in the same map contig. These may be bridged or not. Contig &mdash; non-bridged gaps between map contigs. Centromere &mdash; non-bridged gaps from centromeres. Telomere &mdash; non-bridged gaps from telomeres. Heterochromatin &mdash; non-bridged gaps from large blocks of heterochromatin. Short Arm &mdash; non-bridged long gaps on the short arm of the chromosome. See also NCBI discussion of genome assembly procedures. Credits The Feb. 2009 human reference sequence (GRCh37) was produced by the Genome Reference Consortium. 
gc5Base GC Percent GC Percent in 5-Base Windows Mapping and Sequencing Description The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the &quot;Graph configuration help&quot; link for an explanation of the configuration options. Credits The data and presentation of this graph were prepared by Hiram Clawson. 
genCC GenCC GenCC: The Gene Curation Coalition Annotations Phenotype and Literature Description This track shows annotations from The Gene Curation Coalition (GenCC). The GenCC provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Orphanet, etc.), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry Genetics, Illumina, Invitae, etc.). The GenCC aims to clarify overlap between gene curation efforts and develop consistent terminology for validity, allelic requirement and mechanism of disease. Each item on this track corresponds with a gene, and contains a large number of information such as associated disease, evidence classification, specific submission notes and identifiers from different databases. In cases where multiple annotations exist for the same gene, multiple items are displayed. Display Conventions and Configuration Each item displayed represents a submission to the GenCC database. The displayed name is a combination of the gene symbol and the disease's original submission ID. This submission ID is either the OMIM#, MONDO# or Orphanet#. Clicking on any item will display the complete meta data for that item, including linkouts to the GenCC, NCBI, Ensembl, HGNC, GeneCards, Pombase (MONDO), and Human Phenotype Ontology (HPO). Mousing over any item will display the associated disease title, the classification title, and the mode of inheritance title. Items are colored based on the GenCC classification, or validation, of the evidence in the color scheme seen in the table below. For more information on this process, see the GenCC validity terms FAQ. A filter for the track is also available to display a subset of the items based on their classification. Color Evidence classification Definitive Strong Moderate Supportive Limited Disputed Evidence Refuted Evidence No Known Disease Relationship Limitations: Most entries include both NM_ accessions as well as ENST and ENSG identifiers. From the original file, which contains no coordinates, two genes were not mapped to the hg38 genome, SLCO1B7 and ATXN8. This means that the hg38 track has 2 fewer items than what can be found in the GenCC download file. For hg19, one additional gene was not mapped, KCNJ18. In addition to this, the GenCC data in the Genome Browser does not include OMIM data due to licensing restrictions. For more information, see the Methods section below. Data Access The source data can be explored in GenCC database. The source files can also be found on the GenCC downloads page. The GenCC data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigBed files that can be downloaded from our download server. The data may also be explored interactively using our REST API. The file for this track may also be locally explored using our tools bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to a given range, e.g., bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/genCC.bb stdout Methods The data were downloaded from the GenCC downloads page in tsv format. Manual curation was performed on the file to remove newline characters and tab characters present in the submission notes, in total fewer than 20 manual edits were made. The track was first built on hg38 by associating the gene symbols with the NCBI MANE 1.0 release transcripts. These coordinates were added to the items as well as the NM_ accession, ENST ID and ENSG ID. For items where there was no gene symbol match in MANE (~130), the gene symbols were queried against GENCODEv40 comprehensive set release. In places where multiple transcript matches were found, the earliest transcription start and latest end site was used from among the transcripts to encompass the entire gene coordinates. Two genes were not able to be mapped for hg38, SLCO1B7 and ATXN8, resulting in two missing submissions in the Genome Browser when compared to the raw file. Lastly, the items were colored according to their evidence classification as seen on the GenCC database. For hg19, the hg38 NM_ accessions were used to convert the item coordinates according to the latest hg19 refseq release. For items that failed to convert, the gene symbols were queried using the GENCODEv40 hg19 lift comprehensive set. One additional gene symbol failed to map in hg19, KCNJ18, leading to 3 fewer items on this track when compared to the raw file. For both assemblies, GenCC OMIM data is excluded do to data restrictions. For complete documentation of the processing of these tracks, read the GenCC MakeDoc. Credits Thanks to the entire GenCC committee for creating these annotations and making them available. References DiStefano MT, Goehringer S, Babb L, Alkuraya FS, Amberger J, Amin M, Austin-Tse C, Balzotti M, Berg JS, Birney E et al. The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources. Genet Med. 2022 May 4;. PMID: 35507016 
interactions Gene Interactions Protein Interactions from Curated Databases and Text-Mining Phenotype and Literature Description The Pathways and Gene Interactions track shows a summary of gene interaction and pathway data collected from two sources: curated pathway/protein-interaction databases and interactions found through text mining of PubMed abstracts. Display Conventions and Configuration Track Display The track features a single item for each gene loci in the genome. On the item itself, the gene symbol for the loci is displayed followed by the top gene interactions noted by their gene symbol. Clicking an item will take you a gene interaction graph that includes detailed information on the support for the various interactions. Items are colored based on the number of documents supporting the interactions of a particular gene. Genes with &gt;100 supporting documents are colored black, genes with &gt;10 but &lt;100 supporting documents are colored dark blue, and those with &gt;10 supporting documents are colored light blue. Pathway and Gene Interaction Display See the help documentation accompanying this gene interaction graph for more information on its configuration. Methods The pathways and gene interactions were imported from a number of databases and mined from millions of PubMed abstracts. More information can be found in the &quot;Data Sources and Methods&quot; section of the help page for the gene interaction graph. Data Access The underlying data for this track can be accessed interactively through the Table Browser or Data Integrator. The data for this track is spread across a number of relational tables. The best way to export or analyze the data is using our public MySQL server. The list of tables and how they are linked together are described in the documentation linked at the bottom of the gene interaction viewer. The genome annotation is just a summary of the actual interactions database and therefore often not of interest to most users. It is stored in a bigBed file that can be obtained from the download server. The data underlying the graphical display is in bigBed formatted file named interactions.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed. Instructions for downloading source code and precompiled binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/interactions.bb -chrom=chr6 -start=0 -end=1000000 stdout Credits The text-mined data for the gene interactions and pathways were generated by Chris Quirk and Hoifung Poon as part of Microsoft Research, Project Hanover. Pathway data was provided by the databases listed under &quot;Data Sources and Methods&quot; section of the help page for the gene interaction graph. In particular, thank you to Ian Donaldson from IRef for his unique collection of interaction databases. The short gene descriptions are a merge of the HPRD and PantherDB gene/molecule classifications. Thanks to Arun Patil from HPRD for making them available as a download. The track display and gene interaction graph were developed at the UCSC Genome Browser by Max Haeussler. References Poon H, Quirk C, DeZiel C, Heckerman D. Literome: PubMed-scale genomic knowledge base in the cloud Bioinformatics. 2014 Oct;30(19):2840-2. PMID: 24939151 
geneHancer GeneHancer GeneHancer Regulatory Elements and Gene Interactions Regulation Description GeneHancer is a database of human regulatory elements (enhancers and promoters) and their inferred target genes, which is embedded in GeneCards, a human gene compendium. The GeneHancer database was created by integrating &gt;1 million regulatory elements from multiple genome-wide databases. Associations between the regulatory elements and target genes were based on multiple sources of linking molecular data, along with distance, as described in Methods below. The GeneHancer track set contains tracks representing: Regulatory elements (GeneHancers) Gene transcription start sites Interactions (associations) between regulatory elements and genes Clustered interactions, by gene target or GeneHancer The full set of elements and interactions is included, along with a highly filtered &quot;double elite&quot; subset. Display Conventions Each GeneHancer regulatory element is identified by a GeneHancer id. For example: GH0XJ101383 is located on chromosome X, with starting position of 101,383 kb (GRCh38/hg38 reference). Based on the id, one can obtain full GeneHancer information, as displayed in the Genomics section within the gene-centric web pages of GeneCards. Links to the GeneCards information pages are provided on the track details pages. For the interaction tracks (Clusters and Interactions) a slight offset can be noticed between the line endpoints. This helps to identify the start and end of the feature. In this case, the higher point is the source (enhancers) and the lower point is the target. Regulatory elements Colors are used to distinguish promoters and enhancers and to indicate the GeneHancer element confidence score: Promoters:&nbsp; &emsp;&emsp;&nbsp;High &emsp;&emsp;&nbsp;Medium &emsp;&emsp;&nbsp;Low Enhancers:&nbsp; &emsp;&emsp;&nbsp;High &emsp;&emsp;&nbsp;Medium &emsp;&emsp;&nbsp;Low Gene TSS Colors are used to improve gene and interactions visibility. Successive genes are colored in different colors, and interactions of a gene have the same color. Interactions The Interactions view in Full mode shows GeneHancers and target genes connected by curves or half-rectangles (when one of the connected regions is off-screen). Configuration options are available to change the drawing style, and to limit the view to interactions with one or both connected items in the region. Interactions are identified on mouseover or clicked on for details at the end regions, or at the curve peak, which is marked with a gray ring shape. Interactions in the reverse direction (Gene TSS precedes GeneHancer on the genome) are drawn with a dashed line. Clusters The Clusters view groups interactions by target gene; the target gene and all GeneHancers associated with it are displayed in a single browser item. The gene TSS and associated GeneHancers are shown as blocks linked together, with the TSS drawn as a &quot;tall&quot; item, and the GeneHancers drawn &quot;short&quot;. A user configuration option is provided to change the view to group by GeneHancer (with tall GeneHancer and short TSS's). Clusters composed of interactions with a single gene are colored to correspond to the gene, and those composed of interactions with multiple genes are colored dark gray. Methods GeneHancer identifications were created from &gt;1 million regulatory elements obtained from seven genome-wide databases: ENCODE project Z-Lab Enhancer-like regions (version v3) Ensembl regulatory build (version 92) FANTOM5 atlas of active enhancers VISTA Enhancer Browser dbSUPER super-enhancers EPDnew promoters UCNEbase ultra-conserved noncoding elements Employing an integration algorithm that removes redundancy, the GeneHancer pipeline identified &tilde;250k integrated candidate regulatory elements (GeneHancers). Each GeneHancer is assigned an annotation-derived confidence score. The GeneHancers that are derived from more than one information source are defined as &quot;elite&quot; GeneHancers. Gene-GeneHancer associations, and their likelihood-based scores, were generated using information that helps link regulatory elements to genes: eQTLs (expression quantitative trait loci) from GTEx (version v6p) Capture Hi-C promoter-enhancer long range interactions FANTOM5 eRNA-gene expression correlations Cross-tissue expression correlations between a transcription factor interacting with a GeneHancer and a candidate target gene Distance-based associations, including several approaches: Nearest neighbors, where each GeneHancer is associated with its two proximal genes Overlaps with the gene territory (intragenic) Proximity to the gene TSS (&lt;2kb) Associations that are derived from more than one information source are defined as &quot;elite&quot; associations, which leads to the definition of the &quot;double elite&quot; dataset - elite gene associations of elite GeneHancers. More details are provided at the GeneCards information page. For a full description of the methods used, refer to the GeneHancer manuscript1. Source data for the GeneHancer version 4.8 was downloaded during May 2018. Data Access Due to our agreement with the Weizmann Institute, we cannot allow full genome queries from the Table Browser or share download files. You can still access data for individual chromosomes or positional data from the Table Browser. GeneHancer is the property of the Weizmann Institute of Science and is not available for download or mirroring by any third party without permission. Please contact the Weizmann Institute directly for data inquiries. Credits Thanks to Simon Fishilevich, Marilyn Safran, Naomi Rosen, and Tsippi Iny Stein of the GeneCards group and Shifra Ben-Dor of the Bioinformatics Core group at the Weizmann Institute, for providing this data and documentation, creating track hub versions of these tracks as prototypes, and overall responsiveness during development of these tracks. Contact: &#115;&#105;&#109;&#111;&#110;. &#102;&#105;&#115;&#104;&#105;&#108;ev&#105;&#99;h&#64;&#119;&#101;&#105;&#122;m&#97;&#110;&#110;. a&#99;. &#105;l Supported in part by a grant from LifeMap Sciences Inc. References Fishilevich S., Nudel R., Rappaport N., Hadar R., Plaschkes I., Iny Stein T., Rosen N., Kohn A., Twik M., Safran M., Lancet D. and Cohen D. GeneHancer: genome-wide integration of enhancers and target genes in GeneCards, Database (Oxford) (2017), doi:10.1093/database/bax028. [PDF] PMID 28605766 Stelzer G, Rosen R, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Iny Stein T, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary, D, Warshawsky D, Guan- Golan Y, Kohn A, Rappaport N, Safran M, and Lancet D. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analysis, Current Protocols in Bioinformatics (2016), 54:1.30.1-1.30.33. doi: 10.1002/cpbi.5. PMID 27322403 
ghGeneHancer Reg Elem GeneHancer Regulatory Elements and Gene Interactions Regulation 
geneHancerRegElements GH Reg Elems Enhancers and promoters from GeneHancer Regulation 
geneHancerRegElementsDoubleElite GH Reg Elems (DE) Enhancers and promoters from GeneHancer (Double Elite) Regulation 
ghInteraction Interactions GeneHancer Regulatory Elements and Gene Interactions Regulation 
geneHancerInteractions GH Interactions Interactions between GeneHancer regulatory elements and genes Regulation 
geneHancerInteractionsDoubleElite GH Interactions (DE) Interactions between GeneHancer regulatory elements and genes (Double Elite) Regulation 
ghGeneTss Gene TSS GeneHancer Regulatory Elements and Gene Interactions Regulation 
geneHancerGenes GH genes TSS GH genes TSS Regulation 
geneHancerGenesDoubleElite GH genes TSS (DE) GeneCards genes TSS (Double Elite) Regulation 
ghClusteredInteraction Clustered Interactions GeneHancer Regulatory Elements and Gene Interactions Regulation 
geneHancerClusteredInteractions GH Clusters Clustered interactions of GeneHancer regulatory elements and genes Regulation 
geneHancerClusteredInteractionsDoubleElite GH Clusters (DE) Clustered interactions of GeneHancer regulatory elements and genes (Double Elite) Regulation 
geneid Geneid Genes Geneid Gene Predictions Genes and Gene Predictions Description This track shows gene predictions from the geneid program developed by Roderic Guig&oacute;'s Computational Biology of RNA Processing group which is part of the Centre de Regulaci&oacute; Gen&ograve;mica (CRG) in Barcelona, Catalunya, Spain. Methods Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. Credits Thanks to Computational Biology of RNA Processing for providing these data. References Blanco E, Parra G, Guig&#243; R. Using geneid to identify genes. Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3. PMID: 18428791 Parra G, Blanco E, Guig&#243; R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5. PMID: 10779490; PMC: PMC310871 
geneReviews GeneReviews GeneReviews Phenotype and Literature Description GeneReviews is an online collection of expert-authored, peer-reviewed articles that describe specific gene-related diseases. GeneReviews articles are searchable by disease name, gene symbol, protein name, author, or title. GeneReviews is supported by the National Institutes of Health, hosted at NCBI as part of the Genetic Testing Registry (GTR). The GeneReviews data underlying this track will be updated frequently. The GeneReviews track allows the user to locate the NCBI GeneReviews resource quickly from the Genome Browser. Hovering the mouse on track items shows the gene symbol and associated diseases. A condensed version of the GeneReviews article name and its related diseases are displayed on the item details page as links. Similar information, when available, is provided in the details page of items from the UCSC Genes, RefSeq Genes, and OMIM Genes tracks. Data Access The raw data for the GeneReviews track can be explored interactively with the Table Browser. Cross-referencing can be done with Data Integrator. The complete source file, in bigBed format, can be downloaded from our downloads directory. For automated analysis, the data may be queried from our REST API. Previous versions of this track can be found on our archive download server. References Pagon RA, Adam MP, Bird TD, et al., editors. GeneReviews&reg; [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2014. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1116. 
giab Genome In a Bottle Genome In a Bottle Structural Variants and Trios Variation Description The tracks listed here contain data from The Genome in a Bottle Consortium (GIAB), an open, public consortium hosted by NIST. The priority of GIAB is to develop reference standards, reference methods, and reference data by authoritative characterization of human genomes for use in benchmarking, including analytical validation and technology development that will support translation of whole human genome sequencing to clinical practice. The sole purpose of this work is to provide validated variants and regions to enable technology and bioinformatics developers to benchmark and optimize their detection methods. The Ashkenazim and the Chinese Trio tracks show benchmark SNV calls from two son/father/mother trios of Ashkenazi Jewish and Han Chinese ancestry from the Personal Genome Project, consented for commercial redistribution. The Genome In a Bottle Structural Variants track shows benchmark SV calls (nssv) and variant regions (nsv) (5,262 insertions and 4,095 deletions, &gt 50 bp, in 2.51 Gb of the genome) from the son (HG002/NA24385) from the Ashkenazi Jewish trio. Samples are disseminated as National Institute of Standards and Technology (NIST) Reference Materials. Display Conventions and Configuration These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Unlike a regular genome browser track, the Ashkenazim and the Chinese Trio tracks display the genome variants of each individual as two haplotypes; SNPs, small insertions and deletions are mapped to each haplotype based on the phasing information of the VCF file. The haplotype 1 and the haplotype 2 are displayed as two separate black lanes for the browser window region. Each variant is drawn as a vertical dash. Homozygous variants will show two identical dashes on both haplotype lanes. Phased heterozygous variants are placed on one of the haplotype lanes and unphased heterozygous variants are displayed in the area between the two haplotype lanes. Predicted de novo variants and variants that are inconsistent with phasing in the trio son can be colored in red using the track Configuration options. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Benchmark VCF and BED files for small variants are available for GRCh37 and GRCh38 under each genome at NCBI FTP site. Structural variants are available for GRCh37 at dbVAR nst175. References Zook JM, McDaniel J, Olson ND, Wagner J, Parikh H, Heaton H, Irvine SA, Trigg L, Truty R, McLean CY et al. An open resource for accurately benchmarking small variant and reference calls. Nat Biotechnol. 2019 May;37(5):561-566. PMID: 30936564; PMC: PMC6500473 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC et al. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 Jun 15;. PMID: 32541955 
svView Structural Variants Genome In a Bottle Structural Variants (dbVar nstd175) Variation 
giabSv Structural Variants Genome in a Bottle Structural Variants (dbVar nstd175) Variation 
triosView Genome In a Bottle Trios Genome in a Bottle Ashkenazim and Chinese Trios Variation 
chineseTrio Chinese Trio Genome In a Bottle Chinese  Trio Variation 
ashkenazimTrio Ashkenazim Trio Genome In a Bottle Ashkenazim Trio Variation 
wgEncodeAwgSegmentation Genome Segments Genome Segmentations from ENCODE Regulation Overview This set of tracks represents multivariate genome-segmentation results based on ENCODE data (ENCODE Project Consortium, 2012). Using two different unsupervised machine learning techniques (ChromHMM and Segway), the genome was automatically segmented into disjoint segments. Each segment belongs to one of a few specific genomic "states" which is assigned an intuitive label. Each genomic state represents a particular combination and distribution of different ENCODE functional data tracks such as histone modifications, open chromatin data and specific TF binding data. A consensus unified segmentation was also generated by reconciling results from the individual segmentations. The specific descriptions for each segmentation are listed below. These segmentations were performed on six human cell types (GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for 8 chromatin marks, RNA Polymerase II, the CTCF transcription factor, and input data. In total, twenty-five states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements. Display Conventions and Configuration The number and type of Segmentation states from the individual segmentations differ, but are unified via grouping by color (10 groups for ChromHMM and Segway, 7 for the Combined). The display can be filtered to selected groups using the 'Filter by Segment Type' control on the track configuration page. Groupings that are not represented in the Combined tracks are marked in the menu with an asterisk. Combined Segmentations Description These tracks display chromatin state segmentations from 6 cell lines, using a consensus merge of the segmentations produced by the ChromHMM and Segway software. In both segmentations, twenty-five states were used to segment the genome, however for ease of comprehension and display, the merged segmentation uses only seven states. Display Conventions and Configuration The seven states of the combined segmentation, the candidate annotations and associated segment colors are as follows: TSS Bright Red Predicted promoter region including TSS PF Light Red Predicted promoter flanking region E Orange Predicted enhancer WE Yellow Predicted weak enhancer or open chromatin cis regulatory element CTCFBlue CTCF enriched element T Dark Green Predicted transcribed region R Gray Predicted Repressed or Low Activity region Methods ChIP-seq data from the ENCODE Consortium was used to generate this track, and the ChromHMM and Segway programs were used to perform the segmentation. Methods for the ChromHMM and Segway segmentations are described below. To form the combined segmentation, for each original segmentation, states that could be grouped together based on similar signal patterns were identified. For the ChromHMM segmentation, the states were grouped manually based on the mean signal values across multiple cell lines. For the Segway segmentations run independently over multiple cell lines, multiple hierarchical clustering techniques were applied across all states in the segmentations to identify the most consistent clustering of states, both across cell lines and with respect to existing biological knowledge. Using these criteria, the Ward clustering on euclidean distances between mean signal scores transformed to the unit interval was chosen to cluster the Segway state labels. Subsequently, pairwise relationships between the ChromHMM and Segway merged states were identified using both overlap calculations and manual annotation (Hoffman, Ernst et al. 2013). Pairs of states that were viewed as concordant were assigned to one of the seven state classes. Regions of the genome occupied by concordant states between the two initial segmentations were reassigned to the new summary labels. In some cases there were combinations of states between the two segmentations that could not be reconciled and these combinations were viewed as discordant. Regions with discordant states were not assigned a state label, and were dropped from the summary combined segmentation. ChromHMM Segmentations Description A common set of states across 6 human cell types were learned by computationally integrating ENCODE ChIP-seq, DNase-seq, and FAIRE-seq data using a Hidden Markov Model (HMM). Twenty-five states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements. There are 6 ChromHMM tracks. Each track represents the segmentation results for each of the six cell lines. A related ChromHMM browser track, Chromatin State Segmentation by HMM from ENCODE/Broad (Broad ChromHMM) (Ernst et. al. 2011) reports segmentations for 9 cell types and is based solely on histone data. Display Conventions and Configuration The candidate annotations and associated segment colors are as follows: Tss, TssFBright RedActive Promoter PromFLight RedPromoter Flanking PromPPurpleInactive Promoter Enh, EnhFOrangeCandidate Strong enhancer EnhWF, EnhW, DNaseU, DNaseD, FaireWYellowCandidate Weak enhancer/DNase CtrcfO, CtcfBlueDistal CTCF/Candidate Insulator Gen5', Elon, ElonW, Gen3', Pol2, H4K20Dark GreenTranscription associated LowLight Green Low activity proximal to active states ReprD, Repr, ReprWGrayPolycomb repressed Quies, ArtLight GrayHeterochromatin/Repetitive/Copy Number Variation Methods Data from the ENCODE Consortium was used to generate this track, and the ChromHMM program was used to perform the segmentation. Datasets for 10 factors plus input in 6 cell types were binarized separately at a 200 base pair resolution using a Poisson background model and fold enrichment cut-offs. The chromatin states were learned from this binarized data using a multivariate Hidden Markov Model (HMM) that explicitly models the combinatorial patterns of observed modifications (Ernst and Kellis, 2010). To learn a common set of states across the six cell types, first the genomes were concatenated across the cell types. For each of the six cell types, each 200 base pair interval was then assigned to its most likely state under the model. Segway Segmentations Description Sets of states across 6 human cell types were learned by computationally integrating ENCODE ChIP-seq, DNAse-seq and FAIRE-seq data using a Dynamic Bayesian Network (DBN). Twenty-five states were used to segment the genome (listed below in the Display Conventions and Configuration section by their prefixes - such as PromP for PromP1, PromP2, etc.), and these states were then grouped and colored to highlight predicted functional elements (such as the color purple for an inactive promoter region). There are 6 Segway tracks, each representing the segmentation results for a separate cell line. Not every segmentation state is found in each cell line. If you have further questions about the tracks, please contact the authors listed under the Credits section. Display Conventions and Configuration The segment state prefixes, associated colors, and candidate annotations are: Tss, DnaseDBright RedActive Promoter TssF, PromFLight RedPromoter Flanking PromPPurpleInactive Promoter Enh, EnhF, EnhPr, EnhPOrangeCandidate Strong enhancer EnhW, EnhWfYellowCandidate Weak enhancer Ctcf, CtcfOBlueDistal CTCF/Candidate Insulator Gen3', Gen5', Elon, ElonWDark GreenTranscription associated LowLight GreenLow activity proximal to active states ReprGrayPolycomb repressed QuiescLight GrayHeterochromatin/Repetitive/Copy Number Variation Methods Data from the ENCODE Consortium was used to generate this track, and the Segway program was used to perform the segmentation. Data for 10 factors plus input in 6 cell types was converted to real valued signal data using the Wiggler program. Using the ENCODE regions (spanning 1% of the human genome) the chromatin states were learned from this data using a Dynamic Bayesian Network (DBN) (Hoffman, et al. 2012). Models were learned separately for each of the six cell types. For each cell type, the Viterbi algorithm was used to assign genomic regions to individual state labels at single base pair resolution over the entire genome. Credits The ChromHMM segmentation was produced at the MIT Computational Biology Group (Kellis lab) by Jason Ernst now at UCLA. The Segway segmentation was produced at the Noble Research Lab by Michael Hoffman, now at the Princess Margaret Cancer Center, Toronto. The Combined segmentation was produced at the European Bioinformatics Institute (EMBL-EBI, Flicek team), by Steven Wilder and Ian Dunham, as part of the work of the ENCODE Data Analysis Center (Ewan Birney). References ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMC: PMC3439153 Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012 Feb 28;9(3):215-6. PMID: 22373907; PMC: PMC3577932 Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug;28(8):817-25. PMID: 20657582; PMC: PMC2919626 Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods. 2012 Mar 18;9(5):473-6. PMID: 22426492; PMC: PMC3340533 Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 2013 Jan;41(2):827-41. PMID: 23221638; PMC: PMC3553955 Data Release Policy The data used to generate these segmentations are covered by the ENCODE data release policy here, and so were subject to some usage restrictions for a 9 month period. There are no restrictions on the use of the ENCODE segmentation data. 
wgEncodeAwgSegmentationSegwayHuvec HUVEC Segway HUVEC Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationSegwayHuvec umbilical vein endothelial cells Multi-assay Synthesis HUVEC Genome Segmentation by Segway from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationCombinedHuvec HUVEC Combined HUVEC Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationCombinedHuvec umbilical vein endothelial cells Multi-assay Synthesis HUVEC Genome Segmentation by Combined Segway+ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationChromhmmHuvec HUVEC ChromHMM HUVEC Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationChromhmmHuvec umbilical vein endothelial cells Multi-assay Synthesis HUVEC Genome Segmentation by ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationSegwayHepg2 HepG2 Segway HepG2 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationSegwayHepg2 hepatocellular carcinoma Multi-assay Synthesis HepG2 Genome Segmentation by Segway from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationCombinedHepg2 HepG2 Combined HepG2 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationCombinedHepg2 hepatocellular carcinoma Multi-assay Synthesis HepG2 Genome Segmentation by Combined Segway+ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationChromhmmHepg2 HepG2 ChromHMM HepG2 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationChromhmmHepg2 hepatocellular carcinoma Multi-assay Synthesis HepG2 Genome Segmentation by ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationSegwayHelas3 HeLa-S3 Segway HeLa-S3 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationSegwayHelas3 cervical carcinoma Multi-assay Synthesis HeLa-S3 Genome Segmentation by Segway from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationCombinedHelas3 HeLa-S3 Combined HeLa-S3 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationCombinedHelas3 cervical carcinoma Multi-assay Synthesis HeLa-S3 Genome Segmentation by Combined Segway+ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationChromhmmHelas3 HeLa-S3 ChromHMM HeLa-S3 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationChromhmmHelas3 cervical carcinoma Multi-assay Synthesis HeLa-S3 Genome Segmentation by ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationSegwayK562 K562 Segway K562 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationSegwayK562 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Multi-assay Synthesis K562 Genome Segmentation by Segway from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationCombinedK562 K562 Combined K562 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationCombinedK562 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Multi-assay Synthesis K562 Genome Segmentation by Combined Segway+ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationChromhmmK562 K562 ChromHMM K562 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationChromhmmK562 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Multi-assay Synthesis K562 Genome Segmentation by ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationSegwayH1hesc H1-hESC Segway H1-hESC Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationSegwayH1hesc embryonic stem cells Multi-assay Synthesis H1-hESC Genome Segmentation by Segway from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationCombinedH1hesc H1-hESC Combined H1-hESC Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationCombinedH1hesc embryonic stem cells Multi-assay Synthesis H1-hESC Genome Segmentation by Combined Segway+ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationChromhmmH1hesc H1-hESC ChromHMM H1-hESC Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationChromhmmH1hesc embryonic stem cells Multi-assay Synthesis H1-hESC Genome Segmentation by ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationSegwayGm12878 GM12878 Segway GM12878 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationSegwayGm12878 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Multi-assay Synthesis GM12878 Genome Segmentation by Segway from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationCombinedGm12878 GM12878 Combined GM12878 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationCombinedGm12878 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Multi-assay Synthesis GM12878 Genome Segmentation by Combined Segway+ChromHMM from ENCODE/Analysis Regulation 
wgEncodeAwgSegmentationChromhmmGm12878 GM12878 ChromHMM GM12878 Combined ENCODE Jan 2011 Freeze wgEncodeAwgSegmentationChromhmmGm12878 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Multi-assay Synthesis GM12878 Genome Segmentation by ChromHMM from ENCODE/Analysis Regulation 
pgSnp Genome Variants Personal Genome Variants Variation Description This track displays variant base calls from the publicly released genome sequences of several individuals: 5 Sub-Saharan African genomes sequenced by Penn State University: !Gubi (KB1) G/aq'o (NB1) !Ai (MD8) D#kgao (TK1) Archbishop Desmond Tutu (ABTutu) 6 individuals from the 1000 Genomes Project: a CEU daughter and parents (NA12878, NA12891, NA12892) a YRI daughter and parents (NA19240, NA19238, NA19239) 69 non-diseased individuals sequenced by Complete Genomics: a YRI daughter and parents (NA19240, NA19238, NA19239) a PUR trio (HG00731, HG00732, HG00733) a 17-member, 3-generation CEPH pedigree (Pedigree 1463: NA12877, NA12878, NA12879, NA12880, NA12881, NA12882, NA12883, NA12884, NA12885, NA12886, NA12887, NA12888, NA12889, NA12890, NA12891, NA12892, NA12893) a diversity panel representing unrelated individuals from ten different populations: ASW (NA19700, NA19701, NA19703, NA19704, NA19834) CEU (NA06985, NA06994, NA07357, NA10851, NA12004) CHB (NA18526, NA18537, NA18555, NA18558) GIH (NA20845, NA20846, NA20847, NA20850) JPT (NA18940, NA18942, NA18947, NA18956) LWK (NA19017, NA19020, NA19025, NA19026) MKK (NA21732, NA21733, NA21737, NA21767) MXL (NA19735, NA19648, NA19649, NA19669, NA19670) TSI (NA20502, NA20509, NA20510, NA20511) YRI (NA18501, NA18502, NA18504, NA18505, NA18508, NA18517, NA19129) 5 individuals from the Personal Genome Project: George Church (NA20431) Misha Angrist (NA21677) Rosalynn Gill (NA21833) Henry Louis Gates Sr. Henry Louis Gates Jr. and independently published genomes: Craig Venter James Watson Anonymous Yoruba individual NA18507 Anonymous Han Chinese individual (YH, YanHuang Project) Seong-Jim Kim (SJK) Anonymous Korean individual (AK1) Stephen Quake Anonymous Irish male Marjolein Kriek Gregory Lucier Extinct Palaeo-Eskimo Saqqaq individual Note: The Khoisan languages are characterized by clicks, denoting additional consonants. The ! is a palatal click, / is a dental click, and # is an alveolar click (Le Roux and White, 2004). Display Conventions and Configuration In the genome browser, when viewing the forward strand of the reference genome (the normal case), the displayed alleles are relative to the forward strand. When viewing the reverse strand of the reference genome (&quot;reverse&quot; button), the displayed alleles are reverse-complemented to match the reverse strand. When read frequency data are available, they are displayed in the mouseover text (e.g., &quot;T:8 G:3&quot; means that 8 reads contained a T and 3 reads contained a G at that base position) and box colors are used to show the proportion of alleles. On the details page for each variant, the alleles are given for the forward strand of the reference genome. Frequency data are shown when available. Methods Variants from Complete Genomics and Marjolein Kriek were mapped to the Feb. 2009 (GRCh37/hg19) human genome assembly, so they required no remapping. Variants for all other individuals were originally mapped to the Mar. 2006 (NCBI36/hg18) human genome assembly. Their locations were translated into GRCh37/hg19 coordinates using the liftOver program and the mapping file hg18ToHg19.over.chain.gz. Homozygous matches to the GRCh37/hg19 reference were removed. Sources KB1, NB1, MD8, TK1, ABTutu (Penn State) (Schuster et al.) SNPs are from the allSNPs.txt file which can be downloaded from Galaxy. The indels are also available for download from Galaxy. CEU trio NA12878, NA12891, NA12892; YRI trio NA19240, NA19238, NA19239 (1000 Genomes Project, March 2010 release) (1000 Genomes) The variants shown are from the 1000 Genomes Project's March 2010 release. The CEU variant calls were based on sequence data from the Wellcome Trust Sanger Insititute and the Broad Institute, using the Illumina/Solexa platform. The YRI variant calls were based on sequence data from the Baylor College of Medicine Human Genome Sequencing Center and Applied Biosystems, using the SOLiD platform. For more information on the mapping, variant calling, filtering and validation, see the pilot 2 README file. The variant calls are available from the March 2010 release subdirectory at EBI and at NCBI. Complete Genomics 69 genomes (Complete Genomics, Nov 2011 release) (CG) There are four sets of data: a Yoruba trio; a Puerto Rican trio; a 17-member, 3-generation pedigree; and a diversity panel representing ten different populations. The CEPH samples within the pedigree and diversity sets are from the NIGMS Repository and the remainder from the NHGRI Repository, both housed at the Coriell Institute for Medical Research. The downloaded dataset was generated by the Complete Genomics Analysis Pipeline version 2.0.0. George Church (Personal Genome Project, Complete Genomics) (CG) The variants are from Complete Genomics (Complete Genomics Analysis Pipeline version 1.2.0.14). Misha Angrist, Rosalynn Gill, Henry Louis Gates Sr., Henry Louis Gates Jr. (Personal Genome Project) (PGP) The variants were downloaded from a Trait-o-matic installation that may be out of order.--> Trait-o-matic installation that may be out of order. The numbers for Angrist are read counts; the number supporting each allele was not given. The Personal Genome Project offers whole genome sequences for the original individuals and many more for download. Craig Venter (JCVI) (Levy et al.) An overview is given here. This subtrack contains Venter's single-base variants from the file HuRef.InternalHuRef-NCBI.gff, filtered to include only Method 1 variants (where each variant was kept in its original form and not post-processed), and to exclude any variants that had N as an allele. JCVI hosts a genome browser. James Watson (CSHL) (Wheeler et al.) These single-base variants came from the file watson_snp.gff.gz. CSHL hosts a genome browser. Yoruba NA18507 (Illumina Cambridge/Solexa) (Bentley et al.) Illumina released the read sequences to the NCBI Short Read Archive. Aakrosh Ratan in the Miller Lab at Penn State University (PSU) mapped the sequence reads to the reference genome and called single-base variants using MAQ. YH (YanHuang Project) (Wang et al.) The YanHuang Project released these single-base variants from the genome of a Han Chinese individual. The data are available from the YH database in the file yhsnp_add.gff. The YanHuang Project hosts a genome browser. SJK (GUMS/KOBIC) (Ahn et al.) Researchers at Gachon University of Medicine and Science (GUMS) and the Korean Bioinformation Center (KOBIC) released these single-base variants from the genome of Seong-Jin Kim. The data are available from KOBIC in the file KOREF-solexa-snp-X30_Q40d4D100.gff. AK1 (Genomic Medicine Institute) (Kim et al.) The variants shown are from the AK1_SNP.tar.gz download. Stephen Quake (Stanford) (Pushkarev et al.) The variants were downloaded from a Trait-o-matic installation that may be out of order.--> Trait-o-matic installation that may be out of order. Anonymous Irish male (Tong et al.) The SNPs shown are from the Galaxy library, Irish whole genome. Marjolein Kriek (Leiden) The SNPs shown are called by Belinda Giardine from PSU, from the BAM file provided by Leiden University Medical Center. The reads were aligned to the GRCh37/hg19 build. SNP calls were made using samtools, with a minimum of 4 reads supporting the variant call and a maximum of 45. Those with a quality score of less than 30 were filtered out. Gregory Lucier (Life Technologies) The SNPs shown are from Nimbus Informatics. Sequencing was done using the Life Technologies SOLiD platform. Palaeo-Eskimo Saqqaq individual (Saqqaq Genome Project) (Rasmussen et al.) The variants shown are all non-reference SNPs found by the SNPest program, and in a second track the high confidence SNPs from the first set. The allele counts are not available for these tracks but read depth is available. The read depth was put in place of the allele counts to give a measure of the reliability of the call. Credits Variants shown in this track were determined by the many individuals and institutions listed above. Thanks to Belinda Giardine at PSU for collecting the data and loading them into the UCSC database. References Le Roux W, White A. The voices of the San living in Southern Africa today. Cape Town: Kwela Books; 2004. KB1, NB1, MD8, TK1, ABTutu (Penn State) Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 Feb 18;463(7283):943-7. PMID: 20164927; PMC: PMC3890430 CEU trio NA12878, NA12891, NA12892; YRI trio NA19240, NA19238, NA19239 (1000 Genomes) 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73. PMID: 20981092; PMC: PMC3042601 Complete Genomics 69 genomes Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010 Jan 1;327(5961):78-81. PMID: 19892942 Public Genome Data Repository Service Note, Complete Genomics 2011. George Church Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010 Jan 1;327(5961):78-81. PMID: 19892942 Misha Angrist, Rosalynn Gill, Henry Louis Gates Sr., Henry Louis Gates Jr. Church GM. The personal genome project. Mol Syst Biol. 2005;1:2005.0030. PMID: 16729065; PMC: PMC1681452 Craig Venter (JCVI) Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G et al. The diploid genome sequence of an individual human. PLoS Biol. 2007 Sep 4;5(10):e254. PMID: 17803354; PMC: PMC1964779 James Watson (CSHL) Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008 Apr 17;452(7189):872-6. PMID: 18421352 Yoruba NA18507 (Illumina Cambridge/Solexa) Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9. PMID: 18987734; PMC: PMC2581791 YH (YanHuang Project) Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J et al. The diploid genome sequence of an Asian individual. Nature. 2008 Nov 6;456(7218):60-5. PMID: 18987735; PMC: PMC2716080 SJK (GUMS/KOBIC) Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C et al. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 2009 Sep;19(9):1622-9. PMID: 19470904; PMC: PMC2752128 AK1 (Genomic Medicine Institute) Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ et al. A highly annotated whole-genome sequence of a Korean individual. Nature. 2009 Aug 20;460(7258):1011-5. PMID: 19587683; PMC: PMC2860965 Stephen Quake Pushkarev D, Neff NF, Quake SR. Single-molecule sequencing of an individual human genome. Nat Biotechnol. 2009 Sep;27(9):847-50. PMID: 19668243; PMC: PMC4117198 Anonymous Irish male Tong P, Prendergast JG, Lohan AJ, Farrington SM, Cronin S, Friel N, Bradley DG, Hardiman O, Evans A, Wilson JF et al. Sequencing and analysis of an Irish human genome. Genome Biol. 2010;11(9):R91. PMID: 20822512; PMC: PMC2965383 Marjolein Kriek Not published yet, data provided by Leiden University Medical Center. Gregory Lucier Not published, data provided by Life Technologies and Nimbus Informatics. Palaeo-Eskimo Saqqaq individual Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 2010 Feb 11;463(7282):757-62. PMID: 20148029; PMC: PMC3951495 
pgSnp1off Single Genomes Personal Genome Variants Variation 
pgSaqqaqHc Saqqaq HC Individual from the Extinct Palaeo-Eskimo Saqqaq, high confidence SNPs Variation 
pgSaqqaq Saqqaq Individual from the Extinct Palaeo-Eskimo Saqqaq (Saqqaq Genome Project) Variation 
pgQuake S. Quake Stephen Quake (Stanford) Variation 
pgLucier Greg Lucier Gregory Lucier (Life Technologies) Variation 
pgKriek M. Kriek Marjolein Kriek (Leiden University Medical Centre) Variation 
pgIrish Irish Male Anonymous Irish Male Variation 
pgAk1 AK1 Anonymous Korean individual, AK1 (Genomic Medicine Institute) Variation 
pgSjk SJK Seong-Jin Kim (SJK, GUMS/KOBIC) Variation 
pgYh1 YanHuang Han Chinese Individual (YanHuang Project) Variation 
pgYoruban3 YRI NA18507 YRI NA18507 (Illumina Cambridge/Solexa, SNPs called by PSU) Variation 
pgWatson Watson James Watson (CSHL) Variation 
pgVenter Venter J. Craig Venter - Published Method 1, Variant in Original Form (JCVI) Variation 
pgSnpPSU PSU Bushmen Personal Genome Variants Variation 
pgAbt454indels ABTutu exome indels ABTutu Genome Variants, 454 exome indels Variation 
pgAbtIllum ABTutu Illum ABTutu Genome Variants, Illumina 7.2X Variation 
pgAbt454 ABTutu exome ABTutu Genome Variants, 454 exome Variation 
pgAbtSolid ABTutu ABTutu Genome Variants, SOLiD Variation 
pgTk1Indel TK1 indels TK1 Genome Variants indels Variation 
pgTk1 TK1 TK1 Genome Variants (all SNPs, 16x exome) Variation 
pgMd8Indel MD8 indels MD8 Genome Variants indels Variation 
pgMd8 MD8 MD8 Genome Variants (all SNPs, 16x exome) Variation 
pgNb1Indel NB1 indels NB1 Genome Variants indels Variation 
pgNb1 NB1 NB1 Genome Variants (all SNPs, 2X genome plus 16x exome) Variation 
pgKb1Indel KB1 indels KB1 indels from 454 and Illumina Variation 
pgKb1Illum KB1 Illumina KB1 Genome Variants, Illumina 23.2X Variation 
pgKb1454 KB1 454 KB1 Genome Variants, 454 Variation 
pgKb1Comb KB1 KB1 Genome Variants, combination of 454, Illumina, and genotyping Variation 
pgSnpPGP Personal Genome Project Personal Genome Variants Variation 
pgGill Rosalynn Gill Rosalynn Gill (Personal Genome Project) Variation 
pgGatesSr Gates Sr Henry Louis Gates Sr (Personal Genome Project) Variation 
pgGatesJr Gates Jr Henry Louis Gates Jr (Personal Genome Project) Variation 
pgChurch George Church George Church (Personal Genome Project) Variation 
pgAngrist Misha Angrist Misha Angrist (Personal Genome Project) Variation 
pgSnpCg Complete Genomics Personal Genome Variants Variation 
pgNA12893indel CEU NA12893 indel CEU NA12893 indel (Complete Genomics) Variation 
pgNA12893 CEU NA12893 CEU pedigree 1463, NA12893 (Complete Genomics) Variation 
pgNA12890indel CEU NA12890 indel CEU NA12890 indel (Complete Genomics) Variation 
pgNA12890 CEU NA12890 CEU pedigree 1463, NA12890 (Complete Genomics) Variation 
pgNA12889indel CEU NA12889 indel CEU NA12889 indel (Complete Genomics) Variation 
pgNA12889 CEU NA12889 CEU pedigree 1463, NA12889 (Complete Genomics) Variation 
pgNA12888indel CEU NA12888 indel CEU NA12888 indel (Complete Genomics) Variation 
pgNA12888 CEU NA12888 CEU pedigree 1463, NA12888 (Complete Genomics) Variation 
pgNA12887indel CEU NA12887 indel CEU NA12887 indel (Complete Genomics) Variation 
pgNA12887 CEU NA12887 CEU pedigree 1463, NA12887 (Complete Genomics) Variation 
pgNA12886indel CEU NA12886 indel CEU NA12886 indel (Complete Genomics) Variation 
pgNA12886 CEU NA12886 CEU pedigree 1463, NA12886 (Complete Genomics) Variation 
pgNA12885indel CEU NA12885 indel CEU NA12885 indel (Complete Genomics) Variation 
pgNA12885 CEU NA12885 CEU pedigree 1463, NA12885 (Complete Genomics) Variation 
pgNA12884indel CEU NA12884 indel CEU NA12884 indel (Complete Genomics) Variation 
pgNA12884 CEU NA12884 CEU pedigree 1463, NA12884 (Complete Genomics) Variation 
pgNA12883indel CEU NA12883 indel CEU NA12883 indel (Complete Genomics) Variation 
pgNA12883 CEU NA12883 CEU pedigree 1463, NA12883 (Complete Genomics) Variation 
pgNA12882indel CEU NA12882 indel CEU NA12882 indel (Complete Genomics) Variation 
pgNA12882 CEU NA12882 CEU pedigree 1463, NA12882 (Complete Genomics) Variation 
pgNA12881indel CEU NA12881 indel CEU NA12881 indel (Complete Genomics) Variation 
pgNA12881 CEU NA12881 CEU pedigree 1463, NA12881 (Complete Genomics) Variation 
pgNA12880indel CEU NA12880 indel CEU NA12880 indel (Complete Genomics) Variation 
pgNA12880 CEU NA12880 CEU pedigree 1463, NA12880 (Complete Genomics) Variation 
pgNA12879indel CEU NA12879 indel CEU NA12879 indel (Complete Genomics) Variation 
pgNA12879 CEU NA12879 CEU pedigree 1463, NA12879 (Complete Genomics) Variation 
pgNA12877indel CEU NA12877 indel CEU NA12877 indel (Complete Genomics) Variation 
pgNA12877 CEU NA12877 CEU pedigree 1463, NA12877 (Complete Genomics) Variation 
pgNA19129indel YRI NA19129 indel YRI NA19129 indel (Complete Genomics) Variation 
pgNA19129 YRI NA19129 YRI NA19129 (Complete Genomics) Variation 
pgNA18517indel YRI NA18517 indel YRI NA18517 indel (Complete Genomics) Variation 
pgNA18517 YRI NA18517 YRI NA18517 (Complete Genomics) Variation 
pgNA18508indel YRI NA18508 indel YRI NA18508 indel (Complete Genomics) Variation 
pgNA18508 YRI NA18508 YRI NA18508 (Complete Genomics) Variation 
pgNA18505indel YRI NA18505 indel YRI NA18505 indel (Complete Genomics) Variation 
pgNA18505 YRI NA18505 YRI NA18505 (Complete Genomics) Variation 
pgNA18504indel YRI NA18504 indel YRI NA18504 indel (Complete Genomics) Variation 
pgNA18504 YRI NA18504 YRI NA18504 (Complete Genomics) Variation 
pgNA18502indel YRI NA18502 indel YRI NA18502 indel (Complete Genomics) Variation 
pgNA18502 YRI NA18502 YRI NA18502 (Complete Genomics) Variation 
pgNA18501indel YRI NA18501 indel YRI NA18501 indel (Complete Genomics) Variation 
pgNA18501 YRI NA18501 YRI NA18501 (Complete Genomics) Variation 
pgNA20511indel TSI NA20511 indel TSI NA20511 indel (Complete Genomics) Variation 
pgNA20511 TSI NA20511 TSI NA20511 (Complete Genomics) Variation 
pgNA20510indel TSI NA20510 indel TSI NA20510 indel (Complete Genomics) Variation 
pgNA20510 TSI NA20510 TSI NA20510 (Complete Genomics) Variation 
pgNA20509indel TSI NA20509 indel TSI NA20509 indel (Complete Genomics) Variation 
pgNA20509 TSI NA20509 TSI NA20509 (Complete Genomics) Variation 
pgNA20502indel TSI NA20502 indel TSI NA20502 indel (Complete Genomics) Variation 
pgNA20502 TSI NA20502 TSI NA20502 (Complete Genomics) Variation 
pgNA21767indel MKK NA21767 indel MKK NA21767 indel (Complete Genomics) Variation 
pgNA21767 MKK NA21767 MKK NA21767 (Complete Genomics) Variation 
pgNA21737indel MKK NA21737 indel MKK NA21737 indel (Complete Genomics) Variation 
pgNA21737 MKK NA21737 MKK NA21737 (Complete Genomics) Variation 
pgNA21733indel MKK NA21733 indel MKK NA21733 indel (Complete Genomics) Variation 
pgNA21733 MKK NA21733 MKK NA21733 (Complete Genomics) Variation 
pgNA21732indel MKK NA21732 indel MKK NA21732 indel (Complete Genomics) Variation 
pgNA21732 MKK NA21732 MKK NA21732 (Complete Genomics) Variation 
pgNA19735indel MXL NA19735 indel MXL NA19735 indel (Complete Genomics) Variation 
pgNA19735 MXL NA19735 MXL NA19735 (Complete Genomics) Variation 
pgNA19670indel MXL NA19670 indel MXL NA19670 indel (Complete Genomics) Variation 
pgNA19670 MXL NA19670 MXL NA19670 (Complete Genomics) Variation 
pgNA19669indel MXL NA19669 indel MXL NA19669 indel (Complete Genomics) Variation 
pgNA19669 MXL NA19669 MXL NA19669 (Complete Genomics) Variation 
pgNA19649indel MXL NA19649 indel MXL NA19649 indel (Complete Genomics) Variation 
pgNA19649 MXL NA19649 MXL NA19649 (Complete Genomics) Variation 
pgNA19648indel MXL NA19648 indel MXL NA19648 indel (Complete Genomics) Variation 
pgNA19648 MXL NA19648 MXL NA19648 (Complete Genomics) Variation 
pgNA19026indel LWK NA19026 indel LWK NA19026 indel (Complete Genomics) Variation 
pgNA19026 LWK NA19026 LWK NA19026 (Complete Genomics) Variation 
pgNA19025indel LWK NA19025 indel LWK NA19025 indel (Complete Genomics) Variation 
pgNA19025 LWK NA19025 LWK NA19025 (Complete Genomics) Variation 
pgNA19020indel LWK NA19020 indel LWK NA19020 indel (Complete Genomics) Variation 
pgNA19020 LWK NA19020 LWK NA19020 (Complete Genomics) Variation 
pgNA19017indel LWK NA19017 indel LWK NA19017 indel (Complete Genomics) Variation 
pgNA19017 LWK NA19017 LWK NA19017 (Complete Genomics) Variation 
pgNA18956indel JPT NA18956 indel JPT NA18956 indel (Complete Genomics) Variation 
pgNA18956 JPT NA18956 JPT NA18956 (Complete Genomics) Variation 
pgNA18947indel JPT NA18947 indel JPT NA18947 indel (Complete Genomics) Variation 
pgNA18947 JPT NA18947 JPT NA18947 (Complete Genomics) Variation 
pgNA18942indel JPT NA18942 indel JPT NA18942 indel (Complete Genomics) Variation 
pgNA18942 JPT NA18942 JPT NA18942 (Complete Genomics) Variation 
pgNA18940indel JPT NA18940 indel JPT NA18940 indel (Complete Genomics) Variation 
pgNA18940 JPT NA18940 JPT NA18940 (Complete Genomics) Variation 
pgNA20850indel GIH NA20850 indel GIH NA20850 indel (Complete Genomics) Variation 
pgNA20850 GIH NA20850 GIH NA20850 (Complete Genomics) Variation 
pgNA20847indel GIH NA20847 indel GIH NA20847 indel (Complete Genomics) Variation 
pgNA20847 GIH NA20847 GIH NA20847 (Complete Genomics) Variation 
pgNA20846indel GIH NA20846 indel GIH NA20846 indel (Complete Genomics) Variation 
pgNA20846 GIH NA20846 GIH NA20846 (Complete Genomics) Variation 
pgNA20845indel GIH NA20845 indel GIH NA20845 indel (Complete Genomics) Variation 
pgNA20845 GIH NA20845 GIH NA20845 (Complete Genomics) Variation 
pgNA18558indel CHB NA18558 indel CHB NA18558 indel (Complete Genomics) Variation 
pgNA18558 CHB NA18558 CHB NA18558 (Complete Genomics) Variation 
pgNA18555indel CHB NA18555 indel CHB NA18555 indel (Complete Genomics) Variation 
pgNA18555 CHB NA18555 CHB NA18555 (Complete Genomics) Variation 
pgNA18537indel CHB NA18537 indel CHB NA18537 indel (Complete Genomics) Variation 
pgNA18537 CHB NA18537 CHB NA18537 (Complete Genomics) Variation 
pgNA18526indel CHB NA18526 indel CHB NA18526 indel (Complete Genomics) Variation 
pgNA18526 CHB NA18526 CHB NA18526 (Complete Genomics) Variation 
pgHG00733indel PUR HG00733 indel PUR HG00733 (Daughter) indel (Complete Genomics) Variation 
pgHG00733 PUR daughter '733 PUR Trio Daughter HG00733 (Complete Genomics) Variation 
pgNA12004indel CEU NA12004 indel CEU NA12004 indel (Complete Genomics) Variation 
pgNA12004 CEU NA12004 CEU NA12004 (Complete Genomics) Variation 
pgNA10851indel CEU NA10851 indel CEU NA10851 indel (Complete Genomics) Variation 
pgNA10851 CEU NA10851 CEU NA10851 (Complete Genomics) Variation 
pgNA07357indel CEU NA07357 indel CEU NA07357 indel (Complete Genomics) Variation 
pgNA07357 CEU NA07357 CEU NA07357 (Complete Genomics) Variation 
pgNA06994indel CEU NA06994 indel CEU NA06994 indel (Complete Genomics) Variation 
pgNA06994 CEU NA06994 CEU NA06994 (Complete Genomics) Variation 
pgNA06985indel CEU NA06985 indel CEU NA06985 indel (Complete Genomics) Variation 
pgNA06985 CEU NA06985 CEU NA06985 (Complete Genomics) Variation 
pgHG00732indel PUR HG00732 indel PUR HG00732 (Mother) indel (Complete Genomics) Variation 
pgHG00732 PUR mother '732 PUR Trio Mother HG00732 (Complete Genomics) Variation 
pgNA19834indel ASW NA19834 indel ASW NA19834 indel (Complete Genomics) Variation 
pgNA19834 ASW NA19834 ASW NA19834 (Complete Genomics) Variation 
pgNA19704indel ASW NA19704 indel ASW NA19704 indel (Complete Genomics) Variation 
pgNA19704 ASW NA19704 ASW NA19704 (Complete Genomics) Variation 
pgNA19703indel ASW NA19703 indel ASW NA19703 indel (Complete Genomics) Variation 
pgNA19703 ASW NA19703 ASW NA19703 (Complete Genomics) Variation 
pgNA19701indel ASW NA19701 indel ASW NA19701 indel (Complete Genomics) Variation 
pgNA19701 ASW NA19701 ASW NA19701 (Complete Genomics) Variation 
pgNA19700indel ASW NA19700 indel ASW NA19700 indel (Complete Genomics) Variation 
pgNA19700 ASW NA19700 ASW NA19700 (Complete Genomics) Variation 
pgHG00731indel PUR HG00731 indel PUR HG00731 (Father) indel (Complete Genomics) Variation 
pgHG00731 PUR father '731 PUR Trio Father HG00731 (Complete Genomics) Variation 
pgNA19239indel YRI NA19239 indel YRI NA19239 (Father) indel (Complete Genomics) Variation 
pgNA19239CG YRI NA19239 YRI NA19239 (Father) (Complete Genomics) Variation 
pgNA19238indel YRI NA19238 indel YRI NA19238 (Mother) indel (Complete Genomics) Variation 
pgNA19238CG YRI NA19238 YRI NA19238 (Mother) (Complete Genomics) Variation 
pgNA19240indel YRI NA19240 indel YRI NA19240 (Daughter) indel (Complete Genomics) Variation 
pgNA19240CG YRI NA19240 YRI NA19240 (Daughter) (Complete Genomics) Variation 
pgNA12892indel CEU NA12892 indel CEU NA12892 indel (Complete Genomics) Variation 
pgNA12892CG CEU NA12892 CEU pedigree 1463, NA12892 (Complete Genomics) Variation 
pgNA12891indel CEU NA12891 indel CEU NA12891 indel (Complete Genomics) Variation 
pgNA12891CG CEU NA12891 CEU pedigree 1463, NA12891 (Complete Genomics) Variation 
pgNA12878indel CEU NA12878 indel CEU NA12878 indel (Complete Genomics) Variation 
pgNA12878CG CEU NA12878 CEU pedigree 1463, NA12878 (Complete Genomics) Variation 
pgSnp1kG 1000 Genomes March 2010 Personal Genome Variants Variation 
pgNA19239 YRI father '9239 YRI Trio Father NA19239 (1000 Genomes Project) Variation 
pgNA19238 YRI mother '9238 YRI Trio Mother NA19238 (1000 Genomes Project) Variation 
pgNA19240 YRI daught '9240 YRI Trio Daughter NA19240 (1000 Genomes Project) Variation 
pgNA12892 CEU mother '2892 CEU Trio Mother NA12892 (1000 Genomes Project) Variation 
pgNA12891 CEU father '2891 CEU Trio Father NA12891 (1000 Genomes Project) Variation 
pgNA12878 CEU daught '2878 CEU Trio Daughter NA12878 (1000 Genomes Project) Variation 
genscan Genscan Genes Genscan Gene Predictions Genes and Gene Predictions Description This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The track description page offers the following filter and configuration options: Color track by codons: Select the genomic codons option to color and label each codon in a zoomed-in display to facilitate validation and comparison of gene predictions. Go to the Coloring Gene Predictions and Annotations by Codon page for more information about this feature. Methods For a description of the Genscan program and the model that underlies it, refer to Burge and Karlin (1997) in the References section below. The splice site models used are described in more detail in Burge (1998) below. Credits Thanks to Chris Burge for providing the Genscan program. References Burge C. Modeling Dependencies in Pre-mRNA Splicing Signals. In: Salzberg S, Searls D, Kasif S, editors. Computational Methods in Molecular Biology. Amsterdam: Elsevier Science; 1998. p. 127-163. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 1997 Apr 25;268(1):78-94. PMID: 9149143 
wgEncodeGisDnaPet GIS DNA PET GSE28867 ENCODE Genome Institute of Singapore DNA Paired-End Ditags Variation Description This track is produced as part of the ENCODE Transcriptome Project. It shows the starts and ends of DNA fragments from different cell lines determined by paired-end ditag (PET) sequencing using different DNA fragment sizes for analysis of genome structural variation. Display Conventions and Configuration In the graphical display, the ends are represented by blocks connected by a horizontal line. In full and packed display modes, the arrowheads on the horizontal line represent the strand, and an ID of the format XXXXX-N-M is shown to the left of each PET, where X is the unique ID for each PET, N indicates the number of mapping locations in the genome (1 for a single mapping location, 2 for two mapping locations, and so forth), and M is the number of PET sequences at this location. PETs that mapped to multiple locations may represent low complexity or repetitive sequences. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. The query sequences in the SAM/BAM alignment representation are normalized to the + strand of the reference genome (see the SAM Format Specification for more information on the SAM/BAM file format). If a query sequence was originally the reverse of what has been stored and aligned, it will have the following flag: (0x10) Read is on '-' strand. BAM/SAM alignment representations also have tags. The following tags are associated with this track: RG, CQ, CS, and MD. Mapping quality is not available for this track and so, in accordance with the SAM Format Specification, a score of 255 is used. Methods Sample genomic DNA was isolated, hydrosheared at a given size-range, then ligated with specific DNA linker sequence at both ends, followed by gel-selection of the desired size, e.g., 1 kb, 10 kb, etc. respectively. The DNA fragments modified with linker at both ends (e.g., 10 kb) were then circularized by ligation, followed by restriction digest with enzyme EcoP15I to generate DNA PETs (25 bp tag from each end). The PETs were ligated with SOLiD sequencing adaptors at both ends, then amplified by PCR and purified as complex templates for high throughput DNA sequencing. The current DNA PET data sets submitted are mostly generated by SOLiD platform. Cells were grown according to the approved ENCODE cell culture protocols. Data: Reads of DNA PETs were mapped onto reference genome, GRCh37, hg19, excluding mitochondrion, haplotypes, randoms and chromosome Y. Majority of the PETs mapped on the same chromosome in correct orientations and within expected distance span (e.g., a 10 kb DNA PET was expected mapping on ~10 kb span distance). A small portion of misaligned PETs, called discordant PETs, mapped either too far from each other, had wrong orientations, or in different chromosomes indicating various genome structure or variations observed between the sample and the reference genome. The variations could be due to deletion, inversion, tandem repeats, trans-location, fusion etc. Mapping parameters: Mapping was done using Applied Biosystems' SOLiD alignment and pairing pipeline. The ungapped alignment is done in color space. Seed and extend strategy is adopted where initial seed length of 25 is mapped with maximum of 2 mismatches and then extended to read length, each color space match is awarded a score of +1 and each mismatch is awarded a penalty of -2. Read Score = read length - # of mismatches - 2 * # of mismatches After extension each read is trimmed to its maximum score, shortest length. The color space sequences are then converted into base space and checked to ensure that each sequence has a maximum of 2 base pair mismatches. If any sequence has more than 2 mismatches, then that pair is discarded. The final output is converted into SAM/BAM format. Verification Representative structural variations identified by DNA PET data have been verified by targeted PCR and sequencing analysis to confirm the predicted rearrangement sites. Some of them have also been validated by FISH. Credits The GIS DNA PET libraries and sequence data for genome structural variation analysis were produced at the Genome Institute of Singapore. The data were mapped and analyzed by scientists Xiaoan Ruan, Atif Shahab, Chialin Wei, and Yijun Ruan at the Genome Institute of Singapore. Contact: Yijun Ruan (now at The Jackson Laboratory) Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeGisDnaPetViewAlignments Alignments ENCODE Genome Institute of Singapore DNA Paired-End Ditags Variation 
wgEncodeGisDnaPetK562F20kAln K562 20k K562 DnaPet ENCODE June 2010 Freeze 2010-06-16 2010-04-05 2011-01-05 wgEncodeEH000247 247 GSM714696 Gingeras GIS hg18 wgEncodeGisDnaPetK562F20kAln Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Shows individual reads mapped to the genome and indicates where bases may mismatch ENCODE GIS DNA PET Alignments (20k frags in K562 cells) Variation 
wgEncodeGisDnaPetK562F10kAln K562 10k K562 DnaPet ENCODE Jan 2011 Freeze 2010-07-07 2009-03-11 2009-12-11 wgEncodeEH000243 243 GSM714698 Gingeras GIS hg18 wgEncodeGisDnaPetK562F10kAln Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Shows individual reads mapped to the genome and indicates where bases may mismatch ENCODE GIS DNA PET Alignments (10k frags in K562 cells) Variation 
wgEncodeGisDnaPetK562F1kAln K562 1k K562 DnaPet ENCODE Jan 2011 Freeze 2010-07-07 2009-03-11 2009-12-11 wgEncodeEH000244 244 GSM714693 Gingeras GIS hg18 wgEncodeGisDnaPetK562F1kAln Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Shows individual reads mapped to the genome and indicates where bases may mismatch ENCODE GIS DNA PET Alignments (1k frags in K562 cells) Variation 
wgEncodeGisDnaPetGm12878F10kAln GM12878 10k GM12878 DnaPet ENCODE Jan 2011 Freeze 2010-07-07 2009-03-11 2009-12-11 wgEncodeEH000242 242 GSM714697 Gingeras GIS hg18 wgEncodeGisDnaPetGm12878F10kAln Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Shows individual reads mapped to the genome and indicates where bases may mismatch ENCODE GIS DNA PET Alignments (10k frags in GM12878 cells) Variation 
wgEncodeGisDnaPetGm12878F5kAln GM12878 5k GM12878 DnaPet ENCODE June 2010 Freeze 2010-06-16 2009-04-03 2010-01-03 wgEncodeEH000246 246 GSM714692 Gingeras GIS hg18 wgEncodeGisDnaPetGm12878F5kAln Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Shows individual reads mapped to the genome and indicates where bases may mismatch ENCODE GIS DNA PET Alignments (5k frags in GM12878 cells) Variation 
wgEncodeGisDnaPetGm12878F1kAln GM12878 1k GM12878 DnaPet ENCODE June 2010 Freeze 2010-06-16 2009-04-03 2010-01-03 wgEncodeEH000245 245 GSM714695 Gingeras GIS hg18 wgEncodeGisDnaPetGm12878F1kAln Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Shows individual reads mapped to the genome and indicates where bases may mismatch ENCODE GIS DNA PET Alignments (1k frags in GM12878 cells) Variation 
wgEncodeGisRnaPet GIS RNA PET GSE33600 RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS Expression Description This track was produced as part of the ENCODE Transcriptome Project and shows the starts and ends of full-length mRNA transcripts determined by Gene Identification Signature (GIS) paired-end ditag (PET) sequencing using RNA extracts from different sub-cellular localizations in different cell lines. Short tags used in GIS-PET sequencing provide signatures of the 5' start and the 3' end of individual mRNA transcripts, thus demarcating the first and last exon, and contain enough coding information to map the tags uniquely to the genome, in turn making it possible to identify unconventional fusion transcripts. These 5' and 3' paired-end tags extracted by restriction enzyme are ligated together to form a ditag for sequencing, where the 3' end includes two adenine bases from the polyA tail thereby reducing the relative amount of unique sequence. The RNA-PET information provided in this track is composed of two different PET length versions based on how the PETs were extracted using different restriction enzymes. The cloning-based PET method (18 bp and 16 bp for each of the 5' and 3' ends) is an earlier version (Ng et al., 2006). While the cloning-free PET approach (27 bp and 25 bp for each of the 5' and 3' ends) is a recently modified version which uses Type III restriction enzyme EcoP15I to generate a longer length of PET (Ruan and Ruan, 2012), which results in a significant enhancement in both library construction and mapping efficiency. Both versions of PET templates were sequenced by Illumina platform at 2 x 36 bp paired-end sequencing. See the Methods and References sections below for more details. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types and compartments. Clusters The Clusters view shows clusters built from the alignments. In the graphical display, the ends are represented by blocks connected by a horizontal line. In full and packed display modes, the arrowheads on the horizontal line represent the direction of transcription. Although some of the subtracks have score information most of them do not and score filtering has been disabled. Plus Raw Signal The Plus Raw Signal view graphs the base-by-base density of tags on the forward strand. Minus Raw Signal The Minus Raw Signal view graphs the base-by-base density of tags on the reverse strand. Alignments The Alignments view shows alignment of individual PET sequences. The alignment file follows the standard SAM/BAM format indicated in the SAM Format Specification. Some files also use the tag XA, generated by Bowtie, to represent the total number of mismatches in the tag. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Two different GIS RNA-PET protocols were used to generate the full-length transcriptome PETs: one is based on a cloning-free RNA-PET library construction and sequencing strategy (Ruan and Ruan, 2012), and the other is a cloning-based library construction (Ng et al., 2005) and recent Illumina paired-end sequencing. Cloning-free RNA-PET (52 bp reads, 27 bp and 25 bp tag for each of the 5' and 3' ends) Method: The cloning-free RNA-PET libraries were generated from polyA mRNA samples and constructed using a recently modified GIS protocol (Ruan and Ruan, 2012). High quality total RNA was used as starting material and purified with a MACs polyT column to obtain full-length polyA mRNAs. Approximately 5 &#181;grams of enriched polyA mRNA was used for reverse transcription to convert polyA mRNA to full-length cDNA. Specific linker sequences were ligated to the full-length cDNA. The modified cDNA was circularized by ligation generating circular cDNA molecules. The 27 bp tag from each end of the full-length cDNA was extracted by type III enzyme EcoP15I digestion. The resulting PETs were ligated with sequencing adaptors at both ends, amplified by PCR, and further purified as complex templates for paired-end sequencing using Illumina platforms. Data: The sequenced RNA-PETs resulted in reads of 27 bp and 25 bp corresponding to the 5' and 3' end of each cDNA, respectively. Redundant and noisy reads were excluded from downstream analysis. Strand-specific orientation of each PET was determined using the barcode built into the sequencing template. The oriented RNA-PET was mapped onto the reference genome allowing up to two mismatches. The majority of the PETs mapped to known transcripts. A small portion of misaligned PETs, defined as discordant PETs, mapped too far from each tag, with wrong orientations, or to different chromosomes. These discordant PETs indicated the existence of some transcription variants that could be caused by genomic structural variants such as fusions, deletions, insertions, inversions, tandem repeats, translocations or RNA trans-splicing etc. Cloning-based RNA-PET (34 bp reads, 18 bp and 16 bp tag for each of the 5' and 3' ends) Method: The cloning-based RNA-PET (GIS-PET) libraries were generated from polyA RNA samples and constructed using the protocol described by Ng et al., 2005. Total RNA in good quality was used as starting material and further purified with a MACs polyT column to enrich polyA mRNA. Approximately 10 &#181;grams of polyA enriched mRNA was reverse transcribed resulting in full-length cDNA. The obtained full-length cDNA was modified with specific linker sequences and ligated to a GIS-developed (pGIS4) vector. The resulting plasmids form a complex full-length cDNA library, which was cloned into E. coli. The plasmid DNA was then isolated from the library, followed by MmeI (a type II enzyme) digestion to generate a final length of 18 bp/16 bp ditags from each end of the full-length cDNA. The single ditag (or PET) was then ligated to form a diPET structure (a concatemer with two unrelated PET linked by a linker sequence) to facilitate Illumina paired-end sequencing. Data:Sequencing of clone-based RNA-PETs resulted in paired reads of 18 bp and 16 bp corresponding to the 5' and 3' end of each cDNA, respectively. The redundant reads were filtered out and unique reads were included for analysis. PET sequences were then mapped to (GRCh37, hg19, excluding mitochondrion, haplotypes, randoms and chromosome Y) reference genome using the following specific criteria (Ruan et al., 2007): A minimal continuous 16 bp match must exist for the 5' signature; the 3' signature must have a minimal continuous 14 bp match Both 5' and 3' signatures must be present on the same chromosome Their 5' to 3' orientation must be correct (5' signature followed by 3' signature) The maximal genomic span of a PET genomic alignment must be less than one million bp PETs mapping to 2-10 locations are also included and may represent duplicated genes or pseudogenes in the genome. A majority of the PETs mapped to known transcripts or splice variants. A small portion of misaligned PETs, defined as discordant PETs, mapped either too far from each other, in the wrong orientation, or to different chromosomes. The presence of discordant PETs indicates that some transcriptional variants exist. These variants could be caused by genomic structural variants such as fusions, deletions, insertions, inversions, tandem repeats, translocation or RNA trans-splicing etc. Clusters PETs were clustered using the following procedure. The mapping location of the 5' and 3' tag of a given PET was extended by 100 bp in both directions creating 5' and 3' search windows. If the 5' and 3' tags of a second PET mapped within the 5' and 3' search window of the first PET then the two PETs were clustered and the search windows were adjusted so that they contained the tag extensions of the second PET. PETs which subsequently mapped with their 5' and 3' tags within the adjusted 5' and 3' search window, respectively, were also assigned to this cluster and the search window was readjusted. This iterative process continued until no new PETs fell within the search window. This process is repeated until all PETs were assigned to a cluster. The total count of PET sequences mapped to the same locus but with slight nucleotide differences may reflect the expression level of the transcripts. PETs that mapped to multiple locations may represent low complexity or repetitive sequences. Verification To assess overall PET quality and mapping specificity, the top ten most abundant PET clusters that mapped to well-characterized known genes were examined. Over 99% of the PETs represented full-length transcripts, and the majority fell within 10 bp of the known 5' and 3' boundaries of these transcripts. The PET mapping was further verified by confirming the existence of physical cDNA clones represented by the ditags. PCR primers were designed based on the PET sequences and amplified the corresponding cDNA inserts either from full-length cDNA library (cloning-based PET) or from isolated total RNA (cloning-free PET) for sequencing confirmation. Release Notes This is Release 2 (Aug 2012) of this track. It adds data for tier 2 cell lines (A549, SK-N-SH, IMR90, and MCF-7). This newer data has no scores in the Clusters files. Note: As mentioned above, this track mixes two different methodologies. The clone-based data has functioning score fields in the Cluster files which could be used for filtering or shading. However, the clone-free data either has scores that are not scaled well or scores that are set to zero for all items. Therefore, the scores are useful for some tables and not for others. Credits The GIS RNA-PET libraries and sequence data for transcriptome analysis were generated and analyzed by scientists Xiaoan Ruan, Atif Shahab, Chialin Wei, and Yijun Ruan at the Genome Institute of Singapore. Contact: Yijun Ruan References Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, Fullwood MJ, Srinivasan KG, Perbost C, Du L, Sung WK, et al., Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res. 2006;34:e84. Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, Ang CC, Gupta S, Shahab A, Ridwan A, Wong CH, et al., Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods. 2005;2:105-111. Ng P, Wei CL, Ruan Y, Paired-end diTagging for transcriptome and genome analysis. Curr Protoc Mol Biol. 2007 Jul 21.12. Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, et al., Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res. 2007;17:828-838. Ruan X and Ruan Y, Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeGisRnaPetViewPlusRawSig PlusRawSig RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS Expression 
wgEncodeGisRnaPetProstateCellPapPlusRawSigRep1 Pros cell pA+ + 1 prostate RnaPet ENCODE Jan 2011 Freeze 2010-07-22 2009-11-13 2010-08-13 wgEncodeEH000262 262 GSM830520 Gingeras GIS DHP001 clone-based cell hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetProstateCellPapPlusRawSigRep1 PlusRawSignal prostate tissue purchased for CSHL project RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand Prostate whole cell polyA+ clone-based RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetNhekNucleusPapPlusRawRep1 NHEK nucl pA+ + 1 NHEK RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000261 261 GSM830523 Gingeras GIS IHN012 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetNhekNucleusPapPlusRawRep1 PlusRawSignal epidermal keratinocytes RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA+ clone-free RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetNhekCytosolPapPlusRawRep1 NHEK cyto pA+ + 1 NHEK RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000260 260 GSM830522 Gingeras GIS IHN011 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetNhekCytosolPapPlusRawRep1 PlusRawSignal epidermal keratinocytes RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA+ clone-free RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshNucleusPapPlusRawRep4 SKSH nucl pA+ + 4 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002935 2935 GSM1006906 Gingeras GIS RHS020 clone-free nucleus 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshNucleusPapPlusRawRep4 PlusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ clone-free RNA PET Plus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshNucleusPapPlusRawRep3 SKSH nucl pA+ + 3 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002935 2935 GSM1006906 Gingeras GIS RHS019 clone-free nucleus 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshNucleusPapPlusRawRep3 PlusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ clone-free RNA PET Plus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCytosolPapPlusRawRep4 SKSH cyto pA+ + 4 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002925 2925 GSM1006907 Gingeras GIS RHS018 clone-free cytosol 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCytosolPapPlusRawRep4 PlusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ clone-free RNA PET Plus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCytosolPapPlusRawRep3 SKSH cyto pA+ + 3 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002925 2925 GSM1006907 Gingeras GIS RHS017 clone-free cytosol 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCytosolPapPlusRawRep3 PlusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ clone-free RNA PET Plus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCellPapPlusRawRep4 SKSH cell pA+ + 4 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002926 2926 GSM1006910 Gingeras GIS RHS016 clone-free cell 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCellPapPlusRawRep4 PlusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ clone-free RNA PET Plus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCellPapPlusRawRep3 SKSH cell pA+ + 3 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002926 2926 GSM1006910 Gingeras GIS RHS015 clone-free cell 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCellPapPlusRawRep3 PlusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ clone-free RNA PET Plus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7NucleusPapPlusRawRep4 MCF7 nucl pA+ + 4 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002933 2933 GSM1006912 Gingeras GIS RHM055 clone-free nucleus 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7NucleusPapPlusRawRep4 PlusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ clone-free RNA PET Plus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7NucleusPapPlusRawRep3 MCF7 nucl pA+ + 3 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002933 2933 GSM1006912 Gingeras GIS RHM054 clone-free nucleus 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7NucleusPapPlusRawRep3 PlusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ clone-free RNA PET Plus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CytosolPapPlusRawRep4 MCF7 cyto pA+ + 4 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002932 2932 GSM1006904 Gingeras GIS RHM045 clone-free cytosol 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CytosolPapPlusRawRep4 PlusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ clone-free RNA PET Plus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CytosolPapPlusRawRep3 MCF7 cyto pA+ + 3 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002932 2932 GSM1006904 Gingeras GIS RHM044 clone-free cytosol 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CytosolPapPlusRawRep3 PlusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ clone-free RNA PET Plus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CellPapPlusRawRep4 MCF7 cell pA+ + 4 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002934 2934 GSM1006905 Gingeras GIS RHM047 clone-free cell 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CellPapPlusRawRep4 PlusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ clone-free RNA PET Plus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CellPapPlusRawRep3 MCF7 cell pA+ + 3 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002934 2934 GSM1006905 Gingeras GIS RHM046 clone-free cell 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CellPapPlusRawRep3 PlusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ clone-free RNA PET Plus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90NucleusPapPlusRawRep2 IMR9 nucl pA+ + 2 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002931 2931 GSM1006913 Gingeras GIS RHI006 clone-free nucleus 2x36 2 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90NucleusPapPlusRawRep2 PlusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ clone-free RNA PET Plus signal Rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90NucleusPapPlusRawRep1 IMR9 nucl pA+ + 1 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002931 2931 GSM1006913 Gingeras GIS RHI005 clone-free nucleus 2x36 1 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90NucleusPapPlusRawRep1 PlusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ clone-free RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CytosolPapPlusRawRep2 IMR9 cyto pA+ + 2 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002930 2930 GSM1006911 Gingeras GIS RHI004 clone-free cytosol 2x36 2 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CytosolPapPlusRawRep2 PlusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ clone-free RNA PET Plus signal Rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CytosolPapPlusRawRep1 IMR9 cyto pA+ + 1 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002930 2930 GSM1006911 Gingeras GIS RHI003 clone-free cytosol 2x36 1 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CytosolPapPlusRawRep1 PlusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ clone-free RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CellPapPlusRawRep2 IMR9 cell pA+ + 2 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002924 2924 GSM1006908 Gingeras GIS RHI002 clone-free cell 2x36 2 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CellPapPlusRawRep2 PlusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ clone-free RNA PET Plus signal Rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CellPapPlusRawRep1 IMR9 cell pA+ + 1 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-22 2012-12-22 wgEncodeEH002924 2924 GSM1006908 Gingeras GIS RHI001 clone-free cell 2x36 1 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CellPapPlusRawRep1 PlusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ clone-free RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHuvecNucleusPapPlusRawRep1 HUVE nucl pA+ + 1 HUVEC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000251 251 GSM830519 Gingeras GIS RHH001 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHuvecNucleusPapPlusRawRep1 PlusRawSignal umbilical vein endothelial cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA+ clone-free RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHuvecCytosolPapPlusRawRep1V2 HUVE cyto pA+ + 1 HUVEC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2011-11-09 2012-08-09 wgEncodeEH000266 266 GSM1006915 Gingeras GIS RHH003 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHuvecCytosolPapPlusRawRep1V2 PlusRawSignal umbilical vein endothelial cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA+ clone-free RNA PET Plus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHepg2NucleusPapPlusRawSigRep1 HepG nucl pA+ + 1 HepG2 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000253 253 GSM830531 Gingeras GIS DHH003 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHepg2NucleusPapPlusRawSigRep1 PlusRawSignal hepatocellular carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA+ clone-based RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHepg2CytosolPapPlusRawSigRep1 HepG cyto pA+ + 1 HepG2 RnaPet ENCODE Jan 2011 Freeze 2010-08-19 2009-11-13 2010-08-13 wgEncodeEH000252 252 GSM830525 Gingeras GIS DHH002 clone-based cytosol hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHepg2CytosolPapPlusRawSigRep1 PlusRawSignal hepatocellular carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA+ clone-based RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3NucleusPapPlusRawRep1V2 HeLa nucl pA+ + 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2011-11-09 2012-08-09 wgEncodeEH000267 267 GSM1006914 Gingeras GIS RHH004 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3NucleusPapPlusRawRep1V2 PlusRawSignal cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA+ clone-free RNA PET Plus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3CytosolPapPlusRawRep1 HeLa cyto pA+ + 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-05-17 2009-12-05 2010-09-05 wgEncodeEH000268 268 GSM830533 Gingeras GIS RHH002 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3CytosolPapPlusRawRep1 PlusRawSignal cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA+ clone-free RNA PET Plus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3CellPapPlusRawRep1 HeLa cell pA+ + 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001744 1744 GSM830530 Gingeras GIS RHH014 clone-free cell 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3CellPapPlusRawRep1 PlusRawSignal cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA+ clone-free RNA PET Plus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549NucleusPapPlusRawRep4 A549 nucl pA+ + 4 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002928 2928 GSM1006903 Gingeras GIS RHA014 clone-free nucleus 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549NucleusPapPlusRawRep4 PlusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ clone-free RNA PET Plus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549NucleusPapPlusRawRep3 A549 nucl pA+ + 3 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002928 2928 GSM1006903 Gingeras GIS RHA013 clone-free nucleus 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549NucleusPapPlusRawRep3 PlusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ clone-free RNA PET Plus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CytosolPapPlusRawRep4 A549 cyto pA+ + 4 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002927 2927 GSM1006909 Gingeras GIS RHA012 clone-free cytosol 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CytosolPapPlusRawRep4 PlusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ clone-free RNA PET Plus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CytosolPapPlusRawRep3 A549 cyto pA+ + 3 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002927 2927 GSM1006909 Gingeras GIS RHA011 clone-free cytosol 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CytosolPapPlusRawRep3 PlusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ clone-free RNA PET Plus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CellPapPlusRawRep4 A549 cell pA+ + 4 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002929 2929 GSM1006902 Gingeras GIS RHA010 clone-free cell 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CellPapPlusRawRep4 PlusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ clone-free RNA PET Plus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CellPapPlusRawRep3 A549 cell pA+ + 3 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002929 2929 GSM1006902 Gingeras GIS RHA009 clone-free cell 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CellPapPlusRawRep3 PlusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ clone-free RNA PET Plus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562PolysomePapPlusRawSigRep1 K562 poly pA+ + 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-07-22 2009-11-13 2010-08-13 wgEncodeEH000259 259 GSM830527 Gingeras GIS DHK007 clone-based polysome hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetK562PolysomePapPlusRawSigRep1 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Strand of mRNA with ribosomes attached Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand K562 polysome polyA+ clone-based RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleusPapPlusRawSigRep1 K562 nucl pA+ + 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000258 258 GSM830526 Gingeras GIS DHK006 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetK562NucleusPapPlusRawSigRep1 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA+ clone-based RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleoplasmTotalPlusRawSigRep1 K562 nplm tot + 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000257 257 GSM830524 Gingeras GIS PHK002 clone-based nucleoplasm hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562NucleoplasmTotalPlusRawSigRep1 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore That part of the nuclear content other than the chromosomes or the nucleolus Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand K562 nucleoplasm total clone-based RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleolusTotalPlusRawSigRep1 K562 nlus tot + 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000256 256 GSM830521 Gingeras GIS DHK008 clone-based nucleolus hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562NucleolusTotalPlusRawSigRep1 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The part of the nucleus where ribosomal RNA is actively transcribed Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand K562 nucleolus total clone-based RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562CytosolPapPlusRawRep1 K562 cyto pA+ + 1 K562 RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000255 255 GSM830537 Gingeras GIS IHK009010015 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetK562CytosolPapPlusRawRep1 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ clone-free RNA PET Plus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562ChromatinTotalPlusRawSigRep1 K562 chrm tot + 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000254 254 GSM830536 Gingeras GIS PHK001 clone-based chromatin hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562ChromatinTotalPlusRawSigRep1 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Nuclear DNA and associated proteins Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand K562 chromatin total clone-based RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetH1hescCellPapPlusRawRep1 H1ES cell pA+ + 1 H1-hESC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000250 250 GSM830532 Gingeras GIS IHE001 clone-free cell hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetH1hescCellPapPlusRawRep1 PlusRawSignal embryonic stem cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ clone-free RNA PET Plus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetGm12878NucleusPapPlusRawSigRep1 GM12 nucl pA+ + 1 GM12878 RnaPet ENCODE Jan 2011 Freeze 2010-07-22 2009-11-13 2010-08-13 wgEncodeEH000249 249 GSM830534 Gingeras GIS DHG002 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetGm12878NucleusPapPlusRawSigRep1 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA+ clone-free RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetGm12878CytosolPapPlusRawRep1V2 GM12 cyto pA+ + 1 GM12878 RnaPet ENCODE Mar 2012 Freeze 2010-07-22 2011-11-09 2012-08-09 wgEncodeEH000248 248 GSM830535 Gingeras GIS IHG024 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetGm12878CytosolPapPlusRawRep1V2 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ clone-based RNA PET Plus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetViewMinusRawSig MinusRawSig RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS Expression 
wgEncodeGisRnaPetProstateCellPapMinusRawSigRep1 Pros cell pA+ - 1 prostate RnaPet ENCODE Jan 2011 Freeze 2010-07-22 2009-11-13 2010-08-13 wgEncodeEH000262 262 GSM830520 Gingeras GIS DHP001 clone-based cell hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetProstateCellPapMinusRawSigRep1 MinusRawSignal prostate tissue purchased for CSHL project RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand Prostate whole cell polyA+ clone-based RNA PET Minus sig Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetNhekNucleusPapMinusRawRep1 NHEK nucl pA+ - 1 NHEK RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000261 261 GSM830523 Gingeras GIS IHN012 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetNhekNucleusPapMinusRawRep1 MinusRawSignal epidermal keratinocytes RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA+ clone-free RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetNhekCytosolPapMinusRawRep1 NHEK cyto pA+ - 1 NHEK RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000260 260 GSM830522 Gingeras GIS IHN011 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetNhekCytosolPapMinusRawRep1 MinusRawSignal epidermal keratinocytes RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA+ clone-free RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshNucleusPapMinusRawRep4 SKSH nucl pA+ - 4 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002935 2935 GSM1006906 Gingeras GIS RHS020 clone-free nucleus 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshNucleusPapMinusRawRep4 MinusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ clone-free RNA PET Minus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshNucleusPapMinusRawRep3 SKSH nucl pA+ - 3 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002935 2935 GSM1006906 Gingeras GIS RHS019 clone-free nucleus 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshNucleusPapMinusRawRep3 MinusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ clone-free RNA PET Minus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCytosolPapMinusRawRep4 SKSH cyto pA+ - 4 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002925 2925 GSM1006907 Gingeras GIS RHS018 clone-free cytosol 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCytosolPapMinusRawRep4 MinusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ clone-free RNA PET Minus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCytosolPapMinusRawRep3 SKSH cyto pA+ - 3 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002925 2925 GSM1006907 Gingeras GIS RHS017 clone-free cytosol 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCytosolPapMinusRawRep3 MinusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ clone-free RNA PET Minus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCellPapMinusRawRep4 SKSH cell pA+ - 4 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002926 2926 GSM1006910 Gingeras GIS RHS016 clone-free cell 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCellPapMinusRawRep4 MinusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ clone-free RNA PET Minus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCellPapMinusRawRep3 SKSH cell pA+ - 3 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002926 2926 GSM1006910 Gingeras GIS RHS015 clone-free cell 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCellPapMinusRawRep3 MinusRawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ clone-free RNA PET Minus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7NucleusPapMinusRawRep4 MCF7 nucl pA+ - 4 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002933 2933 GSM1006912 Gingeras GIS RHM055 clone-free nucleus 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7NucleusPapMinusRawRep4 MinusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ clone-free RNA PET Minus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7NucleusPapMinusRawRep3 MCF7 nucl pA+ - 3 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002933 2933 GSM1006912 Gingeras GIS RHM054 clone-free nucleus 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7NucleusPapMinusRawRep3 MinusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ clone-free RNA PET Minus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CytosolPapMinusRawRep4 MCF7 cyto pA+ - 4 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002932 2932 GSM1006904 Gingeras GIS RHM045 clone-free cytosol 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CytosolPapMinusRawRep4 MinusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ clone-free RNA PET Minus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CytosolPapMinusRawRep3 MCF7 cyto pA+ - 3 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002932 2932 GSM1006904 Gingeras GIS RHM044 clone-free cytosol 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CytosolPapMinusRawRep3 MinusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ clone-free RNA PET Minus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CellPapMinusRawRep4 MCF7 cell pA+ - 4 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002934 2934 GSM1006905 Gingeras GIS RHM047 clone-free cell 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CellPapMinusRawRep4 MinusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ clone-free RNA PET Minus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CellPapMinusRawRep3 MCF7 cell pA+ - 3 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002934 2934 GSM1006905 Gingeras GIS RHM046 clone-free cell 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CellPapMinusRawRep3 MinusRawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ clone-free RNA PET Minus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90NucleusPapMinusRawRep2 IMR9 nucl pA+ - 2 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002931 2931 GSM1006913 Gingeras GIS RHI006 clone-free nucleus 2x36 2 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90NucleusPapMinusRawRep2 MinusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ clone-free RNA PET Minus signal Rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90NucleusPapMinusRawRep1 IMR9 nucl pA+ - 1 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002931 2931 GSM1006913 Gingeras GIS RHI005 clone-free nucleus 2x36 1 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90NucleusPapMinusRawRep1 MinusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ clone-free RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CytosolPapMinusRawRep2 IMR9 cyto pA+ - 2 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002930 2930 GSM1006911 Gingeras GIS RHI004 clone-free cytosol 2x36 2 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CytosolPapMinusRawRep2 MinusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ clone-free RNA PET Minus signal Rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CytosolPapMinusRawRep1 IMR9 cyto pA+ - 1 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002930 2930 GSM1006911 Gingeras GIS RHI003 clone-free cytosol 2x36 1 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CytosolPapMinusRawRep1 MinusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ clone-free RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CellPapMinusRawRep2 IMR9 cell pA+ - 2 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002924 2924 GSM1006908 Gingeras GIS RHI002 clone-free cell 2x36 2 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CellPapMinusRawRep2 MinusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ clone-free RNA PET Minus signal Rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CellPapMinusRawRep1 IMR9 cell pA+ - 1 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-22 2012-12-22 wgEncodeEH002924 2924 GSM1006908 Gingeras GIS RHI001 clone-free cell 2x36 1 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CellPapMinusRawRep1 MinusRawSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ clone-free RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHuvecNucleusPapMinusRawRep1 HUVE nucl pA+ - 1 HUVEC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000251 251 GSM830519 Gingeras GIS RHH001 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHuvecNucleusPapMinusRawRep1 MinusRawSignal umbilical vein endothelial cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA+ clone-free RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHuvecCytosolPapMinusRawRep1V2 HUVE cyto pA+ - 1 HUVEC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2011-11-09 2012-08-09 wgEncodeEH000266 266 GSM1006915 Gingeras GIS RHH003 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHuvecCytosolPapMinusRawRep1V2 MinusRawSignal umbilical vein endothelial cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA+ clone-free RNA PET Minus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHepg2NucleusPapMinusRawSigRep1 HepG nucl pA+ - 1 HepG2 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000253 253 GSM830531 Gingeras GIS DHH003 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHepg2NucleusPapMinusRawSigRep1 MinusRawSignal hepatocellular carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA+ clone-based RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHepg2CytosolPapMinusRawSigRep1 HepG cyto pA+ - 1 HepG2 RnaPet ENCODE Jan 2011 Freeze 2010-08-19 2009-11-13 2010-08-13 wgEncodeEH000252 252 GSM830525 Gingeras GIS DHH002 clone-based cytosol hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHepg2CytosolPapMinusRawSigRep1 MinusRawSignal hepatocellular carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA+ clone-based RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3NucleusPapMinusRawRep1V2 HeLa nucl pA+ - 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2011-11-09 2012-08-09 wgEncodeEH000267 267 GSM1006914 Gingeras GIS RHH004 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3NucleusPapMinusRawRep1V2 MinusRawSignal cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA+ clone-free RNA PET Minus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3CytosolPapMinusRawRep1 HeLa cyto pA+ - 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-05-17 2009-12-05 2010-09-05 wgEncodeEH000268 268 GSM830533 Gingeras GIS RHH002 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3CytosolPapMinusRawRep1 MinusRawSignal cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA+ clone-free RNA PET Minus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3CellPapMinusRawRep1 HeLa cell pA+ - 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001744 1744 GSM830530 Gingeras GIS RHH014 clone-free cell 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3CellPapMinusRawRep1 MinusRawSignal cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA+ clone-free RNA PET Minus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549NucleusPapMinusRawRep4 A549 nucl pA+ - 4 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002928 2928 GSM1006903 Gingeras GIS RHA014 clone-free nucleus 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549NucleusPapMinusRawRep4 MinusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ clone-free RNA PET Minus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549NucleusPapMinusRawRep3 A549 nucl pA+ - 3 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002928 2928 GSM1006903 Gingeras GIS RHA013 clone-free nucleus 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549NucleusPapMinusRawRep3 MinusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ clone-free RNA PET Minus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CytosolPapMinusRawRep4 A549 cyto pA+ - 4 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002927 2927 GSM1006909 Gingeras GIS RHA012 clone-free cytosol 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CytosolPapMinusRawRep4 MinusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ clone-free RNA PET Minus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CytosolPapMinusRawRep3 A549 cyto pA+ - 3 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002927 2927 GSM1006909 Gingeras GIS RHA011 clone-free cytosol 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CytosolPapMinusRawRep3 MinusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ clone-free RNA PET Minus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CellPapMinusRawRep4 A549 cell pA+ - 4 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002929 2929 GSM1006902 Gingeras GIS RHA010 clone-free cell 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CellPapMinusRawRep4 MinusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ clone-free RNA PET Minus signal Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CellPapMinusRawRep3 A549 cell pA+ - 3 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002929 2929 GSM1006902 Gingeras GIS RHA009 clone-free cell 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CellPapMinusRawRep3 MinusRawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ clone-free RNA PET Minus signal Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562PolysomePapMinusRawSigRep1 K562 poly pA+ - 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-07-22 2009-11-13 2010-08-13 wgEncodeEH000259 259 GSM830527 Gingeras GIS DHK007 clone-based polysome hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetK562PolysomePapMinusRawSigRep1 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Strand of mRNA with ribosomes attached Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand K562 polysome polyA+ clone-based RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleusPapMinusRawSigRep1 K562 nucl pA+ - 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000258 258 GSM830526 Gingeras GIS DHK006 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetK562NucleusPapMinusRawSigRep1 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA+ clone-based RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleoplasmTotalMinusRawSigRep1 K562 nplm tot - 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000257 257 GSM830524 Gingeras GIS PHK002 clone-based nucleoplasm hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562NucleoplasmTotalMinusRawSigRep1 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore That part of the nuclear content other than the chromosomes or the nucleolus Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand K562 nucleoplasm total clone-based RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleolusTotalMinusRawSigRep1 K562 nlus tot - 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000256 256 GSM830521 Gingeras GIS DHK008 clone-based nucleolus hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562NucleolusTotalMinusRawSigRep1 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The part of the nucleus where ribosomal RNA is actively transcribed Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand K562 nucleolus total clone-based RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562CytosolPapMinusRawRep1 K562 cyto pA+ - 1 K562 RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000255 255 GSM830537 Gingeras GIS IHK009010015 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetK562CytosolPapMinusRawRep1 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ clone-free RNA PET Minus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562ChromatinTotalMinusRawSigRep1 K562 chrm tot - 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000254 254 GSM830536 Gingeras GIS PHK001 clone-based chromatin hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562ChromatinTotalMinusRawSigRep1 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Nuclear DNA and associated proteins Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand K562 chromatin total clone-based RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetH1hescCellPapMinusRawRep1 H1ES cell pA+ - 1 H1-hESC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000250 250 GSM830532 Gingeras GIS IHE001 clone-free cell hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetH1hescCellPapMinusRawRep1 MinusRawSignal embryonic stem cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ clone-free RNA PET Minus Signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetGm12878NucleusPapMinusRawSigRep1 GM12 nucl pA+ - 1 GM12878 RnaPet ENCODE Jan 2011 Freeze 2010-07-22 2009-11-13 2010-08-13 wgEncodeEH000249 249 GSM830534 Gingeras GIS DHG002 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetGm12878NucleusPapMinusRawSigRep1 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA+ clone-free RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetGm12878CytosolPapMinusRawRep1V2 GM12 cyto pA+ - b GM12878 RnaPet ENCODE Mar 2012 Freeze 2010-07-22 2011-11-09 2012-08-09 wgEncodeEH000248 248 GSM830535 Gingeras GIS IHG024 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetGm12878CytosolPapMinusRawRep1V2 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ clone-based RNA PET Minus signal Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetViewClusters Clusters RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS Expression 
wgEncodeGisRnaPetProstateCellPapClustersRep1 Pros cell pA+ 1 prostate RnaPet ENCODE Jan 2011 Freeze 2010-03-08 2009-11-13 2010-08-13 wgEncodeEH000262 262 GSM830520 Gingeras GIS DHP001 clone-based cell hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetProstateCellPapClustersRep1 Clusters prostate tissue purchased for CSHL project RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Clusters built from the alignments Prostate whole cell polyA+ clone-based RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetNhekNucleusPapClustersRep1 NHEK nucl pA+ 1 NHEK RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000261 261 GSM830523 Gingeras GIS IHN012 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetNhekNucleusPapClustersRep1 Clusters epidermal keratinocytes RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Clusters built from the alignments NHEK nucleus polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetNhekCytosolPapClustersRep1 NHEK cyto pA+ 1 NHEK RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000260 260 GSM830522 Gingeras GIS IHN011 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetNhekCytosolPapClustersRep1 Clusters epidermal keratinocytes RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Clusters built from the alignments NHEK cytosol polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshNucleusPapClusters SKSH nucl pA+ SK-N-SH RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002935 2935 GSM1006906 Gingeras GIS RHS019,RHS020 clone-free nucleus 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshNucleusPapClusters Clusters neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments SK-N-SH nucleus polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCytosolPapClusters SKSH cyto pA+ SK-N-SH RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002925 2925 GSM1006907 Gingeras GIS RHS017,RHS018 clone-free cytosol 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCytosolPapClusters Clusters neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments SK-N-SH cytosol polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCellPapClusters SKSH cell pA+ SK-N-SH RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002926 2926 GSM1006910 Gingeras GIS RHS015,RHS016 clone-free cell 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCellPapClusters Clusters neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments SK-N-SH whole cell polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7NucleusPapClusters MCF7 nucl pA+ MCF-7 RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002933 2933 GSM1006912 Gingeras GIS RHM054,RHM055 clone-free nucleus 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7NucleusPapClusters Clusters mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments MCF-7 nucleus polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CytosolPapClusters MCF7 cyto pA+ MCF-7 RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002932 2932 GSM1006904 Gingeras GIS RHM044,RHM045 clone-free cytosol 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CytosolPapClusters Clusters mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments MCF-7 cytosol polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CellPapClusters MCF7 cell pA+ MCF-7 RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002934 2934 GSM1006905 Gingeras GIS RHM046,RHM047 iIDR cell 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CellPapClusters Clusters mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments MCF-7 whole cell polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90NucleusPapClusters IMR9 nucl pA+ IMR90 RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002931 2931 GSM1006913 Gingeras GIS RHI005,RHI006 clone-free nucleus 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90NucleusPapClusters Clusters fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments IMR90 nucleus polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CytosolPapClusters IMR9 cyto pA+ IMR90 RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002930 2930 GSM1006911 Gingeras GIS RHI003,RHI004 clone-free cytosol 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CytosolPapClusters Clusters fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments IMR90 cytosol polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CellPapClusters IMR9 cell pA+ IMR90 RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002924 2924 GSM1006908 Gingeras GIS RHI001,RHI002 clone-free cell 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CellPapClusters Clusters fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments IMR90 whole cell polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetHuvecNucleusPapClustersRep1 HUVE nucl pA+ 1 HUVEC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000251 251 GSM830519 Gingeras GIS RHH001 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHuvecNucleusPapClustersRep1 Clusters umbilical vein endothelial cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Clusters built from the alignments HUVEC nucleus polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHuvecCytosolPapClustersRep1V2 HUVE cyto pA+ 1 HUVEC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2011-11-09 2012-08-09 wgEncodeEH000266 266 GSM1006915 Gingeras GIS RHH003 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHuvecCytosolPapClustersRep1V2 Clusters umbilical vein endothelial cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Clusters built from the alignments HUVEC cytosol polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHepg2NucleusPapClustersRep1 HepG nucl pA+ 1 HepG2 RnaPet ENCODE Jan 2011 Freeze 2010-03-08 2009-11-13 2010-08-13 wgEncodeEH000253 253 GSM830531 Gingeras GIS DHH003 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHepg2NucleusPapClustersRep1 Clusters hepatocellular carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Clusters built from the alignments HepG2 nucleus polyA+ clone-based RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHepg2CytosolPapClustersRep1 HepG cyto pA+ 1 HepG2 RnaPet ENCODE Jan 2011 Freeze 2010-03-08 2009-11-13 2010-08-13 wgEncodeEH000252 252 GSM830525 Gingeras GIS DHH002 clone-based cytosol hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHepg2CytosolPapClustersRep1 Clusters hepatocellular carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Clusters built from the alignments HepG2 cytosol polyA+ clone-based RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3NucleusPapClustersRep1V2 HeLa nucl pA+ 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2011-11-09 2012-08-09 wgEncodeEH000267 267 GSM1006914 Gingeras GIS RHH004 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3NucleusPapClustersRep1V2 Clusters cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Clusters built from the alignments HeLa-S3 nucleus polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3CytosolPapClustersRep1 HeLa cyto pA+ 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-05-17 2009-12-05 2010-09-05 wgEncodeEH000268 268 GSM830533 Gingeras GIS RHH002 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3CytosolPapClustersRep1 Clusters cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Clusters built from the alignments HeLa-S3 cytosol polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3CellPapClustersRep1 HeLa cell pA+ 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001744 1744 GSM830530 Gingeras GIS RHH014 clone-free cell 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3CellPapClustersRep1 Clusters cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Clusters built from the alignments HeLa-S3 whole cell polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549NucleusPapClusters A549 nucl pA+ A549 RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002928 2928 GSM1006903 Gingeras GIS RHA013,RHA014 clone-free nucleus 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549NucleusPapClusters Clusters epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments A549 nucleus polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CytosolPapClusters A549 cyto pA+ A549 RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002927 2927 GSM1006909 Gingeras GIS RHA011,RHA012 clone-free cytosol 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CytosolPapClusters Clusters epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments A549 cytosol polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CellPapClusters A549 cell pA+ A549 RnaPet ENCODE Jul 2012 Freeze 2012-06-29 2012-03-27 2012-12-27 wgEncodeEH002929 2929 GSM1006902 Gingeras GIS RHA009,RHA010 clone-free cell 2x36 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CellPapClusters Clusters epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Clusters built from the alignments A549 whole cell polyA+ clone-free RNA PET Clusters Pooled from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562PolysomePapClustersRep1 K562 poly pA+ 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-03-08 2009-11-13 2010-08-13 wgEncodeEH000259 259 GSM830527 Gingeras GIS DHK007 clone-based polysome hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetK562PolysomePapClustersRep1 Clusters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Strand of mRNA with ribosomes attached Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Clusters built from the alignments K562 polysome polyA+ clone-based RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleusPapClustersRep1 K562 nucl pA+ 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-03-08 2009-11-13 2010-08-13 wgEncodeEH000258 258 GSM830526 Gingeras GIS DHK006 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetK562NucleusPapClustersRep1 Clusters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Clusters built from the alignments K562 nucleus polyA+ clone-based RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleoplasmTotalClustersRep1 K562 nplm tot 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-03-08 2009-11-13 2010-08-13 wgEncodeEH000257 257 GSM830524 Gingeras GIS PHK002 clone-based nucleoplasm hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562NucleoplasmTotalClustersRep1 Clusters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore That part of the nuclear content other than the chromosomes or the nucleolus Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Clusters built from the alignments K562 nucleoplasm total clone-based RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleolusTotalClustersRep1 K562 nlus tot 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-03-08 2009-11-13 2010-08-13 wgEncodeEH000256 256 GSM830521 Gingeras GIS DHK008 clone-based nucleolus hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562NucleolusTotalClustersRep1 Clusters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The part of the nucleus where ribosomal RNA is actively transcribed Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Clusters built from the alignments K562 nucleolus total clone-based RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562CytosolPapClustersRep1 K562 cyto pA+ 1 K562 RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000255 255 GSM830537 Gingeras GIS IHK009010015 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetK562CytosolPapClustersRep1 Clusters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Clusters built from the alignments K562 cytosol polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562ChromatinTotalClustersRep1 K562 chrm tot 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-03-08 2009-11-13 2010-08-13 wgEncodeEH000254 254 GSM830536 Gingeras GIS PHK001 clone-based chromatin hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562ChromatinTotalClustersRep1 Clusters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Nuclear DNA and associated proteins Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Clusters built from the alignments K562 chromatin total clone-based RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetH1hescCellPapClustersRep1 H1ES cell pA+ 1 H1-hESC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000250 250 GSM830532 Gingeras GIS IHE001 clone-free cell hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetH1hescCellPapClustersRep1 Clusters embryonic stem cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Clusters built from the alignments H1-hESC whole cell polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetGm12878NucleusPapClustersRep1 GM12 nucl pA+ 1 GM12878 RnaPet ENCODE Jan 2011 Freeze 2010-03-08 2009-11-13 2010-08-13 wgEncodeEH000249 249 GSM830534 Gingeras GIS DHG002 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetGm12878NucleusPapClustersRep1 Clusters B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Clusters built from the alignments GM12878 nucleus polyA+ clone-free RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetGm12878CytosolPapClustersRep1V2 GM12 cyto pA+ 1 GM12878 RnaPet ENCODE Mar 2012 Freeze 2010-03-08 2011-11-09 2012-08-09 wgEncodeEH000248 248 GSM830535 Gingeras GIS IHG024 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetGm12878CytosolPapClustersRep1V2 Clusters B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Clusters built from the alignments GM12878 cytosol polyA+ clone-based RNA PET Clusters Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetViewAlignments Alignments RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS Expression 
wgEncodeGisRnaPetProstateCellPapAlnRep1 Pros cell pA+ A 1 prostate RnaPet ENCODE Jan 2011 Freeze 2010-07-22 2009-11-13 2010-08-13 wgEncodeEH000262 262 Gingeras GIS DHP001 clone-based cell hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetProstateCellPapAlnRep1 Alignments prostate tissue purchased for CSHL project RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch Prostate whole cell polyA+ clone-based RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetNhekNucleusPapAlnRep1 NHEK nucl pA+ A 1 NHEK RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000261 261 Gingeras GIS IHN012 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetNhekNucleusPapAlnRep1 Alignments epidermal keratinocytes RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetNhekCytosolPapAlnRep1 NHEK cyto pA+ A 1 NHEK RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000260 260 Gingeras GIS IHN011 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetNhekCytosolPapAlnRep1 Alignments epidermal keratinocytes RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshNucleusPapAlnRep4 SKSH nucl pA+ A 4 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002935 2935 Gingeras GIS RHS020 clone-free nucleus 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshNucleusPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH nucleus polyA+ clone-free RNA PET Alignments Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshNucleusPapAlnRep3 SKSH nucl pA+ A 3 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002935 2935 Gingeras GIS RHS019 clone-free nucleus 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshNucleusPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH nucleus polyA+ clone-free RNA PET Alignments Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCytosolPapAlnRep4 SKSH cyto pA+ A 4 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002925 2925 Gingeras GIS RHS018 clone-free cytosol 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCytosolPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH cytosol polyA+ clone-free RNA PET Alignments Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCytosolPapAlnRep3 SKSH cyto pA+ A 3 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002925 2925 Gingeras GIS RHS017 clone-free cytosol 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCytosolPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH cytosol polyA+ clone-free RNA PET Alignments Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCellPapAlnRep4 SKSH cell pA+ A 4 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002926 2926 Gingeras GIS RHS016 clone-free cell 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCellPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH whole cell polyA+ clone-free RNA PET Alignments Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetSknshCellPapAlnRep3 SKSH cell pA+ A 3 SK-N-SH RnaPet ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH002926 2926 Gingeras GIS RHS015 clone-free cell 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetSknshCellPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH whole cell polyA+ clone-free RNA PET Alignments Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7NucleusPapAlnRep4 MCF7 nucl pA+ A 4 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002933 2933 Gingeras GIS RHM055 clone-free nucleus 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7NucleusPapAlnRep4 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 nucleus polyA+ clone-free RNA PET Alignments Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7NucleusPapAlnRep3 MCF7 nucl pA+ A 3 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002933 2933 Gingeras GIS RHM054 clone-free nucleus 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7NucleusPapAlnRep3 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 nucleus polyA+ clone-free RNA PET Alignments Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CytosolPapAlnRep4 MCF7 cyto pA+ A 4 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002932 2932 Gingeras GIS RHM045 clone-free cytosol 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CytosolPapAlnRep4 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 cytosol polyA+ clone-free RNA PET Alignments Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CytosolPapAlnRep3 MCF7 cyto pA+ A 3 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002932 2932 Gingeras GIS RHM044 clone-free cytosol 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CytosolPapAlnRep3 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 cytosol polyA+ clone-free RNA PET Alignments Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CellPapAlnRep4 MCF7 cell pA+ A 4 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002934 2934 Gingeras GIS RHM047 clone-free cell 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CellPapAlnRep4 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA+ clone-free RNA PET Alignments Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetMcf7CellPapAlnRep3 MCF7 cell pA+ A 3 MCF-7 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002934 2934 Gingeras GIS RHM046 clone-free cell 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetMcf7CellPapAlnRep3 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA+ clone-free RNA PET Alignments Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90NucleusPapAlnRep2 IMR9 nucl pA+ A 2 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH002931 2931 Gingeras GIS RHI006 clone-free nucleus 2x36 2 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90NucleusPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 nucleus polyA+ clone-free RNA PET Alignments Rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90NucleusPapAlnRep1 IMR9 nucl pA+ A 1 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002931 2931 Gingeras GIS RHI005 clone-free nucleus 2x36 1 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90NucleusPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 nucleus polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CytosolPapAlnRep2 IMR9 cyto pA+ A 2 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002930 2930 Gingeras GIS RHI004 clone-free cytosol 2x36 2 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CytosolPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 cytosol polyA+ clone-free RNA PET Alignments Rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CytosolPapAlnRep1 IMR9 cyto pA+ A 1 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002930 2930 Gingeras GIS RHI003 clone-free cytosol 2x36 1 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CytosolPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 cytosol polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CellPapAlnRep2 IMR9 cell pA+ A 2 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002924 2924 Gingeras GIS RHI002 clone-free cell 2x36 2 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CellPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell polyA+ clone-free RNA PET Alignments Rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaPetImr90CellPapAlnRep1 IMR9 cell pA+ A 1 IMR90 RnaPet ENCODE Mar 2012 Freeze 2012-03-22 2012-12-22 wgEncodeEH002924 2924 Gingeras GIS RHI001 clone-free cell 2x36 1 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetImr90CellPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHuvecNucleusPapAlnRep1 HUVE nucl pA+ A 1 HUVEC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000251 251 Gingeras GIS RHH001 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHuvecNucleusPapAlnRep1 Alignments umbilical vein endothelial cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHuvecCytosolPapAlnRep1V2 HUVE cyto pA+ A 1 HUVEC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2011-11-09 2012-08-09 wgEncodeEH000266 266 Gingeras GIS RHH003 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHuvecCytosolPapAlnRep1V2 Alignments umbilical vein endothelial cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHepg2NucleusPapAlnRep1 HepG nucl pA+ A 1 HepG2 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000253 253 Gingeras GIS DHH003 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHepg2NucleusPapAlnRep1 Alignments hepatocellular carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA+ clone-based RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHepg2CytosolPapAlnRep1 HepG cyto pA+ A 1 HepG2 RnaPet ENCODE Jan 2011 Freeze 2010-08-19 2009-11-13 2010-08-13 wgEncodeEH000252 252 Gingeras GIS DHH002 clone-based cytosol hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetHepg2CytosolPapAlnRep1 Alignments hepatocellular carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA+ clone-based RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3NucleusPapAlnRep1V2 HeLa nucl pA+ A 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2011-11-09 2012-08-09 wgEncodeEH000267 267 Gingeras GIS RHH004 clone-free nucleus hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3NucleusPapAlnRep1V2 Alignments cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3CytosolPapAlnRep1 HeLa cyto pA+ A 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-05-17 2009-12-05 2010-09-05 wgEncodeEH000268 268 Gingeras GIS RHH002 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3CytosolPapAlnRep1 Alignments cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetHelas3CellPapAlnRep1 HeLa cell pA+ A 1 HeLa-S3 RnaPet ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001744 1744 Gingeras GIS RHH014 clone-free cell 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetHelas3CellPapAlnRep1 Alignments cervical carcinoma RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549NucleusPapAlnRep4 A549 nucl pA+ A 4 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002928 2928 Gingeras GIS RHA014 clone-free nucleus 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549NucleusPapAlnRep4 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 nucleus polyA+ clone-free RNA PET Alignments Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549NucleusPapAlnRep3 A549 nucl pA+ A 3 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002928 2928 Gingeras GIS RHA013 clone-free nucleus 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549NucleusPapAlnRep3 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 nucleus polyA+ clone-free RNA PET Alignments Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CytosolPapAlnRep4 A549 cyto pA+ A 4 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002927 2927 Gingeras GIS RHA012 clone-free cytosol 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CytosolPapAlnRep4 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 cytosol polyA+ clone-free RNA PET Alignments Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CytosolPapAlnRep3 A549 cyto pA+ A 3 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002927 2927 Gingeras GIS RHA011 clone-free cytosol 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CytosolPapAlnRep3 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 cytosol polyA+ clone-free RNA PET Alignments Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CellPapAlnRep4 A549 cell pA+ A 4 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002929 2929 Gingeras GIS RHA010 clone-free cell 2x36 4 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CellPapAlnRep4 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA+ clone-free RNA PET Alignments Rep 4 from ENCODE/GIS Expression 
wgEncodeGisRnaPetA549CellPapAlnRep3 A549 cell pA+ A 3 A549 RnaPet ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002929 2929 Gingeras GIS RHA009 clone-free cell 2x36 3 longPolyA Illumina_HiSeq_2000 wgEncodeGisRnaPetA549CellPapAlnRep3 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA+ clone-free RNA PET Alignments Rep 3 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562PolysomePapAlnRep1 K562 poly pA+ A 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-07-22 2009-11-13 2010-08-13 wgEncodeEH000259 259 Gingeras GIS DHK007 clone-based polysome hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetK562PolysomePapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Strand of mRNA with ribosomes attached Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polysome polyA+ clone-based RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleusPapAlnRep1 K562 nucl pA+ A 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000258 258 Gingeras GIS DHK006 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetK562NucleusPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA+ clone-based RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleoplasmTotalAlnRep1 K562 nplm tot A 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000257 257 Gingeras GIS PHK002 clone-based nucleoplasm hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562NucleoplasmTotalAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore That part of the nuclear content other than the chromosomes or the nucleolus Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleoplasm total clone-based RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562NucleolusTotalAlnRep1 K562 nlus tot A 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000256 256 Gingeras GIS DHK008 clone-based nucleolus hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562NucleolusTotalAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The part of the nucleus where ribosomal RNA is actively transcribed Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleolus total clone-based RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562CytosolPapAlnRep1 K562 cyto pA+ A 1 K562 RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000255 255 Gingeras GIS IHK009010015 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetK562CytosolPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetK562ChromatinTotalAlnRep1 K562 chrm tot A 1 K562 RnaPet ENCODE Jan 2011 Freeze 2010-08-18 2009-11-13 2010-08-13 wgEncodeEH000254 254 Gingeras GIS PHK001 clone-based chromatin hg18 2x36 1 total Illumina_GA2 wgEncodeGisRnaPetK562ChromatinTotalAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Nuclear DNA and associated proteins Paired 36 nt reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch K562 chromatin total clone-based RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetH1hescCellPapAlnRep1 H1ES cell pA+ A 1 H1-hESC RnaPet ENCODE Mar 2012 Freeze 2011-05-05 2009-11-13 2010-08-13 wgEncodeEH000250 250 Gingeras GIS IHE001 clone-free cell hg18 2x36 1 longPolyA Illumina_GA2x wgEncodeGisRnaPetH1hescCellPapAlnRep1 Alignments embryonic stem cells RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Whole cell Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetGm12878NucleusPapAlnRep1 GM12 nucl pA+ A 1 GM12878 RnaPet ENCODE Jan 2011 Freeze 2010-07-22 2009-11-13 2010-08-13 wgEncodeEH000249 249 Gingeras GIS DHG002 clone-based nucleus hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetGm12878NucleusPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA+ clone-free RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaPetGm12878CytosolPapAlnRep1V2 GM12 cyto pA+ A 1 GM12878 RnaPet ENCODE Mar 2012 Freeze 2010-07-22 2011-11-09 2012-08-09 wgEncodeEH000248 248 Gingeras GIS IHG024 clone-free cytosol hg18 2x36 1 longPolyA Illumina_GA2 wgEncodeGisRnaPetGm12878CytosolPapAlnRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA Paired-End Tags Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Paired 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA+ clone-based RNA PET Alignments Rep 1 from ENCODE/GIS Expression 
gnfAtlas2 GNF Atlas 2 GNF Expression Atlas 2 Expression Description This track shows expression data from the GNF Gene Expression Atlas 2. This contains two replicates each of 79 human tissues run over Affymetrix microarrays. By default, averages of related tissues are shown. Display all tissues by selecting &quot;All Arrays&quot; from the &quot;Combine arrays&quot; menu on the track settings page. As is standard with microarray data red indicates overexpression in the tissue, and green indicates underexpression. You may want to view gene expression with the Gene Sorter as well as the Genome Browser. Credits Thanks to the Genomics Institute of the Novartis Research Foundation (GNF) for the data underlying this track. References Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7. PMID: 15075390; PMC: PMC395923 
gnomadPLI gnomAD Constraint Metrics Genome Aggregation Database (gnomAD) - Predicted Constraint Metrics (pLI and Z-scores) Variation Description The Genome Aggregation Database (gnomAD) - Predicted Constraint Metrics track set contains metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1 and identifies genes subject to strong selection against various classes of mutation. This track includes several subtracks of constraint metrics calculated at gene (canonical transcript), transcript and transcript-region level. For more information see the following blog post. The metrics include: Observed and expected variant counts per transcript/gene Observed/Expected ratio (O/E) Z-scores of the observed counts compared to expected Probability of loss of function intolerance (pLI), for predicted loss-of-function (pLoF) variation only Chi-Squared difference of observed to expected counts, for the regional missense constraint track only Display Conventions and Configuration There are three &quot;groups&quot; of tracks in this set: Gene/Transcript LoF Constraint tracks: Predicted constraint metrics at the whole gene level or whole transcript level for three different types of variation: missense, synonymous, and predicted loss of function. The Gene Constraint track displays metrics for a canonical transcript per gene defined as the longest isoform. The Transcript Constraint track displays metrics for all transcript isoforms. Items on both tracks are shaded according to the pLI score, with outlier items shaded in grey. Gene/Transcript Missense Constraint tracks: The missense constraint tracks are built similarly to the LoF constraint tracks, however the items displayed are based on missense Z scores. All items are colored black, and individual Z scores can be seen on mouseover. Regional Constraint track: Missense-variation constrained regions at the sub-genic level. This track displays metrics for transcripts that have two or more regions with significantly different levels of missense constraint. All items are colored black. All tracks follow the general configuration settings for bigBed tracks. Mouseover on the Gene/Transcript Constraint tracks shows the pLI score and the loss of function observed/expected upper bound fraction (LOEUF), while mouseover on the Regional Constraint track shows only the missense O/E ratio. Clicking on items in any track brings up a table of constraint metrics. Clicking the grey box to the left of the track, or right-clicking and choosing the Configure option, brings up the interface for filtering items based on their pLI score, or labeling the items based on their Ensembl identifier and/or Gene Name. Methods Please see the gnomAD browser help page and FAQ for further explanation of the topics below. Observed and Expected Variant Counts Observed count: The number of unique single-nucleotide variants in each transcript/gene with 123 or fewer alternative alleles (MAF &lt; 0.1%). Expected count: A depth-corrected probability prediction model that takes into account sequence context, coverage, and methylation was used to predict expected variant counts. For more information please see Lek et al., 2016. Variants found in exons with a median depth &lt; 1 were removed from both counts. The O/E constraint score is the ratio of the observed/expected variants in that gene. Each item in this track shows the O/E ratio for three different types of variation: missense, synonymous, and loss-of-function. The O/E ratio is a continuous measurement of how tolerant a gene or transcript is to a certain class of variation. When a gene has a low O/E value, it is under stronger selection for that class of variation than a gene with a higher O/E value. Because Counts depend on gene size and sample size, the precision of the values varies a lot from one gene to the next. Therefore, the 90% confidence interval (CI) is also displayed along with the O/E ratio to better assist interpretation of the scores. When evaluating how constrained a gene is, it is essential to consider the CI when using O/E. In research and clinical interpretation of Mendelian cases, pLI > 0.9 has been widely used for filtering. Accordingly, the Gnomad team suggests using the upper bound of the O/E confidence interval LOEUF &lt; 0.35 as a threshold if needed. Please see the Methods section below for more information about how the scores were calculated. pLI and Z-scores The pLI and Z-scores of the deviation of observed variant counts relative to the expected number are intended to measure how constrained or intolerant a gene or transcript is to a specific type of variation. Genes or transcripts that are particularly depleted of a specific class of variation (as observed in the gnomAD data set) are considered intolerant of that specific type of variation. Z-scores are available for the missense and synonynmous categories and pLI scores are available for the loss-of-function variation. NOTE: The Regional Constraint track data reflects regions within transcripts that are intolerant of missense variation within the ExAc dataset and was calculated with the method described by Samocha et al., 2017. Missense and Synonymous: Positive Z-scores indicate more constraint (fewer observed variants than expected), and negative scores indicate less constraint (more observed variants than expected). A greater Z-score indicates more intolerance to the class of variation. Z-scores were generated by a sequence-context-based mutational model that predicted the number of expected rare (&lt; 1% MAF) variants per transcript. The square root of the chi-squared value of the deviation of observed counts from expected counts was multiplied by -1 if the observed count was greater than the expected and vice versa. For the synonymous score, each Z-score was corrected by dividing by the standard deviation of all synonymous Z-scores between -5 and 5. For the missense scores, a mirrored distribution of all Z-scores between -5 and 0 was created, and then all missense Z-scores were corrected by dividing by the standard deviation of the Z-score of the mirror distribution. Loss-of-function: pLI closer to 1 indicates that the gene or transcript cannot tolerate protein truncating variation (nonsense, splice acceptor and splice donor variation). The gnomAD team recommends transcripts with a pLI &gt;= 0.9 for the set of transcripts extremely intolerant to truncating variants. pLI is based on the idea that transcripts can be classified into three categories: null: heterozygous or homozygous protein truncating variation is completely tolerated recessive: heterozygous variants are tolerated but homozygous variants are not haploinsufficient: heterozygous variants are not tolerated An expectation-maximization algorithm was then used to assign a probability of belonging in each class to each gene or transcript. pLI is the probability of belonging in the haploinsufficient class. Please see Samocha et al., 2014 and Lek et al., 2016 for further discussion of these metrics. Transcripts Included Transcripts from GENCODE v19 were filtered according to the following criteria: Must have methionine at start of coding sequence Must have stop codon at end of coding sequence Must be divisible by 3 Must have at least one observed variant when removing exons with median depth &lt; 1 Must have reasonable number of missense and synonymous variants as determined by a Z-score cutoff After filtering the transcript set, 18225 transcripts were left. UCSC Track Methods Gene and Transcript Constraint tracks Per gene and per transcript data were downloaded from the gnomAD Google Storage bucket: gs://gnomad-public/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz gs://gnomad-public/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_transcript.txt.bgz These data were then joined to the Gencode v19 set of genes/transcripts available at the UCSC Genome Browser and then transformed into a bigBed 12+5. For the full list of commands used to make this track please see the &quot;gnomAD 2 pLI and other loss-of-function metrics&quot; section of the makedoc. Regional Constraint track Supplementary Table 4 from the associated publication was downloaded and joined to the Gencode v19 set of transcripts available at UCSC and then transformed into a bigBed 12+6. For the full list of commands used to make this track please the &quot;gnomAD Missense Constraint Scores&quot; section of the makedoc. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed file that can be downloaded from the download server. The exact filenames can be found in the track configuration file. Annotations can be converted to ASCII text by our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/gnomAD/pLI/pliByTranscript.bb -chrom=chr6 -start=0 -end=1000000 stdout Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadSuper gnomAD Genome Aggregation Database (gnomAD) - Variants, Coverage, and Constraint Variation Description The tracks that are listed here contain data from unrelated individuals sequenced as part of various population-genetic and disease-specific studies collected by the Genome Aggregation Database (gnomAD). Individuals affected by severe pediatric diseases and first-degree relatives were excluded from the studies. However, some individuals with severe disease may still have remained in the datasets, although probably at an equivalent or lower frequency than observed in the general population. Raw data from all studies have been reprocessed using a standardized pipeline and jointly variant-called process, which aims to increase consistency between projects. For more information on the processing pipeline and population annotations, see the following blog post gnomAD, gnomAD v2.1 and the 2.0.2 README. The available data tracks are: Genome Variants (gnomAD Genomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 15,708 unrelated individuals' genome sequences from the v2.1.1 release. Exome Variants (gnomAD Exomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 125,748 unrelated individuals' exome sequences from the v2.1.1 release. Genome and Exome Sample Coverage (gnomAD Coverage) - Shows various read depth variant metrics calculated separately for exomes and genomes on a ~10% subset of the v2.0.2 samples. Proportion Expression Across Transcript Scores (pext) - Shows exon-level expression for 53 GTEx tissues. Structural Variants (SV) (gnomAD Structural Variants) - Shows structural variants calls (variants &gt;=50 nucleotides) from the gnomAD v2.1 release on 10,847 unrelated genomes. Predicted Constraint Metrics (gnomAD Constraint Metrics) - Contains metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1. Display Conventions These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Most gnomAD tracks contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, only some subracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details page. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API, and the genome annotations are stored in files that can be downloaded from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Coverage values for the genome are in bigWig files in the coverage/ subdirectory. Variant VCFs can be found in the vcf/ subdirectory. The data can also be found directly from the gnomAD downloads page. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadMissense gnomAD Regional Missense Constraint  (ExAc Dataset, as on DECIPHER Browser) gnomAD Predicted Regional Missense Constraint Metrics (O/E scores from ExAc Dataset) v2.1.1 Variation 
missenseByTranscript gnomAD Transcript Missense Constraint gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) v2.1.1 Variation 
pliByTranscript gnomAD Transcript LoF Constraint gnomAD Predicted Loss of Function Constraint Metrics By Transcript (pLI) v2.1.1 Variation 
missenseByGene gnomAD Gene Missense Constraint gnomAD Predicted Missense Constraint Metrics By Gene (Z-scores) v2.1.1 Variation 
pliByGene gnomAD Gene LoF Constraint gnomAD Predicted Loss of Function Constraint Metrics By Gene (pLI) v2.1.1 Variation 
gnomadCoverage gnomAD Coverage Genome Aggregation Database (gnomAD) - Genome and Exome Sample Coverage Variation Description The Genome Aggregation Database (gnomAD) - Genome and Exome Sample Coverage track set shows various read-depth variant metrics calculated separately for exomes and genomes on a ~10% subset of the v2.0.2 samples. Multiple exome capture methods and sequencing chemistries were used for sequencing, so coverage varies between individuals across sites. This variation of coverage is incorporated in this track. This track includes several subtracks of average coverage metrics and sample percentage of coverage. For more information on the processing pipeline and population annotations, see the following blog post and the 2.0.2 README. Display Conventions The Average Sample Coverage graphs display the mean and median read depth of the samples at each base position. The details page shows calculated sample percentages for the range of sequence within the browser window. The nX Coverage Percentage graphs display the percentage of samples whose read depth is at least 1X, 5X, 10X, 15X, 20X, 25X, 30X, 50X, and 100X at each base position. The details page shows calculated sample percentages for the range of sequence within the browser window. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API, and the genome annotations are stored in files that can be downloaded from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Coverage values for the genome are in bigWig files in the coverage/ subdirectory. Variant VCFs can be found in the vcf/ subdirectory. The data can also be found directly from the gnomAD downloads page. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadGenomesReadDepthPct Genome Coverage % Genome Aggregation Database (gnomAD) Percentage of Genome Samples with at least nX Coverage Variation Description The tracks that are listed here contain data from unrelated individuals sequenced as part of various population-genetic and disease-specific studies collected by the Genome Aggregation Database (gnomAD). Individuals affected by severe pediatric diseases and first-degree relatives were excluded from the studies. However, some individuals with severe disease may still have remained in the datasets, although probably at an equivalent or lower frequency than observed in the general population. Raw data from all studies have been reprocessed using a standardized pipeline and jointly variant-called process, which aims to increase consistency between projects. For more information on the processing pipeline and population annotations, see the following blog post gnomAD, gnomAD v2.1 and the 2.0.2 README. The available data tracks are: Genome Variants (gnomAD Genomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 15,708 unrelated individuals' genome sequences from the v2.1.1 release. Exome Variants (gnomAD Exomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 125,748 unrelated individuals' exome sequences from the v2.1.1 release. Genome and Exome Sample Coverage (gnomAD Coverage) - Shows various read depth variant metrics calculated separately for exomes and genomes on a ~10% subset of the v2.0.2 samples. Proportion Expression Across Transcript Scores (pext) - Shows exon-level expression for 53 GTEx tissues. Structural Variants (SV) (gnomAD Structural Variants) - Shows structural variants calls (variants &gt;=50 nucleotides) from the gnomAD v2.1 release on 10,847 unrelated genomes. Predicted Constraint Metrics (gnomAD Constraint Metrics) - Contains metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1. Display Conventions These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Most gnomAD tracks contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, only some subracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details page. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API, and the genome annotations are stored in files that can be downloaded from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Coverage values for the genome are in bigWig files in the coverage/ subdirectory. Variant VCFs can be found in the vcf/ subdirectory. The data can also be found directly from the gnomAD downloads page. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadGenomes100XPercentage Sample % > 100X gnomAD Percentage of Genome Samples with at least 100X Coverage Variation 
gnomadGenomes50XPercentage Sample % > 50X gnomAD Percentage of Genome Samples with at least 50X Coverage Variation 
gnomadGenomes30XPercentage Sample % > 30X gnomAD Percentage of Genome Samples with at least 30X Coverage Variation 
gnomadGenomes25XPercentage Sample % > 25X gnomAD Percentage of Genome Samples with at least 25X Coverage Variation 
gnomadGenomes20XPercentage Sample % > 20X gnomAD Percentage of Genome Samples with at least 20X Coverage Variation 
gnomadGenomes15XPercentage Sample % > 15X gnomAD Percentage of Genome Samples with at least 15X Coverage Variation 
gnomadGenomes10XPercentage Sample % > 10X gnomAD Percentage of Genome Samples with at least 10X Coverage Variation 
gnomadGenomes5XPercentage Sample % > 5X gnomAD Percentage of Genome Samples with at least 5X Coverage Variation 
gnomadGenomes1XPercentage Sample % > 1X gnomAD Percentage of Genome Samples with at least 1X Coverage Variation 
gnomadGenomesAvgCoverage Genome Avg Cover Genome Aggregation Database (gnomAD) Average Genome Sample Coverage Variation Description The tracks that are listed here contain data from unrelated individuals sequenced as part of various population-genetic and disease-specific studies collected by the Genome Aggregation Database (gnomAD). Individuals affected by severe pediatric diseases and first-degree relatives were excluded from the studies. However, some individuals with severe disease may still have remained in the datasets, although probably at an equivalent or lower frequency than observed in the general population. Raw data from all studies have been reprocessed using a standardized pipeline and jointly variant-called process, which aims to increase consistency between projects. For more information on the processing pipeline and population annotations, see the following blog post gnomAD, gnomAD v2.1 and the 2.0.2 README. The available data tracks are: Genome Variants (gnomAD Genomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 15,708 unrelated individuals' genome sequences from the v2.1.1 release. Exome Variants (gnomAD Exomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 125,748 unrelated individuals' exome sequences from the v2.1.1 release. Genome and Exome Sample Coverage (gnomAD Coverage) - Shows various read depth variant metrics calculated separately for exomes and genomes on a ~10% subset of the v2.0.2 samples. Proportion Expression Across Transcript Scores (pext) - Shows exon-level expression for 53 GTEx tissues. Structural Variants (SV) (gnomAD Structural Variants) - Shows structural variants calls (variants &gt;=50 nucleotides) from the gnomAD v2.1 release on 10,847 unrelated genomes. Predicted Constraint Metrics (gnomAD Constraint Metrics) - Contains metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1. Display Conventions These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Most gnomAD tracks contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, only some subracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details page. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API, and the genome annotations are stored in files that can be downloaded from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Coverage values for the genome are in bigWig files in the coverage/ subdirectory. Variant VCFs can be found in the vcf/ subdirectory. The data can also be found directly from the gnomAD downloads page. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadGenomesMedianCoverage Median Coverage gnomAD Median Genome Sample Coverage Variation 
gnomadGenomesMeanCoverage Mean Coverage gnomAD Mean Genome Sample Coverage Variation 
gnomadExomesReadDepthPct Exome Coverage % Genome Aggregation Database (gnomAD) Percentage of Exome Samples with at least nX Coverage Variation Description The tracks that are listed here contain data from unrelated individuals sequenced as part of various population-genetic and disease-specific studies collected by the Genome Aggregation Database (gnomAD). Individuals affected by severe pediatric diseases and first-degree relatives were excluded from the studies. However, some individuals with severe disease may still have remained in the datasets, although probably at an equivalent or lower frequency than observed in the general population. Raw data from all studies have been reprocessed using a standardized pipeline and jointly variant-called process, which aims to increase consistency between projects. For more information on the processing pipeline and population annotations, see the following blog post gnomAD, gnomAD v2.1 and the 2.0.2 README. The available data tracks are: Genome Variants (gnomAD Genomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 15,708 unrelated individuals' genome sequences from the v2.1.1 release. Exome Variants (gnomAD Exomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 125,748 unrelated individuals' exome sequences from the v2.1.1 release. Genome and Exome Sample Coverage (gnomAD Coverage) - Shows various read depth variant metrics calculated separately for exomes and genomes on a ~10% subset of the v2.0.2 samples. Proportion Expression Across Transcript Scores (pext) - Shows exon-level expression for 53 GTEx tissues. Structural Variants (SV) (gnomAD Structural Variants) - Shows structural variants calls (variants &gt;=50 nucleotides) from the gnomAD v2.1 release on 10,847 unrelated genomes. Predicted Constraint Metrics (gnomAD Constraint Metrics) - Contains metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1. Display Conventions These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Most gnomAD tracks contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, only some subracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details page. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API, and the genome annotations are stored in files that can be downloaded from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Coverage values for the genome are in bigWig files in the coverage/ subdirectory. Variant VCFs can be found in the vcf/ subdirectory. The data can also be found directly from the gnomAD downloads page. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadExomes100XPercentage Sample % > 100X gnomAD Percentage of Exome Samples with at least 100X Coverage Variation 
gnomadExomes50XPercentage Sample % > 50X gnomAD Percentage of Exome Samples with at least 50X Coverage Variation 
gnomadExomes30XPercentage Sample % > 30X gnomAD Percentage of Exome Samples with at least 30X Coverage Variation 
gnomadExomes25XPercentage Sample % > 25X gnomAD Percentage of Exome Samples with at least 25X Coverage Variation 
gnomadExomes20XPercentage Sample % > 20X gnomAD Percentage of Exome Samples with at least 20X Coverage Variation 
gnomadExomes15XPercentage Sample % > 15X gnomAD Percentage of Exome Samples with at least 15X Coverage Variation 
gnomadExomes10XPercentage Sample % > 10X gnomAD Percentage of Exome Samples with at least 10X Coverage Variation 
gnomadExomes5XPercentage Sample % > 5X gnomAD Percentage of Exome Samples with at least 5X Coverage Variation 
gnomadExomes1XPercentage Sample % > 1X gnomAD Percentage of Exome Samples with at least 1X Coverage Variation 
gnomadExomesAvgCoverage Exome Avg Cover Genome Aggregation Database (gnomAD) Average Exome Sample Coverage Variation Description The tracks that are listed here contain data from unrelated individuals sequenced as part of various population-genetic and disease-specific studies collected by the Genome Aggregation Database (gnomAD). Individuals affected by severe pediatric diseases and first-degree relatives were excluded from the studies. However, some individuals with severe disease may still have remained in the datasets, although probably at an equivalent or lower frequency than observed in the general population. Raw data from all studies have been reprocessed using a standardized pipeline and jointly variant-called process, which aims to increase consistency between projects. For more information on the processing pipeline and population annotations, see the following blog post gnomAD, gnomAD v2.1 and the 2.0.2 README. The available data tracks are: Genome Variants (gnomAD Genomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 15,708 unrelated individuals' genome sequences from the v2.1.1 release. Exome Variants (gnomAD Exomes) - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) of 125,748 unrelated individuals' exome sequences from the v2.1.1 release. Genome and Exome Sample Coverage (gnomAD Coverage) - Shows various read depth variant metrics calculated separately for exomes and genomes on a ~10% subset of the v2.0.2 samples. Proportion Expression Across Transcript Scores (pext) - Shows exon-level expression for 53 GTEx tissues. Structural Variants (SV) (gnomAD Structural Variants) - Shows structural variants calls (variants &gt;=50 nucleotides) from the gnomAD v2.1 release on 10,847 unrelated genomes. Predicted Constraint Metrics (gnomAD Constraint Metrics) - Contains metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1. Display Conventions These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Most gnomAD tracks contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, only some subracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details page. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API, and the genome annotations are stored in files that can be downloaded from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Coverage values for the genome are in bigWig files in the coverage/ subdirectory. Variant VCFs can be found in the vcf/ subdirectory. The data can also be found directly from the gnomAD downloads page. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadExomesMedianCoverage Median Coverage gnomAD Median Exome Sample Coverage Variation 
gnomadExomesMeanCoverage Mean Coverage gnomAD Mean Exome Sample Coverage Variation 
gnomadExomes gnomAD Exomes Variants Genome Aggregation Database (gnomAD) Exome Variants v2.1.1 Variation Description The Genome Aggregation Database (gnomAD) - Genome and Exome Variants tracks show single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) from 125,748 exomes and 15,708 whole genomes of unrelated individuals, short variant release 2.1.1. For more information on the processing pipeline and population annotations, see the following blog post and the 2.1.1 README. There are two tracks making up this data set: gnomAD Exome Variants: short variants of 125,748 exomes, release 2.1.1. gnomAD Genome Variants: short variants of 15,708 genomes, release 2.1.1. VCF files were downloaded according to the gnomAD instructions and transformed into one bigBed file per data set, as described in UCSC Methods. Display Conventions and Configuration Display conventions By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters described below), before the track switches to dense display mode. Mouse hover on an item will display many details about each variant, including the affected gene(s), the variant type, and annotation (missense, synonymous, etc). Clicking on an item will display additional details on the variant, including a population frequency table showing allele count in each sub-population. Following the conventions on the gnomAD browser, items are shaded according to their Annotation type: pLoF Missense Synonymous Other Label Options To maintain consistency with the gnomAD website, variants are by default labeled according to their chromosomal start position followed by the reference and alternate alleles, for example &quot;chr1-1234-T-CAG&quot;. dbSNP rsID's are also available as an additional label, if the variant is present in dbSnp. Filtering Options Three filters are available for these tracks: FILTER: Used to exclude/include variants that failed Random Forest (RF), Inbreeding Coefficient (Inbreeding Coeff), or Allele Count (AC0) filters. The PASS option is used to include/exclude variants that pass all of the RF, InbreedingCoeff, and AC0 filters, as denoted in the original VCF. Annotation type: Used to exclude/include variants that are annotated as Probability Loss of Function (pLoF), Missense, Synonymous, or Other, as annotated by VEP version 85 (GENCODE v19). Variant Type: Used to exclude/include variants according to the type of variation, as annotated by VEP v85. For gnomAD Exome Variants v2.1.1, there is a Non-cancer filter used to exclude/include variants from samples of individuals who were not ascertained for having cancer in a cancer study. As an individual variant can possess multiple FILTER and Variant Type values, it is important to select any options of interest (or rather deselect if trying to filter out variants from the display). UCSC Methods Annotations from the Loss-of-function curation results have been added where appropriate to variants in both the exomes and genomes data. For the full steps used to create the track at UCSC, please see the section denoted &quot;gnomAD v2.1.1 update&quot; in the hg19 makedoc. Data Access The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API or downloaded as files from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Please refer to our mailing list archives for questions or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadGenomes gnomAD Genomes Variants Genome Aggregation Database (gnomAD) Genome Variants v2.1.1 Variation Description The Genome Aggregation Database (gnomAD) - Genome and Exome Variants tracks show single nucleotide variants (SNVs) and small insertion/deletion variants of &lt;50 nucleotides (indels) from 125,748 exomes and 15,708 whole genomes of unrelated individuals, short variant release 2.1.1. For more information on the processing pipeline and population annotations, see the following blog post and the 2.1.1 README. There are two tracks making up this data set: gnomAD Exome Variants: short variants of 125,748 exomes, release 2.1.1. gnomAD Genome Variants: short variants of 15,708 genomes, release 2.1.1. VCF files were downloaded according to the gnomAD instructions and transformed into one bigBed file per data set, as described in UCSC Methods. Display Conventions and Configuration Display conventions By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters described below), before the track switches to dense display mode. Mouse hover on an item will display many details about each variant, including the affected gene(s), the variant type, and annotation (missense, synonymous, etc). Clicking on an item will display additional details on the variant, including a population frequency table showing allele count in each sub-population. Following the conventions on the gnomAD browser, items are shaded according to their Annotation type: pLoF Missense Synonymous Other Label Options To maintain consistency with the gnomAD website, variants are by default labeled according to their chromosomal start position followed by the reference and alternate alleles, for example &quot;chr1-1234-T-CAG&quot;. dbSNP rsID's are also available as an additional label, if the variant is present in dbSnp. Filtering Options Three filters are available for these tracks: FILTER: Used to exclude/include variants that failed Random Forest (RF), Inbreeding Coefficient (Inbreeding Coeff), or Allele Count (AC0) filters. The PASS option is used to include/exclude variants that pass all of the RF, InbreedingCoeff, and AC0 filters, as denoted in the original VCF. Annotation type: Used to exclude/include variants that are annotated as Probability Loss of Function (pLoF), Missense, Synonymous, or Other, as annotated by VEP version 85 (GENCODE v19). Variant Type: Used to exclude/include variants according to the type of variation, as annotated by VEP v85. For gnomAD Exome Variants v2.1.1, there is a Non-cancer filter used to exclude/include variants from samples of individuals who were not ascertained for having cancer in a cancer study. As an individual variant can possess multiple FILTER and Variant Type values, it is important to select any options of interest (or rather deselect if trying to filter out variants from the display). UCSC Methods Annotations from the Loss-of-function curation results have been added where appropriate to variants in both the exomes and genomes data. For the full steps used to create the track at UCSC, please see the section denoted &quot;gnomAD v2.1.1 update&quot; in the hg19 makedoc. Data Access The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API or downloaded as files from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Please refer to our mailing list archives for questions or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadPext gnomAD pext gnomAD Proportion Expression Across Transcript Scores (pext) Variation Description The gnomAD Proportion Expression Across Transcript Scores (pext) (pext) track set displays isoform expression levels across 53 tissues, based on 11,706 tissue samples from the Genotype Tissue Expression (GTEx) v7 dataset. The gnomAD pext tracks provide a comprehensive view of the expression of exons across a gene using the proportion expression across transcripts, or pext metric, a transcript-level annotation metric that quantifies isoform expression for variants. This metric was calculated by annotating each variant with the expression of all possible consequences across all transcripts for each tissue and normalizing the expression of the annotation to the total expression of the gene, which can be interpreted as a measure of the proportion of the total transcriptional output from a gene that would be affected by the variant annotation in question. Each of the subtracks shows the pext metric for a specific tissue, except the gnomAD pext Mean Proportion subtrack that shows the average pext metrics calculated from the 53 GTEx tissues. Display Conventions and Configuration The pext graphs display the mean expression at each base position for protein-coding (CDS) regions. While UTRs do have expression in transcriptome datasets, this information is not included for the visualization. The details page shows calculated sample percentages for the range of sequence within the browser window. Methods The pext values are derived from isoform quantifications using the RSEM tool. Detailed information about development and commands to create these files can be found here. Pext values were downloaded from the gnomAD website and transformed into bigWigs, one per tissue. For the full list of UCSC specific steps, please see the &quot;gnomAD PEXT scores&quot; section of the hg19 makedoc from our GitHub repository. Note that isoform quantification tools can be imprecise, especially for longer genes with many annotated isoforms. Regions with low pext values might be enriched for annotation errors (ie. there may be edge cases for which an exon that is established to be critical for gene function may appear unexpressed with pext). Also note that the GTEx dataset is postmortem adult tissue, and thus the possibility that an exon may be development-specific or may be expressed in tissues not represented in GTEx can not be dismissed. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. The data can also be found directly from the gnomAD downloads page. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available, Nick Watts for developing this track on the gnomAD Browser, and Anna Benet-Pag&#232;s and Chris Lee for building this track on the UCSC Genome Browser. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomADPextWholeBlood Whole Blood gnomAD pext Whole Blood Variation 
gnomADPextVagina Vagina gnomAD pext Vagina Variation 
gnomADPextUterus Uterus gnomAD pext Uterus Variation 
gnomADPextThyroid Thyroid gnomAD pext Thyroid Variation 
gnomADPextTestis Testis gnomAD pext Testis Variation 
gnomADPextStomach Stomach gnomAD pext Stomach Variation 
gnomADPextSpleen Spleen gnomAD pext Spleen Variation 
gnomADPextSmallIntestine_TerminalIleum Small Intestine-Terminal Ileum gnomAD pext Small Intestine-Terminal Ileum Variation 
gnomADPextSkin_SunExposed_Lowerleg_ Skin-Sun Exposed (Lowerleg) gnomAD pext Skin-Sun Exposed (Lowerleg) Variation 
gnomADPextSkin_NotSunExposed_Suprapubic_ Skin-Not Sun Exposed (Suprapubic) gnomAD pext Skin-Not Sun Exposed (Suprapubic) Variation 
gnomADPextProstate Prostate gnomAD pext Prostate Variation 
gnomADPextPituitary Pituitary gnomAD pext Pituitary Variation 
gnomADPextPancreas Pancreas gnomAD pext Pancreas Variation 
gnomADPextOvary Ovary gnomAD pext Ovary Variation 
gnomADPextNerve_Tibial Nerve-Tibial gnomAD pext Nerve-Tibial Variation 
gnomADPextMuscle_Skeletal Muscle-Skeletal gnomAD pext Muscle-Skeletal Variation 
gnomADPextMinorSalivaryGland Minor Salivary Gland gnomAD pext Minor Salivary Gland Variation 
gnomADPextLung Lung gnomAD pext Lung Variation 
gnomADPextLiver Liver gnomAD pext Liver Variation 
gnomADPextKidney_Cortex Kidney-Cortex gnomAD pext Kidney-Cortex Variation 
gnomADPextHeart_LeftVentricle Heart-Left Ventricle gnomAD pext Heart-Left Ventricle Variation 
gnomADPextHeart_AtrialAppendage Heart-Atrial Appendage gnomAD pext Heart-Atrial Appendage Variation 
gnomADPextFallopianTube Fallopian Tube gnomAD pext Fallopian Tube Variation 
gnomADPextEsophagus_Muscularis Esophagus-Muscularis gnomAD pext Esophagus-Muscularis Variation 
gnomADPextEsophagus_Mucosa Esophagus-Mucosa gnomAD pext Esophagus-Mucosa Variation 
gnomADPextEsophagus_GastroesophagealJunction Esophagus-Gastroesophageal Junction gnomAD pext Esophagus-Gastroesophageal Junction Variation 
gnomADPextColon_Transverse Colon-Transverse gnomAD pext Colon-Transverse Variation 
gnomADPextColon_Sigmoid Colon-Sigmoid gnomAD pext Colon-Sigmoid Variation 
gnomADPextCervix_Endocervix Cervix-Endocervix gnomAD pext Cervix-Endocervix Variation 
gnomADPextCervix_Ectocervix Cervix-Ectocervix gnomAD pext Cervix-Ectocervix Variation 
gnomADPextCells_Transformedfibroblasts Cells-Transformed Fibroblasts gnomAD pext Cells-Transformed Fibroblasts Variation 
gnomADPextCells_EBV_transformedlymphocytes Cells-EBV-transformed Lymphocytes gnomAD pext Cells-EBV-transformed Lymphocytes Variation 
gnomADPextBreast_MammaryTissue Breast-Mammary Tissue gnomAD pext Breast-Mammary Tissue Variation 
gnomADPextBrain_Substantianigra Brain-Substantia Nigra gnomAD pext Brain-Substantia Nigra Variation 
gnomADPextBrain_Spinalcord_cervicalc_1_ Brain-Spinal Cord (cervicalc 1) gnomAD pext Brain-Spinal Cord (cervicalc 1) Variation 
gnomADPextBrain_Putamen_basalganglia_ Brain-Putamen (basal ganglia) gnomAD pext Brain-Putamen (basal ganglia) Variation 
gnomADPextBrain_Nucleusaccumbens_basalganglia_ Brain-Nucleus Accumbens (basal ganglia) gnomAD pext Brain-Nucleus Accumbens (basal ganglia) Variation 
gnomADPextBrain_Hypothalamus Brain-Hypothalamus gnomAD pext Brain-Hypothalamus Variation 
gnomADPextBrain_Hippocampus Brain-Hippocampus gnomAD pext Brain-Hippocampus Variation 
gnomADPextBrain_FrontalCortex_BA9_ Brain-Frontal Cortex (BA9) gnomAD pext Brain-Frontal Cortex (BA9) Variation 
gnomADPextBrain_Cortex Brain-Cortex gnomAD pext Brain-Cortex Variation 
gnomADPextBrain_Cerebellum Brain-Cerebellum gnomAD pext Brain-Cerebellum Variation 
gnomADPextBrain_CerebellarHemisphere Brain-Cerebellar Hemisphere gnomAD pext Brain-Cerebellar Hemisphere Variation 
gnomADPextBrain_Caudate_basalganglia_ Brain-Caudate (basal ganglia) gnomAD pext Brain-Caudate (basal ganglia) Variation 
gnomADPextBrain_Anteriorcingulatecortex_BA24_ Brain-Anterior Cingulate Cortex (BA24) gnomAD pext Brain-Anterior Cingulate Cortex (BA24) Variation 
gnomADPextBrain_Amygdala Brain-Amygdala gnomAD pext Brain-Amygdala Variation 
gnomADPextBladder Bladder gnomAD pext Bladder Variation 
gnomADPextArtery_Tibial Artery-Tibial gnomAD pext Artery-Tibial Variation 
gnomADPextArtery_Coronary Artery-Coronary gnomAD pext Artery-Coronary Variation 
gnomADPextArtery_Aorta Artery-Aorta gnomAD pext Artery-Aorta Variation 
gnomADPextAdrenalGland Adrenal Gland gnomAD pext Adrenal Gland Variation 
gnomADPextAdipose_Visceral_Omentum_ Adipose-Visceral (Omentum) gnomAD pext Adipose-Visceral (Omentum) Variation 
gnomADPextAdipose_Subcutaneous Adipose-Subcut gnomAD pext Adipose-Subcutaneous Variation 
gnomADPextmean_proportion Mean Proportion gnomAD pext Mean Proportion Variation 
gnomadStructuralVariants gnomAD Structural Variants Genome Aggregation Database (gnomAD) - Structural Variants Variation Description The Genome Aggregation Database (gnomAD) - Structural Variants track set shows structural variants calls (&gt;=50 nucleotides) from the gnomAD v2.1 release on 10,847 unrelated genomes. It mostly (but not entirely) overlaps with the genome set used for the gnomAD short variant release. For more information see the following blog post, Structural variants in gnomAD. There are three subtracks in this track set: All SV's: The full set of variant annotations from all 10,847 samples. Control Only SV's: Only samples from individuals not selected as a case in a case/control study of common disease (5,192 samples). Non-neuro SV's: Only samples from individuals not selected as having a neurological condition in a case/control study (8,342 samples). Display Conventions and Configuration Items in all subtracks follow the same conventions: items are shaded according to variant type, mouseover on items indicates affected protein-coding genes, size of the variant (which may differ from the chromosomal coordinates in cases like insertions), variant type (insertion, duplication, etc), Allele Count, Allele Number, and Allele Frequency. When more than 2 genes are affected by a variant, the full list can be obtained by clicking on the item and reading the details page. A short summary of the 3 datasets is available in the below table: Variant Type All Controls Non-neuro Breakend (BND) 52604 37891 44952 Complex (CPX) 4778 3129 4167 Translocation (CTX) 8 4 5 Deletion (DEL) 169635 116401 145978 Duplication (DUP) 49571 36223 43916 Insertion (INS) 109025 78475 95658 Inversion (INV) 748 492 667 Multi-Allele CNV (MCNV) 1108 1108 1108 Detailed information on the CNV color code is described here. All tracks can be filtered according to the size of the variant and variant type, using the track Configure options. Methods Bed files were obtained from the gnomAD Google Storage bucket: gsutil cp gs://gnomad-public/papers/2019-sv/gnomad_v2.1_sv.*.bed* These data were then transformed into bigBed tracks. For the full list of commands used to make this track please see the &quot;gnomAD Structural Variants v2.1&quot; section of the makedoc. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated access, this track, like all others, is available via our API. However, for bulk processing, it is recommended to download the dataset. The genome annotation is stored in a bigBed file that can be downloaded from the download server. The exact filenames can be found in the track configuration file. Annotations can be converted to ASCII text by our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/gnomAD/structuralVariants/gnomad_v2.1_sv.sites.bb -chrom=chr6 -start=0 -end=1000000 stdout Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site. Credits Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (ODbL) as described here. References Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207 Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alf&#246;ldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197 Collins RL, Brand H, Karczewski KJ, Zhao X, Alf&#246;ldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194 Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198 
gnomadSvNonneuro gnomAD Non-Neuro SV's gnomAD Structural Variants Non-neuro Only Variation 
gnomadSvControls gnomAD Control Only SV's gnomAD Structural Variants Controls Only Variation 
gnomadSvFull gnomAD All SV's gnomAD Structural Variants All Variation 
grcIncidentDb GRC Incident GRC Incident Database Mapping and Sequencing Description This track shows locations in the human assembly where assembly problems have been noted or resolved, as reported by the Genome Reference Consortium (GRC). If you would like to report an assembly problem, please use the GRC issue reporting system. Methods Data for this track are extracted from the GRC incident database from the specific species *_issues.gff3 file. The track is synchronized once daily to incorporate new updates. Credits The data and presentation of this track were prepared by Hiram Clawson. 
ctgPos2 GRC Map Contigs Genome Reference Consortium Map Contigs Mapping and Sequencing Description This track represents the names of the assembled super contigs as established by the Genome Reference Consortium. The contigs in this track are identical to those in the Map Contigs track, the difference being the the contigs in this track track are named according to GRC. Data for this track were obtained from localId2acc files located at NCBI. 
gtexEqtlCluster GTEx Combined eQTL Combined Expression QTLs from 44 Tissues from GTEx (midpoint release, V6) Regulation Description This track shows genetic variants likely affecting proximal gene expression in 44 human tissues from the Genotype-Tissue Expression (GTEx) V6 data release. The data items displayed are gene expression quantitative trait loci within 1MB of gene transcription start sites (cis-eQTLs), significantly associated with gene expression and in the credible set of variants for the gene at a high confidence level (95%). Each eQTL annotation includes the significance of the association, effect size on gene expression, and the probability the eQTL is a member of the 95% credible set (the set containing all causal variants for the gene locus, at 95% confidence level). Display Conventions The eQTL item color indicates the effect size attributed to the eQTL: red&nbsp;&nbsp;high positive light red&nbsp;&nbsp;moderate positive light blue&nbsp;&nbsp;moderate negative blue&nbsp;&nbsp;high negative mixed&nbsp;&nbsp;positive and negative effect in combined eQTL Effect size is the regression slope, computed from the effect of the alternative allele vs. the reference in FPKM units, based on quantile normalized expression tables. For display purposes, An arbitrary cutoff of +- 2.0 FPKM defines high effect size. Combined eQTL track Gene/variant pairs occurring in multiple tissues are combined into a single item in the display. The item label shows the number of tissues where the eQTL was identified, or the tissue name and the GTEx-convention tissue color if the eQTL was identified solely in one tissue. Mouseover lists all tissues affected and the effect size. The item color reflects the largest effect size in any tissue. Track configuration supports filtering by gene, effect size, or probability. Tissues can be selected via checkboxes or from the UCSC GTEx Body Map graphic. GTEx Combined eQTL Track Settings: hg19. Tissue eQTL tracks This track is a composite track containing 44 subtracks representing the GTEx eQTL tissues. Each subtrack contains all GTEx/CAVIAR eQTLs identified for that tissue. GTEx 44 Tissues eQTL Track Settings: hg19. Methods Laboratory and RNA-seq analysis methods for GTEx V6 are summarized in the GTEx Gene Track description page. Cis-eQTL's were identified from GTEx RNA-seq and genotype data (variants with minor allele frequency >= 1%) in 44 tissues (those with sample size >=70) using the FastQTL mapper at 5% FDR threshold, by the GTEx Laboratory, Data Analysis and Coordinating Center (LDACC), as part of the GTEx project v6p analysis. These cis-eQTL's were then analyzed together with genome variation information (LD) using the CAVIAR statistical framework to quantify the probability a variant is causal, at the Eskin lab at UCLA, as part of GTEx downstream analysis. The UCSC track was created using the CAVIAR 95% credible set, with significance p-values and effect sizes from the LDACC analysis. Raw data for these analyses are available from dbGaP (phs000424.v6.p1). Credits Thanks to GTEx investigators and analysts -- particularly Farhad Hormozdiari (currently at the Price lab, Harvard), the Eskin lab at UCLA, the GTEx Laboratory, Data Analysis and Coordinating Center and analysts and portal team for providing this data, and to Christopher Brown (U Penn) , for input on design of the track. References GTEx Consortium., Laboratory, Data Analysis &amp;Coordinating Center (LDACC)&#8212;Analysis Working Group., Statistical Methods groups&#8212;Analysis Working Group., Enhancing GTEx (eGTEx) groups., NIH Common Fund., NIH/NCI., NIH/NHGRI., NIH/NIMH., NIH/NIDA., Biospecimen Collection Source Site&#8212;NDRI. et al. Genetic effects on gene expression across human tissues. Nature. 2017 Oct 11;550(7675):204-213. PMID: 29022597 Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O. Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics. 2016 May 15;32(10):1479-85. PMID: 26708335; PMC: PMC4866519 Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E. Identifying causal variants at loci with multiple signals of association. Genetics. 2014 Oct;198(2):497-508. PMID: 25104515; PMC: PMC4196608 GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun;45(6):580-5. PMID: 23715323; PMC: PMC4010069 GTEx Portal Documentation 
gtexGene GTEx Gene Gene Expression in 53 tissues from GTEx RNA-seq of 8555 samples (570 donors) Expression Description The NIH Genotype-Tissue Expression (GTEx) project was created to establish a sample and data resource for studies on the relationship between genetic variation and gene expression in multiple human tissues. This track shows median gene expression levels in 51 tissues and 2 cell lines, based on RNA-seq data from the GTEx midpoint milestone data release (V6, October 2015). This release is based on data from 8555 tissue samples obtained from 570 adult post-mortem individuals. Display Conventions In Full and Pack display modes, expression for each gene is represented by a colored bargraph, where the height of each bar represents the median expression level across all samples for a tissue, and the bar color indicates the tissue. Tissue colors were assigned to conform to the GTEx Consortium publication conventions. &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The bargraph display has the same width and tissue order for all genes. Mouse hover over a bar will show the tissue and median expression level. The Squish display mode draws a rectangle for each gene, colored to indicate the tissue with highest expression level if it contributes more than 10% to the overall expression (and colored black if no tissue predominates). In Dense mode, the darkness of the grayscale rectangle displayed for the gene reflects the total median expression level across all tissues. The GTEx transcript model used to quantify expression level is displayed below the graph, colored to indicate the transcript class (coding, noncoding, pseudogene, problem), following GENCODE conventions. Click-through on a graph displays a boxplot of expression level quartiles with outliers, per tissue, along with a link to the corresponding gene page on the GTEx Portal. The track configuration page provides controls to limit the genes and tissues displayed, and to select raw or log transformed expression level display. Methods Tissue samples were obtained using the GTEx standard operating procedures for informed consent and tissue collection, in conjunction with the National Cancer Institute Biorepositories and Biospecimen. All tissue specimens were reviewed by pathologists to characterize and verify organ source. Images from stained tissue samples can be viewed via the NCI histopathology viewer. The Qiagen PAXgene non-formalin tissue preservation product was used to stabilize tissue specimens without cross-linking biomolecules. RNA-seq was performed by the GTEx Laboratory, Data Analysis and Coordinating Center (LDACC) at the Broad Institute. The Illumina TruSeq protocol was used to create an unstranded polyA+ library sequenced on the Illumina HiSeq 2000 platform to produce 76-bp paired end reads at a depth averaging 50M aligned reads per sample. Sequence reads were aligned to the hg19/GRCh37 human genome using Tophat v1.4.1 assisted by the GENCODE v19 transcriptome definition. Gene annotations were produced by taking the union of the GENCODE exons for each gene. Gene expression levels in RPKM were called via the RNA-SeQC tool, after filtering for unique mapping, proper pairing, and exon overlap. For further method details, see the GTEx Portal Documentation page. UCSC obtained the gene-level expression files, gene annotations and sample metadata from the GTEx Portal Download page. Median expression level in RPKM was computed per gene/per tissue. Subject and Sample Characteristics The scientific goal of the GTEx project required that the donors and their biospecimen present with no evidence of disease. The tissue types collected were chosen based on their clinical significance, logistical feasibility and their relevance to the scientific goal of the project and the research community. Postmortem samples were collected from non-diseased donors with ages ranging from 20 to 79. 34.4% of donors were female and 65.6% male. Additional summary plots of GTEx sample characteristics are available at the GTEx Portal Tissue Summary page. Data Access The raw data for the GTEx Gene expression track can be accessed interactively through the Table Browser or Data Integrator. Metadata can be found in the connected tables below. gtexGeneModel describes the gene names and coordinates in genePred format. hgFixed.gtexTissue lists each of the 53 tissues in alphabetical order, corresponding to the comma separated expression values in gtexGene. hgFixed.gtexSampleData has RPKM expression scores for each individual gene-sample data point, connected to gtexSample. hgFixed.gtexSample contains metadata about sample time, collection site, and tissue, connected to the donor field in the gtexDonor table. hgFixed.gtexDonor has anonymized information on the tissue donor. For automated analysis and downloads, the track data files can be downloaded from our downloads server or the JSON API. Individual regions or the whole genome annotation can be accessed as text using our utility bigBedToBed. Instructions for downloading the utility can be found here. That utility can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/gtex/gtexTranscExpr.bb -chrom=chr21 -start=0 -end=100000000 stdout Data can also be obtained directly from GTEx at the following link: https://gtexportal.org/home/datasets Credits Statistical analysis and data interpretation was performed by The GTEx Consortium Analysis Working Group. Data was provided by the GTEx LDACC at The Broad Institute of MIT and Harvard. References GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun;45(6):580-5. PMID: 23715323; PMC: PMC4010069 Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, DeLuca DS, Peter-Demchok J, Gelfand ET et al. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. Biopreserv Biobank. 2015 Oct;13(5):311-9. PMID: 26484571; PMC: PMC4675181 Mel&#233; M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ et al. Human genomics. The human transcriptome across tissues and individuals. Science. 2015 May 8;348(6235):660-5. PMID: 25954002; PMC: PMC4547472 DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012 Jun 1;28(11):1530-2. PMID: 22539670; PMC: PMC3356847 
gtexEqtlTissue GTEx Tissue eQTL Expression QTLs in 44 tissues from GTEx (midpoint release, V6) Regulation Description This track shows genetic variants likely affecting proximal gene expression in 44 human tissues from the Genotype-Tissue Expression (GTEx) V6 data release. The data items displayed are gene expression quantitative trait loci within 1MB of gene transcription start sites (cis-eQTLs), significantly associated with gene expression and in the credible set of variants for the gene at a high confidence level (95%). Each eQTL annotation includes the significance of the association, effect size on gene expression, and the probability the eQTL is a member of the 95% credible set (the set containing all causal variants for the gene locus, at 95% confidence level). Display Conventions The eQTL item color indicates the effect size attributed to the eQTL: red&nbsp;&nbsp;high positive light red&nbsp;&nbsp;moderate positive light blue&nbsp;&nbsp;moderate negative blue&nbsp;&nbsp;high negative mixed&nbsp;&nbsp;positive and negative effect in combined eQTL Effect size is the regression slope, computed from the effect of the alternative allele vs. the reference in FPKM units, based on quantile normalized expression tables. For display purposes, An arbitrary cutoff of +- 2.0 FPKM defines high effect size. Combined eQTL track Gene/variant pairs occurring in multiple tissues are combined into a single item in the display. The item label shows the number of tissues where the eQTL was identified, or the tissue name and the GTEx-convention tissue color if the eQTL was identified solely in one tissue. Mouseover lists all tissues affected and the effect size. The item color reflects the largest effect size in any tissue. Track configuration supports filtering by gene, effect size, or probability. Tissues can be selected via checkboxes or from the UCSC GTEx Body Map graphic. GTEx Combined eQTL Track Settings: hg19. Tissue eQTL tracks This track is a composite track containing 44 subtracks representing the GTEx eQTL tissues. Each subtrack contains all GTEx/CAVIAR eQTLs identified for that tissue. GTEx 44 Tissues eQTL Track Settings: hg19. Methods Laboratory and RNA-seq analysis methods for GTEx V6 are summarized in the GTEx Gene Track description page. Cis-eQTL's were identified from GTEx RNA-seq and genotype data (variants with minor allele frequency >= 1%) in 44 tissues (those with sample size >=70) using the FastQTL mapper at 5% FDR threshold, by the GTEx Laboratory, Data Analysis and Coordinating Center (LDACC), as part of the GTEx project v6p analysis. These cis-eQTL's were then analyzed together with genome variation information (LD) using the CAVIAR statistical framework to quantify the probability a variant is causal, at the Eskin lab at UCLA, as part of GTEx downstream analysis. The UCSC track was created using the CAVIAR 95% credible set, with significance p-values and effect sizes from the LDACC analysis. Raw data for these analyses are available from dbGaP (phs000424.v6.p1). Credits Thanks to GTEx investigators and analysts -- particularly Farhad Hormozdiari (currently at the Price lab, Harvard), the Eskin lab at UCLA, the GTEx Laboratory, Data Analysis and Coordinating Center and analysts and portal team for providing this data, and to Christopher Brown (U Penn) , for input on design of the track. References GTEx Consortium., Laboratory, Data Analysis &amp;Coordinating Center (LDACC)&#8212;Analysis Working Group., Statistical Methods groups&#8212;Analysis Working Group., Enhancing GTEx (eGTEx) groups., NIH Common Fund., NIH/NCI., NIH/NHGRI., NIH/NIMH., NIH/NIDA., Biospecimen Collection Source Site&#8212;NDRI. et al. Genetic effects on gene expression across human tissues. Nature. 2017 Oct 11;550(7675):204-213. PMID: 29022597 Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O. Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics. 2016 May 15;32(10):1479-85. PMID: 26708335; PMC: PMC4866519 Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E. Identifying causal variants at loci with multiple signals of association. Genetics. 2014 Oct;198(2):497-508. PMID: 25104515; PMC: PMC4196608 GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun;45(6):580-5. PMID: 23715323; PMC: PMC4010069 GTEx Portal Documentation 
gtexEqtlTissueXformedlymphocytes xformedlymphocytes Expression QTL in Cells_EBV-transformed_lymphocytes from GTEx V6 Regulation 
gtexEqtlTissueXformedfibroblasts xformedfibroblasts Expression QTL in Cells_Transformed_fibroblasts from GTEx V6 Regulation 
gtexEqtlTissueWholeBlood wholeBlood Expression QTL in Whole_Blood from GTEx V6 Regulation 
gtexEqtlTissueVagina vagina Expression QTL in Vagina from GTEx V6 Regulation 
gtexEqtlTissueUterus uterus Expression QTL in Uterus from GTEx V6 Regulation 
gtexEqtlTissueThyroid thyroid Expression QTL in Thyroid from GTEx V6 Regulation 
gtexEqtlTissueTestis testis Expression QTL in Testis from GTEx V6 Regulation 
gtexEqtlTissueStomach stomach Expression QTL in Stomach from GTEx V6 Regulation 
gtexEqtlTissueSpleen spleen Expression QTL in Spleen from GTEx V6 Regulation 
gtexEqtlTissueSmallIntestine smallIntestine Expression QTL in Small_Intestine_Terminal_Ileum from GTEx V6 Regulation 
gtexEqtlTissueSkinNotExposed skinNotExposed Expression QTL in Skin_Not_Sun_Exposed_Suprapubic from GTEx V6 Regulation 
gtexEqtlTissueSkinExposed skinExposed Expression QTL in Skin_Sun_Exposed_Lower_leg from GTEx V6 Regulation 
gtexEqtlTissueProstate prostate Expression QTL in Prostate from GTEx V6 Regulation 
gtexEqtlTissuePituitary pituitary Expression QTL in Pituitary from GTEx V6 Regulation 
gtexEqtlTissuePancreas pancreas Expression QTL in Pancreas from GTEx V6 Regulation 
gtexEqtlTissueOvary ovary Expression QTL in Ovary from GTEx V6 Regulation 
gtexEqtlTissueNerveTibial nerveTibial Expression QTL in Nerve_Tibial from GTEx V6 Regulation 
gtexEqtlTissueMuscleSkeletal muscleSkeletal Expression QTL in Muscle_Skeletal from GTEx V6 Regulation 
gtexEqtlTissueLung lung Expression QTL in Lung from GTEx V6 Regulation 
gtexEqtlTissueLiver liver Expression QTL in Liver from GTEx V6 Regulation 
gtexEqtlTissueHeartLeftVentricl heartLeftVentricl Expression QTL in Heart_Left_Ventricle from GTEx V6 Regulation 
gtexEqtlTissueHeartAtrialAppend heartAtrialAppend Expression QTL in Heart_Atrial_Appendage from GTEx V6 Regulation 
gtexEqtlTissueEsophagusMuscular esophagusMuscular Expression QTL in Esophagus_Muscularis from GTEx V6 Regulation 
gtexEqtlTissueEsophagusMucosa esophagusMucosa Expression QTL in Esophagus_Mucosa from GTEx V6 Regulation 
gtexEqtlTissueEsophagusJunction esophagusJunction Expression QTL in Esophagus_Gastroesophageal_Junction from GTEx V6 Regulation 
gtexEqtlTissueColonTransverse colonTransverse Expression QTL in Colon_Transverse from GTEx V6 Regulation 
gtexEqtlTissueColonSigmoid colonSigmoid Expression QTL in Colon_Sigmoid from GTEx V6 Regulation 
gtexEqtlTissueBreastMamTissue breastMamTissue Expression QTL in Breast_Mammary_Tissue from GTEx V6 Regulation 
gtexEqtlTissueBrainPutamen brainPutamen Expression QTL in Brain_Putamen_basal_ganglia from GTEx V6 Regulation 
gtexEqtlTissueBrainNucAccumbens brainNucAccumbens Expression QTL in Brain_Nucleus_accumbens_basal_ganglia from GTEx V6 Regulation 
gtexEqtlTissueBrainHypothalamus brainHypothalamus Expression QTL in Brain_Hypothalamus from GTEx V6 Regulation 
gtexEqtlTissueBrainHippocampus brainHippocampus Expression QTL in Brain_Hippocampus from GTEx V6 Regulation 
gtexEqtlTissueBrainFrontCortex brainFrontCortex Expression QTL in Brain_Frontal_Cortex_BA9 from GTEx V6 Regulation 
gtexEqtlTissueBrainCortex brainCortex Expression QTL in Brain_Cortex from GTEx V6 Regulation 
gtexEqtlTissueBrainCerebellum brainCerebellum Expression QTL in Brain_Cerebellum from GTEx V6 Regulation 
gtexEqtlTissueBrainCerebelHemi brainCerebelHemi Expression QTL in Brain_Cerebellar_Hemisphere from GTEx V6 Regulation 
gtexEqtlTissueBrainCaudate brainCaudate Expression QTL in Brain_Caudate_basal_ganglia from GTEx V6 Regulation 
gtexEqtlTissueBrainAnCinCortex brainAnCinCortex Expression QTL in Brain_Anterior_cingulate_cortex_BA24 from GTEx V6 Regulation 
gtexEqtlTissueArteryTibial arteryTibial Expression QTL in Artery_Tibial from GTEx V6 Regulation 
gtexEqtlTissueArteryCoronary arteryCoronary Expression QTL in Artery_Coronary from GTEx V6 Regulation 
gtexEqtlTissueArteryAorta arteryAorta Expression QTL in Artery_Aorta from GTEx V6 Regulation 
gtexEqtlTissueAdrenalGland adrenalGland Expression QTL in Adrenal_Gland from GTEx V6 Regulation 
gtexEqtlTissueAdiposeVisceral adiposeVisceral Expression QTL in Adipose_Visceral_Omentum from GTEx V6 Regulation 
gtexEqtlTissueAdiposeSubcut adiposeSubcut Expression QTL in Adipose_Subcutaneous from GTEx V6 Regulation 
gtexTranscExpr GTEx Transcript Transcript Expression in 53 tissues from GTEx RNA-seq of 8555 samples/570 donors Expression Description The NIH Genotype-Tissue Expression (GTEx) project was created to establish a sample and data resource for studies on the relationship between genetic variation and gene expression in multiple human tissues. This track displays median transcript expression levels in 53 tissues, based on RNA-seq data from the GTEx midpoint milestone data release (V6, October 2015). To view the GTEx tissues in anatomical context, see the GTEx Body Map. Data for this track were computed at UCSC from GTEx RNA-seq sequence data using the Toil pipeline running the kallisto transcript-level quantification tool. Display Conventions In Full and Pack display modes, expression for each transcript is represented by a colored bar chart, where the height of each bar represents the median expression level across all samples for a tissue, and the bar color indicates the tissue. The bar chart display has the same width and tissue order for all transcripts. Mouse hover over a bar will show the tissue and median expression level. The Squish display mode draws a rectangle for each gene, colored to indicate the tissue with highest expression level if it contributes more than 10% to the overall expression (and colored black if no tissue predominates). In Dense mode, the darkness of the grayscale rectangle displayed for the transcript reflects the total median expression level across all tissues. Click-through on a graph displays a boxplot of expression level quartiles with outliers, per tissue. Methods Tissue samples were obtained using the GTEx standard operating procedures for informed consent and tissue collection, in conjunction with the National Cancer Institute Biorepositories and Biospecimen. All tissue specimens were reviewed by pathologists to characterize and verify organ source. Images from stained tissue samples can be viewed via the NCI histopathology viewer. The Qiagen PAXgene non-formalin tissue preservation product was used to stabilize tissue specimens without cross-linking biomolecules. RNA-seq was performed by the GTEx Laboratory, Data Analysis and Coordinating Center (LDACC) at the Broad Institute. The Illumina TruSeq protocol was used to create an unstranded polyA+ library sequenced on the Illumina HiSeq 2000 platform to produce 76-bp paired end reads at a depth averaging 50M aligned reads per sample. Sequence reads for this track were quantified to the hg38/GRCh38 human genome using kallisto assisted by the GENCODE v23 transcriptome definition. Read quantification was performed at UCSC by the Computational Genomics lab, using the Toil pipeline. The resulting kallisto files were combined to generate a transcript per million (TPM) expression matrix using the UCSC tool, kallistoToMatrix. Average TPM expression values for each tissue were calculated and used to generate a bed6+5 file that is the base of the track. This was done using the UCSC tool, expMatrixToBarchartBed. The bed track was then converted to a bigBed file using the UCSC tool, bedToBigBed. The data in the hg19/GRCh37 version of this track was generated by converting the coordinates from the hg38/GRCh38 track data. Of the 189,615 BED entries from the original hg38 track, 176,220 were mapped over by transcript name to hg19 using wgEncodeGencodeCompV24lift37 (~93% coverage). Subject and Sample Characteristics The scientific goal of the GTEx project required that the donors and their biospecimen present with no evidence of disease. The tissue types collected were chosen based on their clinical significance, logistical feasibility and their relevance to the scientific goal of the project and the research community. Postmortem samples were collected from non-diseased donors with ages ranging from 20 to 79. 34.4% of donors were female and 65.6% male. Additional summary plots of GTEx sample characteristics are available at the GTEx Portal Tissue Summary page. Credits Samples were collected by the GTEx Consortium. RNA-seq was performed by the GTEx Laboratory, Data Analysis and Coordinating Center (LDACC) at the Broad Institute. John Vivian, Melissa Cline, and Benedict Paten of the UCSC Computational Genomics lab were responsible for the sequence read quantification used to produce this track. Kate Rosenbloom and Chris Eisenhart of the UCSC Genome Browser group were responsible for data file post-processing and track configuration. References J. Vivian et al., Rapid and efficient analysis of 20,000 RNA-seq samples with Toil bioRxiv bioRxiv, vol. 2, p. 62497, 2016. GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun;45(6):580-5. PMID: 23715323; PMC: PMC4010069 Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, DeLuca DS, Peter-Demchok J, Gelfand ET et al. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. Biopreserv Biobank. 2015 Oct;13(5):311-9. PMID: 26484571; PMC: PMC4675181 Mel&#233; M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ et al. Human genomics. The human transcriptome across tissues and individuals. Science. 2015 May 8;348(6235):660-5. PMID: 25954002; PMC: PMC4547472 DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012 Jun 1;28(11):1530-2. PMID: 22539670; PMC: PMC3356847 
gwasCatalog GWAS Catalog NHGRI-EBI Catalog of Published Genome-Wide Association Studies Phenotype and Literature Description This track displays single nucleotide polymorphisms (SNPs) identified by published Genome-Wide Association Studies (GWAS), collected in the NHGRI-EBI GWAS Catalog published jointly by the National Human Genome Research Institute (NHGRI) and the European Bioinformatics Institute (EMBL-EBI). Some abbreviations are used above. From http://www.ebi.ac.uk/gwas/docs/about: The Catalog is a quality controlled, manually curated, literature-derived collection of all published genome-wide association studies assaying at least 100,000 SNPs and all SNP-trait associations with p-values &lt; 1.0 x 10-5 (Hindorff et al., 2009). For more details about the Catalog curation process and data extraction procedures, please refer to the Methods page. Methods From http://www.ebi.ac.uk/gwas/docs/methods: The GWAS Catalog data is extracted from the literature. Extracted information includes publication information, study cohort information such as cohort size, country of recruitment and subject ethnicity, and SNP-disease association information including SNP identifier (i.e. RSID), p-value, gene and risk allele. Each study is also assigned a trait that best represents the phenotype under investigation. When multiple traits are analysed in the same study either multiple entries are created, or individual SNPs are annotated with their specific traits. Traits are used both to query and visualise the data in the Catalog's web form and diagram-based query interfaces. Data extraction and curation for the GWAS Catalog is an expert activity; each step is performed by scientists supported by a web-based tracking and data entry system which allows multiple curators to search, annotate, verify and publish the Catalog data. Papers that qualify for inclusion in the Catalog are identified through weekly PubMed searches. They then undergo two levels of curation. First all data, including association information for SNPs, traits and general information about the study, are extracted by one curator. A second curator then performs an additional round of curation to double-check the accuracy and consistency of all the information. Finally, an automated pipeline performs validation of the extracted data, see the Quality control and SNP mapping section below for more details. This information is then used for queries and in the production of the diagram. Data Access The raw data can be explored interactively with the Table Browser, or Data Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server (gwasCatalog*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Previous versions of this track can be found on our archive download server. References Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7. PMID: 19474294; PMC: PMC2687147 
gwipsvizRiboseq GWIPS-viz Riboseq Ribosome Profiling from GWIPS-viz Expression Description Ribosome profiling (ribo-seq) is a technique that takes advantage of NGS technology to sequence ribosome-protected mRNA fragments and consequently allows the locations of translating ribosomes to be determined at the entire transcriptome level (Ingolia et al., 2009). For a more detailed description of the protocol, see Ingolia et al. (2012). For reviews on this technique and its applications, please refer to Ingolia (2014) and Michel et al. (2013). This track displays cumulative ribo-seq data obtained from human cells under different conditions and can be used for the exploration of human genomic loci that are being translated. The values on the y-axis represent the number of ribosome footprint sequence reads at a given position. As of December 2014, the track contains data from 12 studies (see References section for details). Further details about the aggregated track and additional ribo-seq data from these and other studies including data obtained from other organisms can be found at the specialized ribo-seq browser GWIPS-viz. Methods For each study used to generate this track, raw fastq files were downloaded from a repository (e.g., NCBI GEO datasets). Cutadapt was used to trim the relevant adapter sequence from the reads, after which reads below 25 nt in length were discarded. The trimmed reads were aligned to ribosomal RNA using Bowtie and aligning reads were discarded. The remaining reads were then aligned to the hg19 (GRCh37) genome assembly using RUM. An offset of 15 nt (to infer the position of the A-site) was added to the most 5' nucleotide coordinate of each uniquely-mapped read. The alignment files from each of the included studies were merged to generate this aggregate track. See individual studies at GWIPS-viz for a full description of the methods of data acquisition and processing. Credits Thanks to Audrey Michel and GWIPS-viz for providing the data for this track. If you wish to cite this track, please reference: Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM, Mullan JP, Donohue CA, Higgins DG, Baranov PV. GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res. 2014 Jan;42(Database issue):D859-64. PMID: 24185699; PMC: PMC3965066 References Data Fritsch C, Herrmann A, Nothnagel M, Szafranski K, Huse K, Schumann F, Schreiber S, Platzer M, Krawczak M, Hampe J et al. Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res. 2012 Nov;22(11):2208-18. PMID: 22879431; PMC: PMC3483550 Gonzalez C, Sims JS, Hornstein N, Mela A, Garcia F, Lei L, Gass DA, Amendolara B, Bruce JN, Canoll P et al. Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors. J Neurosci. 2014 Aug 13;34(33):10924-36. PMID: 25122893; PMC: PMC4131009 Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature. 2010 Aug 12;466(7308):835-40. PMID: 20703300; PMC: PMC2990499 Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, Shi EY, Stumpf CR, Christensen C, Bonham MJ et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature. 2012 Feb 22;485(7396):55-61. PMID: 22367541; PMC: PMC3663483 Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):E2424-32. PMID: 22927429; PMC: PMC3443142 Liu B, Han Y, Qian SB. Cotranslational response to proteotoxic stress by elongation pausing of ribosomes. Mol Cell. 2013 Feb 7;49(3):453-63. PMID: 23290916; PMC: PMC3570626 Loayza-Puch F, Drost J, Rooijers K, Lopes R, Elkon R, Agami R. p53 induces transcriptional and translational programs to suppress cell proliferation and growth. Genome Biol. 2013 Apr 17;14(4):R32. PMID: 23594524; PMC: PMC4053767 Reid DW, Nicchitta CV. Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling. J Biol Chem. 2012 Feb 17;287(8):5518-27. PMID: 22199352; PMC: PMC3285328 Stadler M, Fire A. Wobble base-pairing slows in vivo translation elongation in metazoans. RNA. 2011 Dec;17(12):2063-73. PMID: 22045228; PMC: PMC3222120 Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H et al. Decoding human cytomegalovirus. Science. 2012 Nov 23;338(6110):1088-93. PMID: 23180859; PMC: PMC3817102 Stumpf CR, Moreno MV, Olshen AB, Taylor BS, Ruggero D. The translational landscape of the mammalian cell cycle. Mol Cell. 2013 Nov 21;52(4):574-82. PMID: 24120665; PMC: PMC3959127 Wein N, Vulin A, Falzarano MS, Szigyarto CA, Maiti B, Findlay A, Heller KN, Uhl&#233;n M, Bakthavachalu B, Messina S et al. Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. Nat Med. 2014 Sep;20(9):992-1000. PMID: 25108525; PMC: PMC4165597 Protocol/Technique Ingolia NT. Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet. 2014 Mar;15(3):205-13. PMID: 24468696 Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome- protected mRNA fragments. Nat Protoc. 2012 Jul 26;7(8):1534-50. PMID: 22836135; PMC: PMC3535016 Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009 Apr 10;324(5924):218-23. PMID: 19213877; PMC: PMC2746483 Michel AM, Baranov PV. Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale. Wiley Interdiscip Rev RNA. 2013 Sep-Oct;4(5):473-90. PMID: 23696005; PMC: PMC3823065 
ntHumChimpCodingDiff H-C Coding Diffs Neandertal Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage Neandertal Assembly and Analysis Description This track displays Neandertal alleles for human-chimp protein-coding differences on the human lineage using orangutan as the outgroup to determine which allele is more likely to be ancestral. Display Conventions and Configuration Neandertal ancestral alleles are colored blue; derived (human) alleles are colored green. The item names show the number of Neandertal reads for the ancestral and derived alleles, followed by the ancestral and derived codons enclosed in parentheses. For example, if no Neandertal reads matched the ancestral base G and three Neandertal reads matched the derived base A, and the ancestral and derived codons were GTA and ATA respectively, then the item name would be &quot;0G&gt;3A(GTA&gt;ATA)&quot;. If N Neandertal reads match neither ancestral nor derived base, then a &quot;+N?&quot; is added before the codons (i.e. &quot;0G&gt;3A+N?(GTA&gt;ATA)&quot;). Methods Neandertal DNA was extracted from a ~49,000-year-old bone (Sidr&oacute;n 1253), which was excavated in El Sidr&oacute;n cave, Asturias, Spain. Non-synonymous changes that occurred on the human lineage since the ancestral split with chimpanzee were identified by aligning human, chimpanzee and orangutan protein sequences for all orthologous proteins in HomoloGene (Build 58) . Comparison of these three species allowed the assignment of human/chimpanzee differences to their respective evolutionary lineages. An Agilent custom oligonucleotide array covering the 13,841 non-synonymous changes inferred to have occurred in the human lineage was designed and used to capture Neandertal sequences. Reference Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science. 2010 May 7;328(5979):723-5. PMID: 20448179; PMC: PMC3140021 
hinv70Composite H-Inv 7.0 H-Inv 7.0 Gene Predictions Genes and Gene Predictions Description This track shows alignments of full-length cDNAs that were used as the basis of the H-Invitational Gene Database (HInv-DB version 7.0). This is the version 7.0 update from March 2010. HInv-DB entries describe the following entities: gene structures functions novel alternative splicing isoforms non-coding functional RNAs functional domains sub-cellular localizations metabolic pathways predictions of protein 3D structure mapping of SNPs and microsatellite repeat motifs in relation with orphan diseases gene expression profiling comparative results with mouse full-length cDNAs gene structures Methods To cluster redundant cDNAs and alternative splicing variants within the H-Inv cDNAs, a total of 41,118 H-Inv cDNAs were mapped to the human genome using the mapping pipeline developed by the Japan Biological Information Research Center (JBIRC). The mapping yielded 40,140 cDNAs that were aligned against the genome using the stringent criteria of at least 95% identity and 90% length coverage. These 40,140 cDNAs were clustered to 20,190 loci, resulting in an average of 2.0 cDNAs per locus. For the remaining 978 unmapped cDNAs, cDNA-based clustering was applied, yielding 847 clusters. In total, 21,037 clusters (20,190 mapped and 847 unmapped) were identified and integrated into H-InvDB. H-Inv cluster IDs (e.g. HIX0000001) were assigned to these clusters. A representative sequence was selected from each cluster and used for further analyses and annotation. A full description of the construction of the HInv-DB is contained in the report by the H-Inv Consortium (see References section). Credits The H-InvDB is hosted at the Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST) in Japan. The human-curated annotations were produced during invitational annotation meetings held in Japan during the summer of 2002, with a follow-up meeting in November 2004. Participants included 158 scientists representing 67 institutions from 12 countries. The full-length cDNA clones and sequences were produced by the Chinese National Human Genome Center (CHGC), the Deutsches Krebsforschungszentrum (DKFZ/MIPS), Helix Research Institute, Inc. (HRI), the Institute of Medical Science in the University of Tokyo (IMSUT), the Kazusa DNA Research Institute (KDRI), the Mammalian Gene Collection (MGC/NIH) and the Full-Length Long Japan (FLJ) project. References Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S et al. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res. 2008 Jan;36(Database issue):D793-9. PMID: 18089548; PMC: PMC2238988 Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi- Kabata Y, Tanino M et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2004 Jun;2(6):e162. PMID: 15103394; PMC: PMC393292 Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, Habara T, Nakaoka H, Todokoro F, Matsuya A et al. H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res. 2010 Jan;38(Database issue):D626-32. PMID: 19933760; PMC: PMC2808976 
hinv70PseudoGene H-Inv pseudo-genes H-Inv v7.0 Pseudogene Predictions Genes and Gene Predictions 
hinv70NonCoding H-Inv non-coding H-Inv v7.0 Non-coding Gene Predictions Genes and Gene Predictions 
hinv70Coding H-Inv genes H-Inv v7.0 Gene Predictions Genes and Gene Predictions 
wgEncodeHaibGenotype HAIB Genotype GSE40698 Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha Variation Description This track is produced as part of the ENCODE project. The track displays copy number variation (CNV) as determined by the Illumina Human 1M-Duo Infinium HD BeadChip assay and circular binary segmentation (CBS). The Human 1M-Duo contains more than 1,100,000 tagSNP markers and a set of &#126;60,000 additional CNV-targeted markers. The median spacing between markers is 1.5 kb and the mean spacing is 2.4 kb. The B-allele frequency and genotyping single nucleotide polymorphism (SNP) data generated by the experiment are not displayed, but are available for download from the Downloads page. Where applicable, biological replicates of each cell line are reported separately. Possible uses of the data include correction of copy number in peak-calling for ChIP-seq, transcriptome, DNase hypersensitivity, and methylation determinations. Display Conventions and Configuration Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. The track displays regions of the genome where copy number variation has been assessed. CNV regions are colored by type: blue = amplified black = normal orange = heterozygous deletion red = homozygous deletion The mean log R ratio for each region can be seen by clicking on each individual region. See Methods below for significance of log R ratio values. The mean log R ratio for each region is reported in the .bed file available for download. The Illumina 1M-Duo B-allele frequency data is available from the Supplemental Materials directory on the Downloads page. The file (wgEncodeHaibGenotypeBalleleSnp.txt) was generated using the standard Illumina protocol and contains the B-allele frequency for all cell types tested. The genotype calls for all cell types tested are also available for download (wgEncodeHaibGenotypeGtypeSnp.txt). Genotyping calls with a Gencall value greater than 0.6 are considered significant. Replicate Numbering The replicate labeling in the genome browser view is a counter indicating the total number of replicates submitted (UCSC Rep). The producing lab has replicate numbers (Lab Rep) that correspond to their internal bio-replicate numbering. Where these two numbering systems conflict, both are listed in the long label of the specific track. When comparing data across tracks, the lab replicate number should be considered. In the downloads directory both replicate numbers are listed. The files are labeled with the lab replicate number. Methods Isolation of genomic DNA and hybridization Cells were grown according to the approved ENCODE cell culture protocols by the Myers lab and by other ENCODE production groups. The production group is reported in the metadata. Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen). DNA concentration and quality were determined by fluorescence (Invitrogen Quant-iT dsDNA High Sensitivity Kit and Qubit Fluorometer), and 400 nanograms of each sample were hybridized to Illumina 1M-Duo DNA Analysis BeadChips. Processing and Analysis The genotypes from the 1M-Duo Arrays were ascertained with BeadStudio by using default settings and formatting with the A/B genotype designation for each SNP. Primary QC for each sample was a cut-off at a call rate of 0.95. Copy Number Variation (CNV) analysis was performed with circular binary segmentation (DNAcopy) of the log R ratio values at each probe (Olshen et al., 2004). The parameters used were alpha=0.001, nperm=5000, sd.undo=1. The copy number segments are reported with the mean log R ratio for each chromosomal segment called by CBS. Log ratios of ~-0.2 to -1.5 can be considered heterozygous deletions, &lt; -1.5 homozygous deletions, and &gt; 0.2 amplifications. Primary QC for each sample was SD of &lt; 0.6. Release Notes This is release 2 of this track (Jan 2012). This is a correction release. There are no new experiments. The affected tracks are: wgEncodeHaibGenotypeGm12878RegionsRep1 - replaced by wgEncodeHaibGenotypeGm12878RegionsRep1V2 due to mapping off the end of the chromosome in the original version. wgEncodeHaibGenotypeAstrocyRegionsRep1 - renamed to wgEncodeHaibGenotypeNhaDukeRegionsRep1 Astrocytes and NH-A are the same cell line. In addition to the above changes, color values for the files have been corrected as well. This does not affect any data values. This is the NCBI Build37 (hg19) release of this track. This release includes the 3 cell types previously released on NCBI Build36 (hg18) which were lifted to NCBI Build37 (hg19) and adds data for many more cell types. The track includes a single display for each cell type and reports the Log ratio in the .bed files. The B-allele frequency and SNP genotyping files are not displayed, but are available for download for the entire dataset from the downloads page. Credits These data were produced by the Dr. Richard Myers Lab and the Dr. Devin Absher lab at the HudsonAlpha Institute for Biotechnology. Cells were grown by the Myers Lab and other ENCODE production groups. Contact: Dr. Florencia Pauli. References Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004 Oct;5(4):557-72. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeHaibGenotypeU87RegionsRep1 U87 1 U87 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001321 1321 GSM999332 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 1 wgEncodeHaibGenotypeU87RegionsRep1 None CNV glioblastoma, astrocytoma, (PMID: 4332744) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation U87 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeT47dRegionsRep2 T-47D 1 T-47D Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001320 1320 GSM999330 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 2 wgEncodeHaibGenotypeT47dRegionsRep2 None CNV epithelial cell line derived from a mammary ductal carcinoma. Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation T-47D Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeBcsmallintestine0111002RegionsRep1 BC Sm Intest 1 BC_Small_Intestine_01-11002 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001291 1291 GSM999296 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 1 wgEncodeHaibGenotypeBcsmallintestine0111002RegionsRep1 None CNV small intestine, donor 01-11002, age 83, caucasian, DNA and RNA extract Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation BC_Small_Intestine_01-11002 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeSknshraRegionsRep2 SK-N-SH_RA 2 SK-N-SH_RA Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001280 1280 GSM999325 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeSknshraRegionsRep2 None CNV neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation SK-N-SH_RA Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeSknshraRegionsRep1 SK-N-SH_RA 1 SK-N-SH_RA Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001280 1280 GSM999325 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeSknshraRegionsRep1 None CNV neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation SK-N-SH_RA Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeSkmcRegionsRep2 SKMC 2 SKMC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001281 1281 GSM999324 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeSkmcRegionsRep2 None CNV skeletal muscle cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation SKMC Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeSkmcRegionsRep1 SKMC 1 SKMC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001281 1281 GSM999324 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeSkmcRegionsRep1 None CNV skeletal muscle cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation SKMC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeSaecRegionsRep2 SAEC 2 SAEC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001279 1279 GSM999334 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeSaecRegionsRep2 None CNV small airway epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation SAEC Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeSaecRegionsRep1 SAEC 1 SAEC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001279 1279 GSM999334 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeSaecRegionsRep1 None CNV small airway epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation SAEC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeRptecRegionsRep2 RPTEC 2 RPTEC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001278 1278 GSM999288 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeRptecRegionsRep2 None CNV renal proximal tubule epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation RPTEC Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeRptecRegionsRep1 RPTEC 1 RPTEC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001278 1278 GSM999288 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeRptecRegionsRep1 None CNV renal proximal tubule epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation RPTEC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypePrecRegionsRep1 PrEC 1 PrEC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001277 1277 GSM999318 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypePrecRegionsRep1 None CNV prostate epithelial cell line Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation PrEC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypePfsk1RegionsRep1 PFSK-1 1 PFSK-1 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001319 1319 GSM999317 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 1 wgEncodeHaibGenotypePfsk1RegionsRep1 None CNV neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation PFSK-1 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypePanc1RegionsRep2 PANC-1 2 PANC-1 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001276 1276 GSM999315 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 2 wgEncodeHaibGenotypePanc1RegionsRep2 None CNV pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation PANC-1 Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypePanc1RegionsRep1 PANC-1 1 PANC-1 Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001276 1276 GSM999315 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypePanc1RegionsRep1 None CNV pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation PANC-1 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeOvcar3RegionsRep1 Ovcar-3 1 ovcar-3 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001322 1322 GSM999289 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeOvcar3RegionsRep1 None CNV ovarian adenocarcinoma, "the NIH: OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID: 6604576) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation Ovcar-3 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeNt2d1RegionsRep1 NT2-D1 1 NT2-D1 Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001275 1275 GSM999314 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeNt2d1RegionsRep1 None CNV malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation NT2-D1 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeNhdfneoRegionsRep1 NHDF-neo 1 NHDF-neo Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001274 1274 GSM999313 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeNhdfneoRegionsRep1 None CNV neonatal dermal fibroblasts Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation NHDF-neo Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeNhbeRegionsRep2 NHBE 2 NHBE Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001273 1273 GSM999312 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeNhbeRegionsRep2 None CNV bronchial epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation NHBE Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeNhbeRegionsRep1 NHBE 1 NHBE Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001273 1273 GSM999312 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeNhbeRegionsRep1 None CNV bronchial epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation NHBE Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeNhaRegionsRep2 NH-A UW 2 NH-A Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001272 1272 GSM999311 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeNhaRegionsRep2 None CNV astrocytes (also called Astrocy) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation NH-A (UW) Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeNhaRegionsRep1 NH-A UW 1 NH-A Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001272 1272 GSM999311 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeNhaRegionsRep1 None CNV astrocytes (also called Astrocy) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation NH-A (UW) Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeNhaDukeRegionsRep1 NH-A Duke 1 NH-A Genotype ENCODE Mar 2012 Freeze 2011-12-14 2011-01-20 2011-10-20 wgEncodeEH001289 1289 GSM999328 Myers HudsonAlpha Illumina 1MDuo Duke hg19 1 wgEncodeHaibGenotypeNhaDukeRegionsRep1 None CNV astrocytes (also called Astrocy) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation NH-A (Duke) Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeNb4RegionsRep2 NB4 2 NB4 Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001271 1271 GSM999292 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeNb4RegionsRep2 None CNV acute promyelocytic leukemia cell line. (PMID: 1995093) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation NB4 Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeNb4RegionsRep1 NB4 1 NB4 Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001271 1271 GSM999292 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeNb4RegionsRep1 None CNV acute promyelocytic leukemia cell line. (PMID: 1995093) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation NB4 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeMyometrRegionsRep1 Myometr 1 Myometr Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001318 1318 GSM999319 Myers HudsonAlpha Illumina 1MDuo Duke hg19 1 wgEncodeHaibGenotypeMyometrRegionsRep1 None CNV myometrial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation Myometr Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeMelanoRegionsRep2 Melano 2 Melano Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001317 1317 GSM999301 Myers HudsonAlpha Illumina 1MDuo Duke hg19 2 wgEncodeHaibGenotypeMelanoRegionsRep2 None CNV epidermal melanocytes Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation Melano Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeMelanoRegionsRep1 Melano 1 Melano Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001317 1317 GSM999301 Myers HudsonAlpha Illumina 1MDuo Duke hg19 1 wgEncodeHaibGenotypeMelanoRegionsRep1 None CNV epidermal melanocytes Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation Melano Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeMcf10aesTamRegionsRep1 MCF10A Tam 1 MCF10A-Er-Src Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001270 1270 GSM999309 Myers HudsonAlpha Illumina 1MDuo Stanford hg19 1 wgEncodeHaibGenotypeMcf10aesTamRegionsRep1 4OHTAM_1uM_36hr CNV mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Copy Number Variation MCF10A-Er-Src Tamoxifen Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeMcf10aesRegionsRep3 MCF10A-Er-Src 3 MCF10A-Er-Src Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001269 1269 GSM999331 Myers HudsonAlpha Illumina 1MDuo Stanford hg19 3 wgEncodeHaibGenotypeMcf10aesRegionsRep3 None CNV mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation MCF10A-Er-Src Copy number variants Replicate 3 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeMcf10aesRegionsRep2 MCF10A-Er-Src 2 MCF10A-Er-Src Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001269 1269 GSM999331 Myers HudsonAlpha Illumina 1MDuo Stanford hg19 2 wgEncodeHaibGenotypeMcf10aesRegionsRep2 None CNV mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation MCF10A-Er-Src Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeMcf10aesRegionsRep1 MCF10A-Er-Src 1 MCF10A-Er-Src Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001269 1269 GSM999331 Myers HudsonAlpha Illumina 1MDuo Stanford hg19 1 wgEncodeHaibGenotypeMcf10aesRegionsRep1 None CNV mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation MCF10A-Er-Src Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeLncapRegionsRep1 LNCaP 1 LNCaP Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001267 1267 GSM999310 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeLncapRegionsRep1 None CNV prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation LNCaP Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeJurkatRegionsRep2 Jurkat 2 Jurkat Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001266 1266 GSM999316 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeJurkatRegionsRep2 None CNV T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation Jurkat Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeJurkatRegionsRep1 Jurkat 1 Jurkat Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001266 1266 GSM999316 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeJurkatRegionsRep1 None CNV T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation Jurkat Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeBcjejunumh12817nRegionsRep1 BC Jejunum 1 BC_Jejunum_H12817N Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001290 1290 GSM999295 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 1 wgEncodeHaibGenotypeBcjejunumh12817nRegionsRep1 None CNV jejunum, donor H12817N, age 71, caucasian, DNA and RNA extract Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation BC_Jejunum_H12817N Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHtr8RegionsRep1 HTR8svn 1 HTR8svn Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001314 1314 GSM999304 Myers HudsonAlpha Illumina 1MDuo Duke hg19 1 wgEncodeHaibGenotypeHtr8RegionsRep1 None CNV trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HTR8svn Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHsmmtRegionsRep2 HSMMtube 1 HSMMtube Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001313 1313 GSM999305 Myers HudsonAlpha Illumina 1MDuo Duke hg19 2 wgEncodeHaibGenotypeHsmmtRegionsRep2 None CNV skeletal muscle myotubes differentiated from the HSMM cell line Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HSMM tube Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHsmmRegionsRep3 HSMM 1 HSMM Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001312 1312 GSM999306 Myers HudsonAlpha Illumina 1MDuo Duke hg19 3 wgEncodeHaibGenotypeHsmmRegionsRep3 None CNV skeletal muscle myoblasts Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HSMM Copy number variants Replicate 1 (Lab Rep 3) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHrpeRegionsRep2 HRPEpiC 2 HRPEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001264 1264 GSM999284 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHrpeRegionsRep2 None CNV retinal pigment epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HRPEpiC Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHrpeRegionsRep1 HRPEpiC 1 HRPEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001264 1264 GSM999284 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHrpeRegionsRep1 None CNV retinal pigment epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HRPEpiC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHreRegionsRep2 HRE 2 HRE Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001263 1263 GSM999279 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHreRegionsRep2 None CNV renal epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HRE Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHreRegionsRep1 HRE 1 HRE Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001263 1263 GSM999279 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHreRegionsRep1 None CNV renal epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HRE Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHrceRegionsRep2 HRCEpiC 2 HRCEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001262 1262 GSM999280 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHrceRegionsRep2 None CNV renal cortical epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HRCEpiC Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHrceRegionsRep1 HRCEpiC 1 HRCEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001262 1262 GSM999280 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHrceRegionsRep1 None CNV renal cortical epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HRCEpiC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHpaeRegionsRep2 HPAEpiC 2 HPAEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001311 1311 GSM999307 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHpaeRegionsRep2 None CNV pulmonary alveolar epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HPAEpiC Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHpaeRegionsRep1 HPAEpiC 1 HPAEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001311 1311 GSM999307 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHpaeRegionsRep1 None CNV pulmonary alveolar epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HPAEpiC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHnpceRegionsRep1 HNPCEpiC 1 HNPCEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001310 1310 GSM999308 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHnpceRegionsRep1 None CNV non-pigment ciliary epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HNPCEpiC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHmecRegionsRep2 HMEC 1 HMEC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001309 1309 GSM999282 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHmecRegionsRep2 None CNV mammary epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HMEC Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHl60RegionsRep1 HL-60 1 HL-60 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001308 1308 GSM999281 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHl60RegionsRep1 None CNV promyelocytic leukemia cells, (PMID: 276884) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HL-60 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHipeRegionsRep2 HIPEpiC 2 HIPEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001307 1307 GSM999274 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHipeRegionsRep2 None CNV iris pigment epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HIPEpiC Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHipeRegionsRep1 HIPEpiC 1 HIPEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001307 1307 GSM999274 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHipeRegionsRep1 None CNV iris pigment epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HIPEpiC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHek293RegionsRep2 HEK293 1 HEK293 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001306 1306 GSM999273 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHek293RegionsRep2 None CNV embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HEK293 Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHeeRegionsRep2 HEEpiC 1 HEEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001305 1305 GSM999272 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHeeRegionsRep2 None CNV esophageal epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HEEpiC Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHcpeRegionsRep2 HCPEpiC 2 HCPEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001304 1304 GSM999271 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHcpeRegionsRep2 None CNV choroid plexus epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HCPEpiC Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHcpeRegionsRep1 HCPEpiC 1 HCPEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001304 1304 GSM999271 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHcpeRegionsRep1 None CNV choroid plexus epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HCPEpiC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHcmRegionsRep2 HCM 2 HCM Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001303 1303 GSM999278 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHcmRegionsRep2 None CNV cardiac myocytes Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HCM Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHcmRegionsRep1 HCM 1 HCM Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001303 1303 GSM999278 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHcmRegionsRep1 None CNV cardiac myocytes Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HCM Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHcfRegionsRep2 HCF 2 HCF Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001302 1302 GSM999277 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHcfRegionsRep2 None CNV cardiac fibroblasts Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HCF Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHcfRegionsRep1 HCF 1 HCF Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001302 1302 GSM999277 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHcfRegionsRep1 None CNV cardiac fibroblasts Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HCF Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHaeRegionsRep2 HAEpiC 2 HAEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001301 1301 GSM999276 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeHaeRegionsRep2 None CNV amniotic epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HAEpiC Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHaeRegionsRep1 HAEpiC 1 HAEpiC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001301 1301 GSM999276 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeHaeRegionsRep1 None CNV amniotic epithelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HAEpiC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeGm19239RegionsRep1 GM19239 1 GM19239 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001299 1299 GSM999291 Myers HudsonAlpha Illumina 1MDuo Duke hg19 1 wgEncodeHaibGenotypeGm19239RegionsRep1 None CNV B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation GM19239 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeGm12892RegionsRep2 GM12892 1 GM12892 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001298 1298 GSM999290 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 2 wgEncodeHaibGenotypeGm12892RegionsRep2 None CNV B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation GM12892 Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeGm12891RegionsRep2 GM12891 1 GM12891 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001297 1297 GSM999298 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 2 wgEncodeHaibGenotypeGm12891RegionsRep2 None CNV B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation GM12891 Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeGm06990RegionsRep1 GM06990 1 GM06990 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001296 1296 GSM999297 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeGm06990RegionsRep1 None CNV B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation GM06990 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeCmkRegionsRep2 CMK 1 CMK Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001293 1293 GSM999294 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeCmkRegionsRep2 None CNV acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation CMK Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeChorionRegionsRep1 Chorion 1 Chorion Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001295 1295 GSM999300 Myers HudsonAlpha Illumina 1MDuo Duke hg19 1 wgEncodeHaibGenotypeChorionRegionsRep1 None CNV chorion cells (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes. Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation Chorion Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeCaco2RegionsRep1 Caco-2 1 Caco-2 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001294 1294 GSM999299 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeCaco2RegionsRep1 None CNV colorectal adenocarcinoma. (PMID: 1939345) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation Caco-2 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeBjRegionsRep1 BJ 1 BJ Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001292 1292 GSM999293 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeBjRegionsRep1 None CNV skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation BJ Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeAosmcRegionsRep1 AoSMC 1 AoSMC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001288 1288 GSM999329 Myers HudsonAlpha Illumina 1MDuo Duke hg19 1 wgEncodeHaibGenotypeAosmcRegionsRep1 None CNV aortic smooth muscle cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation AoSMC Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeAg10803RegionsRep1 AG10803 1 AG10803 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001287 1287 GSM999322 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeAg10803RegionsRep1 None CNV abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation AG10803 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeAg09319RegionsRep2 AG09319 1 AG09319 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001286 1286 GSM999323 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeAg09319RegionsRep2 None CNV gum tissue fibroblasts from apparently heathly 24 year old Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation AG09319 Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeAg09309RegionsRep1 AG09309 1 AG09309 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001285 1285 GSM999320 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeAg09309RegionsRep1 None CNV adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation AG09309 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeAg04450RegionsRep2 AG04450 1 AG04450 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001284 1284 GSM999321 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeAg04450RegionsRep2 None CNV fetal lung fibroblast Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation AG04450 Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeAg04449RegionsRep1 AG04449 1 AG04449 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001283 1283 GSM999326 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeAg04449RegionsRep1 None CNV fetal buttock/thigh fibroblast Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation AG04449 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeMcf7RegionsRep2 MCF-7 2 MCF-7 Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001268 1268 GSM999333 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeMcf7RegionsRep2 None CNV mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation MCF-7 Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeMcf7RegionsRep1 MCF-7 1 MCF-7 Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001268 1268 GSM999333 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeMcf7RegionsRep1 None CNV mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation MCF-7 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeImr90RegionsRep2 IMR90 2 IMR90 Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001265 1265 GSM999283 Myers HudsonAlpha Illumina 1MDuo UW hg19 2 wgEncodeHaibGenotypeImr90RegionsRep2 None CNV fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation IMR90 Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeImr90RegionsRep1 IMR90 1 IMR90 Genotype ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001265 1265 GSM999283 Myers HudsonAlpha Illumina 1MDuo UW hg19 1 wgEncodeHaibGenotypeImr90RegionsRep1 None CNV fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation IMR90 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHuvecRegionsRep2 HUVEC 1 HUVEC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001315 1315 GSM999303 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 2 wgEncodeHaibGenotypeHuvecRegionsRep2 None CNV umbilical vein endothelial cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HUVEC Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHepg2RegionsRep1 HepG2 1 HepG2 Genotype ENCODE Mar 2012 Freeze 2011-02-17 2011-11-17 wgEncodeEH000274 274 GSM999286 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg18 1 wgEncodeHaibGenotypeHepg2RegionsRep1 None CNV hepatocellular carcinoma Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HepG2 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeHelas3RegionsRep2 HeLa-S3 1 HeLa-S3 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001316 1316 GSM999302 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 2 wgEncodeHaibGenotypeHelas3RegionsRep2 None CNV cervical carcinoma Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation HeLa-S3 Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeA549RegionsRep1 A549 1 A549 Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001282 1282 GSM999327 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 1 wgEncodeHaibGenotypeA549RegionsRep1 None CNV epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation A549 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeK562RegionsRep1 K562 1 K562 Genotype ENCODE Mar 2012 Freeze 2011-02-17 2011-11-17 wgEncodeEH000275 275 GSM999287 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg18 1 wgEncodeHaibGenotypeK562RegionsRep1 None CNV leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation K562 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeH1hescRegionsRep2 H1-hESC 1 H1-hESC Genotype ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001300 1300 GSM999275 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg19 2 wgEncodeHaibGenotypeH1hescRegionsRep2 None CNV embryonic stem cells Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation H1-hESC Copy number variants Replicate 1 (Lab Rep 2) from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeGm12878RegionsRep2 GM12878 2 GM12878 Genotype ENCODE Mar 2012 Freeze 2011-02-17 2011-11-17 wgEncodeEH000273 273 GSM999285 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha hg18 2 wgEncodeHaibGenotypeGm12878RegionsRep2 None CNV B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation GM12878 Copy number variants Replicate 2 from ENCODE/HAIB Variation 
wgEncodeHaibGenotypeGm12878RegionsRep1V2 GM12878 1 GM12878 Genotype ENCODE Mar 2012 Freeze 2011-12-06 2011-05-09 2012-02-09 wgEncodeEH000273 273 GSM999285 Myers HudsonAlpha Illumina 1MDuo HudsonAlpha HudsonAlpha hg19 1 wgEncodeHaibGenotypeGm12878RegionsRep1V2 None CNV B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Genotype CNV and SNP Myers Myers - Hudson Alpha Institute for Biotechnology Copy Number Variation GM12878 Copy number variants Replicate 1 from ENCODE/HAIB Variation 
decipherHaploIns Haploinsufficiency Haploinsufficiency predictions for genes from DECIPHER Phenotype and Literature Description This track displays haploinsufficiency predictions for human genes (Huang 2010). Human cells have two copies of most genes (one from each parent). If a mutation alters one copy, the other is usually still sufficient to maintain gene function. For haploinsufficient genes, however, both copies must be functioning for the organism to have a normal life. Haploinsufficiency is implicated in a number of health disorders. Display Conventions Predictions in this track are provided on a per-gene basis and are displayed in blocks corresponding to each gene's position in the genome (and labeled with that gene's name). The raw prediction scores range from 0 to 1, where 0 is very unlikely to be haploinsufficient and 1 is very likely. Because many of the predicted scores fall toward the lower end of the spectrum, the authors also grouped those scores by quantile. The quantile for each gene is shown as &alpha;-upper percentile, which shows the percentage of genes with a higher predicted score than this one. A gene with a relatively strong prediction of being haploinsufficient will have a quantile close to 0%. A gene with a very low comparative prediction of being haploinsufficient will have a quantile close to 100%. Moving the mouse cursor over any gene will display a pop-up box with the gene name and &alpha;-upper quantile for the prediction. The genes in this track are also color-coded according to quantile: Magenta shades indicate a higher expectation of being haploinsufficient Green shades indicate a lower expectation of being haploinsufficient Credits Data for this track were generously provided by the DECIPHER project at https://decipher.sanger.ac.uk/about/downloads/data. References Huang N, Lee I, Marcotte EM, Hurles ME. Characterising and predicting haploinsufficiency in the human genome. PLoS Genet. 2010 Oct 14;6(10):e1001154. PMID: 20976243; PMC: PMC2954820 
hapmapSnps HapMap SNPs HapMap SNPs (rel27, merged Phase II + Phase III genotypes) Variation Description The HapMap Project identified a set of approximately four million common SNPs, and genotyped these SNPs in four populations in Phase II of the project. In Phase III, it genotyped approximately 1.4 to 1.5 million SNPs in eleven populations. This track shows the combined data from Phases II and III. The intent is that this data can be used as a reference for future studies of human disease. This track displays the genotype counts and allele frequencies of those SNPs, and (when available) shows orthologous alleles from the chimp and macaque reference genome assemblies. The four million HapMap Phase II SNPs were genotyped on individuals from these four human populations: Yoruba in Ibadan, Nigeria (YRI) Japanese in Tokyo, Japan (JPT) Han Chinese in Beijing, China (CHB) CEPH (Utah residents with ancestry from northern and western Europe) (CEU) Phase III expanded to eleven populations: the four above, plus the following: African Ancestry in SouthWestern United States (ASW) Chinese Ancestry in Metropolitan Denver, CO, US (CHD) Gujarati Indians in Houston, TX (GIH) Luhya in Webuye, Kenya (LWK) Mexican Ancestery in Los Angeles, CA, US (MEX) Masai in Kinyawa, Kenya (MKK) Toscani in Italia (TSI) Each of the populations is displayed in a separate subtrack. The HapMap assays provide biallelic results. Over 99.8% of HapMap SNPs are described as biallelic in dbSNP build 129; approximately 6,800 are described as more complex types (in-del, mixed, etc). 70% of the HapMap SNPs are transitions: 35% are A/G, 35% are C/T. The orthologous alleles in chimp (panTro2) and macaque (rheMac2) were derived using liftOver. No two HapMap SNPs occupy the same position. Aside from 430 SNPs from the pseudoautosomal region of chrX and chrY, no SNP is mapped to more than one location in the reference genome. No HapMap SNPs occur on &quot;random&quot; chromosomes (concatenations of unordered and unoriented contigs). Display Conventions and Configuration Note: calculation of heterozygosity has changed since the Phase II (rel22) version of this track. Observed heterozygosity is calculated as follows: each population's heterozygosity is computed as the proportion of heterozygous individuals in the population. The population heterozygosities are averaged to determine the overall observed heterozygosity. [For Phase II genotypes, expected heterozygosity was calculated as follows: the allele counts from all populations were summed (not normalized for population size) and used to determine overall major and minor allele frequencies. Assuming Hardy-Weinberg equilibrium, overall expected heterozygosity was calculated as two times the product of major and minor allele frequencies (see Modern Genetic Analysis, section 17-2).] The human SNPs are displayed in gray using a color gradient based on minor allele frequency. The higher the minor allele frequency, the darker the display. By definition, the maximum minor allele frequency is 50%. When zoomed to base level, the major allele is displayed for each population. The orthologous alleles from chimp and macaque are displayed in brown using a color gradient based on quality score. Quality scores range from 0 to 100 representing low to high quality. For orthologous alleles, the higher the quality, the darker the display. Quality scores are not available for chimp chromosomes chr21 and chrY; these were set to 98, consistent with the panTro2 browser quality track. Filters are provided for the data attributes described above. Additionally, a filter is provided for observed heterozgosity (average of all populations' observed heterozygosities). Filters are applied to all subtracks, even if a subtrack is not displayed. Notes on orthologous allele filters: If a SNP's major allele is different between populations, no overall major allele for human is determined, thus the &quot;matches major human allele&quot; and &quot;matches minor human allele&quot; filters for orthologous alleles do not apply. If a SNP is monomorphic in all populations, the minor allele is not verified in the HapMap dataset. In these cases, the filter to match orthologous alleles to the minor human allele will yield no results. Credits This track is based on International HapMap Project release 27 data, provided by the HapMap Data Coordination Center. References HapMap Project The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18;449(7164):851-61. The International HapMap Consortium. A haplotype map of the human genome. Nature. 2005 Oct 27;437(7063):1299-320. The International HapMap Consortium. The International HapMap Project. Nature. 2003 Dec 18;426(6968):789-96. HapMap Data Coordination Center Thorisson GA, Smith AV, Krishnan L, Stein LD. The International HapMap Project Web site. Genome Res. 2005 Nov;15(11):1592-3. A Sampling of HapMap Literature Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet. 2006 Mar 1; 15(5):789-95. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W et al. Global variation in copy number in the human genome. Nature. 2006 Nov 23;444(7118):444-454. Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG. Common genetic variants account for differences in gene expression among ethnic groups. Nature Genet. 2007 Feb;39(2):226-31. Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, Visscher PM. Recent human effective population size estimated from linkage disequilibrium. Genome Res. 2007 Apr;17(4):520-6. Voight BF, Kudaravalli S, Wen X, Pritchard JK. A Map of Recent Positive Selection in the Human Genome. PLoS Biol. 2006 Mar;4(3):e72. Weir BS, Cardon LR, Anderson AD, Nielsen DM, Hill WG. Measures of human population structure show heterogeneity among genomic regions. Genome Res. 2005 Nov;15(11):1468-76. Data Source The genotypes_chr*_*_r27_nr.b36_fwd.txt.gz files from the HapMap FTP site were processed to make this track. 
hapmapAllelesMacaque Macaque Alleles Orthologous Alleles from Macaque (rheMac2) Variation 
hapmapAllelesChimp Chimp Alleles Orthologous Alleles from Chimp (panTro2) Variation 
hapmapSnpsYRI HapMap SNPs YRI HapMap SNPs from the YRI Population (Yoruba in Ibadan, Nigeria) Variation 
hapmapSnpsTSI HapMap SNPs TSI HapMap SNPs from the TSI Population (Toscani in Italia) Variation 
hapmapSnpsMKK HapMap SNPs MKK HapMap SNPs from the MKK Population (Masai in Kinyawa, Kenya) Variation 
hapmapSnpsMEX HapMap SNPs MEX HapMap SNPs from the MEX Population (Mexican Ancestry in Los Angeles, CA, US) Variation 
hapmapSnpsLWK HapMap SNPs LWK HapMap SNPs from the LWK Population (Luhya in Webuye, Kenya) Variation 
hapmapSnpsJPT HapMap SNPs JPT HapMap SNPs from the JPT Population (Japanese in Tokyo, Japan) Variation 
hapmapSnpsGIH HapMap SNPs GIH HapMap SNPs from the GIH Population (Gujarati Indians in Houston, TX, US) Variation 
hapmapSnpsCHD HapMap SNPs CHD HapMap SNPs from the CHD Population (Chinese Ancestry in Metropolitan Denver, CO, US) Variation 
hapmapSnpsCHB HapMap SNPs CHB HapMap SNPs from the CHB Population (Han Chinese in Beijing, China) Variation 
hapmapSnpsCEU HapMap SNPs CEU HapMap SNPs from the CEU Population (Northern and Western European Ancestry in Utah, US - CEPH) Variation 
hapmapSnpsASW HapMap SNPs ASW HapMap SNPs from the ASW Population (African Ancestry in SouthWestern United States) Variation 
hg19ContigDiff Hg18 Diff Contigs New to GRCh37/(hg19), Not Carried Forward from NCBI Build 36(hg18) Mapping and Sequencing Description This track shows the differences between the GRCh37 (hg19) and previous NCBI Build 36 (hg18) human genome assemblies, indicating contigs (or portions of contigs) that are new to the hg19 assembly. The following color/score key is used: colorscorechange from hg18 to hg19 &nbsp;0New contig added to hg19 to update sequence or fill gaps present in hg18 &nbsp;500Different portions of this same contig used in the construction of hg19 and hg18 assemblies &nbsp;1000Updated version of an hg18 contig in which sequence errors have been corrected Use the score filter to select which categories to show in the display. Methods The contig coordinates were extracted from the AGP files for both assemblies. Contigs that matched the same name, same version, and the same specific portion of sequence in both assemblies were considered identical between the two assemblies and were excluded from this data set. The remaining contigs are shown in this track. Credits The data and presentation of this track were prepared by Hiram Clawson, UCSC Genome Browser engineering. 
hg38ContigDiff Hg38 Diff Contigs Dropped or Changed from GRCh37(hg19) to GRCh38(hg38) Mapping and Sequencing Description This track shows the differences between the GRCh37 (hg19) and GRCh38 (hg38) human genome assemblies, indicating hg19 contigs (or portions of contigs) that were not carried forward to the newer assembly. The following color/score key is used: itemcoloritemscoretype of change from hg19 to hg38 &nbsp;0hg19 contig dropped in the construction of the hg38 assembly &nbsp;500Different portions of this same contig used in the construction of hg38 and hg19 assemblies &nbsp;1000Contig updated in hg38 to correct sequence errors present in hg19 version Use the score filter to select which categories to show in the display. Methods The contig coordinates were extracted from the AGP files for both assemblies. Contigs that matched the same name, same version, and the same specific portion of sequence in both assemblies were considered identical between the two assemblies and were excluded from this data set. The remaining contigs are shown in this track. Credits The data and presentation of this track were prepared by Hiram Clawson, UCSC Genome Browser engineering. 
hgdpGeo HGDP Allele Freq Human Genome Diversity Project SNP Population Allele Frequencies Variation Description This track shows the 657,000 SNPs genotyped in 53 populations worldwide by the Human Genome Diversity Project in collaboration with the Centre d'Etude du Polymorphisme Humain (HGDP-CEPH). This track and several others are available from the HGDP Selection Browser. Methods Samples collected by the HGDP-CEPH from 1,043 individuals from around the world were genotyped for 657,000 SNPs at Stanford. Ancestral states for all SNPs were estimated using whole genome human-chimpanzee alignments from the UCSC database. For each SNP in the human genome (NCBI Build 35, UCSC database hg17), the allele at the corresponding position in the chimp genome (Build 2 version 1, UCSC database pantro2) was used as ancestral. Allele frequencies were plotted on a world map using programs included in the Generic Mapping Tools. Credits Thanks to the HGDP-CEPH, the Pritchard lab at Stanford University, Joe Pickrell and John Novembre for sharing the data and plotting scripts for this track. References Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A et al. A human genome diversity cell line panel. Science. 2002 Apr 12;296(5566):261-2. PMID: 11954565 Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science. 2008 Feb 22;319(5866):1100-4. PMID: 18292342 Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW et al. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 2009 May;19(5):826-37. PMID: 19307593; PMC: PMC2675971 Wessel P, Smith WHF. New, improved version of Generic Mapping Tools released. EOS, Trans. Amer. Geophys. U. 1998;79(47):579. 
hgmd HGMD public Human Gene Mutation Database - Public Version Dec 2023 Phenotype and Literature Description NOTE: HGMD public is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the HGMD public database is open to all academic users, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. DOWNLOADS: As requested by Qiagen, this track is not available for download or mirroring but only for limited API queries, see below. This track shows the genomic positions of variants in the public version of the Human Gene Mutation Database (HGMD). UCSC does not host any further information and provides only the coordinates of mutations. To get details on a mutation (bibliographic reference, phenotype, disease, nucleotide change, etc.), follow the &quot;Link to HGMD&quot; at the top of the details page. Mouse over to show the type of variant (substitution, insertion, deletion, regulatory or splice variant). For deletions, only start coordinates are shown as the end coordinates have not been provided by HGMD. Insertions are located between the two annotated nucleic acids. The HGMD public database is produced at Cardiff University, but is free only for academic use. Academic users can register for a free account at the HGMD User Registration page. Download and commercial use requires a license for the HGMD Professional database, which also contains many mutations not yet added to the public version of HGMD public. The public version is usually 1-2 years behind the professional version. The HGMD database itself does not come with a mapping to genome coordinates, but there is a related product called "GenomeTrax" which includes HGMD in the UCSC Custom Track format. Contact Qiagen for more information. Batch queries Due to license restrictions, the HGMD data is not available for download or for batch queries in the Table Browser. However, it is available for programmatic access via the Global Alliance Beacon API, a web service that accepts queries in the form (genome, chromosome, position, allele) and returns "true" or "false" depending on whether there is information about this allele in the database. For more details see our Beacon Server. Subscribers of the HGMD database can also download the full database or use the HGMD API to retrieve full details, please contact Qiagen support for further information. Academic or non-profit users may be able to obtain a limited version of HGMD public from Qiagen. Display Conventions and Configuration Genomic locations of HGMD variants are labeled with the gene symbol and the accession of the mutation, separated by a colon. All other information is shown on the respective HGMD variation page, accessible via the &quot;Link to HGMD&quot; at the top of the details page. HGMD variants are originally annotated on RefSeq transcripts. You can show all and only those transcripts annotated by HGMD by activating the HGMD subtrack of the track "NCBI RefSeq". Methods The mappings displayed on this track were obtained from Qiagen and reformatted at UCSC as a bigBed file. Credits Thanks to HGMD, Frank Schacherer and Rupert Yip from Qiagen for making these data available. References Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet. 2014 Jan;133(1):1-9. PMID: 24077912; PMC: PMC3898141 
hgnc HGNC HUGO Gene Nomenclature Genes and Gene Predictions Description The HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication. For each known human gene, the HGNC approves a gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC database, www.genenames.org, a curated online repository of HGNC-approved gene nomenclature, gene groups and associated resources including links to genomic, proteomic, and phenotypic information. Each symbol is unique and we ensure that each gene is only given one approved gene symbol. It is necessary to provide a unique symbol for each gene so that we and others can talk about them, and this also facilitates electronic data retrieval from publications and databases. In preference, each symbol maintains parallel construction in different members of a gene family and can also be used in other species, especially other vertebrates including mouse. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For computational analysis, genome annotations are stored in a bigBigFile file that can be downloaded from the download server. Regional or genome-wide annotations can be converted from binary data to human readable text using our command line utility bigBedToBed which can be compiled from source code or downloaded as a precompiled binary for your system. Files and instructions can be found in the utilities directory. The utility can be used to obtain features within a given range, for example: bigBedToBed -chrom=chr6 -start=0 -end=1000000 http://hgdownload.soe.ucsc.edu/gbdb/hg38/hgnc/hgnc.bb stdout Please refer to our Data Access FAQ for more information or our mailing list for archived user questions. Credits HGNC Database, HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom www.genenames.org. References Tweedie S, Braschi B, Gray KA, Jones TEM, Seal RL, Yates B, Bruford EA. Genenames.org: the HGNC and VGNC resources in 2021. Nucleic Acids Res. PMID: 33152070 PMCID: PMC7779007 DOI: 10.1093/nar/gkaa980 
hiSeqDepth Hi Seq Depth Regions of Exceptionally High Depth of Aligned Short Reads Mapping and Sequencing Description This track displays regions of the reference genome that have exceptionally high sequence depth, inferred from alignments of short-read sequences from the 1000 Genomes Project. These regions may be caused by collapsed repetitive sequences in the reference genome assembly; they also have high read depth in assays such as ChIP-seq, and may trigger false positive calls from peak-calling algorithms. Excluding these regions from analysis of short-read alignments should reduce such false positive calls. Methods Pickrell et al. downloaded sequencing reads for 57 Yoruba individuals from the 1000 Genomes Project's low-coverage pilot data, mapped them to the Mar. 2006 human genome assembly (NCBI36/hg18), computed the read depth for every base in the genome, and compiled a distribution of read depths. They then identified contiguous regions where read depth exceeded thresholds corresponding to the top 0.001, 0.005, 0.01, 0.05 and 0.1 of the per-base read depths, merging regions which fall within 50 bases of each other. The regions are available for download from http://eqtl.uchicago.edu/Masking/ (see the readme file). Credits Thanks to Joseph Pickrell at the University of Chicago for these data. References Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics. 2011 Aug 1;27(15):2144-6. Epub 2011 Jun 19. 
hiSeqDepthTop10Pct Top 0.10 Depth Top 0.10 of Read Depth Distribution Mapping and Sequencing 
hiSeqDepthTop5Pct Top 0.05 Depth Top 0.05 of Read Depth Distribution Mapping and Sequencing 
hiSeqDepthTop1Pct Top 0.01 Depth Top 0.01 of Read Depth Distribution Mapping and Sequencing 
hiSeqDepthTopPt5Pct Top 0.005 Depth Top 0.005 of Read Depth Distribution Mapping and Sequencing 
hiSeqDepthTopPt1Pct Top 0.001 Depth Top 0.001 of Read Depth Distribution Mapping and Sequencing 
hgIkmc IKMC Genes Mapped International Knockout Mouse Consortium Genes Mapped to Human Genome Genes and Gene Predictions Description This track shows genes targeted by International Knockout Mouse Consortium (IKMC) mapped to the human genome. IKMC is a collaboration to generate a public resource of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome. Gene targets are color-coded by status: Green: Reagent(s) Available Yellow: In Progress Blue: Not Started/On Hold Black: Withdrawn/Problematic The KnockOut Mouse Project Data Coordination Center (KOMP DCC) is the central database resource for coordinating mouse gene targeting within IKMC and provides web-based query and display tools for IKMC data. In addition, the KOMP DCC website provides a tool for the scientific community to nominate genes of interest to be knocked out by the KOMP initiative. IKMC members include KnockOut Mouse Project (KOMP), a trans-NIH initiative (USA) European Conditional Mouse Mutagenesis Program (EUCOMM), funded by the European Union Framework 6 programme (EU) North American Conditional Mouse Mutagenesis Project (NorCOMM), a Genome Prairie Project (Canada) Texas A&amp;M Institute for Genomic Medicine (TIGM) (USA) KOMP includes two production centers: CSD, a collaborative team at the Children's Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine, and a team at the VelociGene division of Regeneron Pharmaceuticals, Inc. EUCOMM includes 9 participating institutions. NorCOMM includes several participating institutions. Methods Using complementary targeting strategies, the IKMC centers design and create targeting vectors, mutant ES cell lines and, to some extent, mutant mice, embryos or sperm. Materials are distributed to the research community. The KOMP Repository archives, maintains, and distributes IKMC products. Researchers can order products and get product information from the Repository. Researchers can also express interest in products that are still in the pipeline. They will then receive email notification as soon as KOMP generated products are available for distribution. The process for ordering EUCOMM materials can be found here. The process for ordering TIGM materials can be found here. Information on NorCOMM products and services can be found here. Genes were mapped to the human genome by IKMC. Credits Thanks to the International Knockout Mouse Consortium, and Carol Bult in particular, for providing these data. References Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig JT et al. The knockout mouse project. Nat Genet. 2004 Sep;36(9):921-4. PMID: 15340423; PMC: PMC2716027 Collins FS, Finnell RH, Rossant J, Wurst W. A new partner for the international knockout mouse consortium. Cell. 2007 Apr 20;129(2):235. PMID: 17448981 International Mouse Knockout Consortium, Collins FS, Rossant J, Wurst W. A mouse for all reasons. Cell. 2007 Jan 12;128(1):9-13. PMID: 17218247 
illuminaProbes Illumina WG-6 Alignments of Illumina WG-6 3.0 Probe Set Expression Description This track displays the probes from the Illumina WG-6 3.0 BeadChip. The WG-6 BeadChip contains probes for the following set of RNA transcripts: Probe sourceNumber of probes Number of unique probe sources RefSeq NM (well-established coding transcript)27,454 22,435 RefSeq XM (provisional coding transcript)7,870 7,518 RefSeq NR (well-established non-coding transcript)446 358 RefSeq XR (provisional non-coding transcript)196 190 UniGene ESTs12,83712,837 TOTAL48,80343,338 Display The track shows the location of the probes on the genome after the RNAs they correspond to were all aligned to the genome using BLAT. Alignment scores range from 0 to 1000, where 1000 is a perfect score. In the display, darker browns are for higher-scoring alignments. Click on a probe track item to see detailed information about that probe ID. View the base-by-base alignment for that probe by clicking the &quot;View Alignment&quot; link on the details page. Methods The probe set was collected from the NCBI GEO (Gene Expression Omnibus), and the 43,338 RNA sequences were collected from Genbank using NCBI's EUtils interface to Entrez. These RNAs were aligned to the genome using BLAT, and 43,224 of them aligned well to 46,432 locations on the genome. The single best alignment was used, except in 1,789 cases where the RNA mapped equally well to two or more locations. The probes were then aligned to their respective RNAs using BLAT, and if a good alignment resulted, the probe was then mapped through to the genome using the combination of the probe-on-RNA and the RNA-on-genome alignments. Of the 48,803 original probes, 40,852 map well through this procedure to 44,163 locations on the genome. 
ucscToINSDC INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration Mapping and Sequencing Description This track associates UCSC Genome Browser chromosome names to accession names from the International Nucleotide Sequence Database Collaboration (INSDC). The data were downloaded from the NCBI assembly database. Credits The data for this track was prepared by Hiram Clawson. 
nestedRepeats Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID Repeats Description This track shows joined fragments of interrupted repeats extracted from the output of the RepeatMasker program which screens DNA sequences for interspersed repeats and low complexity DNA sequences using the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below. The detailed annotations from RepeatMasker are in the RepeatMasker track. This track shows fragments of original repeat insertions which have been interrupted by insertions of younger repeats or through local rearrangements. The fragments are joined using the ID column of RepeatMasker output. Display Conventions and Configuration In pack or full mode, each interrupted repeat is displayed as boxes (fragments) joined by horizontal lines, labeled with the repeat name. If all fragments are on the same strand, arrows are added to the horizontal line to indicate the strand. In dense or squish mode, labels and arrows are omitted and in dense mode, all items are collapsed to fit on a single row. Items are shaded according to the average identity score of their fragments. Usually, the shade of an item is similar to the shades of its fragments unless some fragments are much more diverged than others. The score displayed above is the average identity score, clipped to a range of 50% - 100% and then mapped to the range 0 - 1000 for shading in the browser. Methods UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet. Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. See the FAQ for more information. Credits Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track. References Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010. Repbase Update is described in: Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072 For a discussion of repeats in mammalian genomes, see: Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616 Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846 
jaspar JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database Regulation Description This track represents genome-wide predicted binding sites for TF (transcription factor) binding profiles in the JASPAR CORE collection. This open-source database contains a curated, non-redundant set of binding profiles derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. Display Conventions and Configuration Shaded boxes represent predicted binding sites for each of the TF profiles in the JASPAR CORE collection. The shading of the boxes indicates the p-value of the profile's match to that position (scaled between 0-1000 scores, where 0 corresponds to a p-value of 1 and 1000 to a p-value &le; 10-10). Thus, the darker the shade, the lower (better) the p-value. The default view shows only predicted binding sites with scores of 400 or greater but can be adjusted in the track settings. Multi-select filters allow viewing of particular transcription factors. At window sizes of greater than 10,000 base pairs, this track turns to density graph mode. Zoom to a smaller region and click into an item to see more detail. From BED format documentation: shade &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; score in range &le; 166 167-277 278-388 389-499 500-611 612-722 723-833 834-944 &ge; 945 Conversion table: Item score 0 100 131 200 300 400 500 600 700 800 900 1000 p-value 1 0.1 0.049 10-2 10-3 10-4 10-5 10-6 10-7 10-8 10-9 &le; 10-10 Methods The JASPAR 2024 update expanded the JASPAR CORE collection by 20% (329 added and 72 upgraded profiles). The new profiles were introduced after manual curation, in which 26 629 TF binding motifs were curated and obtained as PFMs or discovered from ChIP-seq/-exo or DAP-seq data. 2500 profiles from JASPAR 2022 were revised to either promote them to the CORE collection, update the associated metadata, or remove them because of validation inconsistencies or poor quality. The JASPAR database stores and focuses mostly on PFMs as the model of choice for TF-DNA interactions. More information on the methods can be found in the JASPAR 2024 publication or on the JASPAR website. JASPAR 2022 contains updated transcription factor binding sites with additional transcription factor profiles. More information on the methods can be found in the JASPAR 2022 publication JASPAR 2022 publication or on the JASPAR website. JASPAR 2020 scanned DNA sequences with JASPAR CORE TF-binding profiles for each taxa independently using PWMScan. TFBS predictions were selected with a PWM relative score &ge; 0.8 and a p-value &lt; 0.05. P-values were scaled between 0 (corresponding to a p-value of 1) and 1000 (p-value &le; 10-10) for coloring of the genome tracks and to allow for comparison of prediction confidence between different profiles. JASPAR 2018 used the TFBS Perl module (Lenhard and Wasserman 2002) and FIMO (Grant, Bailey, and Noble 2011), as distributed within the MEME suite (version 4.11.2) (Bailey et al. 2009). For scanning genomes with the BioPerl TFBS module, profiles were converted to PWMs and matches were kept with a relative score &ge; 0.8. For the FIMO scan, profiles were reformatted to MEME motifs and matches with a p-value &lt; 0.05 were kept. TFBS predictions that were not consistent between the two methods (TFBS Perl module and FIMO) were removed. The remaining TFBS predictions were colored according to their FIMO p-value to allow for comparison of prediction confidence between different profiles. Please refer to the JASPAR 2024, 2022, 2020, and 2018 publications for more details (citation below). Data Access JASPAR Transcription Factor Binding data includes billions of items. Limited regions can be explored interactively with the Table Browser and cross-referenced with Data Integrator, although positional queries that are too big can lead to timing out. This results in a black page or truncated output. In this case, you may try reducing the chromosomal query to a smaller window. For programmatic access, the track can be accessed using the Genome Browser's REST API. JASPAR annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. The utilities for working with bigBed-formatted binary files can be downloaded here. Run a utility with no arguments to see a brief description of the utility and its options. bigBedInfo provides summary statistics about a bigBed file including the number of items in the file. With the -as option, the output includes an autoSql definition of data columns, useful for interpreting the column values. bigBedToBed converts the binary bigBed data to tab-separated text. Output can be restricted to a particular region by using the -chrom, -start and -end options. Example: retrieve all JASPAR items in chr1:200001-200400 bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/jaspar/JASPAR2024.bb -chrom=chr1 -start=200000 -end=200400 stdout All data are freely available. Additional resources are available directly from the JASPAR group: Binding site predictions for all and individual TF profiles are available for download at http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/. Code and data used to create the UCSC tracks are available at https://github.com/wassermanlab/JASPAR-UCSC-tracks. The underlying JASPAR motif data is available through the JASPAR website at https://jaspar.genereg.net/. Other Genomes The JASPAR group provides TFBS predictions for many additional species and genomes, accessible by connection to their Public Hub or by clicking the assembly links below: Species Genome assembly versions Human - Homo sapiens hg19, hg38 Mouse - Mus musculus mm10, mm39 Zebrafish - Danio rerio danRer11 Fruitfly - Drosophila melanogaster dm6 Nematode - Caenorhabditis elegans ce10, ce11 Vase tunicate - Ciona intestinalis ci3 Thale cress - Arabidopsis thaliana araTha1 Yeast - Saccharomyces cerevisiae sacCer3 Credits The JASPAR database is a joint effort between several labs (please see the latest JASPAR paper, below). Binding site predictions and UCSC tracks were computed by the Wasserman Lab. For enquiries about the data please contact Oriol Fornes ( &#111;&#114;&#105;&#111;l&#64;&#99;&#109;&#109;&#116;. u&#98;&#99;.c&#97; ). Wasserman Lab Centre for Molecular Medicine and Therapeutics BC Children's Hospital Research Institute Department of Medical Genetics University of British Columbia Vancouver, Canada References Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva P&#233;rez N et al. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2021 Nov 30;. PMID: 34850907 Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Barana&#353;i&#263; D et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2020 Jan 8;48(D1):D87-D92. PMID: 31701148; PMC: PMC7145627 Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Ch&#232;neby J, Kulkarni SR, Tan G et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266. PMID: 29140473; PMC: PMC5753243 Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Ch&#232;neby J, Baranasic D et al. JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2023 Nov 14;. PMID: 37962376 
jaspar2018 JASPAR 2018 TFBS JASPAR CORE 2018 - Predicted Transcription Factor Binding Sites Regulation 
jaspar2020 JASPAR 2020 TFBS JASPAR CORE 2020 - Predicted Transcription Factor Binding Sites Regulation 
jaspar2022 JASPAR 2022 TFBS JASPAR CORE 2022 - Predicted Transcription Factor Binding Sites Regulation 
jaspar2024 JASPAR 2024 TFBS JASPAR CORE 2024 - Predicted Transcription Factor Binding Sites Regulation 
laminB1 LaminB1 (Tig3) NKI LaminB1 DamID Map (log2-ratio scores, Tig3 cells) Regulation Description Please see the NKI Nuc Lamina "super-track" link above for description and methods. 
laminB1Super NKI Nuc Lamina NKI Nuclear Lamina Associated Domains (LaminB1 DamID) Regulation Overview Model of chromosome organization in interphase, summarizing the main results presented in this paper. Large, discrete chromosomal domains are dynamically associated (double arrows) with the nuclear lamina, and demarcated by putative insulator elements that include CTCF binding sites, promoters that are oriented away from the lamina, and CpG islands (Fig. S1, Guelen et al., 2008). The architecture of human chromosomes in interphase nuclei is still largely unknown. Microscopy studies have indicated that specific regions of chromosomes are located in close proximity to the nuclear lamina (NL, a dense fibrillar network associated with the inner face of the nuclear envelope). This has led to the idea that certain genomic elements may be attached to the NL, which may contribute to the spatial organization of chromosomes inside the nucleus. This track represents a high-resolution map of genome-NL interactions in human Tig3 lung fibroblasts, as determined by the DamID technique. NKI LaminB1 track The LaminB1 track shows a high resolution map of the interaction sites of the entire genome with Lamin B1, (a key NL component) in human fibroblasts. This map shows that genome-lamina interactions occur through more than 1,300 sharply defined large domains 0.1-10 megabases in size. Microscopy evidence indicates that most of these domains are preferentially located at nuclear periphery. These lamina associated domains (LADs) are characterized by low gene-expression levels, indicating that LADs represent a repressive chromatin environment. The borders of LADs are demarcated by the insulator protein CTCF, by promoters that are oriented away from LADs, or by CpG islands, suggesting possible mechanisms of LAD confinement. Taken together, these results demonstrate that the human genome is divided into large, discrete domains that are units of chromosome organization within the nucleus (see Guelen et al., 2008). NKI LADs track The LADs track shows Lamina Associated Domains, or LADs, based on a genome-wide DamID profile of LaminB1 (above). For the definition of LADs, the full-genome lamin B1 DamID data set was binarized by setting tiling array probes with positive DamID log ratios to 1 and otherwise to 21. Next, a two-step algorithm was used to identify LADs. First, sharp transitions were identified with a sliding edge filter, which calculates the difference in average binary values in two windows of 99 neighbouring probes immediately left and right of a queried probe. The cutoff for this difference was chosen such that the number of edges detected in randomly permuted data sets was less than 5% of the number of edges detected in the original lamin B1 data set. Second, pairs of adjacent 'left' and 'right' edges were identified that together enclosed a region of arbitrary size with at least 70% of the enclosed probes reporting a positive log2 ratio. A total of 1,344 regions fulfilled these criteria and were termed LADs. In 20 randomly permuted data sets, fewer than 13 domains were identified by the same criteria. Note that there are also lamin-B1-positive domains flanked by one or two gradual or irregular transitions. Because it is difficult to define the borders of such domains precisely, these 'fuzzy' domains are not analyzed here. (see Guelen et al., 2008). Display Conventions and Configuration The LaminB1 wiggle track values range from -6.602 to 5.678 and were normalized so have a median of 0 and standard deviation of 1.037. The default vertical viewing range for the wiggle track was chosen from -2 to 2 because this is roughly +/- 2 standard deviations. For an example region see genomic location: chr4:35,000,001-45,000,000 (Fig 1, Guelen et al., 2008). Methods The DamID technique was applied to generate a high-resolution map of NL interactions for the entire human genome. DamID is based on targeted adenine methylation of DNA sequences that interact in vivo with a protein of interest. DamID was performed with lentiviral transduction as described (Guelen et al., 2008). In short, a fusion protein consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to human LaminB1 was introduced into cultured Tig3 human lung fibroblasts. Dam methylates adenines in the sequence GATC, a mark absent in most eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. Unfused Dam was used as a reference (http://research.nki.nl/vansteensellab/DamID.htm). The data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only. Sample labelling and hybridizations were performed by NimbleGen Inc., on a set of 8 custom-designed oligonucleotide arrays, with a median probe spacing of ~750 bp. All probes recognize unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized. Between array median/scale normalization was based on 6979 probes common to all arrays. Replicate arrays were averaged and the full data set normalized to genome-wide median. Verification The data are based on two independent biological replicates. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1 associated regions are preferentially located at the nuclear periphery. The array platform, the raw and normalized data have been deposited at the NCBI Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE8854. Credits The data for this track were generated by Lars Guelen, Ludo Pagie, and Bas van Steensel at the Van Steensel Lab, Netherlands Cancer Institute. References Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature. 2008 Jun 12;453(7197):948-51. PMID: 18463634 
patSeq Lens Patents Lens PatSeq Patent Document Sequences Phenotype and Literature Description This track shows genome matches to biomedical sequences submitted with patent application documents to patent offices around the world. The sequences, their mappings, and selected patent information were graciously provided by PatSeq, a search tool part of The Lens, Cambia. This track contains more data than the NCBI Genbank Division &quot;Patents&quot;, as the sequences were extracted from patents directly. Display Convention and Configuration The data is split into two subtracks: one for sequences that are only part of patents that have submitted more than 100 sequences (&quot;bulk patents&quot;) and a second track for all other sequences (&quot;non-bulk patents&quot;). A sequence can be part of many patent documents, with some being found in several thousand patents. This track shows only a single alignment for every sequence, colored based on its occurrence in the different patent documents and using a color schema similar to The Lens. Based on the first sequence match, the four different item colors follow this priority ranking in descending order: the sequence is referenced in the claims of a granted patent the sequence is disclosed in a granted patent the sequence is referenced in the claims of a patent application the sequence is disclosed in a patent application Sequences referenced in the claims section of a patent document define the scope of the invention and are important during litigation. Therefore, they are given priority in the color scheme. Patent grant documents form the basis of patent protection and are prioritized over applications. Hover over a feature with the mouse to see the total number of documents where the sequence has been referenced, how many of these documents are granted patents and how often the sequence has been referenced in the claims. A randomly selected document title is also shown in the mouseover. Clicking on a feature will bring up the details page, which contains information about the sequence and alignment of that feature. The link at the top of the page opens the PatSeq Analyzer with the chromosomal region covered by the feature that was clicked. The PatSeq Analyzer is a specialized genome browser that allows for the viewing and filtering of patent sequence matches in detail. The next section of the details page is a list of up to ten patent documents that include this sequence, with the number of occurrences within each document in parentheses. This is followed by up to thirty links to patent documents. The patent documents listed in these sections are displayed in order of the number of sequence occurrences in the document. Shown below these are the links to the sequence in The Lens, in the format &quot;patentDocumentIdentifier-SEQIDNO (docSequenceCount)&quot;. The &quot;SEQ ID NO&quot; is an integer number, the unique identifier of a patent sequence in a patent document. When a protein sequence has been annotated on a nucleotide sequence, the &quot;SEQ ID NO&quot; contains the reading frame separated by a &quot;.&quot;, e.g. &quot;1.1&quot; would indicate the first frame of SEQIDNO 1. The total number of sequences submitted with the patent document (&quot;docSequenceCount&quot;) is shown in parentheses after the SEQIDNO. The links to the sequence are separated into the categories &quot;granted and in claims&quot;, &quot;granted&quot;, &quot;in claims&quot; and &quot;applications&quot; (=all others). Sequence identifiers link to the respective pages on PatSeq. A maximum of thirty documents are linked from this page per category listed in order of the number of sequence occurrences; please use PatSeq Analyzer to view all matching documents. The score of the features in this track is the number of documents where the sequence appears in the claims. For example, by setting the score filter to 1, only sequences are shown that have been referenced at least once in the claims. Methods More than 96 million patent document files were collected by The Lens. The ST.25-formatted sequences were extracted and mapped to genomes with the aligners BLAT and BWA. The minimal identity of the query over the alignment is 95%. Note that for hg19, no patents are shown on chrM, as the mitochondrial chromosome used for the mapping was the one from the Ensembl genome FASTA files. Credits Thanks to the team behind The Lens, in particular, Osmat Jefferson and Deniz Koellhofer, for making these data available. Feedback Send suggestions on the way data in this track is visualized to our support address &#103;e&#110;&#111;&#109;e&#64;&#115;&#111;&#101;.&#117;&#99;&#115;&#99;.e&#100;&#117;. Questions on the data itself are best directed to &#115;u&#112;&#112;&#111;&#114;&#116;&#64;&#99;&#97;&#109;&#98;&#105;a.o&#114;&#103;. Data access The raw data can be explored interactively with the Table Browser. For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called patNonBulk.bb and patBulk.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The command to obtain the data as a tab-separated table looks like this: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/patNonBulk.bb -chrom=chr5 -start=1000000 -end=2000000 output.tsv A full log of the commands that were used to build this annotation is available from our database build description. In this text file, search for "patNonBulk" to find the right section. References Editorial: The patent bargain Nature. 2013 Dec 12;504(7479):187-188. Patently transparent. Nat Biotechnol. 2006 May;24(5):474. PMID: 16680110 Jefferson OA, K&#246;llhofer D, Ehrich TH, Jefferson RA. Transparency tools in gene patenting for informing policy and practice. Nat Biotechnol. 2013 Dec;31(12):1086-93. PMID: 24316644 
patBulk Bulk patents Patent Lens Bulk patents Phenotype and Literature 
patNonBulk Non-bulk patents Patent Lens Non-bulk patents Phenotype and Literature 
liftHg38 liftOver & ReMap UCSC LiftOver and NCBI ReMap: Genome alignments to convert annotations to hg38 Mapping and Sequencing Description This track shows alignments from the hg19 to the hg38 genome assembly, used by the UCSC liftOver tool and NCBI's ReMap service, respectively. Display Conventions and Configuration The track has three subtracks, one for UCSC and two for NCBI alignments. The alignments are shown as &quot;chains&quot; of alignable regions. The display is similar to the other chain tracks, see our chain display documentation for more information. Data access UCSC liftOver chain files for hg19 to hg38 can be obtained from a dedicated directory on our Download server. The NCBI chain file can be obtained from the MySQL tables directory on our download server, the filename is 'chainHg38ReMap.txt.gz'. Both tables can also be explored interactively with the Table Browser or the Data Integrator. Methods ReMap 2.2 alignments were downloaded from the NCBI FTP site and converted with the UCSC kent command line tools. Like all data processing for the genome browser, the procedure is documented in our hg19 makeDoc file. Credits Thanks to NCBI for making the ReMap data available and to Angie Hinrichs for the file conversion. 
chainHg38ReMapAxtChain ReMap + axtChain hg38 Lifting: NCBI ReMap alignments to hg38/GRCh38, joined by axtChain Mapping and Sequencing 
chainHg38ReMap NCBI ReMap hg38 Lifting: NCBI ReMap alignments to hg38/GRCh38 Mapping and Sequencing 
liftOverHg38 UCSC liftOver to hg38 Lifting: UCSC liftOver alignments to hg38 Mapping and Sequencing 
lincRNAsTranscripts lincRNA Transcripts lincRNA and TUCP transcripts Genes and Gene Predictions Description This track displays the Human Body Map lincRNAs (large intergenic non coding RNAs) and TUCPs (transcripts of uncertain coding potential), as well as their expression levels across 22 human tissues and cell lines. The Human Body Map catalog was generated by integrating previously existing annotation sources with transcripts that were de-novo assembled from RNA-Seq data. These transcripts were collected from ~4 billion RNA-Seq reads across 24 tissues and cell types. Expression abundance was estimated by Cufflinks (Trapnell et al., 2010) based on RNA-Seq. Expression abundances were estimated on the gene locus level, rather than for each transcript separately and are given as raw FPKM. The prefixes tcons_ and tcons_l2_ are used to describe lincRNAs and TUCP transcripts, respectively. Specific details about the catalog generation and data sets used for this study can be found in Cabili et al (2011). Extended characterization of each transcript in the human body map catalog can be found at the Human lincRNA Catalog website. Expression abundance scores range from 0 to 1000, and are displayed from light blue to dark blue respectively: 01000 Credits The body map RNA-Seq data was kindly provided by the Gene Expression Applications research group at Illumina. References Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15;25(18):1915-27. PMID: 21890647; PMC: PMC3185964 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. PMID: 20436464; PMC: PMC3146043 
lovdComp LOVD Variants LOVD: Leiden Open Variation Database Public Variants Phenotype and Literature Description NOTE: LOVD is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the LOVD database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. Further, please be sure to visit the LOVD web site for the very latest, as they are continually updating data. DOWNLOADS: LOVD databases are owned by their respective curators and are not available for download or mirroring by any third party without their permission. Batch queries on this track are only available via the UCSC Beacon API (see below). See also the LOVD web site for a list of database installations and the respective curators. This track shows the genomic positions of all public entries in public installations of the Leiden Open Variation Database system (LOVD) and the effect of the variant, if annotated. Due to the copyright restrictions of the LOVD databases, UCSC is not allowed to host any further information. To get details on a variant (bibliographic reference, phenotype, disease, patient, etc.), follow the &quot;Link to LOVD&quot; to the central server at Leiden, which will then redirect you to the details page on the particular LOVD server reporting this variant. Since Apr 2020, similar to the ClinVar track, the data is split into two subtracks, for variants with a length of &lt; 50 bp and &gt;= 50 bp, respectively. LOVD is a flexible, freely-available tool for gene-centered collection and display of DNA variations. It is not a database itself, but rather a platform where curators store and analyze data. While the LOVD team and the biggest LOVD sites are run at the Leiden University Medical Center, LOVD installations and their curators are spread over the whole world. Most LOVD databases report at least some of their content back to Leiden to allow global cross-database search, which is, among others, exported to this UCSC Genome Browser track every month. A few LOVD databases are entirely missing from this track. Reasons include configuration issues and intentionally blocked data search. During the last check in November 2019, the following databases did not export any variants: https://databases.lovd.nl/shared/genes/LDLR http://sysbio.org.cn/ https://ab-openlab.csir.res.in/mitolsdb/ Curators who want to share data in their database so it is present in this track can find more details in the LOVD FAQ. Batch queries The LOVD data is not available for download or for batch queries in the Table Browser. However, it is available for programmatic access via the Global Alliance Beacon API, a web service that accepts queries in the form (genome, chromosome, position, allele) and returns &quot;true&quot; or &quot;false&quot; depending on whether there is information about this allele in the database. For more details see our Beacon Server. To find all LOVD databases that contain variants of a given gene, you can get a list of databases by constructing a url in the format geneSymbol.lovd.nl, for example, tp53.lovd.nl. You can then use the LOVD API to retrieve more detailed information from a particular database. See the LOVD FAQ. Display Conventions and Configuration Genomic locations of LOVD variation entries are labeled with the gene symbol and the description of the mutation according to Human Gene Variation Society standards. For instance, the label AGRN:c.172G&gt;A means that the cDNA of AGRN is mutated from G to A at position 172. Since October 2017, the functional effect for variants is shown on the details page, if annotated. The possible values are: notClassified functionAffected notThisDisease notAnyDisease functionProbablyAffected functionProbablyNotAffected functionNotAffected unknown LOVD does not use the term &quot;pathogenic&quot;, please see the HGVS Terminology page for more details. All other information is shown on the respective LOVD variation page, accessible via the &quot;Link to LOVD&quot; above. Methods The mappings displayed in this track were provided by LOVD. Credits Thanks to the LOVD team, Ivo Fokkema, Peter Taschner, Johan den Dunnen, and all LOVD curators who gave permission to show their data. References Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT. LOVD v.2.0: the next generation in gene variant databases. Hum Mutat. 2011 May;32(5):557-63. PMID: 21520333 
lovdLong LOVD Variants >= 50 bp LOVD: Leiden Open Variation Database Public Variants, long >= 50 bp variants Phenotype and Literature 
lovdShort LOVD Variants < 50 bp + ins LOVD: Leiden Open Variation Database, short < 50 bp variants and insertions of any length Phenotype and Literature 
lrg LRG Regions Locus Reference Genomic (LRG) / RefSeqGene Sequences Mapped to Feb. 2009 (GRCh37/hg19) Assembly Mapping and Sequencing Description Locus Reference Genomic (LRG) sequences are manually curated, stable DNA sequences that surround a locus (typically a gene) and provide an unchanging coordinate system for reporting sequence variants. They are not necessarily identical to the corresponding sequence in a particular reference genome assembly (such as Feb. 2009 (GRCh37/hg19)), but can be mapped to each version of a reference genome assembly in order to convert between the stable LRG variant coordinates and the various assembly coordinates. We import the data from the LRG database at the EBI. The NCBI RefSeqGene database is almost identical to LRG, but it may contain a few more sequences. See the NCBI documentation. Each LRG record also includes at least one stable transcript on which variants may be reported. These transcripts appear in the LRG Transcripts track in the Gene and Gene Predictions track section. Methods LRG sequences are suggested by the community studying a locus (for example, Locus-Specific Database curators, research laboratories, mutation consortia). LRG curators then examine the submitted transcript as well as other known transcripts at the locus, in the context of alignment and public expression data. For more information on the selection and annotation process, see the LRG FAQ, (Dalgleish, et al.) and (MacArthur, et al.). Credits This track was produced at UCSC using LRG XML files. Thanks to LRG collaborators for making these data available. References Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW et al. Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Med. 2010 Apr 15;2(4):24. PMID: 20398331; PMC: PMC2873802 MacArthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR et al. Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants. Nucleic Acids Res. 2014 Jan;42(Database issue):D873-8. PMID: 24285302; PMC: PMC3965024 
lrgTranscriptAli LRG Transcripts Locus Reference Genomic (LRG) / RefSeqGene Fixed Transcript Annotations Genes and Gene Predictions Description This track shows the fixed (unchanging) transcript(s) associated with each Locus Reference Genomic (LRG) sequence. LRG sequences are manually curated, stable DNA sequences that surround a locus (typically a gene) and provide an unchanging coordinate system for reporting sequence variants. They are not necessarily identical to the corresponding sequence in a particular reference genome assembly (such as Feb. 2009 (GRCh37/hg19)), but can be mapped to each version of a reference genome assembly in order to convert between the stable LRG variant coordinates and the various assembly coordinates. We import the data from the LRG database at the EBI. The NCBI RefSeqGene database is almost identical to LRG, but it may contain a few more sequences. See the NCBI documentation. The LRG Regions track, in the Mapping and Sequencing Tracks section, includes more information about the LRG including the HGNC gene symbol for the gene at that locus, source of the LRG sequence, and summary of differences between LRG sequence and the genome assembly. Methods LRG sequences are suggested by the community studying a locus (for example, Locus-Specific Database curators, research laboratories, mutation consortia). LRG curators then examine the submitted transcript as well as other known transcripts at the locus, in the context of alignment and public expression data. For more information on the selection and annotation process, see the LRG FAQ, (Dalgleish, et al.) and (MacArthur, et al.). Credits This track was produced at UCSC using LRG XML files. Thanks to LRG collaborators for making these data available. References Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW et al. Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Med. 2010 Apr 15;2(4):24. PMID: 20398331; PMC: PMC2873802 MacArthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR et al. Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants. Nucleic Acids Res. 2014 Jan;42(Database issue):D873-8. PMID: 24285302; PMC: PMC3965024 
ctgPos Map Contigs Physical Map Contigs Mapping and Sequencing Description This track shows the locations of human contigs on the physical map. The underlying data is derived from the GRCh37 AGP file that accompanies this assembly. The contigs in this track are identical to those in the GRC Map Contigs track, the difference being the the contigs in the GRC Map Contigs track are named according to GRC. All contigs in this track are oriented to the &quot;+&quot; strand. Methods For human genome reference sequences dated April 2003 and later, the individual chromosome sequencing centers are responsible for preparing the assembly of their chromosomes in AGP format (see also: AGP File Specification). The files provided by these centers are checked and validated at NCBI, and form the basis for the AGP file that defines the physical map contigs. For more information on the human genome assembly process, see NCBI Assembly Primer. 
wgEncodeMapability Mappability Mappability or Uniqueness of Reference Genome from ENCODE Mapping and Sequencing Description These tracks display the level of sequence uniqueness of the reference GRCh37/hg19 genome assembly. They were generated using different window sizes, and high signal will be found in areas where the sequence is unique. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types separated as separate (views). For each view, there are multiple subtracks representing different sequence lengths or methods of preparation. Instructions for configuring multi-view tracks are here. Mappability tracks consist of the following views: Alignability These tracks provide a measure of how often the sequence found at the particular location will align within the whole genome. Unlike measures of uniqueness, alignability will tolerate up to 2 mismatches. These tracks are in the form of signals ranging from 0 to 1 and have several configuration options. Uniqueness These tracks are a direct measure of sequence uniqueness throughout the reference genome. These tracks are in the form of signals ranging from 0 to 1 and have several configuration options. Blacklisted Regions Both tracks of blacklisted regions attempt to identify regions of the reference genome which are troublesome for high throughput sequencing aligners. Troubled regions may be due to repetitive elements or other anomalies. Each track contains a set of regions of varying length with no special configuration options. Methods Alignability The CRG Alignability tracks display how uniquely k-mer sequences align to a region of the genome. To generate the data, the GEM-mappability program has been employed. The method is equivalent to mapping sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts to produce these tracks) back to the genome using the GEM mapper aligner (up to 2 mismatches were allowed in this case). For each window, a mappability score was computed (S = 1/(number of matches found in the genome): S=1 means one match in the genome, S=0.5 is two matches in the genome, and so on). The CRG Alignability tracks were generated independently of the ENCODE project, in the framework of the GEM (GEnome Multitool) project. Uniqueness The Duke Uniqueness tracks display how unique each sequence is on the positive strand starting at a particular base and of a particular length. Thus, the 20 bp track reflects the uniqueness of all 20 base sequences with the score being assigned to the first base of the sequence. Scores are normalized to between 0 and 1, with 1 representing a completely unique sequence and 0 representing a sequence that occurs more than 4 times in the genome (excluding chrN_random and alternative haplotypes). A score of 0.5 indicates the sequence occurs exactly twice, likewise 0.33 for three times and 0.25 for four times. The Duke Uniqueness tracks were generated for the ENCODE project as tools in the development of the Open Chromatin: DNaseI HS, FAIRE, TFBS and Synthesis tracks. Blacklisted Regions The DAC Blacklisted Regions aim to identify a comprehensive set of regions in the human genome that have anomalous, unstructured, high signal/read counts in next gen sequencing experiments independent of cell line and type of experiment. There were 80 open chromatin tracks (DNase and FAIRE datasets) and 20 ChIP-seq input/control tracks spanning &#126;60 human tissue types/cell lines in total used to identify these regions with signal artifacts. These regions tend to have a very high ratio of multi-mapping to unique mapping reads and high variance in mappability. Some of these regions overlap pathological repeat elements such as satellite, centromeric and telomeric repeats. However, simple mappability based filters do not account for most of these regions. Hence, it is recommended to use this blacklist alongside mappability filters. The DAC Blacklisted Regions track was generated for the ENCODE project. here. --> The Duke Excluded Regions track displays genomic regions for which mapped sequence tags were filtered out before signal generation and peak calling for Open Chromatin: DNaseI HS and FAIRE tracks. This track contains problematic regions for short sequence tag signal detection (such as satellites and rRNA genes). The Duke Excluded Regions track was generated for the ENCODE project. Release Notes This is Release 3 (October 2011) of this track, which now includes the DAC Blacklisted regions, Duke Uniqueness and Duke Excluded regions. Credits The CRG Alignability track was created by Thomas Derrien and Paolo Ribeca in Roderic Guigo's lab at the Centre for Genomic Regulation (CRG), Barcelona, Spain. Thomas Derrien was supported by funds from NHGRI for the ENCODE project, while Paolo Ribeca was funded by a Consolider grant CDS2007-00050 from the Spanish Ministerio de Educaci&#243;n y Ciencia. The Duke Uniqueness and Duke Excluded Regions tracks were created by Terry Furey and Debbie Winter at Duke Univerisity's Institute for Genome Sciences & Policy (IGSP); and Stefan Graf at the University of Cambridge, Department of Oncology and CR-UK Cambridge Research Institute (CRI). We thank NHGRI for ENCODE funding support. The DAC Blacklisted Regions were created by Anshul Kundaje at Stanford University in the labs of Batzoglou and Sidow and in cooperation with Ewan Birney at the European Bioinformatics Insitute (EBI). We thank NHGRI for ENCODE funding support. (Contact: Anshul Kundaje). References Derrien T, Estelle J, Marco Sola S, Knowles DG, Raineri E, Guigo R, Ribeca P. Fast computation and applications of genome mappability. PLoS One. 2012;7(1):e30377. Data Release Policy Data users may freely use all data in this track. ENCODE labs that contributed annotations have exempted the data displayed here from the ENCODE data release policy restrictions. 
wgEncodeMapabilityViewDuniq Duke Uniqueness Mappability or Uniqueness of Reference Genome from ENCODE Mapping and Sequencing 
wgEncodeDukeMapabilityUniqueness35bp Duke Uniq 35 Mapability ENCODE Mar 2012 Freeze 2011-03-28 wgEncodeEH000325 325 Crawford Duke 1.0 - 4 or less wgEncodeDukeMapabilityUniqueness35bp Uniqueness Short Read Mappability Crawford Crawford - Duke University Displays how unique is each sequence on the positive strand starting at a particular base and of a particular length. The score of 1 represents completely unique, 0.5 occurs exactly twice, 0.33 three times, 0.25 four times and 0 occurs > 4 times (excluding chrN_random and alternative haplotypes). The Duke uniqueness tracks were generated for the ENCODE project. Uniqueness of 35bp Windows from ENCODE/OpenChrom(Duke) Mapping and Sequencing 
wgEncodeDukeMapabilityUniqueness20bp Duke Uniq 20 Mapability ENCODE Mar 2012 Freeze 2011-03-28 wgEncodeEH000323 323 Crawford Duke 1.0 - 4 or less wgEncodeDukeMapabilityUniqueness20bp Uniqueness Short Read Mappability Crawford Crawford - Duke University Displays how unique is each sequence on the positive strand starting at a particular base and of a particular length. The score of 1 represents completely unique, 0.5 occurs exactly twice, 0.33 three times, 0.25 four times and 0 occurs > 4 times (excluding chrN_random and alternative haplotypes). The Duke uniqueness tracks were generated for the ENCODE project. Uniqueness of 20bp Windows from ENCODE/OpenChrom(Duke) Mapping and Sequencing 
wgEncodeMapabilityViewCRGMAP CRG GEM Alignability Mappability or Uniqueness of Reference Genome from ENCODE Mapping and Sequencing 
wgEncodeCrgMapabilityAlign100mer CRG Align 100 Mapability January 2010 wgEncodeEH000317 317 Gingeras CRG-Guigo wgEncodeCrgMapabilityAlign100mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 100mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeCrgMapabilityAlign75mer CRG Align 75 Mapability January 2010 wgEncodeEH000321 321 Gingeras CRG-Guigo wgEncodeCrgMapabilityAlign75mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 75mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeCrgMapabilityAlign50mer CRG Align 50 Mapability January 2010 wgEncodeEH000320 320 Gingeras CRG-Guigo wgEncodeCrgMapabilityAlign50mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 50mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeCrgMapabilityAlign40mer CRG Align 40 Mapability January 2010 wgEncodeEH000319 319 Gingeras CRG-Guigo wgEncodeCrgMapabilityAlign40mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 40mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeCrgMapabilityAlign36mer CRG Align 36 Mapability January 2010 wgEncodeEH000318 318 Gingeras CRG-Guigo wgEncodeCrgMapabilityAlign36mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 36mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeCrgMapabilityAlign24mer CRG Align 24 Mapability April 2010 wgEncodeEH000608 608 Gingeras CRG-Guigo wgEncodeCrgMapabilityAlign24mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 24mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeMapabilityViewXR Blacklisted Regions Mappability or Uniqueness of Reference Genome from ENCODE Mapping and Sequencing 
wgEncodeDukeMapabilityRegionsExcludable Duke Excluded Mapability ENCODE Mar 2012 Freeze 2011-03-28 wgEncodeEH000322 322 Crawford Duke satellite_rna_chrM_500.bed.20080925 wgEncodeDukeMapabilityRegionsExcludable Excludable Short Read Mappability Crawford Crawford - Duke University Genomic regions for which mapped sequence tags were filtered out before signal generation and peak calling, problematic regions for short sequence tag signal detection (such as satellites and rRNA genes) Duke Excluded Regions from ENCODE/OpenChrom(Duke) Mapping and Sequencing 
wgEncodeDacMapabilityConsensusExcludable DAC Blacklist Mapability ENCODE Mar 2012 Freeze 2011-05-04 wgEncodeEH001432 1432 Birney DAC-Stanford consensus: Duke Excluded and DAC UltraHighSignal blacklist wgEncodeDacMapabilityConsensusExcludable Excludable Short Read Mappability Birney Batzoglou & Sidow - Stanford University Genomic regions for which mapped sequence tags were filtered out before signal generation and peak calling, problematic regions for short sequence tag signal detection (such as satellites and rRNA genes) DAC Blacklisted Regions from ENCODE/DAC(Kundaje) Mapping and Sequencing 
mastermind Mastermind Variants Genomenon Mastermind Variants extracted from full text publications Phenotype and Literature Description This track shows most variants found in the full text of scientific publications gathered by Genomenon Mastermind. Mastermind uses a software that searches for disease-gene-variant associations in the scientific literature. The genome browser track shows only if a variant has been indexed by the search engine. To get details on a variant (bibliographic references, disease, etc) click it and follow the &quot;Protein change and link to details&quot; at the top of the details page. Mouse over an item to show the gene and amino acid change and the scores MMCNT1, MMCNT2 and MMCNT3, explained below. Genomenon Mastermind Genomic Search Engine is a commercial database of variants likely to be mentioned in full text scientific articles. A limited number of queries per week is free for healthcare professionals and researchers, if they register on the signup page page. Advanced features require a license for the Mastermind Professional Edition, which contains the same content but allows more comprehensive searches. Display Conventions and Configuration Genomic locations of variants are labeled with the nucleotide change. Hover over the features to see the gene, the amino acid change and the scores MMCNT1, MMCNT2 and MMCNT3, described below. All other information is shown on the respective Mastermind variant detail page, accessible via the &quot;Protein change and link to details&quot; at the top of the details page. The features are colored based on their evidence: As suggested by Genomenom, we added a filter on all variants, so the data are not exactly identical to their website. We skip variants with more than one nucleotide and a MMCNT of 0 and where the variant is not an indel. This means that for longer variants, only variants are shown that are explicitly mentioned in the papers. This makes the data more specific. Color Level of support High: at least one paper mentions this exact cDNA change Medium: at least two papers mention a variant that leads to the same amino acid change Low: only a single paper mentions a variant that leads to the same amino acid change The three numbers that are shown on the mouse-over and the details page have the following meaning (MM=Mastermind): MMCNT1: cDNA-level exact matches. This is the number of articles that mention the variant at the nucleotide level in either the title/abstract or the full-text. MMCNT2: cDNA-level possible matches. This is the number of articles with nucleotide-level matches (from 1) plus articles with protein-level matches in which the publication did not specify the cDNA-level change, meaning they could be referring to this nucleotide-level variant but there is insufficient data in these articles to determine conclusively. MMCNT3: This is the number of articles citing any variant resulting in the same biological effect as this variant. This includes the articles from MMCNT1 and MMCNT2 plus articles with alternative cDNA-level variants that result in the same protein effect. On the track settings page one can filter on these scores under the display mode section by entering a minimum number of articles for each kind of evidence. Data access The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can be accessed from scripts through our API, the track name is "mastermind". For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called mastermind.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/mastermind.bb -chrom=chr21 -start=0 -end=100000000 stdout Previous versions of this track can be found on our archive download server. Methods The Mastermind Cited Variants file was downloaded, converted to BED format with scripts that are available in our Git repository and converted to a bigBed file with the UCSC genome browser tool bedToBigBed. This track is automatically updated two weeks after every Mastermind CVR release, which happens every three months. Credits Thanks to Mark Kiel, Steve Schwartz and Clayton Wheeler from Genomenon for making these data available. References Chunn LM, Nefcy DC, Scouten RW, Tarpey RP, Chauhan G, Lim MS, Elenitoba-Johnson KSJ, Schwartz SA, Kiel MJ. Mastermind: A Comprehensive Genomic Association Search Engine for Empirical Evidence Curation and Genetic Variant Interpretation. Front Genet. 2020 Nov 13;11:577152. doi: 10.3389/fgene.2020.577152. PMID: 33281875; PMC: PMC7691534 
mgcFullMrna MGC Genes Mammalian Gene Collection Full ORF mRNAs Genes and Gene Predictions Description This track show alignments of human mRNAs from the Mammalian Gene Collection (MGC) having full-length open reading frames (ORFs) to the genome. The goal of the Mammalian Gene Collection is to provide researchers with unrestricted access to sequence-validated full-length protein-coding cDNA clones for human, mouse, rat, xenopus, and zerbrafish genes. Display Conventions and Configuration The track follows the display conventions for gene prediction tracks. An optional codon coloring feature is available for quick validation and comparison of gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Methods GenBank human MGC mRNAs identified as having full-length ORFs were aligned against the genome using blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 1% of the best and at least 95% base identity with the genomic sequence were kept. Credits The human MGC full-length mRNA track was produced at UCSC from mRNA sequence data submitted to GenBank by the Mammalian Gene Collection project. References Mammalian Gene Collection project references. Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
mgcOrfeomeMrna MGC/ORFeome Genes MGC/ORFeome Full ORF mRNA Clones Genes and Gene Predictions Description These tracks show alignments of human mRNAs from the Mammalian Gene Collection (MGC) and ORFeome Collaboration having full-length open reading frames (ORFs) to the genome. The goal of the Mammalian Gene Collection is to provide researchers with unrestricted access to sequence-validated full-length protein-coding cDNA clones for human, mouse, and rat genes. The ORFeome project extended MGC to provide additional human, mouse, and zebrafish clones. Display Conventions and Configuration The track follows the display conventions for gene prediction tracks. An optional codon coloring feature is available for quick validation and comparison of gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Methods GenBank human MGC mRNAs identified as having full-length ORFs were aligned against the genome using blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 1% of the best and at least 95% base identity with the genomic sequence were kept. Credits The human MGC full-length mRNA track was produced at UCSC from mRNA sequence data submitted to GenBank by the Mammalian Gene Collection project. Visit the ORFeome Collaboration members page for a list of credits and references. References Mammalian Gene Collection project references. Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
jaxQtlMapped MGI Mouse QTL MGI Mouse Quantitative Trait Loci Coarsely Mapped to Human Phenotype and Literature Description This track shows Mouse quantitative trait loci (QTLs) from Mouse Genome Informatics (MGI) at the Jackson Laboratory that have been coarsely mapped by UCSC to the Human genome using stringently filtered cross-species alignments. A quantitative trait locus (QTL) is a polymorphic locus that contains alleles which differentially affect the expression of a continuously distributed phenotypic trait. Usually a QTL is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. To map the Mouse QTLs to Human, UCSC's chained and netted blastz alignments of Mouse to Human were filtered to retain only those with minimum length of 20,000 bases in both Mouse and Human, and minimum score of 10,000. This removed many valid-but-short alignments. This choice was made because QTLs in general are extremely large and approximate regions. After the alignment filtering, UCSC's liftOver program was used to map Mouse regions to Human via the filtered alignments. For the purpose of cross-species mapping, MGI QTLs were divided into two categories: QTLs whose genomic coordinates span the entire confidence interval (often several million bases), and QTLs for which only the STS marker with the peak score was given, resulting in genomic coordinates for very small regions (most less than 300 bases). QTLs in the latter set were so small as to make mapping impossible in many cases, so their coordinates were padded by 50,000 bases before and after, for a total size of approximately 100,000 bases, a conservative proxy for the unknown confidence interval. The two categories of QTL are displayed in subtracks: MGI Mouse QTL for the unmodified QTLs and MGI Mouse QTL Padded for the single-marker QTLs that were padded to 100,000 bases. To get a sense of how many genomic rearrangments between Mouse and Human are in the region of a particular Mouse QTL, you may want to view the Human Nets track in the Mouse Feb. 2006 (NCBI36/mm8) genome browser. In the position/search box, enter the name of the Mouse QTL of interest. Credits Thanks to MGI at the Jackson Laboratory, and Bob Sinclair in particular, for providing these data. 
jaxQtlPadded MGI Mouse QTL Padded MGI Mouse QTL Peak-Score Markers Padded to 100k and Coarsely Mapped to Human Phenotype and Literature 
jaxQtlAsIs MGI Mouse QTL MGI Mouse QTLs Coarsely Mapped to Human Phenotype and Literature 
microsat Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats Repeats Description This track displays regions that are likely to be useful as microsatellite markers. These are sequences of at least 15 perfect di-nucleotide and tri-nucleotide repeats and tend to be highly polymorphic in the population. Methods The data shown in this track are a subset of the Simple Repeats track, selecting only those repeats of period 2 and 3, with 100% identity and no indels and with at least 15 copies of the repeat. The Simple Repeats track is created using the Tandem Repeats Finder. For more information about this program, see Benson (1999). Credits Tandem Repeats Finder was written by Gary Benson. References Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217 
dhcVcfModern Mod Hum Variants Variant Calls from 11 Modern Human Genome Sequences Denisova Assembly and Analysis Description The Modern Human Variants track shows variant calls made from sequence reads of eleven individuals mapped to the human genome. The purpose of this track is to put the divergence of the Denisova genome into perspective with regard to present-day humans. Methods DNA was obtained for each of ten individuals from the CEPH-Human Genome Diversity Panel (HGDP): HGDP00456 (Mbuti) HGDP00521 (French) HGDP00542 (Papuan) HGDP00665 (Sardinian) HGDP00778 (Han) HGDP00927 (Yoruba) HGDP00998 (Karitiana) HGDP01029 (San) HGDP01284 (Mandenka) HGDP01307 (Dai) DNA was also extracted from a Dinka individual from Sudan (DNK02). To minimize biases due to instrument variability, the samples were pooled for sequencing, using four barcoded libraries per sample. The paired-end reads were aligned to the human genome using the Burrows-Wheeler Aligner and potential PCR duplicates were filtered using Picard. Genotype calls for single nucleotide variants and small insertions and deletions were made using the Unified Genotyper from the Genome Analysis Toolkit (GATK), with an additional iteration using a modified reference genome in order to reduce reference bias (Note 6, supplementary online materials of Meyer, 2012). Variant Call Format (VCF) files were enhanced by adding information from Ensembl Compara EPO alignments of 6 primates and of 35 Eutherian mammals, phastCons conservation scores generated using EPO alignments, 1000 Genomes Project integrated variant call files, University of Washington background selection scores, ENCODE/Duke Uniqueness of 20mers (see the Mappability track), segmental duplications from the Eichler lab (see the Segmental Dups track), and samtools mpileup summaries of mapped reads. Credits Thanks to the Max Planck Institute for Evolutionary Anthropology for providing the variant-only VCF files used for this track. References Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Pr&#252;fer K, de Filippo C et al. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012 Oct 12;338(6104):222-6. PMID: 22936568; PMC: PMC3617501; supplementary online materials, Note 6. 
dhcVcfHGDP01307 Dai Variants Dai Individual (HGDP01307) Variant Calls Denisova Assembly and Analysis 
dhcVcfHGDP01284 Mandenka Variants Mandenka Individual (HGDP01284) Variant Calls Denisova Assembly and Analysis 
dhcVcfHGDP01029 San Variants San Individual (HGDP01029) Variant Calls Denisova Assembly and Analysis 
dhcVcfHGDP00998 Karit. Variants Karitiana Individual (HGDP00998) Variant Calls Denisova Assembly and Analysis 
dhcVcfHGDP00927 Yoruba Variants Yoruba Individual (HGDP00927) Variant Calls Denisova Assembly and Analysis 
dhcVcfHGDP00778 Han Variants Han Individual (HGDP00778) Variant Calls Denisova Assembly and Analysis 
dhcVcfHGDP00665 Sardin. Variants Sardinian Individual (HGDP00665) Variant Calls Denisova Assembly and Analysis 
dhcVcfHGDP00542 Papuan Variants Papuan Individual (HGDP00542) Variant Calls Denisova Assembly and Analysis 
dhcVcfHGDP00521 French Variants French Individual (HGDP00521) Variant Calls Denisova Assembly and Analysis 
dhcVcfHGDP00456 Mbuti Variants Mbuti Individual (HGDP00456) Variant Calls Denisova Assembly and Analysis 
dhcVcfDNK02 Dinka Variants Dinka Individual Variant Calls Denisova Assembly and Analysis 
dhcHumDerDenAnc Modern Derived Modern Human Derived, Denisova Ancestral Denisova Assembly and Analysis Description This track shows mutations in the modern human lineage that rose to fixation or near fixation since the split from the last common ancestor with Denisovans, along with predicted functional effects from Ensembl's Variant Effect Predictor (VEP). Methods Methods and analysis are described in detail in Note 19 of supplementary online materials of (Meyer, 2012). Whole genome Enredo-Pecan-Ortheus (EPO) alignments of human, chimpanzee, gorilla and orangutan were combined with modern human genotypes from the 1000 Genomes Project Phase 1 (1000G) to identify sites that are fixed (&gt;99.0% frequency in 1000G) or high frequency (&gt;90.0% frequency in 1000G) derived in modern humans and ancestral in chimpanzee and at least one other great ape (gorilla or orangutan). In order to avoid paralogous regions, human and chimpanzee sequences were required to appear in only one EPO alignment block. Some "fixed" sites are in dbSNP; these were separated out from fixed sites not in dbSNP, so three categories of frequency are displayed: Fixed, Fixed+dbSNP, and High Frequency. Various quality filters were applied to Denisova genotypes: minimum 40 PHRED genotype likelihood from the Genome Analysis Toolkit (GATK); minimum 30 RMS map quality score; coverage at least 14X and at most 66X; no sites in positions identified as systematic errors or deemed to be of low quality due to conflicting genotype calls in a second iteration of GATK (Note 6, supplementary online materials of Meyer, 2012). The derived-in-modern-human sites were intersected with the high-confidence-in-Denisova sites and annotated using VEP to predict effects on protein structure and transcriptional regulation. Credits Thanks to the Max Planck Institute for Evolutionary Anthropology for providing the data files used for this track. References Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Pr&#252;fer K, de Filippo C et al. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012 Oct 12;338(6104):222-6. PMID: 22936568; PMC: PMC3617501; supplementary online materials, Note 19 
dhcHumDerDenAncReg Modern Derivd Reg Modern Human Derived, Denisova Ancestral Denisova Assembly and Analysis 
dhcHumDerDenAncRegHighFreq RegRegion HiF Modern Human Derived (HighFreq), Denisova Ancestral: Regulatory Region Denisova Assembly and Analysis 
dhcHumDerDenAncRegFixedDbSnp RegRegion FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: Regulatory Region Denisova Assembly and Analysis 
dhcHumDerDenAncRegFixed RegRegion Fxd Modern Human Derived (Fixed), Denisova Ancestral: Regulatory Region Denisova Assembly and Analysis 
dhcHumDerDenAncRegMotifHighFreq RegMotif HiF Modern Human Derived (HighFreq), Denisova Ancestral: Regulatory Motif Denisova Assembly and Analysis 
dhcHumDerDenAncRegMotifFixedDbSnp RegMotif FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: Regulatory Motif Denisova Assembly and Analysis 
dhcHumDerDenAncRegMotifFixed RegMotif Fxd Modern Human Derived (Fixed), Denisova Ancestral: Regulatory Motif Denisova Assembly and Analysis 
dhcHumDerDenAncRegMotifHighInfoHighFreq RgMoHiInf HiF Modern Human Derived (HighFreq), Denisova Ancestral: High Inf Pos in TFBP Denisova Assembly and Analysis 
dhcHumDerDenAncRegMotifHighInfoFixedDbSnp RgMoHiInf FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: High Inf Pos in TFBP Denisova Assembly and Analysis 
dhcHumDerDenAncRegMotifHighInfoFixed RgMoHiInf Fxd Modern Human Derived (Fixed), Denisova Ancestral: High Inf Pos in TFBP Denisova Assembly and Analysis 
dhcHumDerDenAncEns Modern Derivd Ens Modern Human Derived, Denisova Ancestral Denisova Assembly and Analysis 
dhcHumDerDenAncSynHighFreq Syn HiF Modern Human Derived (HighFreq), Denisova Ancestral: Syn Denisova Assembly and Analysis 
dhcHumDerDenAncSynFixedDbSnp Syn FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: Syn Denisova Assembly and Analysis 
dhcHumDerDenAncSynFixed Syn Fxd Modern Human Derived (Fixed), Denisova Ancestral: Syn Denisova Assembly and Analysis 
dhcHumDerDenAncUtr5HighFreq Utr5 HiF Modern Human Derived (HighFreq), Denisova Ancestral: 5' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncUtr5FixedDbSnp Utr5 FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: 5' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncUtr5Fixed Utr5 Fxd Modern Human Derived (Fixed), Denisova Ancestral: 5' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncUtr3HighFreq Utr3 HiF Modern Human Derived (HighFreq), Denisova Ancestral: 3' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncUtr3FixedDbSnp Utr3 FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: 3' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncUtr3Fixed Utr3 Fxd Modern Human Derived (Fixed), Denisova Ancestral: 3' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncSpliceHighFreq Splice HiF Modern Human Derived (HighFreq), Denisova Ancestral: Splice Denisova Assembly and Analysis 
dhcHumDerDenAncSpliceFixedDbSnp Splice FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: Splice Denisova Assembly and Analysis 
dhcHumDerDenAncSpliceFixed Splice Fxd Modern Human Derived (Fixed), Denisova Ancestral: Splice Denisova Assembly and Analysis 
dhcHumDerDenAncNonsynHighFreq Nonsyn HiF Modern Human Derived (HighFreq), Denisova Ancestral: Non-synonymous Denisova Assembly and Analysis 
dhcHumDerDenAncNonsynFixedDbSnp Nonsyn FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: Non-synonymous Denisova Assembly and Analysis 
dhcHumDerDenAncNonsynFixed Nonsyn Fxd Modern Human Derived (Fixed), Denisova Ancestral: Non-synonymous Denisova Assembly and Analysis 
dhcHumDerDenAncInFrameNonsynFixed InFrNS Fxd Modern Human Derived (Fixed), Denisova Ancestral: In-frame Non-synonymous Denisova Assembly and Analysis 
dhcHumDerDenAncFrameshiftCodingHighFreq FrShft HiF Modern Human Derived (HighFreq), Denisova Ancestral: Frameshift Coding Denisova Assembly and Analysis 
dhcHumDerDenAncFrameshiftCodingFixedDbSnp FrShft FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: Frameshift Coding Denisova Assembly and Analysis 
dhcHumDerDenAncFrameshiftCodingFixed FrShft Fxd Modern Human Derived (Fixed), Denisova Ancestral: Frameshift Coding Denisova Assembly and Analysis 
dhcHumDerDenAncCcds Modern Derivd CC Modern Human Derived, Denisova Ancestral Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsSynHighFreq CC Syn HiF Modern Human Derived (HighFreq), Denisova Ancestral: CCDS Syn Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsSynFixedDbSnp CC Syn FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: CCDS Syn Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsSynFixed CC Syn Fxd Modern Human Derived (Fixed), Denisova Ancestral: CCDS Syn Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsUtr5HighFreq CC Utr5 HiF Modern Human Derived (HighFreq), Denisova Ancestral: CCDS 5' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsUtr5FixedDbSnp CC Utr5 FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: CCDS 5' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsUtr5Fixed CC Utr5 Fxd Modern Human Derived (Fixed), Denisova Ancestral: CCDS 5' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsUtr3HighFreq CC Utr3 HiF Modern Human Derived (HighFreq), Denisova Ancestral: CCDS 3' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsUtr3FixedDbSnp CC Utr3 FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: CCDS 3' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsUtr3Fixed CC Utr3 Fxd Modern Human Derived (Fixed), Denisova Ancestral: CCDS 3' UTR Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsSpliceHighFreq CC Splice HiF Modern Human Derived (HighFreq), Denisova Ancestral: CCDS Splice Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsSpliceFixedDbSnp CC Splice FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: CCDS Splice Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsSpliceFixed CC Splice Fxd Modern Human Derived (Fixed), Denisova Ancestral: CCDS Splice Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsNonsynHighFreq CC Nonsyn HiF Modern Human Derived (HighFreq), Denisova Ancestral: CCDS Non-synonymous Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsNonsynFixedDbSnp CC Nonsyn FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: CCDS Non-synonymous Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsNonsynFixed CC Nonsyn Fxd Modern Human Derived (Fixed), Denisova Ancestral: CCDS Non-synonymous Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsInFrameNonsynFixed CC InFrNS Fxd Modern Human Derived (Fixed), Denisova Ancestral: CCDS In-frame Non-synonymous Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsFrameshiftCodingHighFreq CC FrShft HiF Modern Human Derived (HighFreq), Denisova Ancestral: CCDS Frameshift Coding Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsFrameshiftCodingFixedDbSnp CC FrShft FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: CCDS Frameshift Coding Denisova Assembly and Analysis 
dhcHumDerDenAncCcdsFrameshiftCodingFixed CC FrShft Fxd Modern Human Derived (Fixed), Denisova Ancestral: CCDS Frameshift Coding Denisova Assembly and Analysis 
dhcHumDerDenAncAll Modern Derivd All Modern Human Derived, Denisova Ancestral Denisova Assembly and Analysis 
dhcHumDerDenAncAllHighFreq HiF Modern Human Derived (HighFreq), Denisova Ancestral: All Denisova Assembly and Analysis 
dhcHumDerDenAncAllFixedDbSnp FxS Modern Human Derived (Fixed+dbSNP), Denisova Ancestral: All Denisova Assembly and Analysis 
dhcHumDerDenAncAllFixed Fxd Modern Human Derived (Fixed), Denisova Ancestral: All Denisova Assembly and Analysis 
nscanGene N-SCAN N-SCAN Gene Predictions Genes and Gene Predictions Description This track shows gene predictions using the N-SCAN gene structure prediction software provided by the Computational Genomics Lab at Washington University in St. Louis, MO, USA. Methods N-SCAN combines biological-signal modeling in the target genome sequence along with information from a multiple-genome alignment to generate de novo gene predictions. It extends the TWINSCAN target-informant genome pair to allow for an arbitrary number of informant sequences as well as richer models of sequence evolution. N-SCAN models the phylogenetic relationships between the aligned genome sequences, context-dependent substitution rates, insertions, and deletions. Human N-SCAN Human N-SCAN uses mouse (mm9) as the informant and iterative pseudogene masking. Credits Thanks to Michael Brent's Computational Genomics Group at Washington University St. Louis for providing this data. Special thanks for this implementation of N-SCAN to Aaron Tenney in the Brent lab, and Robert Zimmermann, currently at Max F. Perutz Laboratories in Vienna, Austria. References Gross SS, Brent MR. Using multiple alignments to improve gene prediction. J Comput Biol. 2006 Mar;13(2):379-93. PMID: 16597247 Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003 Oct 1;31(19):5654-66. PMID: 14500829; PMC: PMC206470 Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001;17 Suppl 1:S140-8. PMID: 11473003 van Baren MJ, Brent MR. Iterative gene prediction and pseudogene removal improves genome annotation. Genome Res. 2006 May;16(5):678-85. PMID: 16651666; PMC: PMC1457044 
neandertalMethylation Neandertal Methyl Neandertal Reconstructed DNA Methylation Map Neandertal Assembly and Analysis Description This track shows the reconstructed DNA methylation map of the Neandertal genome, derived from bone tissues. Display conventions and configuration Green to red scaling is used as a rough indicator of methylation. Values range from 0% (green, unmethylated) to 100% (red, methylated). Data are displayed for CpG positions across the genome. Methods Gokhman et al. reconstructed the DNA methylation maps of two archaic humans, the Neandertal and the Denisovan, based on the natural deamination of cytosines in ancient DNA. With time, cytosines (C's) in post-mortem DNA lose their amine group (deamination). However, deamination of methylated vs. unmethylated C's results in different products - Methylated C's are deaminated with time to T's, whereas unmethylated C's are deaminated to U's. The U's are later removed during ancient DNA library preparation and as a result, a distinct pattern is observed: methylated regions in the genome display high C--&gt;T conversion rate, whereas unmethylated regions display a low C--&gt;T conversion rate. These patterns were used to reconstruct the full DNA methylation maps of the archaic humans. Credits This track was produced at UCSC using data generated by Gokhman et al., 2014. References Gokhman D, Lavi E, Pr&#252;fer K, Fraga MF, Riancho JA, Kelso J, P&#228;&#228;bo S, Meshorer E, Carmel L. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science. 2014 May 2;344(6183):523-7. PMID: 24786081 
ntMito Neandertal Mito Neandertal Mitochondrial Sequence (Vi33.16, 2008) Neandertal Assembly and Analysis Description This track shows the alignment of a complete Neandertal mitochondrial sequence to a modern human mitochondrial sequence. Note: the mitochondrion used as the genome browser reference sequence &quot;chrM&quot; in hg18 and hg19 is NC_001807, which has been deprecated. Future human genome browsers will use the revised Cambridge Reference Sequence (rCRS) NC_012920. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. Mismatching bases are highlighted as described here. Several types of alignment gap may also be colored; for more information, click here. Methods DNA was extracted from a 38,000-year-old bone and sequenced using methods described in Green, et al. The Neandertal mitochondrial sequence (NC_011137) was downloaded from GenBank and aligned to chrM (NC_001807) using BLAT. Reference Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell. 2008 Aug 8;134(3):416-26. 
ntSeqReads Neandertal Seq Neandertal Sequence Reads Neandertal Assembly and Analysis Description The Neandertal Seq track shows Neandertal sequence reads mapped to the human genome. The Neandertal sequence was generated from six Neandertal fossils found in Croatia, Germany, Spain and Russia. Display Conventions and Configuration The sequence reads (query sequences) from each of the six samples are contained in separate subtracks. Use the checkboxes to select which samples will be displayed in the browser. Click and drag the sample name to reorder the subtracks. The order in which the subtracks appear in the subtrack list will be the order in which they display in the browser. The query sequences in the SAM/BAM alignment representation are normalized to the + strand of the reference genome (see the SAM Format Specification for more information on the SAM/BAM file format). If a query sequence was originally the reverse of what has been stored and aligned, it will have the following flag: (0x10) Read is on '-' strand. BAM/SAM alignment representations also have tags. Some tags are predefined and others (those beginning with X, Y or Z) are defined by the aligner or data submitter. The following tag is associated with this track: AS: Alignment score generated by aligner The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. Display Read Names: By default, read names are not displayed. To display the read names, selected the check box next to "Display read names". Minimum alignment quality: Excludes alignments with quality less than the given number. The default is 0. Color track by bases: By default, mismatching bases are highlighted in the display. Change the selection to &quot;item bases&quot; to see all base values from the query sequence, or &quot;OFF&quot; to ignore query sequence. Click here for additional information. Alignment Gap/Insertion Display Options: Click here for help with these options. Additional coloring modes: Other aspects of the alignments can be displayed in color or grayscale. Color by strand: Alignments on the reverse strand are colored dark red, alignments on the forward strand are colored dark blue. Grayscale: Items are shaded according to the chosen method: alignment quality or base qualities. The alignment qualities of individual items are shaded on a scale of 0 (lightest) to 99 (darkest). Base qualities are shaded on a scale of 0 (lightest) to 40 (darkest). Alignment quality is the default. Methods The Neandertal sequence was genereated from six Neandertal fossils. Vi33.16 (54.1% genome coverage), Vi33.25 (46.6%) and Vi33.26 (45.2%) were discovered in the Vindija cave in Croatia. Feld1 (0.1%) is from the Neandertal type specimen from the Neander Valley in Germany, Sid1253 (0.1%) is from El Sidron cave in Asturias, Spain, and Mez1 (2%) is from Mezmaiskaya in the Altai Mountains, Russia. To increase the fraction of endogenous Neandertal DNA in the sequencing libraries, restriction enzymes were used to deplete libraries of microbial DNA. This was done by identifying Neandertal sequencing reads whose best alignment was to a primate sequence, and selecting enzymes that would differentially cut non-primate fragments. These enzymes all contained CpG dinucleotides in their recognition sequences, reflecting the particularly low abundance of this dinucleotide in mammalian DNA. Sequencing was carried out on the 454 FLX and Titanium platforms and the Illumina GA. Neandertal reads were mapped to the human genome (hg19) using a custom mapper called ANFO. This custom alignment program was developed to take into account the characteristics of ancient DNA. Following the observation and implementation by Briggs et al., ANFO uses different substitution matrices for DNA thought to be double-stranded versus single-stranded and changes between them if doing so affords a better score. Credits This track was produced at UCSC using data generated by Ed Green. References Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Pr&#252;fer K, Meyer M, Krause J, Ronan MT, Lachmann M et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14616-21. PMID: 17715061; PMC: PMC1976210 Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. PMID: 20448178 
bamSLVi33dot26 Vi33.26 Sequence Vi33.26 Sequence Reads Neandertal Assembly and Analysis 
bamSLVi33dot25 Vi33.25 Sequence Vi33.25 Sequence Reads Neandertal Assembly and Analysis 
bamSLVi33dot16 Vi33.16 Sequence Vi33.16 Sequence Reads Neandertal Assembly and Analysis 
bamSLSid1253 Sid1253 Sequence Sid1253 Sequence Reads Neandertal Assembly and Analysis 
bamSLMez1 Mez1 Sequence Mez1 Sequence Reads Neandertal Assembly and Analysis 
bamSLFeld1 Feld1 Sequence Feld1 Sequence Reads Neandertal Assembly and Analysis 
laminB1Lads NKI LADs (Tig3) NKI LADs (Lamina Associated Domains, Tig3 cells) Regulation Description Please see the NKI Nuc Lamina "super-track" link above for description and methods. 
numtSeq NumtS Sequence Human NumtS mitochondrial sequence Repeats Description and display conventions NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear genomic sequences. The most credited hypothesis concerning their generation suggests that in presence of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during break repair; although NumtS can also derive from duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing and hence frequent false low heteroplasmic evidences have been reported.The Bioinformatics group chaired by M.Attimonelli (University of Bari, Italy) has produced the RHNumtS (Reference Human NumtS) compilation annotating more than 500 Human NumtS. To allow the scientific community to access the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the group has designed the Human NumtS tracks described below. The NumtS tracks show nuclear and mitochondrial regions, the former derived from the application of the Lift-Over (Galaxy) tool on the High Score Pairs (HSPs) obtained by aligning the mitochondrial reference genome (NC_012920) with the hg18 release of the human genome then converted to hg19. "NumtS (Nuclear mitochondrial Sequences)" Track The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear genome. The shading of the items reflect the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. "NumtS assembled" Track The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the "NumtS" track fulfilling the following conditions: The orientation of their alignments must be concordant. The distance between them must be less than 2 kb, on the mitochondrial genome as well as on the nuclear genome. Exceptions for the second condition arise when a long repetitive element is present between two HSPs. "NumtS on mitochondrion" Track The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the nuclear mapping is provided. "Human NumtS on mitochondrion SNP" Track The "Human NumtS SNP" shows the mapping of the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from the comparison with the hg19 build. No shading is provided here. For every item, a link pointing to the nuclear mapping is provided. Methods NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome of the Human Genome (hg18 build) and the human mitochondrial reference sequence (rCRS, AC: NC_012920), fixing the e-value threshold to 1e-03. Mapping coordinates were converted from hg18 to the hg19 assemby by using the Lift-Over software part of Galaxy suite. The assembling of the HSPs was performed with spreadsheet interpolation and manual inspection. BED format is used for the first three annotation tracks, while for the last one the BAM format is implemented. Verification NumtS predicted in silico were validated by carrying out PCR amplification and sequencing on blood-extracted DNA of a healthy individual of European origin. PCR amplification was successful for 275 NumtS and provided amplicons of the expected length. All PCR fragments were sequenced on both strands, and submitted to the EMBL databank. Furthermore, 541 NumtS were validated by merging NumtS nuclear coordinates with HapMap annotations. The analysis was carried on eight HapMap individuals (NA18517, NA18507, NA18956, NA19240, NA18555, NA12878, NA19129, NA12156). For each sample, clones with a single best concordant placement (according to the fosmid end-sequence-pair analysis described in Kidd et al., 2008), have been considered. The analysis showed that 541 NumtS (at least 30bp for each one) had been sequenced in such samples. Credits These data were provided by Domenico Simone, Francesco Maria Calabrese and Marcella Attimonelli at the Department of Biochemistry and Molecular Biology "Ernesto Quagliariello" (University of Bari, Italy). Primer design was carried out by Francesco Calabrese and Giuseppe Mineccia. PCR validation was carried out by Martin Lang, Domenico Simone and Giuseppe Gasparre. Merging with HapMap annotations was performed by Domenico Simone. References Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 2008 May 1;453(7191):56-64. PMID: 18451855; PMC: PMC2424287 Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics. 2008 Jun 3;9:267. PMID: 18522722; PMC: PMC2447851 Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011 Oct 20;12:517. PMID: 22013967; PMC: PMC3228558 
bamAllNumtSSorted NumtS SNPs Human NumtS on Mitochondrion SNPs Repeats 
numtSMitochondrion NumtS on mitochon Human NumtS on Mitochondrion Repeats Description and display conventions NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear genomic sequences. The most credited hypothesis concerning their generation suggests that in presence of mutagenic agents or under stress conditions fragments of mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during break repair, although NumtS can derive from duplication of genomic fragments. NumtS may be cause of contamination during human mtDNA sequencing and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group chaired by M.Attimonelli (Bari, Italy) has produced the RHNumtS compilation annotating more than 500 Human NumtS. To allow the scientific community to access to the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the group has designed the Human NumtS tracks below described. The NumtS tracks show the High Score Pairs (HSPs) obtained by aligning the mitochondrial reference genome (NC_012920) with the hg18 release of the human genome. "NumtS (Nuclear mitochondrial Sequences)" Track The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. "NumtS assembled" Track The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the "NumtS" track fulfilling the following conditions: the orientation of their alignments must be concordant. the distance between them must be less than 2 kb, on the mitochondrial genome as well as on the nuclear genome. Exceptions for the second condition arise when a long repetitive element is present between two HSPs. "NumtS on mitochondrion" Track The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the nuclear mapping is provided. "NumtS on mitochondrion with chromosome placement" Track The "NumtS on mitochondrion with chromosome placement" shows the mapping of the HSPs on the mitochondrial genome, but the items are coloured according to the colours assigned to each human chromosome on the UCSC genome browser. No shading is here provided. For every item, a link pointing to the nuclear mapping is provided. Methods NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome of of the Human Genome hg18 build and the human mitochondrial reference sequence (rCRS, AC: NC_012920), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with spreadsheet interpolation and manual inspection. Verification NumtS predicted in silico were validated by carrying out PCR amplification and sequencing on blood-extracted DNA of a healthy individual of European origin. PCR amplification was successful for 275 NumtS and provided amplicons of the expected length. All PCR fragments were sequenced on both strands, and submitted to the EMBL databank. Furthermore, 541 NumtS were validated by merging NumtS nuclear coordinates with HapMap annotations. Our analysis has been carried on eight HapMap individuals (NA18517, NA18507, NA18956, NA19240, NA18555, NA12878, NA19129, NA12156). For each sample, clones with a single best concordant placement (according to the fosmid end-sequence-pair analysis described in Kidd et al., 2008), have been considered. The analysis showed that 541 NumtS (at least 30bp for each one) had been sequenced in such samples. Credits These data were provided by Domenico Simone and Marcella Attimonelli at Department of Biochemistry and Molecular Biology "Ernesto Quagliariello" (University of Bari, Italy). Primer designing was carried out by Francesco Calabrese and Giuseppe Mineccia. PCR validation was carried out by Martin Lang, Domenico Simone and Giuseppe Gasparre. Merging with HapMap annotations has been performed by Domenico Simone. References Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 2008 May 1;453(7191):56-64. PMID: 18451855; PMC: PMC2424287 Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics. 2008 Jun 3;9:267. PMID: 18522722; PMC: PMC2447851 Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011 Oct 20;12:517. PMID: 22013967; PMC: PMC3228558 
numtSAssembled NumtS assembled Human NumtS Assembled Repeats Description and display conventions NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear genomic sequences. The most credited hypothesis concerning their generation suggests that in presence of mutagenic agents or under stress conditions fragments of mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during break repair, although NumtS can derive from duplication of genomic fragments. NumtS may be cause of contamination during human mtDNA sequencing and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group chaired by M.Attimonelli (Bari, Italy) has produced the RHNumtS compilation annotating more than 500 Human NumtS. To allow the scientific community to access to the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the group has designed the Human NumtS tracks below described. The NumtS tracks show the High Score Pairs (HSPs) obtained by aligning the mitochondrial reference genome (NC_012920) with the hg18 release of the human genome. "NumtS (Nuclear mitochondrial Sequences)" Track The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. "NumtS assembled" Track The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the "NumtS" track fulfilling the following conditions: the orientation of their alignments must be concordant. the distance between them must be less than 2 kb, on the mitochondrial genome as well as on the nuclear genome. Exceptions for the second condition arise when a long repetitive element is present between two HSPs. "NumtS on mitochondrion" Track The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the nuclear mapping is provided. "NumtS on mitochondrion with chromosome placement" Track The "NumtS on mitochondrion with chromosome placement" shows the mapping of the HSPs on the mitochondrial genome, but the items are coloured according to the colours assigned to each human chromosome on the UCSC genome browser. No shading is here provided. For every item, a link pointing to the nuclear mapping is provided. Methods NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome of of the Human Genome hg18 build and the human mitochondrial reference sequence (rCRS, AC: NC_012920), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with spreadsheet interpolation and manual inspection. Verification NumtS predicted in silico were validated by carrying out PCR amplification and sequencing on blood-extracted DNA of a healthy individual of European origin. PCR amplification was successful for 275 NumtS and provided amplicons of the expected length. All PCR fragments were sequenced on both strands, and submitted to the EMBL databank. Furthermore, 541 NumtS were validated by merging NumtS nuclear coordinates with HapMap annotations. Our analysis has been carried on eight HapMap individuals (NA18517, NA18507, NA18956, NA19240, NA18555, NA12878, NA19129, NA12156). For each sample, clones with a single best concordant placement (according to the fosmid end-sequence-pair analysis described in Kidd et al., 2008), have been considered. The analysis showed that 541 NumtS (at least 30bp for each one) had been sequenced in such samples. Credits These data were provided by Domenico Simone and Marcella Attimonelli at Department of Biochemistry and Molecular Biology "Ernesto Quagliariello" (University of Bari, Italy). Primer designing was carried out by Francesco Calabrese and Giuseppe Mineccia. PCR validation was carried out by Martin Lang, Domenico Simone and Giuseppe Gasparre. Merging with HapMap annotations has been performed by Domenico Simone. References Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 2008 May 1;453(7191):56-64. PMID: 18451855; PMC: PMC2424287 Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics. 2008 Jun 3;9:267. PMID: 18522722; PMC: PMC2447851 Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011 Oct 20;12:517. PMID: 22013967; PMC: PMC3228558 
numtS NumtS Human NumtS Repeats Description and display conventions NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear genomic sequences. The most credited hypothesis concerning their generation suggests that in presence of mutagenic agents or under stress conditions fragments of mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during break repair, although NumtS can derive from duplication of genomic fragments. NumtS may be cause of contamination during human mtDNA sequencing and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group chaired by M.Attimonelli (Bari, Italy) has produced the RHNumtS compilation annotating more than 500 Human NumtS. To allow the scientific community to access to the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the group has designed the Human NumtS tracks below described. The NumtS tracks show the High Score Pairs (HSPs) obtained by aligning the mitochondrial reference genome (NC_012920) with the hg18 release of the human genome. "NumtS (Nuclear mitochondrial Sequences)" Track The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. "NumtS assembled" Track The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the "NumtS" track fulfilling the following conditions: the orientation of their alignments must be concordant. the distance between them must be less than 2 kb, on the mitochondrial genome as well as on the nuclear genome. Exceptions for the second condition arise when a long repetitive element is present between two HSPs. "NumtS on mitochondrion" Track The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the nuclear mapping is provided. "NumtS on mitochondrion with chromosome placement" Track The "NumtS on mitochondrion with chromosome placement" shows the mapping of the HSPs on the mitochondrial genome, but the items are coloured according to the colours assigned to each human chromosome on the UCSC genome browser. No shading is here provided. For every item, a link pointing to the nuclear mapping is provided. Methods NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome of of the Human Genome hg18 build and the human mitochondrial reference sequence (rCRS, AC: NC_012920), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with spreadsheet interpolation and manual inspection. Verification NumtS predicted in silico were validated by carrying out PCR amplification and sequencing on blood-extracted DNA of a healthy individual of European origin. PCR amplification was successful for 275 NumtS and provided amplicons of the expected length. All PCR fragments were sequenced on both strands, and submitted to the EMBL databank. Furthermore, 541 NumtS were validated by merging NumtS nuclear coordinates with HapMap annotations. Our analysis has been carried on eight HapMap individuals (NA18517, NA18507, NA18956, NA19240, NA18555, NA12878, NA19129, NA12156). For each sample, clones with a single best concordant placement (according to the fosmid end-sequence-pair analysis described in Kidd et al., 2008), have been considered. The analysis showed that 541 NumtS (at least 30bp for each one) had been sequenced in such samples. Credits These data were provided by Domenico Simone and Marcella Attimonelli at Department of Biochemistry and Molecular Biology "Ernesto Quagliariello" (University of Bari, Italy). Primer designing was carried out by Francesco Calabrese and Giuseppe Mineccia. PCR validation was carried out by Martin Lang, Domenico Simone and Giuseppe Gasparre. Merging with HapMap annotations has been performed by Domenico Simone. References Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 2008 May 1;453(7191):56-64. PMID: 18451855; PMC: PMC2424287 Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics. 2008 Jun 3;9:267. PMID: 18522722; PMC: PMC2447851 Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011 Oct 20;12:517. PMID: 22013967; PMC: PMC3228558 
knownGeneOld6 Old UCSC Genes Previous Version of UCSC Genes Genes and Gene Predictions Description The Old UCSC Genes track shows genes from the previous version of the UCSC Genes build. This is similar to the current version but without explicitly including Rfam or tRNA sequences. The new release has 82,960 total transcripts, compared with 80,922 in the previous version. The total number of canonical genes has increased from 31,227 to 31,848. Comparing the new gene set with the previous version: 74,657 transcripts did not change between versions. 88 transcripts were not carried forward to the new version. 5,556 transcripts are &quot;compatible&quot; with those in the previous set, meaning that the two transcripts show consistent splicing. In most cases, the old and new transcripts differ in the lengths of their UTRs. 621 transcripts overlap with those in the previous set but do not show consistent splicing, i.e., they contain overlapping introns with differing splice sites. Read the description of how the current version of the UCSC Genes track was built. 
oreganno ORegAnno Regulatory elements from ORegAnno Regulation Description This track displays literature-curated regulatory regions, transcription factor binding sites, and regulatory polymorphisms from ORegAnno (Open Regulatory Annotation). For more detailed information on a particular regulatory element, follow the link to ORegAnno from the details page. ORegAnno (Open Regulatory Annotation). --> Display Conventions and Configuration The display may be filtered to show only selected region types, such as: regulatory regions (shown in light blue) regulatory polymorphisms (shown in dark blue) transcription factor binding sites (shown in orange) regulatory haplotypes (shown in red) miRNA binding sites (shown in blue-green) To exclude a region type, uncheck the appropriate box in the list at the top of the Track Settings page. Methods An ORegAnno record describes an experimentally proven and published regulatory region (promoter, enhancer, etc.), transcription factor binding site, or regulatory polymorphism. Each annotation must have the following attributes: A stable ORegAnno identifier. A valid taxonomy ID from the NCBI taxonomy database. A valid PubMed reference. A target gene that is either user-defined, in Entrez Gene or in EnsEMBL. A sequence with at least 40 flanking bases (preferably more) to allow the site to be mapped to any release of an associated genome. At least one piece of specific experimental evidence, including the biological technique used to discover the regulatory sequence. (Currently only the evidence subtypes are supplied with the UCSC track.) A positive, neutral or negative outcome based on the experimental results from the primary reference. (Only records with a positive outcome are currently included in the UCSC track.) The following attributes are optionally included: A transcription factor that is either user-defined, in Entrez Gene or in EnsEMBL. A specific cell type for each piece of experimental evidence, using the eVOC cell type ontology. A specific dataset identifier (e.g. the REDfly dataset) that allows external curators to manage particular annotation sets using ORegAnno's curation tools. A &quot;search space&quot; sequence that specifies the region that was assayed, not just the regulatory sequence. A dbSNP identifier and type of variant (germline, somatic or artificial) for regulatory polymorphisms. Mapping to genome coordinates is performed periodically to current genome builds by BLAST sequence alignment. The information provided in this track represents an abbreviated summary of the details for each ORegAnno record. Please visit the official ORegAnno entry (by clicking on the ORegAnno link on the details page of a specific regulatory element) for complete details such as evidence descriptions, comments, validation score history, etc. Credits ORegAnno core team and principal contacts: Stephen Montgomery, Obi Griffith, and Steven Jones from Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada. The ORegAnno community (please see individual citations for various features): ORegAnno Citation. References Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL, Open Regulatory Annotation Consortium.. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 2016 Jan 4;44(D1):D126-32. PMID: 26578589; PMC: PMC4702855 Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. PMID: 18006570; PMC: PMC2239002 Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics. 2006 Mar 1;22(5):637-40. PMID: 16397004 
orfeomeMrna ORFeome Clones ORFeome Collaboration Gene Clones Genes and Gene Predictions Description This track show alignments of human clones from the ORFeome Collaboration. The goal of the project is to be an &quot;unrestricted source of fully sequence-validated full-ORF human cDNA clones in a format allowing easy transfer of the ORF sequences into virtually any type of expression vector. A major goal is to provide at least one fully-sequenced full-ORF clone for each human, mouse, and zebrafish gene. This track is updated automatically as new clones become available. Display Conventions and Configuration The track follows the display conventions for gene prediction tracks. Methods ORFeome human clones were obtained from GenBank and aligned against the genome using the blat program. When a single clone aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits and References Visit the ORFeome Collaboration members page for a list of credits and references. 
orphadata Orphanet Orphadata: Aggregated Data From Orphanet Phenotype and Literature Description NOTE: These data are for research purposes only. While the Orphadata data is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal medical questions. UCSC presents these data for use by qualified professionals, and even such professionals should use caution in interpreting the significance of information found here. No single data point should be taken at face value and such data should always be used in conjunction with as much corroborating data as possible. No treatment protocols should be developed or patient advice given on the basis of these data without careful consideration of all possible sources of information. No attempt to identify individual patients should be undertaken. No one is authorized to attempt to identify patients by any means. The Orphadata: Aggregated data from Orphanet (Orphanet) track shows genomic positions of genes and their association to human disorders, related epidemiological data, and phenotypic annotations. As a consortium of 40 countries throughout the world, Orphanet gathers and improves knowledge regarding rare diseases and maintains the Orphanet rare disease nomenclature (ORPHAcode), essential in improving the visibility of rare diseases in health and research information systems. The data is updated monthly by Orphanet and updated monthly on the UCSC Genome Browser. Display Conventions Mouseover on items shows the gene name, disorder name, modes of inheritance(s) (if available), and age(s) of onset (if available). Tracks can be filtered according to gene-disorder association types, modes of inheritance, and ages of onset. Clicking an item from the browser will return the complete entry, including gene linkouts to Ensembl, OMIM, and HGNC, as well as phenotype information using HPO (human phenotype ontology) terms. For more information on the use of this data, see the Orphadata FAQs. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Data is also freely available through Orphadata datasets. Methods Orphadata files were reformatted at UCSC to the bigBed format. Credits Thank you to the Orphanet and Orphadata team and to Tiana Pereira, Christopher Lee, Daniel Schmelter, and Anna Benet-Pages of the Genome Browser team. References Pavan S, Rommel K, Mateo Marquina ME, H&#246;hn S, Lanneau V, Rath A. Clinical Practice Guidelines for Rare Diseases: The Orphanet Database. PLoS One. 2017;12(1):e0170365. PMID: 28099516; PMC: PMC5242437 Nguengang Wakap S, Lambert DM, Olry A, Rodwell C, Gueydan C, Lanneau V, Murphy D, Le Cam Y, Rath A. Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database. Eur J Hum Genet. 2020 Feb;28(2):165-173. PMID: 31527858; PMC: PMC6974615 
xenoRefGene Other RefSeq Non-Human RefSeq Genes Genes and Gene Predictions Description This track shows known protein-coding and non-protein-coding genes for organisms other than human, taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark). The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely. Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box. Methods The RNAs were aligned against the human genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 25% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
panelApp PanelApp Genomics England PanelApp Diagnostics Phenotype and Literature Description The Genomics England PanelApp tracks show gene panels that are related to human disorders. Originally developed to aid interpretation of participant genomes in the 100,000 Genomes Project, PanelApp is now also being used as the platform for achieving consensus on gene panels in the NHS Genomic Medicine Service (GMS). As panels in PanelApp are publicly available, they can also be used by other groups and projects. Panels are maintained and updated by Genomics England curators. Genes and genomic entities (short tandem repeats/STRs and copy number variants/CNVs) have been reviewed by experts to enable a community consensus to be reached on which genes and genomic entities should appear on a diagnostics grade panel for each disorder. A rating system (confidence level 0 - 3) is used to classify the level of evidence supporting association with phenotypes covered by the gene panel in question. The available data tracks are: Genomics England PanelApp Genes (PanelApp Genes): shows genes with evidence supporting a gene-disease relationship. NOTE: Due to a bug in the PanelApp gene API, between 5 and 20% of gene entries are missing as of 11/2/22. Genomics England PanelApp STRs (PanelApp STRs): shows short tandem repeats that can be disease-causing when a particular number of repeats is present. Only on hg38: Genomics England PanelApp Regions (PanelApp CNV Regions): shows copy-number variants (region-loss and region-gain) with evidence supporting a gene-disease relationship. Display Conventions The individual tracks are colored by confidence level: Score 3 (lime green) - High level of evidence for this gene-disease association. Demonstrates confidence that this gene should be used for genome interpretation. Score 2 (amber) - Moderate evidence for this gene-disease association. This gene should not be used for genomic interpretation. Score 0 or 1 (red) - Not enough evidence for this gene-disease association. This gene should not be used for genomic interpretation. Mouseover on items shows the gene name, panel associated, mode of inheritance (if known), phenotypes related to the gene, and confidence level. Tracks can be filtered according to the confidence level of disease association evidence. For more information on the use of this data, see the PanelApp FAQs. Data Access The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API. For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called genes.bb, tandRep.bb and cnv.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/panelApp/genes.bb -chrom=chr21 -start=0 -end=100000000 stdout Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Data is also freely available on the PanelApp API. Updates and archiving of old releases This track is updated automatically every week. If you need to access older releases of the data, you can download them from our archive directory on the download server. To load them into the browser, select a week on the archive directory, copy the link to a file, go to My Data &gt; Custom Tracks, click "Add custom track", paste the link into the box and click "Submit". Methods PanelApp files were reformatted at UCSC to the bigBed format. The script that updates the track is called updatePanelApp and can be found in our Github repository. Credits Thank you to Genomics England PanelApp, especially Catherine Snow for technical coordination and consultation. Thank you to Beagan Nguy, Christopher Lee, Daniel Schmelter, Ana Benet-Pag&egrave;s and Maximilian Haeussler of the Genome Browser team for the creation of the tracks. Reference Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR, Gerasimenko O, Haraldsdottir E et al. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat Genet. 2019 Nov;51(11):1560-1565. PMID: 31676867 
panelAppTandRep PanelApp STRs Genomics England PanelApp Short Tandem Repeats Phenotype and Literature 
panelAppGenes PanelApp Genes Genomics England PanelApp Genes Phenotype and Literature 
peptideAtlas2014 PeptideAtlas Peptide sequences identified from MS spectra of 971 samples by PeptideAtlas Expression Description PeptideAtlas collects raw mass spectrometry proteomics datasets from laboratories around the world and reprocesses them in a uniform bioinformatics workflow using the Trans-Proteomic Pipeline . This track displays peptide identifications from the PeptideAtlas August 2014 (Build 433) Human build. This build, based on 971 samples containing 420,607,360 spectra, identified 1,021,823 distinct peptides, covering 15,136 canonical proteins. Each PeptideAtlas build comprises a set of reprocessed experiments from a single species or subset of samples (such has human plasma) from a species. Processed results are filtered to a quality level such that there is a 1% false discovery rate at the protein level. All peptide identifications of sufficient quality to enter a build are mapped to the Ensembl genome (v75) using the Ensembl toolkit. Genomic coordinates for all identified peptides to all their Ensembl protein, transcript, and gene mappings, including intron spans, as calculated by the Ensembl toolkit are stored in the PeptideAtlas database. All peptide sequences in the August 2014 human build (including unmapped sequences) are available for download in FASTA format. Methods Mass spectrometer spectra are compared to theoretical spectra (SEQUEST, X!Tandem) or actual spectra (SpectraST) to identify possible peptides. These peptide identifications are scored and filtered (using PeptideProphet) to retain only the highest scoring identifications. The filtered sequences are compared to protein sequence databases (for human, Ensembl, IPI, and Swiss-Prot). The CDS coordinates relative to protein start of matched sequences are used to then calculate genomic coordinates. The protein identifications are then clustered and annotated using ProteinProphet, and stored in the SBEAMS database, where they assigned a unique identifer of the form PAp[8 digit number], e.g. PAp00000001. The processing pipeline is summarized in the graphic below. --> Credits Eric Deutsch, Zhi Sun, and the PeptideAtlas team at the Institute for Systems Biology, Seattle. References Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D655-8. PMID: 16381952; PMC: PMC1347403 Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, Yamamoto T, Shteynberg D, Harris MM, Moritz RL. State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res. 2014 Jan 3;13(1):60-75. PMID: 24261998; PMC: PMC3951210 Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 2002 Oct 15;74(20):5383-92. PMID: 12403597 Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 2003 Sep 1;75(17):4646-58. PMID: 14632076 
ucscGenePfam Pfam in UCSC Gene Pfam Domains in UCSC Genes Genes and Gene Predictions Description Most proteins are composed of one or more conserved functional regions called domains. This track shows the high-quality, manually-curated Pfam-A domains found in transcripts located in the UCSC Genes track by the software HMMER3. Display Conventions and Configuration This track follows the display conventions for gene tracks. Methods The sequences from the knownGenePep table (see UCSC Genes description page) are submitted to the set of Pfam-A HMMs which annotate regions within the predicted peptide that are recognizable as Pfam protein domains. These regions are then mapped to the transcripts themselves using the pslMap utility. A complete shell script log for every version of UCSC genes can be found in our GitHub repository under hg/makeDb/doc/ucscGenes, e.g. mm10.knownGenes17.csh is for the database mm10 and version 17 of UCSC known genes. Of the several options for filtering out false positives, the &quot;Trusted cutoff (TC)&quot; threshold method is used in this track to determine significance. For more information regarding thresholds and scores, see the HMMER documentation and results interpretation pages. Note: There is currently an undocumented but known HMMER problem which results in lessened sensitivity and possible missed searches for some zinc finger domains. Until a fix is released for HMMER /PFAM thresholds, please also consult the "UniProt Domains" subtrack of the UniProt track for more comprehensive zinc finger annotations. Credits pslMap was written by Mark Diekhans at UCSC. References Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K et al. The Pfam protein families database. Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. PMID: 19920124; PMC: PMC2808889 
platinumGenomes Platinum Genomes Platinum genome variants Variation Description These tracks show high-confidence &quot;Platinum Genome&quot; variant calls for two individuals, NA12877 and NA12878, part of a sequenced 17 member pedigree for family number 1463, from the Centre d'Etude du Polymorphisme Humain (CEPH). The hybrid track displays a merging of the NA12878 results with variant calls produced by Genome in a Bottle, discussed further below. CEPH is an international genetic research center that provides a resource of immortalized cell cultures used to map genetic markers, and pedigree 1463 represents a family lineage from Utah of four grandparents, two parents, and 11 children. The whole pedigree was sequenced to 50x depth on a HiSeq 2000 Illumina system, which is considered a platinum standard, where platinum refers to the quality and completeness of the resulting assembly, such as providing full chromosome scaffolds with phasing and haplotypes resolved across the entire genome. This figure depicts the pedigree of the family sequenced for this study, where the ID for each sample is defined by adding the prefix NA128 to each numbered individual, so that 77 = NA12877 and 78 = NA12878, corresponding to the VCF tracks available in this track set. The dark orange individuals indicate sequences used in the analysis methods, whereas the blue represent the founder generations (grandparents), which were also sequenced and used in validation steps. The genomes of the parent-child trio on the top right side, 91-92-78, were also sequenced during Phase I of the 1000 Genomes Project. These tracks represent a comprehensive genome-wide set of phased small variants that have been validated to high confidence. Sequencing and phasing a larger pedigree, beyond the two parents and one child, increases the ability to detect errors and assess the accuracy of more of the variants compared to a standard trio analysis. The genetic inheritance data enables creating a more comprehensive catalog of &quot;platinum variants&quot; that reflects both high accuracy and completeness. These results are significant as a comprehensive set of valid single-nucleotide variants (SNVs) and insertions and deletions (indels), in both the easy and difficult parts of the genome, provides a vital resource for software developers creating the next generation of variant callers, because these are the areas where the current methods most need training data to improve their methods. Since every one of the variants in this catalog is phased, this data set provides a resource to better assess emerging technologies designed to generate valid phasing information. To generate the calls, six analysis pipelines to call SNVs and indels were used and merged into one catalog, where the sensitivity of the genetic inheritance aided to detect genotyping errors and maximize the chance of only including true variants, that might otherwise be removed by suboptimal filtering. Read more about the detailed methods in the referenced paper, further describing this variant catalog of 4.7 million SNVs plus 0.7 million small (1-50 bp) indels, that are all consistent with the pattern of inheritance in the parents and 11 children of this pedigree. The hybrid track in this set extends the characterization of NA12878 by incorporating high confidence calls produced by Genome in a Bottle analysis. The resulting merged files contain more comprehensive coverage of variation than either set independently, for instance, the hg19 version contains over 80,000 more indels than either input set. Read more about the hybrid methods at the following link: https://github.com/Illumina/PlatinumGenomes/wiki/Hybrid-truthset Data Access The VCF files for this track can be obtained from the download server: https://hgdownload.soe.ucsc.edu/gbdb/hg19/platinumGenomes/. These files were obtained from the Platinum genomes source archive: https://s3.eu-central-1.amazonaws.com/platinum-genomes/2017-1.0/ReleaseNotes.txt. Reference Eberle MA, Fritzilas E, Krusche P, K&#228;llberg M, Moore BL, Bekritsky MA, Iqbal Z, Chuang HY, Humphray SJ, Halpern AL et al. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Res. 2017 Jan;27(1):157-164. PMID: 27903644; PMC: PMC5204340 
platinumNA12878 NA12878 Platinum genome variant NA12878 Variation 
platinumNA12877 NA12877 Platinum genome variant NA12877 Variation 
platinumHybrid hybrid Platinum genome hybrid Variation 
problematic Problematic Regions Problematic Regions for NGS or Sanger sequencing or very variable regions Mapping and Sequencing Description This track helps call out sections of the genome that often cause problems for bioinformaticians. The 12 subtracks identify genomic regions known to cause analysis artifacts for common sequencing downstream computations, such as alignment, variant calling, or peak calling. The underlying data was imported from the NCBI GeT-RM, the Genome-in-a-Bottle, and Anshul Kundaje's ENCODE Blacklist projects. The only exception is the UCSC Unusual Regions subtrack, which contains annotations of a few special gene clusters (IGH, IGL, PAR1/2, TCRA, TCRB, etc) and fixed sequences, alternate haplotypes, unplaced contigs, pseudo-autosomal regions, and mitochondria. These loci can yield alignments with low-quality mapping scores and discordant read pairs. This data set was manually curated, based on the Genome Browser's assembly description, the FAQs about assembly, and the NCBI RefSeq "other" annotations track data. The ENCODE Blacklist subtrack contains a comprehensive set of regions which are troublesome for high-throughput Next-Generation Sequencing (NGS) aligners. These regions tend to have a very high ratio of multi-mapping to unique mapping reads and high variance in mappability due to repetitive elements such as satellite, centromeric and telomeric repeats. The Genome-In-A-Bottle (GIAB) track set contains defined regions where it is difficult to make a confident call, due to low coverage, systematic sequencing errors, and local alignment problems. These regions were identified from sequencing data generated by multiple technologies. The NCBI GeT-RM, Genetic Testing Reference Materials, track set contains highly homologous gene- and exon-level regions difficult or impossible to analyze with standard Sanger or short-read NGS approaches and are relevant to current clinical testing. Display Conventions and Configuration Each track contains a set of regions of varying length with no special configuration options. The UCSC Unusual Regions track has a mouse-over description, all other tracks have at most a name field, which can be shown in pack mode. The tracks are usually kept in dense mode. The Hide empty subtracks control hides subtracks with no data in the browser window. Changing the browser window by zooming or scrolling may result in the display of a different selection of tracks. Data access The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored in bigBed files that can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/problematic/deadZone.bb -chrom=chr21 -start=0 -end=100000000 stdout Methods Files were downloaded from the respective databases and converted to bigBed format. The procedure is documented in our hg19 makeDoc file (search problematic). Credits Thanks to Anna Benet-Pages, Max Haeussler, Angie Hinrichs, and Daniel Schmelter at the UCSC Genome Browser for planning, building, and testing these tracks. The underlying data comes from the ENCODE Blacklist, the GeT-RM, and the Genome-in-a-Bottle projects. References Amemiya HM, Kundaje A, Boyle AP. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Sci Rep. 2019 Jun 27;9(1):9354. PMID: 31249361; PMC: PMC6597582 Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, Salit M. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014 Mar;32(3):246-51. PMID: 24531798 Mandelker D, Schmidt RJ, Ankala A, McDonald Gibson K, Bowser M, Sharma H, Duffy E, Hegde M, Santani A, Lebo M et al. Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next- generation sequencing. Genet Med. 2016 Dec;18(12):1282-1289. PMID: 27228465 
filterConflicting GIAB genotype conflict NIST Genome-in-a-bottle: calls with unresolved conflicting genotypes after arbitration Mapping and Sequencing 
filterAlign GIAB align problem NIST Genome-in-a-bottle: calls with evidence of local alignment problems like clipped reads Mapping and Sequencing 
filterABQD GIAB allele imbalance NIST Genome-in-a-bottle: calls with abnormal allele balance Mapping and Sequencing 
filterMap GIAB quality issue NIST Genome-in-a-bottle: calls with low mapping quality or high coverage Mapping and Sequencing 
filterHapNoVar GIAB call conflict NIST Genome-in-a-bottle: HaplotypeCaller makes no call and UnifiedGenotyper makes a variant call Mapping and Sequencing 
filterSSE GIAB filter SSE NIST Genome-in-a-bottle: calls with evidence of systematic sequencing errors Mapping and Sequencing 
getRmNgsProblemHigh NCBI NGS High Stringency NCBI GeT-RM NGS Problem List, High Stringency Mapping and Sequencing 
getRmNgsProblemLow NCBI NGS Low Stringency NCBI GeT-RM NGS Problem List, Low Stringency Mapping and Sequencing 
getRmSangerDeadZone NCBI Sanger Dead Zone NCBI GeT-RM Sanger Dead Zone Mapping and Sequencing 
getRmNgsDeadZone NCBI NGS Dead Zone NCBI GeT-RM NGS Dead Zone Mapping and Sequencing 
encBlacklist ENCODE Blacklist V2 ENCODE Blacklist V2 Mapping and Sequencing 
comments UCSC Unusual Regions UCSC unusual regions on assembly structure (manually annotated) Mapping and Sequencing 
prsEmerge PRS eMERGE Polygenic Risk Scores from NHGRI Electronic Medical Records and Genomics (eMERGE) project Phenotype and Literature Description The Polygenic Risk Scores eMERGE track shows variants that are part of selected polygenic risk scores for ten common diseases. Polygenic risk scores (PRS) have clinical utility and are the result of many years of GWAS studies. A score is given for a combination of SNPs to calculate the risk of getting a disease in a healthy population. The risk scores were selected by the NHGRI eMERGE project, and the selection process is described in Lennon et al. 2023. Many PRS models were evaluated, and the 9 models shown here were selected based on quality and are part of this track: Asthma Atrial Fibrillation Breast Cancer Coronary Heart Disease Chronic Kidney Disease Hypercholesterolemia Prostate Cancer T1 Diabetes T2 Diabetes The BMI (body mass index) model cannot currently be shown on the browser, pending publication. Methods Text files provided by eMerge were converted to bigBed format. The scripts are available in our GitHub repo. Data access The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can be accessed from scripts through our API, the track name is &quot;prsEmerge&quot;. For automated download and analysis, the genome annotations are stored in files that can be obtained from our download server. The data is stored in our bigBed format. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can be used to obtain all features or only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/prsEmerge/t2d.bb -chrom=chr21 -start=0 -end=100000000 stdout Credits Thanks to Elisabeth McNally for advice, to Zia Truong for building this track and to Niall Lennon for sharing the data with us. References Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn N, Arias J, Belbin G, Below JE, Berndt S, Chung W, Cimino JJ et al. Selection, optimization, and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse populations. medRxiv. 2023 Jun 5;. PMID: 37333246; PMC: PMC10275001 
prs Polygenic Risk Scores Polygenic Risk Scores Phenotype and Literature Description The Polygenic Risk Scores eMERGE track shows variants that are part of selected polygenic risk scores for ten common diseases. Polygenic risk scores (PRS) have clinical utility and are the result of many years of GWAS studies. A score is given for a combination of SNPs to calculate the risk of getting a disease in a healthy population. The risk scores were selected by the NHGRI eMERGE project, and the selection process is described in Lennon et al. 2023. Many PRS models were evaluated, and the 9 models shown here were selected based on quality and are part of this track: Asthma Atrial Fibrillation Breast Cancer Coronary Heart Disease Chronic Kidney Disease Hypercholesterolemia Prostate Cancer T1 Diabetes T2 Diabetes The BMI (body mass index) model cannot currently be shown on the browser, pending publication. Methods Text files provided by eMerge were converted to bigBed format. The scripts are available in our GitHub repo. Data access The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can be accessed from scripts through our API, the track name is &quot;prsEmerge&quot;. For automated download and analysis, the genome annotations are stored in files that can be obtained from our download server. The data is stored in our bigBed format. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can be used to obtain all features or only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/prsEmerge/t2d.bb -chrom=chr21 -start=0 -end=100000000 stdout Credits Thanks to Elisabeth McNally for advice, to Zia Truong for building this track and to Niall Lennon for sharing the data with us. References Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn N, Arias J, Belbin G, Below JE, Berndt S, Chung W, Cimino JJ et al. Selection, optimization, and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse populations. medRxiv. 2023 Jun 5;. PMID: 37333246; PMC: PMC10275001 
prsT2Diabetes PRS-E T2 Diabetes Polygenic Risk Scores eMERGE: T2 Diabetes Phenotype and Literature 
prsT1Diabetes PRS-E T1 Diabetes Polygenic Risk Scores eMERGE: T1 Diabetes Phenotype and Literature 
prsProstateCancer PRS-E Prost. Cancer Polygenic Risk Scores eMERGE: Prostate Cancer Phenotype and Literature 
prsHypercholest PRS-E Hypercholest. Polygenic Risk Scores eMERGE: Hypercholesterolemia Phenotype and Literature 
prsCorHeartDis PRS-E Cor Heart Dis Polygenic Risk Scores eMERGE: Coronary Heart Disease Phenotype and Literature 
prsChKidneyDis PRS-E Ch Kidney Dis Polygenic Risk Scores eMERGE: Chronic Kidney Disease Phenotype and Literature 
prsBrCancer PRS-E Breast Cancer Polygenic Risk Scores eMERGE: Breast Cancer Phenotype and Literature 
prsAtrialFib PRS-E Atrial Fib Polygenic Risk Scores eMERGE: Atrial Fibrillation Phenotype and Literature 
prsEmergeAsthma PRS-E Asthma Polygenic Risk Scores eMERGE: Asthma Phenotype and Literature 
qPcrPrimers qPCR Primers Human (hg19) Whole Transcriptome qPCR Primers Expression Description This track provides automatically-designed RT-qPCR primers for measuring the abundance of human and mouse transcripts using SYBR-based qPCR (qPCR with double-stranded DNA-binding reporter dye). The primers were generated by a procedure that targets all transcripts and all &quot;possible&quot; exon-exon and intron-exon junctions in the human and mouse transcriptomes. Not all consecutive exon-intron-exon triplets generate &quot;possible&quot; primer pairs. &quot;Possible&quot; primer pairs are defined as satisfying a set of imposed design rules: The first exon-exon junction is not addressed, to avoid problems related to abortive transcription. Intron length should be more than 800 bp to avoid problems of double products in amplification. Only junction primers are designed: forward and reverse primers must flank the junction. Melting temperature of the primers should be between 60&deg;C and 63&deg;C (optimally 60.5&deg;C, according to Breslauer et al., 1986). Primer length should be 18-25 bp. Product size should be 60-125 bp. Primers are designed first for the intron-exon (pre-mRNA) junctions, and the two best primer pairs for each junction are chosen. Then, for the reverse primer of each pair, two options are designed for the corresponding forward primer of the exon-exon (mRNA) junction. The &quot;Primer Mispriming Library&quot; of the primer3 software is used: &quot;human&quot; for the human transcriptome and &quot;rodent&quot; for the mouse transcriptome. The track provides easy access to primers for almost all transcripts in the transcriptome, eliminating the need for a tedious, error-prone design process. Methods The UCSC Genes model was used as a reference of the gene structure and the primer3 software as the design engine. The software goes over all possible exon-exon junctions in the transcriptome and applies our design rules/parameters to provide two primer pairs for every &quot;possible&quot; intron-exon junction and four pairs for every &quot;possible&quot; exon-exon junction. Display Conventions The primers to amplify pre-mRNA (intron-exon junctions) are shown in red and the primers to amplify mRNA (exon-exon junctions) in blue. For each pre-mRNA primer pair, there are two corresponding mRNA primers (that use the same reverse primer, if possible). Each pair has a unique code which stands for the gene name and the junction name. For example, the human pair &quot;JAG1_uc002wnw.2_11_1&quot; amplifies pre-mRNA, and the corresponding mRNA primers are &quot;JAG1_uc002wnw.2_11_1_1&quot; and &quot;JAG1_uc002wnw.2_11_1_2.&quot; Using JAG1_uc002wnw.2_11_1_2 to illustrate the naming scheme: JAG1 is the gene symbol. uc002wnw.2 is the UCSC Genes identifier of the isoform. 11 identifies the exon-intron-exon triplet. 1 is the number (1 or 2) of the intron-exon junction (step 7 in the Description section above). The names of primer pairs that cover intron-exon junctions end here. For the exon-exon junctions that use the same reverse primer, there is one additional number. 2 is the number (1 or 2) of the exon-exon junction pair (step 8 in the Description section above). Clicking on a primer pair will take you to a new page with details for that pair. Additional properties for the primer pair, including forward and reverse sequence, melting temperature, GC%, and product size, are available by clicking on the number next to the instruction &quot;Click here for primer details.&quot; There is also a batch query website available to download details for a large number of primers. References Breslauer KJ, Frank R, Bl&#246;cker H, Marky LA. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746-50. PMID: 3459152; PMC: PMC323600 Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000;132:365-86. PMID: 10547847 Zeisel A, Yitzhaky A, Bossel Ben-Moshe N, Domany E. An accessible database for mouse and human whole transcriptome qPCR primers. Bioinformatics. 2013 May 15;29(10):1355-6. PMID: 23539303 
rao2014Hic Rao 2014 Hi-C Hi-C on 7 cell lines from Rao 2014 Regulation Description These tracks provide heatmaps of chromatin folding data from in situ Hi-C experiments on the seven cell lines (Rao et al., 2014). Two other cell lines were also part of this project, but are not included in this track: CH12-LX (mouse B-lymphoblasts) and HeLa (the Henrietta Lacks tumor cell line). Below are the seven types of cells sequenced with a short description: GM12878 B-Lymphocyte Cells HMEC Mammary Epithelial Cells HUVEC Umbilical Endothelial Cells IMR90 Fetal Lung Cells K562 Immortalised Leukemia Cells KBM7 Immortalised Leukemia Cells NHEK Epidermal Keratinocyte Cells The data indicate how many interactions were detected between regions of the genome. A high score between two regions suggests that they are probably in close proximity in 3D space within the nucleus of a cell. In the track display, this is shown by a more intense color in the heatmap. Display Conventions This is a composite track with data from seven cell lines. Individual subtrack settings can be adjusted by clicking the wrench next to the subtrack name, and all subtracks can be configured simultaneously using the track controls at the top of the page. Note that some controls (specifically, resolution and normalization options) are only available in the subtrack-specific configuration. The proximity data in these tracks are displayed as heatmaps, with high scores (and more intense colors) corresponding to closer proximity. Draw modes There are three display methods available for Hi-C heatmaps: square, triangle, and arc. Square mode provides a traditional Hi-C display in which chromosome positions are mapped along the top-left-to-bottom-right diagonal, and interaction values are plotted on both sides of that diagonal to form a square. The upper-left corner of the square corresponds to the left-most position of the window in view, while the bottom-right corner corresponds to the right-most position of the window. The color shade at any point within the square shows the proximity score for two genomic regions: the region where a vertical line drawn from that point intersects with the diagonal, and the region where a horizontal line from that point intersects with the diagonal. A point directly on the diagonal shows the score for how proximal a region is to itself (scores on the diagonal are usually quite high unless no data are available). A point at the extreme bottom left of the square shows the score for how proximal the left-most position within the window is to the right-most position within the window. In triangle mode, the display is quite similar to square except that only the top half of the square is drawn (eliminating the redundancy), and the image is rotated so that the diagonal of the square now lies on the horizontal axis. This display consumes less vertical space in the image, although it may be more difficult to ascertain exactly which positions correspond to a point within the triangle. In arc mode, simple arcs are drawn between the centers of interacting regions. The color of each arc corresponds to the proximity score. Self-interactions are not displayed. Score normalization settings Score values for this type of display correspond to how close two genomic regions are in 3D space. A high score indicates more links were formed between them in the experiment, which suggests that the regions are near to each other. A low score suggests that the regions are farther apart. High scores are displayed with a more intense color value; low scores are displayed in paler shades. There are four score values available in this display: NONE, VC, VC_SQRT, and KR. NONE provides raw, un-normalized counts for the number of interactions between regions. VC, or Vanilla Coverage, normalization (Lieberman-Aiden et al., 2009) and the VC_SQRT variant normalize these count values based on the overall count values for each of the two interacting regions. Knight-Ruiz, or KR, matrix balancing (Knight and Ruiz, 2013) provides an alternative normalization method where the row and column sums of the contact matrix equal 1. Color intensity in the heatmap goes up to indicate higher scores, but eventually saturates at a maximum beyond which all scores share the same color intensity. The value of this maximum score for saturation can be set manually by un-checking the &quot;Auto-scale&quot; box. When the &quot;Auto-scale&quot; box is checked, it automatically sets the saturation maximum to be double (2x) the median score in the current display window. Resolution settings The resolution for each track is measured in base pairs and represents the size of the bins into which proximity data are gathered. The list of available resolutions ranges from 1kb to 10Mb. There is also an &quot;Auto&quot; setting, which attempts to use the coarsest resolution that still displays at least 500 bins in the current window. Methods The protocol described in this paper, in situ Hi-C, is a refinement of an earlier method originally called Hi-C and now referred to as dilution Hi-C. Both methods involve cross-linking DNA with formaldehyde, cleaving it with a restriction enzyme, forming local bonds between the cleaved DNA ends, and sequencing the resulting junctions. The primary refinement for in situ Hi-C is that it keeps cell nuclei intact during cross-linking, which reduces the number of spurious contacts in the resulting contact matrix. The protocol also takes less time (3 days instead of 7) and can make use of higher-resolution restriction enzymes. The cell lines in this paper were processed using the in situ Hi-C protocol to produce contact matrices in the .hic format. We downloaded a subset of those files from the GEO repository at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525. The files used for this track are the &quot;combined.hic&quot; files, which combine the results from multiple experimental replicates without imposing a cutoff on the data values. The files are parsed for display using the Straw library from the Aiden lab at Baylor College of Medicine. Data Access The data for this track can be explored interactively with the Table Browser in the interact format. Direct access to the raw data files in .hic format can be obtained from GEO at the URL provided in the Methods section or from our own download server. The following files for this track can be found in the /gbdb/hg19/hic/ subdirectory: GSE63525_GM12878_insitu_primary+replicate_combined.hic, GSE63525_HUVEC_combined.hic, GSE63525_K562_combined.hic, GSE63525_NHEK_combined.hic, GSE63525_HMEC_combined.hic, GSE63525_IMR90_combined.hic, and GSE63525_KBM7_combined.hic. Details on working with .hic files can be found at https://www.aidenlab.org/documentation.html. References Knight P, Ruiz D. A fast algorithm for matrix balancing. IMA J Numer Anal. 2013 Jul;33(3):1029-1047. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 9;326(5950):289-93. PMID: 19815776; PMC: PMC2858594 Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014 Dec 18;159(7):1665-80. PMID: 25497547; PMC: PMC5635824 
nhekInsitu NHEK Hi-C In situ Hi-C Chromatin Structure on NHEK Regulation 
kbm7Insitu KBM7 Hi-C In situ Hi-C Chromatin Structure on KBM7 Regulation 
k562Insitu K562 Hi-C In situ Hi-C Chromatin Structure on K562 Regulation 
imr90Insitu IMR90 Hi-C In situ Hi-C Chromatin Structure on IMR90 Regulation 
huvecInsitu HUVEC Hi-C In situ Hi-C Chromatin Structure on HUVEC Regulation 
hmecInsitu HMEC Hi-C In situ Hi-C Chromatin Structure on HMEC Regulation 
gm12878Insitu GM12878 Hi-C In situ Hi-C Chromatin Structure on GM12878 Regulation 
recombRate Recomb Rate Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default) Mapping and Sequencing Description The recombination rate track represents calculated sex-averaged rates of recombination based on either the deCODE, Marshfield, or Genethon genetic maps. By default, the deCODE map rates are displayed. Female- and male-specific recombination rates, as well as rates from the Marshfield and Genethon maps, can also be displayed by choosing the appropriate filter option on the track description page. Methods The deCODE genetic map was created at deCODE Genetics and is based on 5,136 microsatellite markers for 146 families with a total of 1,257 meiotic events. For more information on this map, see Kong, et al., 2002. The Marshfield genetic map was created at the Center for Medical Genetics and is based on 8,325 short tandem repeat polymorphisms (STRPs) for 8 CEPH families consisting of 134 individuals with 186 meioses. For more information on this map, see Broman et al., 1998. The Genethon genetic map was created at Genethon and is based on 5,264 microsatellites for 8 CEPH families consisting of 134 individuals with 186 meioses. For more information on this map, see Dib et al., 1996. Each base is assigned the recombination rate calculated by assuming a linear genetic distance across the immediately flanking genetic markers. The recombination rate assigned to each 1 Mb window is the average recombination rate of the bases contained within the window. Using the Filter This track has a filter that can be used to change the map or gender-specific rate displayed. The filter is located at the top of the track description page, which is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu. To view a particular map or gender-specific rate, select the corresponding option from the &quot;Map Distances&quot; pulldown list. By default, the browser displays the deCODE sex-averaged distances. When you have finished configuring the filter, click the Submit button. Credits This track was produced at UCSC using data that are freely available for the Genethon, Marshfield, and deCODE genetic maps (see above links). Thanks to all who played a part in the creation of these maps. References Broman KW, Murray JC, Sheffield VC, White RL, Weber JL. Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am J Hum Genet. 1998 Sep;63(3):861-9. PMID: 9718341; PMC: PMC1377399 Dib C, Faur&#233; S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E et al. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. 1996 Mar 14;380(6570):152-4. PMID: 8600387 Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G et al. A high-resolution recombination map of the human genome. Nat Genet. 2002 Jul;31(3):241-7. PMID: 12053178 
ucscToRefSeq RefSeq Acc RefSeq Accession Mapping and Sequencing Description This track associates UCSC Genome Browser chromosome names to accession identifiers from the NCBI Reference Sequence Database (RefSeq). The data were downloaded from the NCBI assembly database. Credits The data for this track was prepared by Hiram Clawson. 
ReMap ReMap ChIP-seq ReMap Atlas of Regulatory Regions Regulation Description This track represents the ReMap Atlas of regulatory regions, which consists of a large-scale integrative analysis of all Public ChIP-seq data for transcriptional regulators from GEO, ArrayExpress, and ENCODE. Below is a schematic diagram of the types of regulatory regions: ReMap 2022 Atlas (all peaks for each analyzed data set) ReMap 2022 Non-redundant peaks (merged similar target) ReMap 2022 Cis Regulatory Modules Display Conventions and Configuration Each transcription factor follows a specific RGB color. ChIP-seq peak summits are represented by vertical bars. Hsap: A data set is defined as a ChIP/Exo-seq experiment in a given GEO/ArrayExpress/ENCODE series (e.g. GSE41561), for a given TF (e.g. ESR1), in a particular biological condition (e.g. MCF-7). Data sets are labeled with the concatenation of these three pieces of information (e.g. GSE41561.ESR1.MCF-7). Atha: The data set is defined as a ChIP-seq experiment in a given series (e.g. GSE94486), for a given target (e.g. ARR1), in a particular biological condition (i.e. ecotype, tissue type, experimental conditions; e.g. Col-0_seedling_3d-6BA-4h). Data sets are labeled with the concatenation of these three pieces of information (e.g. GSE94486.ARR1.Col-0_seedling_3d-6BA-4h). Methods This 4th release of ReMap (2022) presents the analysis of a total of 8,103 quality controlled ChIP-seq (n=7,895) and ChIP-exo (n=208) data sets from public sources (GEO, ArrayExpress, ENCODE). The ChIP-seq/exo data sets have been mapped to the GRCh38/hg38 human assembly. The data set is defined as a ChIP-seq experiment in a given series (e.g. GSE46237), for a given TF (e.g. NR2C2), in a particular biological condition (i.e. cell line, tissue type, disease state, or experimental conditions; e.g. HELA). Data sets were labeled by concatenating these three pieces of information, such as GSE46237.NR2C2.HELA. Those merged analyses cover a total of 1,211 DNA-binding proteins (transcriptional regulators) such as a variety of transcription factors (TFs), transcription co-activators (TCFs), and chromatin-remodeling factors (CRFs) for 182 million peaks. GEO & ArrayExpress Public ChIP-seq data sets were extracted from Gene Expression Omnibus (GEO) and ArrayExpress (AE) databases. For GEO, the query &apos;(&apos;chip seq&apos; OR &apos;chipseq&apos; OR &apos;chip sequencing&apos;) AND &apos;Genome binding/occupancy profiling by high throughput sequencing&apos; AND &apos;homo sapiens&apos;[organism] AND NOT &apos;ENCODE&apos;[project]&apos; was used to return a list of all potential data sets to analyze, which were then manually assessed for further analyses. Data sets involving polymerases (i.e. Pol2 and Pol3), and some mutated or fused TFs (e.g. KAP1 N/C terminal mutation, GSE27929) were excluded. ENCODE Available ENCODE ChIP-seq data sets for transcriptional regulators from the ENCODE portal were processed with the standardized ReMap pipeline. The list of ENCODE data was retrieved as FASTQ files from the ENCODE portal using the following filters: Assay: &quot;ChIP-seq&quot; Organism: &quot;Homo sapiens&quot; Target of assay: &quot;transcription factor&quot; Available data: &quot;fastq&quot; on 2016 June 21st Metadata information in JSON format and FASTQ files were retrieved using the Python requests module. ChIP-seq processing Both Public and ENCODE data were processed similarly. Bowtie 2 (PMC3322381) (version 2.2.9) with options -end-to-end -sensitive was used to align all reads on the genome. Biological and technical replicates for each unique combination of GSE/TF/Cell type or Biological condition were used for peak calling. TFBS were identified using MACS2 peak-calling tool (PMC3120977) (version 2.1.1.2) in order to follow ENCODE ChIP-seq guidelines, with stringent thresholds (MACS2 default thresholds, p-value: 1e-5). An input data set was used when available. Quality assessment To assess the quality of public data sets, a score was computed based on the cross-correlation and the FRiP (fraction of reads in peaks) metrics developed by the ENCODE Consortium (https://genome.ucsc.edu/ENCODE/qualityMetrics.html). Two thresholds were defined for each of the two cross-correlation ratios (NSC, normalized strand coefficient: 1.05 and 1.10; RSC, relative strand coefficient: 0.8 and 1.0). Detailed descriptions of the ENCODE quality coefficients can be found at https://genome.ucsc.edu/ENCODE/qualityMetrics.html. The phantompeak tools suite was used (https://code.google.com/p/phantompeakqualtools/) to compute RSC and NSC. Please refer to the ReMap 2022, 2020, and 2018 publications for more details (citation below). This is a detailled view of the data increase in ReMap v2 with FOXA1 peaks at a specific location. --> Data Access ReMap Atlas of regulatory regions data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. Individual BED files for specific TFs, cells/biotypes, or data sets can be found and downloaded on the ReMap website. References Ch&#232;neby J, Gheorghe M, Artufel M, Mathelier A, Ballester B. ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP- seq experiments. Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275. PMID: 29126285; PMC: PMC5753247 Ch&#232;neby J, M&#233;n&#233;trier Z, Mestdagh M, Rosnet T, Douida A, Rhalloussi W, Bergon A, Lopez F, Ballester B. ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments. Nucleic Acids Res. 2020 Jan 8;48(D1):D180-D188. PMID: 31665499; PMC: PMC7145625 Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B. Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res. 2015 Feb 27;43(4):e27. PMID: 25477382; PMC: PMC4344487 Hammal F, de Langen P, Bergon A, Lopez F, Ballester B. ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. Nucleic Acids Res. 2022 Jan 7;50(D1):D316-D325. PMID: 34751401; PMC: PMC8728178 
ReMapTFs ReMap ChIP-seq ReMap Atlas of Regulatory Regions Regulation Description This track represents the ReMap Atlas of regulatory regions, which consists of a large-scale integrative analysis of all Public ChIP-seq data for transcriptional regulators from GEO, ArrayExpress, and ENCODE. Below is a schematic diagram of the types of regulatory regions: ReMap 2022 Atlas (all peaks for each analyzed data set) ReMap 2022 Non-redundant peaks (merged similar target) ReMap 2022 Cis Regulatory Modules Display Conventions and Configuration Each transcription factor follows a specific RGB color. ChIP-seq peak summits are represented by vertical bars. Hsap: A data set is defined as a ChIP/Exo-seq experiment in a given GEO/ArrayExpress/ENCODE series (e.g. GSE41561), for a given TF (e.g. ESR1), in a particular biological condition (e.g. MCF-7). Data sets are labeled with the concatenation of these three pieces of information (e.g. GSE41561.ESR1.MCF-7). Atha: The data set is defined as a ChIP-seq experiment in a given series (e.g. GSE94486), for a given target (e.g. ARR1), in a particular biological condition (i.e. ecotype, tissue type, experimental conditions; e.g. Col-0_seedling_3d-6BA-4h). Data sets are labeled with the concatenation of these three pieces of information (e.g. GSE94486.ARR1.Col-0_seedling_3d-6BA-4h). Methods This 4th release of ReMap (2022) presents the analysis of a total of 8,103 quality controlled ChIP-seq (n=7,895) and ChIP-exo (n=208) data sets from public sources (GEO, ArrayExpress, ENCODE). The ChIP-seq/exo data sets have been mapped to the GRCh38/hg38 human assembly. The data set is defined as a ChIP-seq experiment in a given series (e.g. GSE46237), for a given TF (e.g. NR2C2), in a particular biological condition (i.e. cell line, tissue type, disease state, or experimental conditions; e.g. HELA). Data sets were labeled by concatenating these three pieces of information, such as GSE46237.NR2C2.HELA. Those merged analyses cover a total of 1,211 DNA-binding proteins (transcriptional regulators) such as a variety of transcription factors (TFs), transcription co-activators (TCFs), and chromatin-remodeling factors (CRFs) for 182 million peaks. GEO & ArrayExpress Public ChIP-seq data sets were extracted from Gene Expression Omnibus (GEO) and ArrayExpress (AE) databases. For GEO, the query &apos;(&apos;chip seq&apos; OR &apos;chipseq&apos; OR &apos;chip sequencing&apos;) AND &apos;Genome binding/occupancy profiling by high throughput sequencing&apos; AND &apos;homo sapiens&apos;[organism] AND NOT &apos;ENCODE&apos;[project]&apos; was used to return a list of all potential data sets to analyze, which were then manually assessed for further analyses. Data sets involving polymerases (i.e. Pol2 and Pol3), and some mutated or fused TFs (e.g. KAP1 N/C terminal mutation, GSE27929) were excluded. ENCODE Available ENCODE ChIP-seq data sets for transcriptional regulators from the ENCODE portal were processed with the standardized ReMap pipeline. The list of ENCODE data was retrieved as FASTQ files from the ENCODE portal using the following filters: Assay: &quot;ChIP-seq&quot; Organism: &quot;Homo sapiens&quot; Target of assay: &quot;transcription factor&quot; Available data: &quot;fastq&quot; on 2016 June 21st Metadata information in JSON format and FASTQ files were retrieved using the Python requests module. ChIP-seq processing Both Public and ENCODE data were processed similarly. Bowtie 2 (PMC3322381) (version 2.2.9) with options -end-to-end -sensitive was used to align all reads on the genome. Biological and technical replicates for each unique combination of GSE/TF/Cell type or Biological condition were used for peak calling. TFBS were identified using MACS2 peak-calling tool (PMC3120977) (version 2.1.1.2) in order to follow ENCODE ChIP-seq guidelines, with stringent thresholds (MACS2 default thresholds, p-value: 1e-5). An input data set was used when available. Quality assessment To assess the quality of public data sets, a score was computed based on the cross-correlation and the FRiP (fraction of reads in peaks) metrics developed by the ENCODE Consortium (https://genome.ucsc.edu/ENCODE/qualityMetrics.html). Two thresholds were defined for each of the two cross-correlation ratios (NSC, normalized strand coefficient: 1.05 and 1.10; RSC, relative strand coefficient: 0.8 and 1.0). Detailed descriptions of the ENCODE quality coefficients can be found at https://genome.ucsc.edu/ENCODE/qualityMetrics.html. The phantompeak tools suite was used (https://code.google.com/p/phantompeakqualtools/) to compute RSC and NSC. Please refer to the ReMap 2022, 2020, and 2018 publications for more details (citation below). This is a detailled view of the data increase in ReMap v2 with FOXA1 peaks at a specific location. --> Data Access ReMap Atlas of regulatory regions data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. Individual BED files for specific TFs, cells/biotypes, or data sets can be found and downloaded on the ReMap website. References Ch&#232;neby J, Gheorghe M, Artufel M, Mathelier A, Ballester B. ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP- seq experiments. Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275. PMID: 29126285; PMC: PMC5753247 Ch&#232;neby J, M&#233;n&#233;trier Z, Mestdagh M, Rosnet T, Douida A, Rhalloussi W, Bergon A, Lopez F, Ballester B. ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments. Nucleic Acids Res. 2020 Jan 8;48(D1):D180-D188. PMID: 31665499; PMC: PMC7145625 Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B. Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res. 2015 Feb 27;43(4):e27. PMID: 25477382; PMC: PMC4344487 Hammal F, de Langen P, Bergon A, Lopez F, Ballester B. ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. Nucleic Acids Res. 2022 Jan 7;50(D1):D316-D325. PMID: 34751401; PMC: PMC8728178 
ReMapDensity ReMap density ReMap density Regulation Description This track represents the ReMap Atlas of regulatory regions, which consists of a large-scale integrative analysis of all Public ChIP-seq data for transcriptional regulators from GEO, ArrayExpress, and ENCODE. Below is a schematic diagram of the types of regulatory regions: ReMap 2022 Atlas (all peaks for each analyzed data set) ReMap 2022 Non-redundant peaks (merged similar target) ReMap 2022 Cis Regulatory Modules Display Conventions and Configuration Each transcription factor follows a specific RGB color. ChIP-seq peak summits are represented by vertical bars. Hsap: A data set is defined as a ChIP/Exo-seq experiment in a given GEO/ArrayExpress/ENCODE series (e.g. GSE41561), for a given TF (e.g. ESR1), in a particular biological condition (e.g. MCF-7). Data sets are labeled with the concatenation of these three pieces of information (e.g. GSE41561.ESR1.MCF-7). Atha: The data set is defined as a ChIP-seq experiment in a given series (e.g. GSE94486), for a given target (e.g. ARR1), in a particular biological condition (i.e. ecotype, tissue type, experimental conditions; e.g. Col-0_seedling_3d-6BA-4h). Data sets are labeled with the concatenation of these three pieces of information (e.g. GSE94486.ARR1.Col-0_seedling_3d-6BA-4h). Methods This 4th release of ReMap (2022) presents the analysis of a total of 8,103 quality controlled ChIP-seq (n=7,895) and ChIP-exo (n=208) data sets from public sources (GEO, ArrayExpress, ENCODE). The ChIP-seq/exo data sets have been mapped to the GRCh38/hg38 human assembly. The data set is defined as a ChIP-seq experiment in a given series (e.g. GSE46237), for a given TF (e.g. NR2C2), in a particular biological condition (i.e. cell line, tissue type, disease state, or experimental conditions; e.g. HELA). Data sets were labeled by concatenating these three pieces of information, such as GSE46237.NR2C2.HELA. Those merged analyses cover a total of 1,211 DNA-binding proteins (transcriptional regulators) such as a variety of transcription factors (TFs), transcription co-activators (TCFs), and chromatin-remodeling factors (CRFs) for 182 million peaks. GEO & ArrayExpress Public ChIP-seq data sets were extracted from Gene Expression Omnibus (GEO) and ArrayExpress (AE) databases. For GEO, the query &apos;(&apos;chip seq&apos; OR &apos;chipseq&apos; OR &apos;chip sequencing&apos;) AND &apos;Genome binding/occupancy profiling by high throughput sequencing&apos; AND &apos;homo sapiens&apos;[organism] AND NOT &apos;ENCODE&apos;[project]&apos; was used to return a list of all potential data sets to analyze, which were then manually assessed for further analyses. Data sets involving polymerases (i.e. Pol2 and Pol3), and some mutated or fused TFs (e.g. KAP1 N/C terminal mutation, GSE27929) were excluded. ENCODE Available ENCODE ChIP-seq data sets for transcriptional regulators from the ENCODE portal were processed with the standardized ReMap pipeline. The list of ENCODE data was retrieved as FASTQ files from the ENCODE portal using the following filters: Assay: &quot;ChIP-seq&quot; Organism: &quot;Homo sapiens&quot; Target of assay: &quot;transcription factor&quot; Available data: &quot;fastq&quot; on 2016 June 21st Metadata information in JSON format and FASTQ files were retrieved using the Python requests module. ChIP-seq processing Both Public and ENCODE data were processed similarly. Bowtie 2 (PMC3322381) (version 2.2.9) with options -end-to-end -sensitive was used to align all reads on the genome. Biological and technical replicates for each unique combination of GSE/TF/Cell type or Biological condition were used for peak calling. TFBS were identified using MACS2 peak-calling tool (PMC3120977) (version 2.1.1.2) in order to follow ENCODE ChIP-seq guidelines, with stringent thresholds (MACS2 default thresholds, p-value: 1e-5). An input data set was used when available. Quality assessment To assess the quality of public data sets, a score was computed based on the cross-correlation and the FRiP (fraction of reads in peaks) metrics developed by the ENCODE Consortium (https://genome.ucsc.edu/ENCODE/qualityMetrics.html). Two thresholds were defined for each of the two cross-correlation ratios (NSC, normalized strand coefficient: 1.05 and 1.10; RSC, relative strand coefficient: 0.8 and 1.0). Detailed descriptions of the ENCODE quality coefficients can be found at https://genome.ucsc.edu/ENCODE/qualityMetrics.html. The phantompeak tools suite was used (https://code.google.com/p/phantompeakqualtools/) to compute RSC and NSC. Please refer to the ReMap 2022, 2020, and 2018 publications for more details (citation below). This is a detailled view of the data increase in ReMap v2 with FOXA1 peaks at a specific location. --> Data Access ReMap Atlas of regulatory regions data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser&apos;s REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. Individual BED files for specific TFs, cells/biotypes, or data sets can be found and downloaded on the ReMap website. References Ch&#232;neby J, Gheorghe M, Artufel M, Mathelier A, Ballester B. ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP- seq experiments. Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275. PMID: 29126285; PMC: PMC5753247 Ch&#232;neby J, M&#233;n&#233;trier Z, Mestdagh M, Rosnet T, Douida A, Rhalloussi W, Bergon A, Lopez F, Ballester B. ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments. Nucleic Acids Res. 2020 Jan 8;48(D1):D180-D188. PMID: 31665499; PMC: PMC7145625 Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B. Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res. 2015 Feb 27;43(4):e27. PMID: 25477382; PMC: PMC4344487 Hammal F, de Langen P, Bergon A, Lopez F, Ballester B. ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. Nucleic Acids Res. 2022 Jan 7;50(D1):D316-D325. PMID: 34751401; PMC: PMC8728178 
ucscRetroAli5 Retroposed Genes Retroposed Genes V5, Including Pseudogenes Genes and Gene Predictions Description Retrotransposition is a process involving the copying of DNA by a group of enzymes that have the ability to reverse transcribe spliced mRNAs, resulting in single-exon copies of genes and sometime chimeric genes. RetroGenes can be either functional genes that have acquired a promoter from a neighboring gene, non-functional pseudogenes, or transcribed pseudogenes. Methods All mRNAs of a species from GenBank were aligned to the genome using lastz (Miller lab, Pennsylvania State University). mRNAs that aligned twice in the genome (once with introns and once without introns) were initially screened. Next, a series of features were scored to determine candidates for retrotransposition events. These features included position and length of the polyA tail, degree of synteny with mouse, coverage of repetitive elements, number of exons that can still be aligned to the retrogene and degree of divergence from the parent gene. Retrogenes were classified using a threshold score function that is a linear combination of this set of features. Retrogenes in the final set were selected using a score threshold based on a ROC plot against the Vega annotated pseudogenes. Retrogene Statistics table: Expression of Retrogene: The following values are possible where those that are not expressed are classed as pseudogene or mrna: pseudogene indicates that the parent gene has been annotated by one of NCBI's RefSeq, UCSC Genes or Mammalian Gene Collection (MGC). mrna indicates that the parent gene is a spliced mrna that has no annotation in NCBI's RefSeq, UCSC Genes or Mammalian Gene Collection (MGC). Therefore, the retrogene is a product of a potentially non-annotated parent gene and is a putative pseudogene of that putative parent gene. expressed weak indicates that there is a mRNA overlapping the retrogene, indicating possible transcription. noOrf indicates that an ORF was not identified by BESTORF. expressed indicates that there is a medium level of mRNAs/ESTs mapping to the retrogene locus, indicating possible transcription. expressed strong indicates that there is a mRNA overlapping the retrogene, and at least five spliced ESTs indicating probable transcription. noOrf indicates that an ORF was not identified by BESTORF. expressed shuffle indicates that the retrogene was inserted into a pre-existing annotated gene. Score: Based on features of the potential retrogene. Percent Gene Alignment Coverage (Bases Matching Parent): Shows the percentage of the parent gene aligning to this region. Intron Count: Number of introns is the number of gaps in the alignment between the parent mRNA and the genome where gaps are &gt;80 bp and the ratio of the mRNA alignment gap to the genome alignment gap is less than 30% after removing repeats. Gap Count: Numer of gaps in the alignment of between the parent mRNA and the genome after removing repeats. Gaps are not counted if the gap on the mRNA side of the alignment is a similar size to the gap in the genome alignment. BESTORF Score: BESTORF (written by Victor Solovyev) predicts potential open reading frames (ORFs) in mRNAs/ESTs with very high accuracy using a Markov chain model of coding regions and a probabilistic model of translation start codon potential. The score threshold for finding an ORF is 50 (Jim Kent, personal communication). Break in Orthology table: Retrogenes inserted into the genome since the human/mouse divergence show a break in the mouse genome syntenic net alignments to the human genome. The percentage break represents the portion of the genome that is missing in each species relative to the reference genome (human hg19) at the retrogene locus as defined by syntenic alignment nets. Breaks in orthology with mouse and dog tend to be due to genomic insertions in the primate lineage. Relative orthology of dog/human and rhesus macque/human nets are used to avoid false positives due to deletions in the mouse genome. Older retrogenes will not show a break in orthology, so this feature is weighted lower than other features when scoring putative retrogenes. These features can be downloaded from the table retroMrnaInfo in many formats using the Table Browser option from the Tools menu in the top blue navigation bar. Credits The RetroFinder program and browser track were developed by Robert Baertsch at UCSC. References Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics. 2008 Oct 8;9:466. PMID: 18842134; PMC: PMC2584115 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M et al. The GENCODE pseudogene resource. Genome Biol. 2012 Sep 26;13(9):R51. PMID: 22951037; PMC: PMC3491395 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res. 2007 Jun;17(6):839-51. PMID: 17568002; PMC: PMC1891343 
revel REVEL Scores REVEL Pathogenicity Score for single-base coding mutations (zoom for exact score) Phenotype and Literature Description This track collection shows Rare Exome Variant Ensemble Learner (REVEL) scores for predicting the deleteriousness of each nucleotide change in the genome. REVEL is an ensemble method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. REVEL was trained using recently discovered pathogenic and rare neutral missense variants, excluding those previously used to train its constituent tools. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. Most authors of deleteriousness scores argue against using fixed cutoffs in diagnostics. But to give an idea of the meaning of the score value, the REVEL authors note: "For example, 75.4% of disease mutations but only 10.9% of neutral variants (and 12.4% of all ESVs) have a REVEL score above 0.5, corresponding to a sensitivity of 0.754 and specificity of 0.891. Selecting a more stringent REVEL score threshold of 0.75 would result in higher specificity but lower sensitivity, with 52.1% of disease mutations, 3.3% of neutral variants, and 4.1% of all ESVs being classified as pathogenic". (Figure S1 of the reference below) Display Conventions and Configuration There are five subtracks for this track: Four lettered subtracks, one for every nucleotide, showing scores for mutation from the reference to that nucleotide. All subtracks show the REVEL ensemble score on mouseover. Across the exome, there are three values per position, one for every possible nucleotide mutation. The fourth value, &quot;no mutation&quot;, representing the reference allele, e.g. A to A, is always set to zero, "0.0". REVEL only takes into account amino acid changes, so a nucleotide change that results in no amino acid change (synonymous) also receives the score "0.0". In rare cases, two scores are output for the same variant at a genome position. This happens when there are two transcripts with different splicing patterns and since some input scores for REVEL take into account the sequence context, the same mutation can get two different scores. In these cases, only the maximum score is shown in the four per-nucleotide subtracks. The complete set of scores are shown in the Overlaps track. One subtrack, Overlaps, shows alternate REVEL scores when applicable. In rare cases (0.05% of genome positions), multiple scores exist with a single variant, due to multiple, overlapping transcripts. For example, if there are two transcripts and one covers only half of an exon, then the amino acids that overlap both transcripts will get two different REVEL scores, since some of the underlying scores (polyPhen for example) take into account the amino acid sequence context and this context is different depending on the transcript. For these cases, this subtrack contains at least two graphical features, for each affected genome position. Each feature is labeled with the mutation (A, C, T or G). The transcript IDs and resulting score is shown when hovering over the feature or clicking it. For the large majority of the genome, this subtrack has no features. This is because REVEL usually outputs only a single score per nucleotide and most transcript-derived amino acid sequence contexts are identical. Note that in most diagnostic assays, variants are called using WGS pipelines, not RNA-seq. As a result, variants are originally located on the genome, not on transcripts, and the choice of transcript is made by a variant calling software using a heuristic. In addition, clinically, in the field, some transcripts have been agreed-on as more relevant for a disease, e.g. because only certain transcripts may be expressed in the relevant tissue. So the choice of the most relevant transcript, and as such the REVEL score, may be a question of manual curation standards rather than a result of the variant itself. When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and no score will be shown on the mouseover tooltip. For hg38, note that the data was converted from the hg19 data using the UCSC liftOver program, by the REVEL authors. This can lead to missing values or duplicated values. When a hg38 position is annotated with two scores due to the lifting, the authors removed all the scores for this position. They did the same when the reference allele has changed from hg19 to hg38. Also, on hg38, the track has the "lifted" icon to indicate this. You can double-check if a nucleotide position is possibly affected by the lifting procedure by activating the track "Hg19 Mapping" under "Mapping and Sequencing". Data access REVEL scores are available at the REVEL website. The site provides precomputed REVEL scores for all possible human missense variants to facilitate the identification of pathogenic variants among the large number of rare variants discovered in sequencing studies. The REVEL data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig files that can be downloaded from our download server. The files for this track are called a.bw, c.bw, g.bw, t.bw. Individual regions or the whole genome annotation can be obtained using our tool bigWigToWig which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tools can also be used to obtain features confined to given range, e.g. &nbsp; bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/hg19/revel/a.bw stdout Methods Data were converted from the files provided on the REVEL Downloads website. As with all other tracks, a full log of all commands used for the conversion is available in our source repository, for hg19 and hg38. The release used for each assembly is shown on the track description page. Credits Thanks to the REVEL development team for providing precomputed data and fixing duplicated values in the hg38 files. References Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, Musolf A, Li Q, Holzinger E, Karyadi D, et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants Am J Hum Genet. 2016 Oct 6;99(4):877-885. PMID: 27666373; PMC: PMC5065685 
revelOverlaps REVEL overlaps REVEL: Positions with >1 score due to overlapping transcripts (mouseover for details) Phenotype and Literature 
revelT Mutation: T REVEL: Mutation is T Phenotype and Literature 
revelG Mutation: G REVEL: Mutation is G Phenotype and Literature 
revelC Mutation: C REVEL: Mutation is C Phenotype and Literature 
revelA Mutation: A REVEL: Mutation is A Phenotype and Literature 
rgdQtl RGD Human QTL Human Quantitative Trait Locus from RGD Phenotype and Literature Description A quantitative trait locus (QTL) is a polymorphic locus that contains alleles which differentially affect the expression of a continuously distributed phenotypic trait. Usually a QTL is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. Credits Thanks to the RGD for providing this annotation. RGD is funded by grant HL64541 entitled "Rat Genome Database", awarded to Dr. Howard J Jacob, Medical College of Wisconsin, from the National Heart Lung and Blood Institute (NHLBI) of the National Institutes of Health (NIH). References Rapp JP. Genetic analysis of inherited hypertension in the rat. Physiol Rev. 2000 Jan;80(1):135-72. PMID: 10617767 
rgdRatQtl RGD Rat QTL Rat Quantitative Trait Locus from RGD Coarsely Mapped to Human Phenotype and Literature Description This track shows Rat quantitative trait loci (QTLs) from the Rat Genome Database (RGD) that have been coarsely mapped by UCSC to the Human genome using stringently filtered cross-species alignments. A quantitative trait locus (QTL) is a polymorphic locus that contains alleles which differentially affect the expression of a continuously distributed phenotypic trait. Usually a QTL is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. For a comprehensive review of QTL mapping techniques in the rat, see Rapp, 2000. To map the Rat QTLs to Human, UCSC's chained and netted blastz alignments of Rat to Human were filtered to retain only those with high chain scores (&gt;=500,000). This removed many valid-but-short alignments and in general retained only very long chains (&gt;10,000, usually &gt;100,000 bp), so that only large regions could be mapped. This choice was made because QTLs in general are extremely large and approximate regions. After the alignment filtering, UCSC's liftOver program was used to map Rat regions to Human via the filtered alignments. To get a sense of how many genomic rearrangments between Rat and Human are in the region of a particular Rat QTL, you may want to view the Human Nets track in the Rat Nov. 2004 (Baylor 3.4/rn4) genome browser. In the position/search box, enter the name of the Rat QTL of interest. Credits Thanks to the RGD for providing the Rat QTLs. RGD is funded by grant HL64541 entitled "Rat Genome Database", awarded to Dr. Howard J Jacob, Medical College of Wisconsin, from the National Heart Lung and Blood Institute (NHLBI) of the National Institutes of Health (NIH). References Rapp JP. Genetic analysis of inherited hypertension in the rat. Physiol Rev. 2000 Jan;80(1):135-72. PMID: 10617767 
wgEncodeRikenCage RIKEN CAGE Loc GSE34448 RNA Subcellular CAGE Localization from ENCODE/RIKEN Expression Description This track shows 5' cap analysis gene expression (CAGE) tags and clusters in RNA extracts from different sub-cellular localizations in multiple cell lines. A CAGE cluster is a region of overlapping tags with an assigned value that represents the expression level. The data in this track were produced as part of the ENCODE Transcriptome Project. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. This track contains the following views: Clusters Pooled clusters generated by merging clusters from individual bioreplicates using mergedBed (where two bioreplicates were available). Expression was scored individually for each replicate. The score represents the average expression score of the pooled replicates. Non-parametric Irreproducible Discovery Rate (np-IDR) was run on the normalized expression scores. The expression score is number of reads mapping to a merged cluster divided by the number of total mapped reads. A complete description of the Cluster files is located in the supplemental materials directory of our downloads page. --> TSS HMM Transcriptional Start Sites based on Hidden Markov Modeling for pooled replicates where two replicates exist. Expression levels are shown in reads per kilobase of exon per million reads mapped (RPKM). The IDR value is the irreproducible discovery rate. This is a measurement that measures expression variances between genomic replicates in large scale experiments. Plus and Minus Signals These views display signals representing the amount of overlapping CAGE reads (clusters) mapped on the forward and reverse genomic strands. Alignments The Alignments view shows reads mapped to the genome and indicates where bases may mismatch. Every mapped read is displayed, i.e. uncollapsed. The alignment file follows the standard SAM format of Bowtie output. The custom tag XP can be ignored. See the Bowtie Manual for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format. Where mapping quality is not available for this track, a score of 255 is used in accordance with the SAM Format Specification. Also, where the sequence quality scores are not available, all scores are displayed as 40. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Replicate numbering in the track display page is done by rank. The first replicate available may be replicate number three. Color differences in subtracks may be set as a visual cue to distinguish between the different cell types or between annotations on the plus and minus strand. Downloadable Files TSS GencV7 For some samples, there are download files in a modified gtf format with Transcriptional Start Sites based on GENCODE V7. A complete description of the TSS files is located in the supplemental materials directory. Methods Cells were grown according to the approved ENCODE cell culture protocols. RNA molecules longer than 200 nt were isolated from each subcellular compartment and then were fractionated into polyA+ and polyA- fractions as described in these protocols. The CAGE tags were sequenced from the 5' ends of cap-trapped cDNAs produced using RIKEN CAGE technology (Kodzius et al. 2006; Valen et al. 2009). To create the tag, a linker was attached to the 5' end of polyA+ or polyA- reverse-transcribed cDNAs which were selected by cap trapping (Carninci et al. 1996). The first 27 bp of the cDNA were cleaved using class II restriction enzymes. A linker was then attached to the 3' end of the cDNA. After PCR amplification, the tags were sequenced using Illumina's Genome analyzer or HiSeq. The read lengths for each sample are specified in the metadata. Tags were mapped to the human genome (hg19) using the program Delve (T. Lassmann manuscript in preparation). Delve is a new probabilistic aligner focused on giving the best possible alignment of reads to a genome rather than focusing on speed. It calculates the mapping accuracy (probability of each alignment being true or not) for each alignment. There is no set limit on the number of errors allowed and therefore the mapping rate is commonly 100%. However, for analysis it is recommended to discard alignments with low mapping qualities. Exceptions to the above protocol are the polyA- RNA samples from K562 cytosol, K562 nucleus, and prostate whole cell which were sequenced using ABI SOLiD technology. These reads were mapped using Bowtie with its default parameters. Clusters were defined as regions of overlapping CAGE reads. The expression level was computed as the number of reads making up the cluster, divided by the total number of reads sequenced, times 1 million. Release Notes This is Release 4 (July 2012) of Riken CAGE. Three missing Transcription Start Sites determined by Hidden Markov Models (TssHmm) tables have been added (H1-hesc Nucleus, H1-hesc Cytosol and NHEK Nucleus polyA+ samples). As with previous releases, the orignal data from the hg18 version of this track is still included and can be noted in the metadata as having a bioRepId that starts with gen0. This older data may be missing some information and does not have replicates. If there are new data available for an older sample, only the newer data is displayed. The older data is still availble for downloads. Release 1 on hg19 contained the original data on hg18 that was remapped and indicated in this release as Generation 0 since that data had no replicates. If there is both old and new generation data available for a particular experiment, only the new generation data is displayed and the older data is available for download. The new data for this track was done with a different process and has standard replicate numbers. The replicate labeling in the genome browser view is a counter indicating the total number of replicates submitted. The producing lab has replicate numbers that correspond to their internal bio-replicate numbering. Where these two numbering systems conflict, both are listed in the long label of the specific track. ---> Credits These data were generated and analyzed by Timo Lassmann, Phil Kapranov, Hazuki Takahashi, Yoshihide Hayashizaki, Carrie Davis, Tom Gingeras, and Piero Carninci. Contact: Piero Carninci at RIKEN Omics Science Center References Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N, Izawa M, et al. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics. 1996 November 1; 37(3):327-336. Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M, et al. CAGE: cap analysis of gene expression. Nat Methods. 2006 March 1; 3(3):211-222. Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res. 2009 February; 19(2):255-265. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeRikenCageViewTssHmm TssHmm RNA Subcellular CAGE Localization from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshraCellPapTssHmm SKRA cell pA+ SK-N-SH_RA Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001157 1157 GSM849362 Gingeras RIKEN K14,K15 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageSknshraCellPapTssHmm TssHmm neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) SK-N-SH RA whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageSkmcCellPapTssHmm SkMC cell pA+ SkMC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002764 2764 GSM979653 Gingeras RIKEN CThi10030,CThi10031 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSkmcCellPapTssHmm TssHmm Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) SkMC whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemm2CellPapTssHmm NHEM cell pA+ NHEM_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002760 2760 GSM979649 Gingeras RIKEN CThi10056,CThi10102GAT cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemm2CellPapTssHmm TssHmm Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) NHEM M2 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemfm2CellPapTssHmm NHEf cell pA+ NHEM.f_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002759 2759 GSM979663 Gingeras RIKEN CThi10102CTT,CThi10055 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemfm2CellPapTssHmm TssHmm Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) NHEM.f M2 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCellPapTssHmm NHEK cell pA+ NHEK Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001152 1152 GSM849367 Gingeras RIKEN J76,J77 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageNhekCellPapTssHmm TssHmm epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) NHEK whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPapTssHmmV3 NHEK nucl pA+ NHEK Cage ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH001154 1154 GSM849361 Gingeras RIKEN CTig10011,K09 nucleus 1x36 longPolyA Illumina_GA2x F wgEncodeRikenCageNhekNucleusPapTssHmmV3 TssHmm epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Female Expression level estimates for transcription start sites (TSS) NHEK nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPamTssHmmV2 NHEK nucl pA- NHEK Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000347 347 GSM849347 Gingeras RIKEN I71 nucleus longNonPolyA wgEncodeRikenCageNhekNucleusPamTssHmmV2 TssHmm epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) NHEK nucleus polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPapTssHmm NHEK cyto pA+ NHEK Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001153 1153 GSM849366 Gingeras RIKEN K08,K20 IDR cytosol longPolyA Illumina_GA2x wgEncodeRikenCageNhekCytosolPapTssHmm TssHmm epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) NHEK cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPamTssHmmV2 NHEK cyto pA- NHEK Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000346 346 GSM849346 Gingeras RIKEN I70 cytosol longNonPolyA wgEncodeRikenCageNhekCytosolPamTssHmmV2 TssHmm epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) NHEK cytosol polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhdfCellPapTssHmm NHDF cell pA+ NHDF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002758 2758 GSM979662 Gingeras RIKEN CThi10032,CThi10033 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhdfCellPapTssHmm TssHmm Dermal Fibroblasts from temple / breast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) NHDF whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHwpCellPapTssHmm HWP cell pA+ HWP Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002751 2751 GSM979661 Gingeras RIKEN CThi10101ACA,CThi10101ATC cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHwpCellPapTssHmm TssHmm Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HWP whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHvmfCellPapTssHmm HVMF cell pA+ HVMF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002750 2750 GSM979660 Gingeras RIKEN CThi10034,CThi10035 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHvmfCellPapTssHmm TssHmm villous mesenchymal fibroblast cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HVMF whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHsavecCellPapTssHmm HSaV cell pA+ HSaVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002748 2748 GSM979645 Gingeras RIKEN CThi10102ACA,CThi10102ATC cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHsavecCellPapTssHmm TssHmm Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HSaVEC whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpiepcCellPapTssHmm HPIE cell pA+ HPIEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002747 2747 GSM979642 Gingeras RIKEN CThi10104ATC,CThi10101GAT cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpiepcCellPapTssHmm TssHmm Placental Epithelial Cells amniotic membrane CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HPIEpC whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpcplCellPapTssHmm HPCP cell pA+ HPC-PL Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002746 2746 GSM979643 Gingeras RIKEN CThi10057,CThi10105ATC cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpcplCellPapTssHmm TssHmm Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HPC-PL whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHobCellPapTssHmm HOB cell pA+ HOB Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002745 2745 GSM979640 Gingeras RIKEN CThi10036,CThi10037 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHobCellPapTssHmm TssHmm Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HOB whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscucCellPapTssHmm hMUC cell pA+ hMSC-UC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002767 2767 GSM979650 Gingeras RIKEN CThi10101CTT,CThi10100ATC cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscucCellPapTssHmm TssHmm Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) hMSC-UC whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscbmCellPapTssHmm hMBM cell pA+ hMSC-BM Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002766 2766 GSM979651 Gingeras RIKEN CThi10103ATC,CThi10100ACA cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscbmCellPapTssHmm TssHmm Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) hMSC-BM whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscatCellPapTssHmm hMAT cell pA+ hMSC-AT Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002765 2765 GSM979652 Gingeras RIKEN CThi10105ACA,CThi10104GAT cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscatCellPapTssHmm TssHmm Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) hMSC-AT whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmepcCellPapTssHmm HMEp cell pA+ HMEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002744 2744 GSM979641 Gingeras RIKEN CThi10105GAT cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmepcCellPapTssHmm TssHmm Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HMEpC whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHfdpcCellPapTssHmm HFDP cell pA+ HFDPC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002743 2743 GSM979638 Gingeras RIKEN CThi10103ACA,CThi10100GAT cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHfdpcCellPapTssHmm TssHmm Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HFDPC whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHchCellPapTssHmm HCH cell pA+ HCH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002742 2742 GSM979639 Gingeras RIKEN CThi10104CTT,CThi10104ACA cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHchCellPapTssHmm TssHmm Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HCH whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoecCellPapTssHmm HAoE cell pA+ HAoEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002741 2741 GSM979636 Gingeras RIKEN CThi10103GAT,CThi10105CTT cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoecCellPapTssHmm TssHmm Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HAoEC whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoafCellPapTssHmm HAoA cell pA+ HAoAF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002740 2740 GSM979637 Gingeras RIKEN CThi10100CTT,CThi10103CTT cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoafCellPapTssHmm TssHmm Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) HAoAF whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd34mobilizedCellPapTssHmm CD34 cell pA+ CD34+_Mobilized Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002739 2739 GSM979635 Gingeras RIKEN CThi10058 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd34mobilizedCellPapTssHmm TssHmm hematopoietic progenitor cells- mobilized, from donor RO01679. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) CD34+ Mobilized whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageBjCellPapTssHmm BJ cell pA+ BJ Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001160 1160 GSM849328 Gingeras RIKEN K18,K19 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageBjCellPapTssHmm TssHmm skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) BJ whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageAg04450CellPapTssHmm AG50 cell pA+ AG04450 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001159 1159 GSM849358 Gingeras RIKEN K12,K13 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageAg04450CellPapTssHmm TssHmm fetal lung fibroblast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) AG04450 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCellPapTssHmm SKSH cell pA+ SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002763 2763 GSM979646 Gingeras RIKEN CThi10043,CThi10046 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCellPapTssHmm TssHmm neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) SK-N-SH whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshNucleusPapTssHmm SKSH nucl pA+ SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002762 2762 GSM979647 Gingeras RIKEN CThi10045,CThi10048 nucleus 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshNucleusPapTssHmm TssHmm neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) SK-N-SH nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCytosolPapTssHmm SKSH cyto pA+ SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002761 2761 GSM979648 Gingeras RIKEN CThi10044,CThi10047 cytosol 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCytosolPapTssHmm TssHmm neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) SK-N-SH cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageMonocd14CellPapTssHmm CD14 cell pA+ Monocytes-CD14+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002757 2757 GSM979655 Gingeras RIKEN CThi10021,CThi10022 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMonocd14CellPapTssHmm TssHmm Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) Monocytes-CD14+ whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CellPapTssHmm MCF7 cell pA+ MCF-7 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001151 1151 GSM849364 Gingeras RIKEN K07,K11 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageMcf7CellPapTssHmm TssHmm mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) MCF-7 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7NucleusPapTssHmm MCF7 nucl pA+ MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002756 2756 GSM979654 Gingeras RIKEN CThi10052,CThi10054 nucleus 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7NucleusPapTssHmm TssHmm mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) MCF-7 nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CytosolPapTssHmm MCF7 cyto pA+ MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002755 2755 GSM979657 Gingeras RIKEN CThi10051,CThi10053 cytosol 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7CytosolPapTssHmm TssHmm mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) MCF-7 cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CellPapTssHmm IMR9 cell pA+ IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002754 2754 GSM979656 Gingeras RIKEN CThi10016,CThi10018 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CellPapTssHmm TssHmm fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) IMR90 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90NucleusPapTssHmm IMR9 nucl pA+ IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002753 2753 GSM979659 Gingeras RIKEN CThi10025,CThi10026 nucleus 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90NucleusPapTssHmm TssHmm fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) IMR90 nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CytosolPapTssHmm IMR9 cyto pA+ IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002752 2752 GSM979658 Gingeras RIKEN CThi10017,CThi10019 cytosol 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CytosolPapTssHmm TssHmm fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) IMR90 cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCellPapTssHmm HUVE cell pA+ HUVEC Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001141 1141 GSM849327 Gingeras RIKEN J78,J79 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCellPapTssHmm TssHmm umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HUVEC whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPapTssHmm HUVE nucl pA+ HUVEC Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001143 1143 GSM849325 Gingeras RIKEN K05,K06 IDR nucleus longPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPapTssHmm TssHmm umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HUVEC nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPamTssHmm HUVE nucl pA- HUVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002749 2749 GSM979644 Gingeras RIKEN CTig10027 nucleus 1x36 longNonPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPamTssHmm TssHmm umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HUVEC nucleus polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPapTssHmm HUVE cyto pA+ HUVEC Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001142 1142 GSM849324 Gingeras RIKEN K03,K04 IDR cytosol longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCytosolPapTssHmm TssHmm umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HUVEC cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPamTssHmmV2 HUVE cyto pA- HUVEC Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000342 342 GSM849350 Gingeras RIKEN I72 cytosol longNonPolyA wgEncodeRikenCageHuvecCytosolPamTssHmmV2 TssHmm umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) HUVEC cytosol polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CellPapTssHmmV2 HepG cell pA+ HepG2 Cage ENCODE Mar 2012 Freeze 2011-12-09 2012-09-09 wgEncodeEH001149 1149 GSM849335 Gingeras RIKEN K01,K02 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CellPapTssHmmV2 TssHmm hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HepG2 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPapTssHmm HepG nucl pA+ HepG2 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001148 1148 GSM849334 Gingeras RIKEN J98,J99 IDR nucleus longPolyA Illumina_GA2x wgEncodeRikenCageHepg2NucleusPapTssHmm TssHmm hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HepG2 nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPamTssHmmV2 HepG nucl pA- HepG2 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000345 345 GSM849345 Gingeras RIKEN I44 nucleus longNonPolyA wgEncodeRikenCageHepg2NucleusPamTssHmmV2 TssHmm hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) HepG2 nucleus polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleolusTotalTssHmmV3 HepG nlos tot HepG2 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000344 344 GSM849344 Gingeras RIKEN I68 nucleolus total wgEncodeRikenCageHepg2NucleolusTotalTssHmmV3 TssHmm hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Expression level estimates for transcription start sites (TSS) HepG2 nucleolus total CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPapTssHmm HepG cyto pA+ HepG2 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001147 1147 GSM849343 Gingeras RIKEN J89,J90 IDR cytosol longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CytosolPapTssHmm TssHmm hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HepG2 cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPamTssHmmV2 HepG cyto pA- HepG2 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000343 343 GSM849351 Gingeras RIKEN I42 cytosol longNonPolyA wgEncodeRikenCageHepg2CytosolPamTssHmmV2 TssHmm hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) HepG2 cytosol polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CellPapTssHmm HeLa cell pA+ HeLa-S3 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001146 1146 GSM849342 Gingeras RIKEN J80,J81 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CellPapTssHmm TssHmm cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HeLa-S3 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPapTssHmm HeLa nucl pA+ HeLa-S3 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001145 1145 GSM849331 Gingeras RIKEN J96,J97 IDR nucleus longPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPapTssHmm TssHmm cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HeLa-S3 nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPamTssHmm HeLa nucl pA- HeLa-S3 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002775 2775 GSM979631 Gingeras RIKEN CTig10028 nucleus 1x36 longNonPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPamTssHmm TssHmm cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HeLa-S3 nucleus polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleolusTotalTssHmmV2 HeLa nlos tot HeLa-S3 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001156 1156 GSM849363 Gingeras RIKEN J58 nucleolus total wgEncodeRikenCageHelas3NucleolusTotalTssHmmV2 TssHmm cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Expression level estimates for transcription start sites (TSS) HeLa-S3 nucleolus total CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPapTssHmm HeLa cyto pA+ HeLa-S3 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001144 1144 GSM849330 Gingeras RIKEN J87,J88 IDR cytosol longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CytosolPapTssHmm TssHmm cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) HeLa-S3 cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPamTssHmmV2 HeLa cyto pA- HeLa-S3 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001155 1155 GSM849360 Gingeras RIKEN J56 cytosol longNonPolyA wgEncodeRikenCageHelas3CytosolPamTssHmmV2 TssHmm cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) HeLa-S3 cytosol polyA - CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd20CellPapTssHmm CD20 cell pA+ CD20+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002738 2738 GSM979634 Gingeras RIKEN CThi10023,CThi10024 cell 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd20CellPapTssHmm TssHmm B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) CD20+ whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CellPapTssHmm A549 cell pA+ A549 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001158 1158 GSM849359 Gingeras RIKEN K16,K17 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageA549CellPapTssHmm TssHmm epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) A549 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549NucleusPapTssHmm A549 nucl pA+ A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002737 2737 GSM979633 Gingeras RIKEN CThi10106,CThi10060 nucleus 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549NucleusPapTssHmm TssHmm epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) A549 nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CytosolPapTssHmm A549 cyto pA+ A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002736 2736 GSM979632 Gingeras RIKEN CThi10049,CThi10059 cytosol 1x50 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549CytosolPapTssHmm TssHmm epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Expression level estimates for transcription start sites (TSS) A549 cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CellPapTssHmm K562 cell pA+ K562 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001150 1150 GSM849365 Gingeras RIKEN J70,J71 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageK562CellPapTssHmm TssHmm leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) K562 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562PolysomePamTssHmmV2 K562 poly pA- K562 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000337 337 GSM849354 Gingeras RIKEN I32 polysome longNonPolyA wgEncodeRikenCageK562PolysomePamTssHmmV2 TssHmm leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Strand of mRNA with ribosomes attached Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) K562 polysome polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPapTssHmm K562 nucl pA+ K562 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000333 333 GSM849338 Gingeras RIKEN J91,J92 IDR nucleus longPolyA Illumina_GA2x wgEncodeRikenCageK562NucleusPapTssHmm TssHmm leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) K562 nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPamTssHmmV2 K562 nucl pA- K562 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000330 330 GSM849337 Gingeras RIKEN I23 nucleus longNonPolyA wgEncodeRikenCageK562NucleusPamTssHmmV2 TssHmm leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) K562 nucleus polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleoplasmTotalTssHmmV3 K562 nplm tot K562 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000336 336 GSM849340 Gingeras RIKEN I34 nucleoplasm total wgEncodeRikenCageK562NucleoplasmTotalTssHmmV3 TssHmm leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center That part of the nuclear content other than the chromosomes or the nucleolus Total RNA extract (longer than 200 nt) Expression level estimates for transcription start sites (TSS) K562 nucleoplasm total CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleolusTotalTssHmmV3 K562 nlos tot K562 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000335 335 GSM849332 Gingeras RIKEN I33 nucleolus total wgEncodeRikenCageK562NucleolusTotalTssHmmV3 TssHmm leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Expression level estimates for transcription start sites (TSS) K562 nucleolus total CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPapTssHmm K562 cyto pA+ K562 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000332 332 GSM849339 Gingeras RIKEN J82,J83 IDR cytosol longPolyA Illumina_GA2x wgEncodeRikenCageK562CytosolPapTssHmm TssHmm leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) K562 cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPamTssHmmV2 K562 cyto pA- K562 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000329 329 GSM849353 Gingeras RIKEN I22 cytosol longNonPolyA wgEncodeRikenCageK562CytosolPamTssHmmV2 TssHmm leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) K562 cytosol polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562ChromatinTotalTssHmmV3 K562 chrm tot K562 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000334 334 GSM849333 Gingeras RIKEN I35 chromatin total wgEncodeRikenCageK562ChromatinTotalTssHmmV3 TssHmm leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Nuclear DNA and associated proteins Total RNA extract (longer than 200 nt) Expression level estimates for transcription start sites (TSS) K562 chromatin total CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPapTssHmm H1ES cell pA+ H1-hESC Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001138 1138 GSM849357 Gingeras RIKEN J74,J75 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCellPapTssHmm TssHmm embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) H1-hESC whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPamTssHmmV2 H1ES cell pA- H1-hESC Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000341 341 GSM849355 Gingeras RIKEN I67 cell longNonPolyA wgEncodeRikenCageH1hescCellPamTssHmmV2 TssHmm embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) H1-hESC whole cell polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescNucleusPapTssHmm H1ES nucl pA+ H1-hESC Cage ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH001140 1140 GSM849326 Gingeras RIKEN J95 nucleus 1x36 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescNucleusPapTssHmm TssHmm embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) H1-hESC nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCytosolPapTssHmm H1ES cyto pA+ H1-hESC Cage ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH001139 1139 GSM849356 Gingeras RIKEN J86 cytosol 1x36 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCytosolPapTssHmm TssHmm embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) H1-hESC cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CellPapTssHmm GM78 cell pA+ GM12878 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001680 1680 GSM849368 Gingeras RIKEN J72,J73 IDR cell longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CellPapTssHmm TssHmm B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) GM12878 whole cell polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPapTssHmm GM78 nucl pA+ GM12878 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001678 1678 GSM849348 Gingeras RIKEN J93,J94 IDR nucleus longPolyA Illumina_GA2x wgEncodeRikenCageGm12878NucleusPapTssHmm TssHmm B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) GM12878 nucleus polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPamTssHmmV2 GM78 nucl pA- GM12878 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000339 339 GSM849341 Gingeras RIKEN J59 nucleus longNonPolyA wgEncodeRikenCageGm12878NucleusPamTssHmmV2 TssHmm B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) GM12878 nucleus polyA - CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleolusTotalTssHmmV2 GM78 nlos tot GM12878 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000340 340 GSM849352 Gingeras RIKEN I69 nucleolus total wgEncodeRikenCageGm12878NucleolusTotalTssHmmV2 TssHmm B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Expression level estimates for transcription start sites (TSS) GM12878 nucleolus total CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPapTssHmm GM78 cyto pA+ GM12878 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH001679 1679 GSM849349 Gingeras RIKEN J84,J85 IDR cytosol longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CytosolPapTssHmm TssHmm B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Expression level estimates for transcription start sites (TSS) GM12878 cytosol polyA+ CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPamTssHmmV2 GM78 cyto pA- GM12878 Cage ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000338 338 GSM849329 Gingeras RIKEN I27 cytosol longNonPolyA wgEncodeRikenCageGm12878CytosolPamTssHmmV2 TssHmm B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Expression level estimates for transcription start sites (TSS) GM12878 cytosol polyA- CAGE TSS HMM from ENCODE/RIKEN Expression 
wgEncodeRikenCageViewPlusSignal Plus Signal RNA Subcellular CAGE Localization from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshraCellPapPlusSignalRep2 SKSH cell pA+ + 2 SK-N-SH_RA Cage ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001157 1157 GSM849362 Gingeras RIKEN K15 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageSknshraCellPapPlusSignalRep2 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH_RA whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshraCellPapPlusRawRep1 SKSH cell pA+ + 1 SK-N-SH_RA Cage ENCODE Mar 2012 Freeze 2011-05-31 2012-03-02 wgEncodeEH001157 1157 GSM849362 Gingeras RIKEN K14 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageSknshraCellPapPlusRawRep1 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH_RA whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSkmcCellPapPlusRawRep2 SkMC cell pA+ + 2 SkMC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002764 2764 GSM979653 Gingeras RIKEN CThi10031 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSkmcCellPapPlusRawRep2 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSkmcCellPapPlusRawRep1 SkMC cell pA+ + 1 SkMC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002764 2764 GSM979653 Gingeras RIKEN CThi10030 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSkmcCellPapPlusRawRep1 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageProstateCellPamPlusSignal Pros cell pA- + 1 prostate Cage ENCODE Jan 2011 Freeze 2010-09-22 2008-12-09 2009-09-09 wgEncodeEH000331 331 GSM849336 Gingeras RIKEN I09 cell longNonPolyA bedtools v2.7.1 wgEncodeRikenCageProstateCellPamPlusSignal PlusSignal prostate tissue purchased for CSHL project CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand Prostate whole cell polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemm2CellPapPlusRawRep2 NHEM cell pA+ + 2 NHEM_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002760 2760 GSM979649 Gingeras RIKEN CThi10102GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemm2CellPapPlusRawRep2 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM M2 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemm2CellPapPlusRawRep1 NHEM cell pA+ + 1 NHEM_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002760 2760 GSM979649 Gingeras RIKEN CThi10056 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemm2CellPapPlusRawRep1 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM M2 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemfm2CellPapPlusRawRep2 NHEf cell pA+ + 2 NHEM.f_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002759 2759 GSM979663 Gingeras RIKEN CThi10055 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemfm2CellPapPlusRawRep2 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f M2 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemfm2CellPapPlusRawRep1 NHEf cell pA+ + 1 NHEM.f_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002759 2759 GSM979663 Gingeras RIKEN CThi10102CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemfm2CellPapPlusRawRep1 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f M2 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCellPapPlusSignalRep2 NHEK cell pA+ + 2 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001152 1152 GSM849367 Gingeras RIKEN J77 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCellPapPlusSignalRep2 PlusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCellPapPlusSignalRep1 NHEK cell pA+ + 1 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001152 1152 GSM849367 Gingeras RIKEN J76 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCellPapPlusSignalRep1 PlusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPapPlusRawRep4 NHEK nucl pA+ + 4 NHEK Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH001154 1154 GSM849361 Gingeras RIKEN CTig10011 nucleus 1x36 4 longPolyA Illumina_GA2x F wgEncodeRikenCageNhekNucleusPapPlusRawRep4 PlusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Female Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPapPlusSignalRep3 NHEK nucl pA+ + 1 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001154 1154 GSM849361 Gingeras RIKEN K09 nucleus 3 longPolyA Illumina_GA2x wgEncodeRikenCageNhekNucleusPapPlusSignalRep3 PlusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPamPlusSignal NHEK nucl pA- + 1 NHEK Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000347 347 GSM849347 Gingeras RIKEN I71 bedtools v2.7.1 nucleus longNonPolyA wgEncodeRikenCageNhekNucleusPamPlusSignal PlusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPapPlusRawRep4 NHEK cyto pA+ + 2 NHEK Cage ENCODE Mar 2012 Freeze 2011-05-31 2012-03-02 wgEncodeEH001153 1153 GSM849366 Gingeras RIKEN K20 cytosol 4 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCytosolPapPlusRawRep4 PlusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPapPlusSignalRep3 NHEK cyto pA+ + 1 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001153 1153 GSM849366 Gingeras RIKEN K08 cytosol 3 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCytosolPapPlusSignalRep3 PlusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPamPlusSignal NHEK cyto pA- + 1 NHEK Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000346 346 GSM849346 Gingeras RIKEN I70 bedtools v2.7.1 cytosol longNonPolyA wgEncodeRikenCageNhekCytosolPamPlusSignal PlusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhdfCellPapPlusRawRep2 NHDF cell pA+ + 2 NHDF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002758 2758 GSM979662 Gingeras RIKEN CThi10033 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhdfCellPapPlusRawRep2 PlusSignal Dermal Fibroblasts from temple / breast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhdfCellPapPlusRawRep1 NHDF cell pA+ + 1 NHDF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002758 2758 GSM979662 Gingeras RIKEN CThi10032 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhdfCellPapPlusRawRep1 PlusSignal Dermal Fibroblasts from temple / breast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHwpCellPapPlusRawRep2 HWP cell pA+ + 2 HWP Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002751 2751 GSM979661 Gingeras RIKEN CThi10101ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHwpCellPapPlusRawRep2 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHwpCellPapPlusRawRep1 HWP cell pA+ + 1 HWP Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002751 2751 GSM979661 Gingeras RIKEN CThi10101ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHwpCellPapPlusRawRep1 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHvmfCellPapPlusRawRep2 HVMF cell pA+ + 2 HVMF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002750 2750 GSM979660 Gingeras RIKEN CThi10035 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHvmfCellPapPlusRawRep2 PlusSignal villous mesenchymal fibroblast cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHvmfCellPapPlusRawRep1 HVMF cell pA+ + 1 HVMF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002750 2750 GSM979660 Gingeras RIKEN CThi10034 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHvmfCellPapPlusRawRep1 PlusSignal villous mesenchymal fibroblast cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHsavecCellPapPlusRawRep2 HSaV cell pA+ + 2 HSaVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002748 2748 GSM979645 Gingeras RIKEN CThi10102ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHsavecCellPapPlusRawRep2 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHsavecCellPapPlusRawRep1 HSaV cell pA+ + 1 HSaVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002748 2748 GSM979645 Gingeras RIKEN CThi10102ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHsavecCellPapPlusRawRep1 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpiepcCellPapPlusRawRep2 HPIE cell pA+ + 2 HPIEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002747 2747 GSM979642 Gingeras RIKEN CThi10101GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpiepcCellPapPlusRawRep2 PlusSignal Placental Epithelial Cells amniotic membrane CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpiepcCellPapPlusRawRep1 HPIE cell pA+ + 1 HPIEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002747 2747 GSM979642 Gingeras RIKEN CThi10104ATC cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpiepcCellPapPlusRawRep1 PlusSignal Placental Epithelial Cells amniotic membrane CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpcplCellPapPlusRawRep2 HPCP cell pA+ + 2 HPC-PL Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002746 2746 GSM979643 Gingeras RIKEN CThi10105ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpcplCellPapPlusRawRep2 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpcplCellPapPlusRawRep1 HPCP cell pA+ + 1 HPC-PL Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002746 2746 GSM979643 Gingeras RIKEN CThi10057 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpcplCellPapPlusRawRep1 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHobCellPapPlusRawRep2 HOB cell pA+ + 2 HOB Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002745 2745 GSM979640 Gingeras RIKEN CThi10037 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHobCellPapPlusRawRep2 PlusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHobCellPapPlusRawRep1 HOB cell pA+ + 1 HOB Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002745 2745 GSM979640 Gingeras RIKEN CThi10036 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHobCellPapPlusRawRep1 PlusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscucCellPapPlusRawRep2 hMUC cell pA+ + 2 hMSC-UC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002767 2767 GSM979650 Gingeras RIKEN CThi10100ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscucCellPapPlusRawRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscucCellPapPlusRawRep1 hMUC cell pA+ + 1 hMSC-UC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002767 2767 GSM979650 Gingeras RIKEN CThi10101CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscucCellPapPlusRawRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscbmCellPapPlusRawRep2 hMBM cell pA+ + 2 hMSC-BM Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002766 2766 GSM979651 Gingeras RIKEN CThi10100ACA cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscbmCellPapPlusRawRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscbmCellPapPlusRawRep1 hMBM cell pA+ + 1 hMSC-BM Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002766 2766 GSM979651 Gingeras RIKEN CThi10103ATC cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscbmCellPapPlusRawRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscatCellPapPlusRawRep2 hMAT cell pA+ + 2 hMSC-AT Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002765 2765 GSM979652 Gingeras RIKEN CThi10104GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscatCellPapPlusRawRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscatCellPapPlusRawRep1 hMAT cell pA+ + 1 hMSC-AT Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002765 2765 GSM979652 Gingeras RIKEN CThi10105ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscatCellPapPlusRawRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmepcCellPapPlusRawRep1 HMEp cell pA+ + 1 HMEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002744 2744 GSM979641 Gingeras RIKEN CThi10105GAT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmepcCellPapPlusRawRep1 PlusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HMEpC whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHfdpcCellPapPlusRawRep2 HFDP cell pA+ + 2 HFDPC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002743 2743 GSM979638 Gingeras RIKEN CThi10100GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHfdpcCellPapPlusRawRep2 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHfdpcCellPapPlusRawRep1 HFDP cell pA+ + 1 HFDPC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002743 2743 GSM979638 Gingeras RIKEN CThi10103ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHfdpcCellPapPlusRawRep1 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHchCellPapPlusRawRep2 HCH cell pA+ + 2 HCH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002742 2742 GSM979639 Gingeras RIKEN CThi10104ACA cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHchCellPapPlusRawRep2 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHchCellPapPlusRawRep1 HCH cell pA+ + 1 HCH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002742 2742 GSM979639 Gingeras RIKEN CThi10104CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHchCellPapPlusRawRep1 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoecCellPapPlusRawRep2 HAoE cell pA+ + 2 HAoEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002741 2741 GSM979636 Gingeras RIKEN CThi10105CTT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoecCellPapPlusRawRep2 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoecCellPapPlusRawRep1 HAoE cell pA+ + 1 HAoEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002741 2741 GSM979636 Gingeras RIKEN CThi10103GAT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoecCellPapPlusRawRep1 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoafCellPapPlusRawRep2 HAoA cell pA+ + 2 HAoAF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002740 2740 GSM979637 Gingeras RIKEN CThi10103CTT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoafCellPapPlusRawRep2 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoafCellPapPlusRawRep1 HAoA cell pA+ + 1 HAoAF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002740 2740 GSM979637 Gingeras RIKEN CThi10100CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoafCellPapPlusRawRep1 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd34mobilizedCellPapPlusRawRep1 CD34 cell pA+ + 1 CD34+_Mobilized Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002739 2739 GSM979635 Gingeras RIKEN CThi10058 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd34mobilizedCellPapPlusRawRep1 PlusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand CD34+ Mobilized whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageBjCellPapPlusSignalRep2 BJ cell pA+ + 2 BJ Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001160 1160 GSM849328 Gingeras RIKEN K19 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageBjCellPapPlusSignalRep2 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageBjCellPapPlusSignalRep1 BJ cell pA+ + 1 BJ Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001160 1160 GSM849328 Gingeras RIKEN K18 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageBjCellPapPlusSignalRep1 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageAg04450CellPapPlusSignalRep2 AG50 cell pA+ + 2 AG04450 Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001159 1159 GSM849358 Gingeras RIKEN K13 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageAg04450CellPapPlusSignalRep2 PlusSignal fetal lung fibroblast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageAg04450CellPapPlusSignalRep1 AG50 cell pA+ + 1 AG04450 Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001159 1159 GSM849358 Gingeras RIKEN K12 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageAg04450CellPapPlusSignalRep1 PlusSignal fetal lung fibroblast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCellPapPlusRawRep4 SKSH cell pA+ + 4 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002763 2763 GSM979646 Gingeras RIKEN CThi10046 cell 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCellPapPlusRawRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCellPapPlusRawRep3 SKSH cell pA+ + 3 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002763 2763 GSM979646 Gingeras RIKEN CThi10043 cell 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCellPapPlusRawRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshNucleusPapPlusRawRep4 SKSH nucl pA+ + 4 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002762 2762 GSM979647 Gingeras RIKEN CThi10048 nucleus 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshNucleusPapPlusRawRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshNucleusPapPlusRawRep3 SKSH nucl pA+ + 3 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002762 2762 GSM979647 Gingeras RIKEN CThi10045 nucleus 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshNucleusPapPlusRawRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCytosolPapPlusRawRep4 SKSH cyto pA+ + 4 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002761 2761 GSM979648 Gingeras RIKEN CThi10047 cytosol 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCytosolPapPlusRawRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCytosolPapPlusRawRep3 SKSH cyto pA+ + 3 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002761 2761 GSM979648 Gingeras RIKEN CThi10044 cytosol 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCytosolPapPlusRawRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMonocd14CellPapPlusRawRep2 CD14 cell pA+ + 2 Monocytes-CD14+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002757 2757 GSM979655 Gingeras RIKEN CThi10022 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMonocd14CellPapPlusRawRep2 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand Monocytes-CD14+ whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMonocd14CellPapPlusRawRep1 CD14 cell pA+ + 1 Monocytes-CD14+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002757 2757 GSM979655 Gingeras RIKEN CThi10021 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMonocd14CellPapPlusRawRep1 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand Monocytes-CD14+ whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CellPapPlusRawRep2 MCF7 cell pA+ + 2 MCF-7 Cage ENCODE Mar 2012 Freeze 2011-06-17 2012-03-17 wgEncodeEH001151 1151 GSM849364 Gingeras RIKEN K11 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageMcf7CellPapPlusRawRep2 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CellPapPlusSignalRep1 MCF7 cell pA+ + 1 MCF-7 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001151 1151 GSM849364 Gingeras RIKEN K07 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageMcf7CellPapPlusSignalRep1 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7NucleusPapPlusRawRep4 MCF7 nucl pA+ + 4 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002756 2756 GSM979654 Gingeras RIKEN CThi10054 nucleus 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7NucleusPapPlusRawRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7NucleusPapPlusRawRep3 MCF7 nucl pA+ + 3 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002756 2756 GSM979654 Gingeras RIKEN CThi10052 nucleus 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7NucleusPapPlusRawRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CytosolPapPlusRawRep4 MCF7 cyto pA+ + 4 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002755 2755 GSM979657 Gingeras RIKEN CThi10053 cytosol 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7CytosolPapPlusRawRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CytosolPapPlusRawRep3 MCF7 cyto pA+ + 3 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002755 2755 GSM979657 Gingeras RIKEN CThi10051 cytosol 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7CytosolPapPlusRawRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CellPapPlusRawRep2 IMR9 cell pA+ + 2 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002754 2754 GSM979656 Gingeras RIKEN CThi10018 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CellPapPlusRawRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CellPapPlusRawRep1 IMR9 cell pA+ + 1 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002754 2754 GSM979656 Gingeras RIKEN CThi10016 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CellPapPlusRawRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90NucleusPapPlusRawRep2 IMR9 nucl pA+ + 2 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002753 2753 GSM979659 Gingeras RIKEN CThi10026 nucleus 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90NucleusPapPlusRawRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90NucleusPapPlusRawRep1 IMR9 nucl pA+ + 1 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002753 2753 GSM979659 Gingeras RIKEN CThi10025 nucleus 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90NucleusPapPlusRawRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CytosolPapPlusRawRep2 IMR9 cyto pA+ + 2 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002752 2752 GSM979658 Gingeras RIKEN CThi10019 cytosol 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CytosolPapPlusRawRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CytosolPapPlusRawRep1 IMR9 cyto pA+ + 1 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002752 2752 GSM979658 Gingeras RIKEN CThi10017 cytosol 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CytosolPapPlusRawRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCellPapPlusSignalRep2 HUVE cell pA+ + 2 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001141 1141 GSM849327 Gingeras RIKEN J79 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCellPapPlusSignalRep2 PlusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCellPapPlusSignalRep1 HUVE cell pA+ + 1 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001141 1141 GSM849327 Gingeras RIKEN J78 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCellPapPlusSignalRep1 PlusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPapPlusSignalRep4 HUVE nucl pA+ + 2 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001143 1143 GSM849325 Gingeras RIKEN K06 nucleus 4 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPapPlusSignalRep4 PlusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPapPlusSignalRep3 HUVE nucl pA+ + 1 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001143 1143 GSM849325 Gingeras RIKEN K05 nucleus 3 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPapPlusSignalRep3 PlusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPamPlusRawRep1 HUVE nucl pA- + 1 HUVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-31 wgEncodeEH002749 2749 GSM979644 Gingeras RIKEN CTig10027 nucleus 1x36 1 longNonPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPamPlusRawRep1 PlusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPapPlusSignalRep4 HUVE cyto pA+ + 2 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001142 1142 GSM849324 Gingeras RIKEN K04 cytosol 4 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCytosolPapPlusSignalRep4 PlusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPapPlusSignalRep3 HUVE cyto pA+ + 1 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001142 1142 GSM849324 Gingeras RIKEN K03 cytosol 3 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCytosolPapPlusSignalRep3 PlusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPamPlusSignal HUVE cyto pA- + 1 HUVEC Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-13 2010-10-13 wgEncodeEH000342 342 GSM849350 Gingeras RIKEN I72 bedtools v2.7.1 cytosol longNonPolyA wgEncodeRikenCageHuvecCytosolPamPlusSignal PlusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CellPapPlusSignalRep2 HepG cell pA+ + 2 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001149 1149 GSM849335 Gingeras RIKEN K02 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CellPapPlusSignalRep2 PlusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CellPapPlusSignalRep1 HepG cell pA+ + 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001149 1149 GSM849335 Gingeras RIKEN K01 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CellPapPlusSignalRep1 PlusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPapPlusSignalRep2 HepG nucl pA+ + 2 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001148 1148 GSM849334 Gingeras RIKEN J99 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2NucleusPapPlusSignalRep2 PlusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPapPlusSignalRep1 HepG nucl pA+ + 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001148 1148 GSM849334 Gingeras RIKEN J98 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2NucleusPapPlusSignalRep1 PlusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPamPlusSignal HepG nucl pA- + 1 HepG2 Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-13 2010-10-13 wgEncodeEH000345 345 GSM849345 Gingeras RIKEN I44 bedtools v2.7.1 nucleus longNonPolyA wgEncodeRikenCageHepg2NucleusPamPlusSignal PlusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleolusTotalPlusSignal HepG nlus tot + 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-08-23 2010-01-13 2010-10-13 wgEncodeEH000344 344 GSM849344 Gingeras RIKEN I68 nucleolus total wgEncodeRikenCageHepg2NucleolusTotalPlusSignal PlusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the plus strand HepG2 nucleolus total CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPapPlusSignalRep2 HepG cyto pA+ + 2 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001147 1147 GSM849343 Gingeras RIKEN J90 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CytosolPapPlusSignalRep2 PlusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPapPlusSignalRep1 HepG cyto pA+ + 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001147 1147 GSM849343 Gingeras RIKEN J89 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CytosolPapPlusSignalRep1 PlusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPamPlusSignal HepG cyto pA- + 1 HepG2 Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-13 2010-10-13 wgEncodeEH000343 343 GSM849351 Gingeras RIKEN I42 bedtools v2.7.1 cytosol longNonPolyA wgEncodeRikenCageHepg2CytosolPamPlusSignal PlusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CellPapPlusSignalRep2 HeLa cell pA+ + 2 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001146 1146 GSM849342 Gingeras RIKEN J81 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CellPapPlusSignalRep2 PlusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CellPapPlusSignalRep1 HeLa cell pA+ + 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001146 1146 GSM849342 Gingeras RIKEN J80 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CellPapPlusSignalRep1 PlusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPapPlusSignalRep2 HeLa nucl pA+ + 2 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001145 1145 GSM849331 Gingeras RIKEN J97 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPapPlusSignalRep2 PlusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPapPlusSignalRep1 HeLa nucl pA+ + 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001145 1145 GSM849331 Gingeras RIKEN J96 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPapPlusSignalRep1 PlusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPamPlusRawRep1 HeLa nucl pA- + 1 HeLa-S3 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-31 wgEncodeEH002775 2775 GSM979631 Gingeras RIKEN CTig10028 nucleus 1x36 1 longNonPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPamPlusRawRep1 PlusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleolusTotalPlusSignal HeLa nlus tot + 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-10-29 2011-07-29 wgEncodeEH001156 1156 GSM849363 Gingeras RIKEN J58 nucleolus total wgEncodeRikenCageHelas3NucleolusTotalPlusSignal PlusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the plus strand Hela-S3 nucleolus total CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPapPlusSignalRep2 HeLa cyto pA+ + 2 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001144 1144 GSM849330 Gingeras RIKEN J88 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CytosolPapPlusSignalRep2 PlusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPapPlusSignalRep1 HeLa cyto pA+ + 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001144 1144 GSM849330 Gingeras RIKEN J87 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CytosolPapPlusSignalRep1 PlusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPamPlusSignal HeLa cyto pA- + 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-10-29 2011-07-29 wgEncodeEH001155 1155 GSM849360 Gingeras RIKEN J56 cytosol longNonPolyA wgEncodeRikenCageHelas3CytosolPamPlusSignal PlusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd20CellPapPlusRawRep2 CD20 cell pA+ + 2 CD20+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002738 2738 GSM979634 Gingeras RIKEN CThi10024 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd20CellPapPlusRawRep2 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd20CellPapPlusRawRep1 CD20 cell pA+ + 1 CD20+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002738 2738 GSM979634 Gingeras RIKEN CThi10023 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd20CellPapPlusRawRep1 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CellPapPlusSignalRep2 A549 cell pA+ + 2 A549 Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001158 1158 GSM849359 Gingeras RIKEN K17 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageA549CellPapPlusSignalRep2 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CellPapPlusSignalRep1 A549 cell pA+ + 1 A549 Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001158 1158 GSM849359 Gingeras RIKEN K16 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageA549CellPapPlusSignalRep1 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549NucleusPapPlusRawRep4 A549 nucl pA+ + 4 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002737 2737 GSM979633 Gingeras RIKEN CThi10060 nucleus 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549NucleusPapPlusRawRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549NucleusPapPlusRawRep3 A549 nucl pA+ + 3 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002737 2737 GSM979633 Gingeras RIKEN CThi10106 nucleus 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549NucleusPapPlusRawRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CytosolPapPlusRawRep4 A549 cyto pA+ + 4 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002736 2736 GSM979632 Gingeras RIKEN CThi10059 cytosol 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549CytosolPapPlusRawRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ CAGE Plus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CytosolPapPlusRawRep3 A549 cyto pA+ + 3 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002736 2736 GSM979632 Gingeras RIKEN CThi10049 cytosol 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549CytosolPapPlusRawRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ CAGE Plus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CellPapPlusSignalRep2 K562 cell pA+ + 2 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001150 1150 GSM849365 Gingeras RIKEN J71 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageK562CellPapPlusSignalRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CellPapPlusSignalRep1 K562 cell pA+ + 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001150 1150 GSM849365 Gingeras RIKEN J70 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageK562CellPapPlusSignalRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562PolysomePamPlusSignal K562 psom pA- + 1 K562 Cage ENCODE June 2010 Freeze 2010-06-21 2009-02-19 2009-11-19 wgEncodeEH000337 337 GSM849354 Gingeras RIKEN I32 bedtools v2.7.1 polysome longNonPolyA wgEncodeRikenCageK562PolysomePamPlusSignal PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Strand of mRNA with ribosomes attached Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand K562 polysome polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPapPlusSignalRep2 K562 nucl pA+ + 2 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000333 333 GSM849338 Gingeras RIKEN J92 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageK562NucleusPapPlusSignalRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPapPlusSignalRep1 K562 nucl pA+ + 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000333 333 GSM849338 Gingeras RIKEN J91 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageK562NucleusPapPlusSignalRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPamPlusSignal K562 nucl pA- + 1 K562 Cage ENCODE Jan 2011 Freeze 2010-08-26 2008-12-09 2009-09-09 wgEncodeEH000330 330 GSM849337 Gingeras RIKEN I23 nucleus longNonPolyA wgEncodeRikenCageK562NucleusPamPlusSignal PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleoplasmTotalPlusSignal K562 nplm tot + 1 K562 Cage ENCODE June 2010 Freeze 2010-06-21 2009-02-19 2009-11-19 wgEncodeEH000336 336 GSM849340 Gingeras RIKEN I34 bedtools v2.7.1 nucleoplasm total wgEncodeRikenCageK562NucleoplasmTotalPlusSignal PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center That part of the nuclear content other than the chromosomes or the nucleolus Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the plus strand K562 nucleoplasm total CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleolusTotalPlusSignal K562 nlus tot + 1 K562 Cage ENCODE Jan 2011 Freeze 2010-11-09 2011-08-09 wgEncodeEH000335 335 GSM849332 Gingeras RIKEN I33 nucleolus total wgEncodeRikenCageK562NucleolusTotalPlusSignal PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the plus strand K562 nucleolus total CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPapPlusSignalRep2 K562 cyto pA+ + 2 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000332 332 GSM849339 Gingeras RIKEN J83 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageK562CytosolPapPlusSignalRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPapPlusSignalRep1 K562 cyto pA+ + 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000332 332 GSM849339 Gingeras RIKEN J82 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageK562CytosolPapPlusSignalRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPamPlusSignal K562 cyto pA- + 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-22 2008-12-09 2009-09-09 wgEncodeEH000329 329 GSM849353 Gingeras RIKEN I22 cytosol longNonPolyA bedtools v2.7.1 wgEncodeRikenCageK562CytosolPamPlusSignal PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562ChromatinTotalPlusSignal K562 chrm tot + 1 K562 Cage ENCODE June 2010 Freeze 2010-06-21 2009-02-19 2009-11-19 wgEncodeEH000334 334 GSM849333 Gingeras RIKEN I35 bedtools v2.7.1 chromatin total wgEncodeRikenCageK562ChromatinTotalPlusSignal PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Nuclear DNA and associated proteins Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the plus strand K562 chromatin total CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPapPlusSignalRep2 H1ES cell pA+ + 2 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001138 1138 GSM849357 Gingeras RIKEN J75 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCellPapPlusSignalRep2 PlusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPapPlusSignalRep1 H1ES cell pA+ + 1 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001138 1138 GSM849357 Gingeras RIKEN J74 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCellPapPlusSignalRep1 PlusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPamPlusSignal H1ES cell pA- + 1 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-22 2010-01-13 2010-10-13 wgEncodeEH000341 341 GSM849355 Gingeras RIKEN I67 cell longNonPolyA bedtools v2.7.1 wgEncodeRikenCageH1hescCellPamPlusSignal PlusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescNucleusPapPlusSignalRep2 H1ES nucl pA+ + 2 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001140 1140 GSM849326 Gingeras RIKEN J95 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescNucleusPapPlusSignalRep2 PlusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC nucleus polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCytosolPapPlusSignalRep2 H1ES cyto pA+ + 2 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001139 1139 GSM849356 Gingeras RIKEN J86 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCytosolPapPlusSignalRep2 PlusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC cytosol polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CellPapPlusSignalRep2 GM78 cell pA+ + 2 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001680 1680 GSM849368 Gingeras RIKEN J73 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CellPapPlusSignalRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CellPapPlusSignalRep1 GM78 cell pA+ + 1 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001680 1680 GSM849368 Gingeras RIKEN J72 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CellPapPlusSignalRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPapPlusSignalRep2 GM78 nucl pA+ + 2 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001678 1678 GSM849348 Gingeras RIKEN J94 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878NucleusPapPlusSignalRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPapPlusSignalRep1 GM78 nucl pA+ + 1 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001678 1678 GSM849348 Gingeras RIKEN J93 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878NucleusPapPlusSignalRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPamPlusSignalRep1 GM78 nucl pA- + 1 GM12878 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000339 339 GSM849341 Gingeras RIKEN J59 nucleus longNonPolyA wgEncodeRikenCageGm12878NucleusPamPlusSignalRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleolusTotalPlusSignal GM78 nlus tot + 1 GM12878 Cage ENCODE Jan 2011 Freeze 2010-08-23 2010-01-14 2010-10-13 wgEncodeEH000340 340 GSM849352 Gingeras RIKEN I69 nucleolus total wgEncodeRikenCageGm12878NucleolusTotalPlusSignal PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the plus strand GM12878 nucleolus total CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPapPlusSignalRep2 GM78 cyto pA+ + 2 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEH001679 1679 GSM849349 Gingeras RIKEN J85 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CytosolPapPlusSignalRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ CAGE Plus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPapPlusSignalRep1 GM78 cyto pA+ + 1 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001679 1679 GSM849349 Gingeras RIKEN J84 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CytosolPapPlusSignalRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPamPlusSignal GM78 cyto pA- + 1 GM12878 Cage ENCODE June 2010 Freeze 2010-06-21 2009-03-09 2009-12-09 wgEncodeEH000338 338 GSM849329 Gingeras RIKEN I27 bedtools v2.7.1 cytosol longNonPolyA wgEncodeRikenCageGm12878CytosolPamPlusSignal PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA- CAGE Plus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageViewMinusSignal Minus Signal RNA Subcellular CAGE Localization from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshraCellPapMinusSignalRep2 SKSH cell pA+ - 2 SK-N-SH_RA Cage ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001157 1157 GSM849362 Gingeras RIKEN K15 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageSknshraCellPapMinusSignalRep2 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH_RA whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshraCellPapMinusRawRep1 SKSH cell pAP - 1 SK-N-SH_RA Cage ENCODE Mar 2012 Freeze 2011-05-31 2012-03-02 wgEncodeEH001157 1157 GSM849362 Gingeras RIKEN K14 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageSknshraCellPapMinusRawRep1 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH_RA whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSkmcCellPapMinusRawRep2 SkMC cell pA+ - 2 SkMC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002764 2764 GSM979653 Gingeras RIKEN CThi10031 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSkmcCellPapMinusRawRep2 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSkmcCellPapMinusRawRep1 SkMC cell pA+ - 1 SkMC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002764 2764 GSM979653 Gingeras RIKEN CThi10030 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSkmcCellPapMinusRawRep1 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageProstateCellPamMinusSignal Pros cell pA- - 1 prostate Cage ENCODE Jan 2011 Freeze 2010-09-22 2008-12-09 2009-09-09 wgEncodeEH000331 331 GSM849336 Gingeras RIKEN I09 cell longNonPolyA bedtools v2.7.1 wgEncodeRikenCageProstateCellPamMinusSignal MinusSignal prostate tissue purchased for CSHL project CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand Prostate whole cell polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemm2CellPapMinusRawRep2 NHEM cell pA+ - 2 NHEM_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002760 2760 GSM979649 Gingeras RIKEN CThi10102GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemm2CellPapMinusRawRep2 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM M2 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemm2CellPapMinusRawRep1 NHEM cell pA+ - 1 NHEM_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002760 2760 GSM979649 Gingeras RIKEN CThi10056 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemm2CellPapMinusRawRep1 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM M2 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemfm2CellPapMinusRawRep2 NHEf cell pA+ - 2 NHEM.f_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002759 2759 GSM979663 Gingeras RIKEN CThi10055 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemfm2CellPapMinusRawRep2 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f M2 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemfm2CellPapMinusRawRep1 NHEf cell pA+ - 1 NHEM.f_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002759 2759 GSM979663 Gingeras RIKEN CThi10102CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemfm2CellPapMinusRawRep1 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f M2 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCellPapMinusSignalRep2 NHEK cell pA+ - 2 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001152 1152 GSM849367 Gingeras RIKEN J77 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCellPapMinusSignalRep2 MinusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCellPapMinusSignalRep1 NHEK cell pA+ - 1 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001152 1152 GSM849367 Gingeras RIKEN J76 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCellPapMinusSignalRep1 MinusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPapMinusRawRep4 NHEK nucl pA+ - 4 NHEK Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH001154 1154 GSM849361 Gingeras RIKEN CTig10011 nucleus 1x36 4 longPolyA Illumina_GA2x F wgEncodeRikenCageNhekNucleusPapMinusRawRep4 MinusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Female Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPapMinusSignalRep3 NHEK nucl pA+ - 1 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001154 1154 GSM849361 Gingeras RIKEN K09 nucleus 3 longPolyA Illumina_GA2x wgEncodeRikenCageNhekNucleusPapMinusSignalRep3 MinusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPamMinusSignal NHEK nucl pA- - 1 NHEK Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000347 347 GSM849347 Gingeras RIKEN I71 bedtools v2.7.1 nucleus longNonPolyA wgEncodeRikenCageNhekNucleusPamMinusSignal MinusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPapMinusRawRep4 NHEK cyto pA+ - 2 NHEK Cage ENCODE Mar 2012 Freeze 2011-05-31 2012-03-02 wgEncodeEH001153 1153 GSM849366 Gingeras RIKEN K20 cytosol 4 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCytosolPapMinusRawRep4 MinusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPapMinusSignalRep3 NHEK cyto pA+ - 1 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001153 1153 GSM849366 Gingeras RIKEN K08 cytosol 3 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCytosolPapMinusSignalRep3 MinusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPamMinusSignal NHEK cyto pA- - 1 NHEK Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000346 346 GSM849346 Gingeras RIKEN I70 bedtools v2.7.1 cytosol longNonPolyA wgEncodeRikenCageNhekCytosolPamMinusSignal MinusSignal epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhdfCellPapMinusRawRep2 NHDF cell pA+ - 2 NHDF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002758 2758 GSM979662 Gingeras RIKEN CThi10033 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhdfCellPapMinusRawRep2 MinusSignal Dermal Fibroblasts from temple / breast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhdfCellPapMinusRawRep1 NHDF cell pA+ - 1 NHDF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002758 2758 GSM979662 Gingeras RIKEN CThi10032 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhdfCellPapMinusRawRep1 MinusSignal Dermal Fibroblasts from temple / breast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHwpCellPapMinusRawRep2 HWP cell pA+ - 2 HWP Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002751 2751 GSM979661 Gingeras RIKEN CThi10101ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHwpCellPapMinusRawRep2 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHwpCellPapMinusRawRep1 HWP cell pA+ - 1 HWP Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002751 2751 GSM979661 Gingeras RIKEN CThi10101ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHwpCellPapMinusRawRep1 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHvmfCellPapMinusRawRep2 HVMF cell pA+ - 2 HVMF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002750 2750 GSM979660 Gingeras RIKEN CThi10035 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHvmfCellPapMinusRawRep2 MinusSignal villous mesenchymal fibroblast cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHvmfCellPapMinusRawRep1 HVMF cell pA+ - 1 HVMF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002750 2750 GSM979660 Gingeras RIKEN CThi10034 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHvmfCellPapMinusRawRep1 MinusSignal villous mesenchymal fibroblast cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHsavecCellPapMinusRawRep2 HSaV cell pA+ - 2 HSaVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002748 2748 GSM979645 Gingeras RIKEN CThi10102ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHsavecCellPapMinusRawRep2 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHsavecCellPapMinusRawRep1 HSaV cell pA+ - 1 HSaVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002748 2748 GSM979645 Gingeras RIKEN CThi10102ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHsavecCellPapMinusRawRep1 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpiepcCellPapMinusRawRep2 HPIE cell pA+ - 2 HPIEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002747 2747 GSM979642 Gingeras RIKEN CThi10101GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpiepcCellPapMinusRawRep2 MinusSignal Placental Epithelial Cells amniotic membrane CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpiepcCellPapMinusRawRep1 HPIE cell pA+ - 1 HPIEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002747 2747 GSM979642 Gingeras RIKEN CThi10104ATC cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpiepcCellPapMinusRawRep1 MinusSignal Placental Epithelial Cells amniotic membrane CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpcplCellPapMinusRawRep2 HPCP cell pA+ - 2 HPC-PL Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002746 2746 GSM979643 Gingeras RIKEN CThi10105ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpcplCellPapMinusRawRep2 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpcplCellPapMinusRawRep1 HPCP cell pA+ - 1 HPC-PL Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002746 2746 GSM979643 Gingeras RIKEN CThi10057 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpcplCellPapMinusRawRep1 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHobCellPapMinusRawRep2 HOB cell pA+ - 2 HOB Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002745 2745 GSM979640 Gingeras RIKEN CThi10037 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHobCellPapMinusRawRep2 MinusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHobCellPapMinusRawRep1 HOB cell pA+ - 1 HOB Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002745 2745 GSM979640 Gingeras RIKEN CThi10036 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHobCellPapMinusRawRep1 MinusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscucCellPapMinusRawRep2 hMUC cell pA+ - 2 hMSC-UC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002767 2767 GSM979650 Gingeras RIKEN CThi10100ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscucCellPapMinusRawRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscucCellPapMinusRawRep1 hMUC cell pA+ - 1 hMSC-UC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002767 2767 GSM979650 Gingeras RIKEN CThi10101CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscucCellPapMinusRawRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscbmCellPapMinusRawRep2 hMBM cell pA+ - 2 hMSC-BM Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002766 2766 GSM979651 Gingeras RIKEN CThi10100ACA cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscbmCellPapMinusRawRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscbmCellPapMinusRawRep1 hMBM cell pA+ - 1 hMSC-BM Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002766 2766 GSM979651 Gingeras RIKEN CThi10103ATC cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscbmCellPapMinusRawRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscatCellPapMinusRawRep2 hMAT cell pA+ - 2 hMSC-AT Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002765 2765 GSM979652 Gingeras RIKEN CThi10104GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscatCellPapMinusRawRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscatCellPapMinusRawRep1 hMAT cell pA+ - 1 hMSC-AT Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002765 2765 GSM979652 Gingeras RIKEN CThi10105ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscatCellPapMinusRawRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmepcCellPapMinusRawRep1 HMEp cell pA+ - 1 HMEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002744 2744 GSM979641 Gingeras RIKEN CThi10105GAT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmepcCellPapMinusRawRep1 MinusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HMEpC whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHfdpcCellPapMinusRawRep2 HFDP cell pA+ - 2 HFDPC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002743 2743 GSM979638 Gingeras RIKEN CThi10100GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHfdpcCellPapMinusRawRep2 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHfdpcCellPapMinusRawRep1 HFDP cell pA+ - 1 HFDPC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002743 2743 GSM979638 Gingeras RIKEN CThi10103ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHfdpcCellPapMinusRawRep1 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHchCellPapMinusRawRep2 HCH cell pA+ - 2 HCH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002742 2742 GSM979639 Gingeras RIKEN CThi10104ACA cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHchCellPapMinusRawRep2 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHchCellPapMinusRawRep1 HCH cell pA+ - 1 HCH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002742 2742 GSM979639 Gingeras RIKEN CThi10104CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHchCellPapMinusRawRep1 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoecCellPapMinusRawRep2 HAoE cell pA+ - 2 HAoEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002741 2741 GSM979636 Gingeras RIKEN CThi10105CTT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoecCellPapMinusRawRep2 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoecCellPapMinusRawRep1 HAoE cell pA+ - 1 HAoEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002741 2741 GSM979636 Gingeras RIKEN CThi10103GAT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoecCellPapMinusRawRep1 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoafCellPapMinusRawRep2 HAoA cell pA+ - 2 HAoAF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002740 2740 GSM979637 Gingeras RIKEN CThi10103CTT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoafCellPapMinusRawRep2 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoafCellPapMinusRawRep1 HAoA cell pA+ - 1 HAoAF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002740 2740 GSM979637 Gingeras RIKEN CThi10100CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoafCellPapMinusRawRep1 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd34mobilizedCellPapMinusRawRep1 CD34 cell pA+ - 1 CD34+_Mobilized Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002739 2739 GSM979635 Gingeras RIKEN CThi10058 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd34mobilizedCellPapMinusRawRep1 MinusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand CD34+ Mobilized whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageBjCellPapMinusSignalRep2 BJ cell pA+ - 2 BJ Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001160 1160 GSM849328 Gingeras RIKEN K19 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageBjCellPapMinusSignalRep2 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageBjCellPapMinusSignalRep1 BJ cell pA+ - 1 BJ Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001160 1160 GSM849328 Gingeras RIKEN K18 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageBjCellPapMinusSignalRep1 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageAg04450CellPapMinusSignalRep2 AG50 cell pA+ - 2 AG04450 Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001159 1159 GSM849358 Gingeras RIKEN K13 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageAg04450CellPapMinusSignalRep2 MinusSignal fetal lung fibroblast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageAg04450CellPapMinusSignalRep1 AG50 cell pA+ - 1 AG04450 Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001159 1159 GSM849358 Gingeras RIKEN K12 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageAg04450CellPapMinusSignalRep1 MinusSignal fetal lung fibroblast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCellPapMinusRawRep4 SKSH cell pA+ - 4 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002763 2763 GSM979646 Gingeras RIKEN CThi10046 cell 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCellPapMinusRawRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCellPapMinusRawRep3 SKSH cell pA+ - 3 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002763 2763 GSM979646 Gingeras RIKEN CThi10043 cell 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCellPapMinusRawRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshNucleusPapMinusRawRep4 SKSH nucl pA+ - 4 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002762 2762 GSM979647 Gingeras RIKEN CThi10048 nucleus 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshNucleusPapMinusRawRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshNucleusPapMinusRawRep3 SKSH nucl pA+ - 3 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002762 2762 GSM979647 Gingeras RIKEN CThi10045 nucleus 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshNucleusPapMinusRawRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCytosolPapMinusRawRep4 SKSH cyto pA+ - 4 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002761 2761 GSM979648 Gingeras RIKEN CThi10047 cytosol 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCytosolPapMinusRawRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCytosolPapMinusRawRep3 SKSH cyto pA+ - 3 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002761 2761 GSM979648 Gingeras RIKEN CThi10044 cytosol 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCytosolPapMinusRawRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMonocd14CellPapMinusRawRep2 CD14 cell pA+ - 2 Monocytes-CD14+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002757 2757 GSM979655 Gingeras RIKEN CThi10022 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMonocd14CellPapMinusRawRep2 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand Monocytes-CD14+ whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMonocd14CellPapMinusRawRep1 CD14 cell pA+ - 1 Monocytes-CD14+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002757 2757 GSM979655 Gingeras RIKEN CThi10021 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMonocd14CellPapMinusRawRep1 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand Monocytes-CD14+ whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CellPapMinusRawRep2 MCF7 cell pA+ - 2 MCF-7 Cage ENCODE Mar 2012 Freeze 2011-06-17 2012-03-17 wgEncodeEH001151 1151 GSM849364 Gingeras RIKEN K11 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageMcf7CellPapMinusRawRep2 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CellPapMinusSignalRep1 MCF7 cell pA+ - 1 MCF-7 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001151 1151 GSM849364 Gingeras RIKEN K07 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageMcf7CellPapMinusSignalRep1 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7NucleusPapMinusRawRep4 MCF7 nucl pA+ - 4 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002756 2756 GSM979654 Gingeras RIKEN CThi10054 nucleus 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7NucleusPapMinusRawRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7NucleusPapMinusRawRep3 MCF7 nucl pA+ - 3 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002756 2756 GSM979654 Gingeras RIKEN CThi10052 nucleus 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7NucleusPapMinusRawRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CytosolPapMinusRawRep4 MCF7 cyto pA+ - 4 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002755 2755 GSM979657 Gingeras RIKEN CThi10053 cytosol 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7CytosolPapMinusRawRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CytosolPapMinusRawRep3 MCF7 cyto pA+ - 3 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002755 2755 GSM979657 Gingeras RIKEN CThi10051 cytosol 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7CytosolPapMinusRawRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CellPapMinusRawRep2 IMR9 cell pA+ - 2 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002754 2754 GSM979656 Gingeras RIKEN CThi10018 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CellPapMinusRawRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CellPapMinusRawRep1 IMR9 cell pA+ - 1 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002754 2754 GSM979656 Gingeras RIKEN CThi10016 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CellPapMinusRawRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90NucleusPapMinusRawRep2 IMR9 nucl pA+ - 2 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002753 2753 GSM979659 Gingeras RIKEN CThi10026 nucleus 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90NucleusPapMinusRawRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90NucleusPapMinusRawRep1 IMR9 nucl pA+ - 1 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002753 2753 GSM979659 Gingeras RIKEN CThi10025 nucleus 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90NucleusPapMinusRawRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CytosolPapMinusRawRep2 IMR9 cyto pA+ - 2 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002752 2752 GSM979658 Gingeras RIKEN CThi10019 cytosol 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CytosolPapMinusRawRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CytosolPapMinusRawRep1 IMR9 cyto pA+ - 1 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002752 2752 GSM979658 Gingeras RIKEN CThi10017 cytosol 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CytosolPapMinusRawRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCellPapMinusSignalRep2 HUVE cell pA+ - 2 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001141 1141 GSM849327 Gingeras RIKEN J79 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCellPapMinusSignalRep2 MinusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCellPapMinusSignalRep1 HUVE cell pA+ - 1 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001141 1141 GSM849327 Gingeras RIKEN J78 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCellPapMinusSignalRep1 MinusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPapMinusSignalRep4 HUVE nucl pA+ - 2 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001143 1143 GSM849325 Gingeras RIKEN K06 nucleus 4 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPapMinusSignalRep4 MinusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPapMinusSignalRep3 HUVE nucl pA+ - 1 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001143 1143 GSM849325 Gingeras RIKEN K05 nucleus 3 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPapMinusSignalRep3 MinusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPamMinusRawRep1 HUVE nucl pA- - 1 HUVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-31 wgEncodeEH002749 2749 GSM979644 Gingeras RIKEN CTig10027 nucleus 1x36 1 longNonPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPamMinusRawRep1 MinusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA- CAGE Raw signal - Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPapMinusSignalRep4 HUVE cyto pA+ - 2 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001142 1142 GSM849324 Gingeras RIKEN K04 cytosol 4 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCytosolPapMinusSignalRep4 MinusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPapMinusSignalRep3 HUVE cyto pA+ - 1 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001142 1142 GSM849324 Gingeras RIKEN K03 cytosol 3 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCytosolPapMinusSignalRep3 MinusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPamMinusSignal HUVE cyto pA- - 1 HUVEC Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-13 2010-10-13 wgEncodeEH000342 342 GSM849350 Gingeras RIKEN I72 bedtools v2.7.1 cytosol longNonPolyA wgEncodeRikenCageHuvecCytosolPamMinusSignal MinusSignal umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CellPapMinusSignalRep2 HepG cell pA+ - 2 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001149 1149 GSM849335 Gingeras RIKEN K02 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CellPapMinusSignalRep2 MinusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CellPapMinusSignalRep1 HepG cell pA+ - 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001149 1149 GSM849335 Gingeras RIKEN K01 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CellPapMinusSignalRep1 MinusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPapMinusSignalRep2 HepG nucl pA+ - 2 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001148 1148 GSM849334 Gingeras RIKEN J99 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2NucleusPapMinusSignalRep2 MinusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPapMinusSignalRep1 HepG nucl pA+ - 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001148 1148 GSM849334 Gingeras RIKEN J98 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2NucleusPapMinusSignalRep1 MinusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPamMinusSignal HepG nucl pA- - 1 HepG2 Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-13 2010-10-13 wgEncodeEH000345 345 GSM849345 Gingeras RIKEN I44 bedtools v2.7.1 nucleus longNonPolyA wgEncodeRikenCageHepg2NucleusPamMinusSignal MinusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleolusTotalMinusSignal HepG nlus tot - 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-08-23 2010-01-13 2010-10-13 wgEncodeEH000344 344 GSM849344 Gingeras RIKEN I68 nucleolus total wgEncodeRikenCageHepg2NucleolusTotalMinusSignal MinusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the minus strand HepG2 nucleolus total CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPapMinusSignalRep2 HepG cyto pA+ - 2 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001147 1147 GSM849343 Gingeras RIKEN J90 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CytosolPapMinusSignalRep2 MinusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPapMinusSignalRep1 HepG cyto pA+ - 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001147 1147 GSM849343 Gingeras RIKEN J89 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CytosolPapMinusSignalRep1 MinusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPamMinusSignal HepG cyto pA- - 1 HepG2 Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-13 2010-10-13 wgEncodeEH000343 343 GSM849351 Gingeras RIKEN I42 bedtools v2.7.1 cytosol longNonPolyA wgEncodeRikenCageHepg2CytosolPamMinusSignal MinusSignal hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CellPapMinusSignalRep2 HeLa cell pA+ - 2 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001146 1146 GSM849342 Gingeras RIKEN J81 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CellPapMinusSignalRep2 MinusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CellPapMinusSignalRep1 HeLa cell pA+ - 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001146 1146 GSM849342 Gingeras RIKEN J80 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CellPapMinusSignalRep1 MinusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPapMinusSignalRep2 HeLa nucl pA+ - 2 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001145 1145 GSM849331 Gingeras RIKEN J97 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPapMinusSignalRep2 MinusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPapMinusSignalRep1 HeLa nucl pA+ - 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001145 1145 GSM849331 Gingeras RIKEN J96 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPapMinusSignalRep1 MinusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPamMinusRawRep1 HeLa nucl pA- - 1 HeLa-S3 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-31 wgEncodeEH002775 2775 GSM979631 Gingeras RIKEN CTig10028 nucleus 1x36 1 longNonPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPamMinusRawRep1 MinusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA- CAGE Raw signal - Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleolusTotalMinusSignal HeLa nlus tot - 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-10-29 2011-07-29 wgEncodeEH001156 1156 GSM849363 Gingeras RIKEN J58 nucleolus total wgEncodeRikenCageHelas3NucleolusTotalMinusSignal MinusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the minus strand Hela-S3 nucleolus total CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPapMinusSignalRep2 HeLa cyto pA+ - 2 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001144 1144 GSM849330 Gingeras RIKEN J88 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CytosolPapMinusSignalRep2 MinusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPapMinusSignalRep1 HeLa cyto pA+ - 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001144 1144 GSM849330 Gingeras RIKEN J87 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CytosolPapMinusSignalRep1 MinusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPamMinusSignal HeLa cyto pA- - 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-10-29 2011-07-29 wgEncodeEH001155 1155 GSM849360 Gingeras RIKEN J56 cytosol longNonPolyA wgEncodeRikenCageHelas3CytosolPamMinusSignal MinusSignal cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd20CellPapMinusRawRep2 CD20 cell pA+ - 2 CD20+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002738 2738 GSM979634 Gingeras RIKEN CThi10024 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd20CellPapMinusRawRep2 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd20CellPapMinusRawRep1 CD20 cell pA+ - 1 CD20+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002738 2738 GSM979634 Gingeras RIKEN CThi10023 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd20CellPapMinusRawRep1 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CellPapMinusSignalRep2 A549 cell pA+ - 2 A549 Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001158 1158 GSM849359 Gingeras RIKEN K17 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageA549CellPapMinusSignalRep2 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CellPapMinusSignalRep1 A549 cell pA+ - 1 A549 Cage ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001158 1158 GSM849359 Gingeras RIKEN K16 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageA549CellPapMinusSignalRep1 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549NucleusPapMinusRawRep4 A549 nucl pA+ - 4 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002737 2737 GSM979633 Gingeras RIKEN CThi10060 nucleus 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549NucleusPapMinusRawRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549NucleusPapMinusRawRep3 A549 nucl pA+ - 3 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002737 2737 GSM979633 Gingeras RIKEN CThi10106 nucleus 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549NucleusPapMinusRawRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CytosolPapMinusRawRep4 A549 cyto pA+ - 4 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002736 2736 GSM979632 Gingeras RIKEN CThi10059 cytosol 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549CytosolPapMinusRawRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ CAGE Minus start sites Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CytosolPapMinusRawRep3 A549 cyto pA+ - 3 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002736 2736 GSM979632 Gingeras RIKEN CThi10049 cytosol 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549CytosolPapMinusRawRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ CAGE Minus start sites Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CellPapMinusSignalRep2 K562 cell pA+ - 2 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001150 1150 GSM849365 Gingeras RIKEN J71 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageK562CellPapMinusSignalRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CellPapMinusSignalRep1 K562 cell pA+ - 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001150 1150 GSM849365 Gingeras RIKEN J70 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageK562CellPapMinusSignalRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562PolysomePamMinusSignal K562 psom pA- - 1 K562 Cage ENCODE June 2010 Freeze 2010-06-21 2009-02-19 2009-11-19 wgEncodeEH000337 337 GSM849354 Gingeras RIKEN I32 bedtools v2.7.1 polysome longNonPolyA wgEncodeRikenCageK562PolysomePamMinusSignal MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Strand of mRNA with ribosomes attached Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand K562 polysome polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPapMinusSignalRep2 K562 nucl pA+ - 2 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000333 333 GSM849338 Gingeras RIKEN J92 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageK562NucleusPapMinusSignalRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPapMinusSignalRep1 K562 nucl pA+ - 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000333 333 GSM849338 Gingeras RIKEN J91 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageK562NucleusPapMinusSignalRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPamMinusSignal K562 nucl pA- - 1 K562 Cage ENCODE Jan 2011 Freeze 2010-08-26 2008-12-09 2009-09-09 wgEncodeEH000330 330 GSM849337 Gingeras RIKEN I23 nucleus longNonPolyA wgEncodeRikenCageK562NucleusPamMinusSignal MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleoplasmTotalMinusSignal K562 nplm tot - 1 K562 Cage ENCODE June 2010 Freeze 2010-06-21 2009-02-19 2009-11-19 wgEncodeEH000336 336 GSM849340 Gingeras RIKEN I34 bedtools v2.7.1 nucleoplasm total wgEncodeRikenCageK562NucleoplasmTotalMinusSignal MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center That part of the nuclear content other than the chromosomes or the nucleolus Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the minus strand K562 nucleoplasm total CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleolusTotalMinusSignal K562 nlus tot - 1 K562 Cage ENCODE Jan 2011 Freeze 2010-11-09 2011-08-09 wgEncodeEH000335 335 GSM849332 Gingeras RIKEN I33 nucleolus total wgEncodeRikenCageK562NucleolusTotalMinusSignal MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the minus strand K562 nucleolus total CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPapMinusSignalRep2 K562 cyto pA+ - 2 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000332 332 GSM849339 Gingeras RIKEN J83 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageK562CytosolPapMinusSignalRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPapMinusSignalRep1 K562 cyto pA+ - 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000332 332 GSM849339 Gingeras RIKEN J82 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageK562CytosolPapMinusSignalRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPamMinusSignal K562 cyto pA- - 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-22 2008-12-09 2009-09-09 wgEncodeEH000329 329 GSM849353 Gingeras RIKEN I22 cytosol longNonPolyA bedtools v2.7.1 wgEncodeRikenCageK562CytosolPamMinusSignal MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562ChromatinTotalMinusSignal K562 chrm tot - 1 K562 Cage ENCODE June 2010 Freeze 2010-06-21 2009-02-19 2009-11-19 wgEncodeEH000334 334 GSM849333 Gingeras RIKEN I35 bedtools v2.7.1 chromatin total wgEncodeRikenCageK562ChromatinTotalMinusSignal MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Nuclear DNA and associated proteins Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the minus strand K562 chromatin total CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPapMinusSignalRep2 H1ES cell pA+ - 2 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001138 1138 GSM849357 Gingeras RIKEN J75 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCellPapMinusSignalRep2 MinusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPapMinusSignalRep1 H1ES cell pA+ - 1 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001138 1138 GSM849357 Gingeras RIKEN J74 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCellPapMinusSignalRep1 MinusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPamMinusSignal H1ES cell pA- - 1 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-22 2010-01-13 2010-10-13 wgEncodeEH000341 341 GSM849355 Gingeras RIKEN I67 cell longNonPolyA bedtools v2.7.1 wgEncodeRikenCageH1hescCellPamMinusSignal MinusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescNucleusPapMinusSignalRep2 H1ES nucl pA+ - 2 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001140 1140 GSM849326 Gingeras RIKEN J95 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescNucleusPapMinusSignalRep2 MinusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC nucleus polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCytosolPapMinusSignalRep2 H1ES cyto pA+ - 2 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001139 1139 GSM849356 Gingeras RIKEN J86 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCytosolPapMinusSignalRep2 MinusSignal embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC cytosol polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CellPapMinusSignalRep2 GM78 cell pA+ - 2 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001680 1680 GSM849368 Gingeras RIKEN J73 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CellPapMinusSignalRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CellPapMinusSignalRep1 GM78 cell pA+ - 1 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001680 1680 GSM849368 Gingeras RIKEN J72 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CellPapMinusSignalRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPapMinusSignalRep2 GM78 nucl pA+ - 2 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001678 1678 GSM849348 Gingeras RIKEN J94 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878NucleusPapMinusSignalRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPapMinusSignalRep1 GM78 nucl pA+ - 1 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001678 1678 GSM849348 Gingeras RIKEN J93 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878NucleusPapMinusSignalRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPamMinusSignalRep1 GM78 nucl pA- - 1 GM12878 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000339 339 GSM849341 Gingeras RIKEN J59 nucleus longNonPolyA wgEncodeRikenCageGm12878NucleusPamMinusSignalRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleolusTotalMinusSignal GM78 nlus tot - 1 GM12878 Cage ENCODE Jan 2011 Freeze 2010-08-23 2010-01-14 2010-10-13 wgEncodeEH000340 340 GSM849352 Gingeras RIKEN I69 nucleolus total wgEncodeRikenCageGm12878NucleolusTotalMinusSignal MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Graphs the base-by-base density of tags on the minus strand GM12878 nucleolus total CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPapMinusSignalRep2 GM78 cyto pA+ - 2 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEH001679 1679 GSM849349 Gingeras RIKEN J85 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CytosolPapMinusSignalRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ CAGE Minus start sites Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPapMinusSignalRep1 GM78 cyto pA+ - 1 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001679 1679 GSM849349 Gingeras RIKEN J84 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CytosolPapMinusSignalRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPamMinusSignal GM78 cyto pA- - 1 GM12878 Cage ENCODE June 2010 Freeze 2010-06-21 2009-03-09 2009-12-09 wgEncodeEH000338 338 GSM849329 Gingeras RIKEN I27 bedtools v2.7.1 cytosol longNonPolyA wgEncodeRikenCageGm12878CytosolPamMinusSignal MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA- CAGE Minus start sites Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageViewAlignments Alignments RNA Subcellular CAGE Localization from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshraCellPapAlnRep2 SKSH cell pA+ A 2 SK-N-SH_RA Cage ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001157 1157 Gingeras RIKEN K15 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageSknshraCellPapAlnRep2 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH_RA whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshraCellPapAlnRep1 SKSH cell pA+ A 1 SK-N-SH_RA Cage ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001157 1157 Gingeras RIKEN K14 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageSknshraCellPapAlnRep1 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH_RA whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSkmcCellPapAlnRep2 SkMC cell pA+ A 2 SkMC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002764 2764 Gingeras RIKEN CThi10031 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSkmcCellPapAlnRep2 Alignments Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SkMC whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSkmcCellPapAlnRep1 SkMC cell pA+ A 1 SkMC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002764 2764 Gingeras RIKEN CThi10030 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSkmcCellPapAlnRep1 Alignments Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SkMC whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageProstateCellPamAln Pros cell pA- A 1 prostate Cage ENCODE Jan 2011 Freeze 2010-09-22 2008-12-09 2009-09-09 wgEncodeEH000331 331 Gingeras RIKEN I09 cell longNonPolyA Delve version 0.9 wgEncodeRikenCageProstateCellPamAln Alignments prostate tissue purchased for CSHL project CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch Prostate whole cell polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemm2CellPapAlnRep2 NHEM cell pA+ A 2 NHEM_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002760 2760 Gingeras RIKEN CThi10102GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemm2CellPapAlnRep2 Alignments Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM M2 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemm2CellPapAlnRep1 NHEM cell pA+ A 1 NHEM_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002760 2760 Gingeras RIKEN CThi10056 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemm2CellPapAlnRep1 Alignments Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM M2 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemfm2CellPapAlnRep2 NHEf cell pA+ A 2 NHEM.f_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002759 2759 Gingeras RIKEN CThi10055 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemfm2CellPapAlnRep2 Alignments Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM.f M2 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhemfm2CellPapAlnRep1 NHEf cell pA+ A 1 NHEM.f_M2 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002759 2759 Gingeras RIKEN CThi10102CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhemfm2CellPapAlnRep1 Alignments Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM.f M2 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCellPapAlnRep2 NHEK cell pA+ A 2 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001152 1152 Gingeras RIKEN J77 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCellPapAlnRep2 Alignments epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCellPapAlnRep1 NHEK cell pA+ A 1 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001152 1152 Gingeras RIKEN J76 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCellPapAlnRep1 Alignments epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPapAlnRep4 NHEK nucl pA+ A 4 NHEK Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH001154 1154 Gingeras RIKEN CTig10011 nucleus 1x36 4 longPolyA Illumina_GA2x F wgEncodeRikenCageNhekNucleusPapAlnRep4 Alignments epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Female Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPapAlnRep3 NHEK nucl pA+ A 1 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001154 1154 Gingeras RIKEN K09 nucleus 3 longPolyA Illumina_GA2x wgEncodeRikenCageNhekNucleusPapAlnRep3 Alignments epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekNucleusPamAln NHEK nucl pA- A 1 NHEK Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000347 347 Gingeras RIKEN I71 Delve version 0.9 nucleus longNonPolyA wgEncodeRikenCageNhekNucleusPamAln Alignments epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPapAlnRep4 NHEK cyto pA+ A 2 NHEK Cage ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001153 1153 Gingeras RIKEN K20 cytosol 4 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCytosolPapAlnRep4 Alignments epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPapAlnRep3 NHEK cyto pA+ A 1 NHEK Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001153 1153 Gingeras RIKEN K08 cytosol 3 longPolyA Illumina_GA2x wgEncodeRikenCageNhekCytosolPapAlnRep3 Alignments epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhekCytosolPamAln NHEK cyto pA- A 1 NHEK Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000346 346 Gingeras RIKEN I70 Delve version 0.9 cytosol longNonPolyA wgEncodeRikenCageNhekCytosolPamAln Alignments epidermal keratinocytes CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhdfCellPapAlnRep2 NHDF cell pA+ A 2 NHDF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002758 2758 Gingeras RIKEN CThi10033 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhdfCellPapAlnRep2 Alignments Dermal Fibroblasts from temple / breast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHDF whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageNhdfCellPapAlnRep1 NHDF cell pA+ A 1 NHDF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002758 2758 Gingeras RIKEN CThi10032 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageNhdfCellPapAlnRep1 Alignments Dermal Fibroblasts from temple / breast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHDF whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHwpCellPapAlnRep2 HWP cell pA+ A 2 HWP Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002751 2751 Gingeras RIKEN CThi10101ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHwpCellPapAlnRep2 Alignments Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HWP whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHwpCellPapAlnRep1 HWP cell pA+ A 1 HWP Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002751 2751 Gingeras RIKEN CThi10101ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHwpCellPapAlnRep1 Alignments Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HWP whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHvmfCellPapAlnRep2 HVMF cell pA+ A 2 HVMF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002750 2750 Gingeras RIKEN CThi10035 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHvmfCellPapAlnRep2 Alignments villous mesenchymal fibroblast cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HVMF whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHvmfCellPapAlnRep1 HVMF cell pA+ A 1 HVMF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002750 2750 Gingeras RIKEN CThi10034 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHvmfCellPapAlnRep1 Alignments villous mesenchymal fibroblast cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HVMF whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHsavecCellPapAlnRep2 HSaV cell pA+ A 2 HSaVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002748 2748 Gingeras RIKEN CThi10102ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHsavecCellPapAlnRep2 Alignments Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HSaVEC whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHsavecCellPapAlnRep1 HSaV cell pA+ A 1 HSaVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002748 2748 Gingeras RIKEN CThi10102ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHsavecCellPapAlnRep1 Alignments Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HSaVEC whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpiepcCellPapAlnRep2 HPIE cell pA+ A 2 HPIEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002747 2747 Gingeras RIKEN CThi10101GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpiepcCellPapAlnRep2 Alignments Placental Epithelial Cells amniotic membrane CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPIEpC whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpiepcCellPapAlnRep1 HPIE cell pA+ A 1 HPIEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002747 2747 Gingeras RIKEN CThi10104ATC cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpiepcCellPapAlnRep1 Alignments Placental Epithelial Cells amniotic membrane CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPIEpC whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpcplCellPapAlnRep2 HPCP cell pA+ A 2 HPC-PL Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002746 2746 Gingeras RIKEN CThi10105ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpcplCellPapAlnRep2 Alignments Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPC-PL whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHpcplCellPapAlnRep1 HPCP cell pA+ A 1 HPC-PL Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002746 2746 Gingeras RIKEN CThi10057 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHpcplCellPapAlnRep1 Alignments Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPC-PL whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHobCellPapAlnRep2 HOB cell pA+ A 2 HOB Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002745 2745 Gingeras RIKEN CThi10037 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHobCellPapAlnRep2 Alignments Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HOB whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHobCellPapAlnRep1 HOB cell pA+ A 1 HOB Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002745 2745 Gingeras RIKEN CThi10036 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHobCellPapAlnRep1 Alignments Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HOB whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscucCellPapAlnRep2 hMUC cell pA+ A 2 hMSC-UC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002767 2767 Gingeras RIKEN CThi10100ATC cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscucCellPapAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-UC whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscucCellPapAlnRep1 hMUC cell pA+ A 1 hMSC-UC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002767 2767 Gingeras RIKEN CThi10101CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscucCellPapAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-UC whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscbmCellPapAlnRep2 hMBM cell pA+ A 2 hMSC-BM Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002766 2766 Gingeras RIKEN CThi10100ACA cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscbmCellPapAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-BM whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscbmCellPapAlnRep1 hMBM cell pA+ A 1 hMSC-BM Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002766 2766 Gingeras RIKEN CThi10103ATC cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscbmCellPapAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-BM whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscatCellPapAlnRep2 hMAT cell pA+ A 2 hMSC-AT Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002765 2765 Gingeras RIKEN CThi10104GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscatCellPapAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-AT whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmscatCellPapAlnRep1 hMAT cell pA+ A 1 hMSC-AT Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002765 2765 Gingeras RIKEN CThi10105ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmscatCellPapAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-AT whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHmepcCellPapAlnRep1 HMEp cell pA+ A 1 HMEpC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002744 2744 Gingeras RIKEN CThi10105GAT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHmepcCellPapAlnRep1 Alignments Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HMEpC whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHfdpcCellPapAlnRep2 HFDP cell pA+ A 2 HFDPC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002743 2743 Gingeras RIKEN CThi10100GAT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHfdpcCellPapAlnRep2 Alignments Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HFDPC whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHfdpcCellPapAlnRep1 HFDP cell pA+ A 1 HFDPC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002743 2743 Gingeras RIKEN CThi10103ACA cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHfdpcCellPapAlnRep1 Alignments Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HFDPC whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHchCellPapAlnRep2 HCH cell pA+ A 2 HCH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002742 2742 Gingeras RIKEN CThi10104ACA cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHchCellPapAlnRep2 Alignments Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HCH whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHchCellPapAlnRep1 HCH cell pA+ A 1 HCH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002742 2742 Gingeras RIKEN CThi10104CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHchCellPapAlnRep1 Alignments Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HCH whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoecCellPapAlnRep2 HAoE cell pA+ A 2 HAoEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002741 2741 Gingeras RIKEN CThi10105CTT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoecCellPapAlnRep2 Alignments Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoEC whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoecCellPapAlnRep1 HAoE cell pA+ A 1 HAoEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002741 2741 Gingeras RIKEN CThi10103GAT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoecCellPapAlnRep1 Alignments Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoEC whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoafCellPapAlnRep2 HAoA cell pA+ A 2 HAoAF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002740 2740 Gingeras RIKEN CThi10103CTT cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoafCellPapAlnRep2 Alignments Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoAF whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHaoafCellPapAlnRep1 HAoA cell pA+ A 1 HAoAF Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002740 2740 Gingeras RIKEN CThi10100CTT cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageHaoafCellPapAlnRep1 Alignments Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoAF whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd34mobilizedCellPapAlnRep1 CD34 cell pA+ A 1 CD34+_Mobilized Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002739 2739 Gingeras RIKEN CThi10058 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd34mobilizedCellPapAlnRep1 Alignments hematopoietic progenitor cells- mobilized, from donor RO01679. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch CD34+ Mobilized whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageBjCellPapAlnRep2 BJ cell pA+ A 2 BJ Cage ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001160 1160 Gingeras RIKEN K19 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageBjCellPapAlnRep2 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageBjCellPapAlnRep1 BJ cell pA+ A 1 BJ Cage ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001160 1160 Gingeras RIKEN K18 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageBjCellPapAlnRep1 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageAg04450CellPapAlnRep2 AG50 cell pA+ A 2 AG04450 Cage ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001159 1159 Gingeras RIKEN K13 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageAg04450CellPapAlnRep2 Alignments fetal lung fibroblast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageAg04450CellPapAlnRep1 AG50 cell pA+ A 1 AG04450 Cage ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001159 1159 Gingeras RIKEN K12 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageAg04450CellPapAlnRep1 Alignments fetal lung fibroblast CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCellPapAlnRep4 SKSH cell pA+ A 4 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002763 2763 Gingeras RIKEN CThi10046 cell 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCellPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH whole cell polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCellPapAlnRep3 SKSH cell pA+ A 3 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002763 2763 Gingeras RIKEN CThi10043 cell 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCellPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH whole cell polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshNucleusPapAlnRep4 SKSH nucl pA+ A 4 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002762 2762 Gingeras RIKEN CThi10048 nucleus 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshNucleusPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH nucleus polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshNucleusPapAlnRep3 SKSH nucl pA+ A 3 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002762 2762 Gingeras RIKEN CThi10045 nucleus 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshNucleusPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH nucleus polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCytosolPapAlnRep4 SKSH cyto pA+ A 4 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002761 2761 Gingeras RIKEN CThi10047 cytosol 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCytosolPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH cytosol polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageSknshCytosolPapAlnRep3 SKSH cyto pA+ A 3 SK-N-SH Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002761 2761 Gingeras RIKEN CThi10044 cytosol 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageSknshCytosolPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH cytosol polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMonocd14CellPapAlnRep2 CD14 cell pA+ A 2 Monocytes-CD14+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002757 2757 Gingeras RIKEN CThi10022 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMonocd14CellPapAlnRep2 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch Monocytes-CD14+ whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMonocd14CellPapAlnRep1 CD14 cell pA+ A 1 Monocytes-CD14+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002757 2757 Gingeras RIKEN CThi10021 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMonocd14CellPapAlnRep1 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch Monocytes-CD14+ whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CellPapAlnRep2 MCF7 cell pA+ A 2 MCF-7 Cage ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001151 1151 Gingeras RIKEN K11 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageMcf7CellPapAlnRep2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CellPapAlnRep1 MCF7 cell pA+ A 1 MCF-7 Cage ENCODE Mar 2012 Freeze 2010-09-21 2011-06-21 wgEncodeEH001151 1151 Gingeras RIKEN K07 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageMcf7CellPapAlnRep1 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7NucleusPapAlnRep4 MCF7 nucl pA+ A 4 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002756 2756 Gingeras RIKEN CThi10054 nucleus 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7NucleusPapAlnRep4 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 nucleus polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7NucleusPapAlnRep3 MCF7 nucl pA+ A 3 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002756 2756 Gingeras RIKEN CThi10052 nucleus 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7NucleusPapAlnRep3 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 nucleus polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CytosolPapAlnRep4 MCF7 cyto pA+ A 4 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002755 2755 Gingeras RIKEN CThi10053 cytosol 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7CytosolPapAlnRep4 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 cytosol polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageMcf7CytosolPapAlnRep3 MCF7 cyto pA+ A 3 MCF-7 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002755 2755 Gingeras RIKEN CThi10051 cytosol 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageMcf7CytosolPapAlnRep3 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 cytosol polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CellPapAlnRep2 IMR9 cell pA+ A 2 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002754 2754 Gingeras RIKEN CThi10018 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CellPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CellPapAlnRep1 IMR9 cell pA+ A 1 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002754 2754 Gingeras RIKEN CThi10016 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CellPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90NucleusPapAlnRep2 IMR9 nucl pA+ A 2 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002753 2753 Gingeras RIKEN CThi10026 nucleus 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90NucleusPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 nucleus polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90NucleusPapAlnRep1 IMR9 nucl pA+ A 1 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002753 2753 Gingeras RIKEN CThi10025 nucleus 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90NucleusPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 nucleus polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CytosolPapAlnRep2 IMR9 cyto pA+ A 2 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002752 2752 Gingeras RIKEN CThi10019 cytosol 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CytosolPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 cytosol polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageImr90CytosolPapAlnRep1 IMR9 cyto pA+ A 1 IMR90 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002752 2752 Gingeras RIKEN CThi10017 cytosol 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageImr90CytosolPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 cytosol polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCellPapAlnRep2 HUVE cell pA+ A 2 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001141 1141 Gingeras RIKEN J79 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCellPapAlnRep2 Alignments umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCellPapAlnRep1 HUVE cell pA+ A 1 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001141 1141 Gingeras RIKEN J78 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCellPapAlnRep1 Alignments umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPapAlnRep4 HUVE nucl pA+ A 2 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001143 1143 Gingeras RIKEN K06 nucleus 4 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPapAlnRep4 Alignments umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPapAlnRep3 HUVE nucl pA+ A 1 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001143 1143 Gingeras RIKEN K05 nucleus 3 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPapAlnRep3 Alignments umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecNucleusPamAlnRep1 HUVE nucl pA- A 1 HUVEC Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-31 wgEncodeEH002749 2749 Gingeras RIKEN CTig10027 nucleus 1x36 1 longNonPolyA Illumina_GA2x wgEncodeRikenCageHuvecNucleusPamAlnRep1 Alignments umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPapAlnRep4 HUVE cyto pA+ A 2 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001142 1142 Gingeras RIKEN K04 cytosol 4 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCytosolPapAlnRep4 Alignments umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPapAlnRep3 HUVE cyto pA+ A 1 HUVEC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001142 1142 Gingeras RIKEN K03 cytosol 3 longPolyA Illumina_GA2x wgEncodeRikenCageHuvecCytosolPapAlnRep3 Alignments umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHuvecCytosolPamAln HUVE cyto pA- A 1 HUVEC Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-13 2010-10-13 wgEncodeEH000342 342 Gingeras RIKEN I72 Delve version 0.9 cytosol longNonPolyA wgEncodeRikenCageHuvecCytosolPamAln Alignments umbilical vein endothelial cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CellPapAlnRep2 HepG cell pA+ A 2 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001149 1149 Gingeras RIKEN K02 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CellPapAlnRep2 Alignments hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CellPapAlnRep1 HepG cell pA+ A 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001149 1149 Gingeras RIKEN K01 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CellPapAlnRep1 Alignments hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPapAlnRep2 HepG nucl pA+ A 2 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001148 1148 Gingeras RIKEN J99 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2NucleusPapAlnRep2 Alignments hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPapAlnRep1 HepG nucl pA+ A 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001148 1148 Gingeras RIKEN J98 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2NucleusPapAlnRep1 Alignments hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleusPamAln HepG nucl pA- A 1 HepG2 Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-13 2010-10-13 wgEncodeEH000345 345 Gingeras RIKEN I44 Delve version 0.9 nucleus longNonPolyA wgEncodeRikenCageHepg2NucleusPamAln Alignments hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2NucleolusTotalAln HepG nlus tot A 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-08-23 2010-01-13 2010-10-13 wgEncodeEH000344 344 Gingeras RIKEN I68 nucleolus total wgEncodeRikenCageHepg2NucleolusTotalAln Alignments hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleolus total CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPapAlnRep2 HepG cyto pA+ A 2 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001147 1147 Gingeras RIKEN J90 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CytosolPapAlnRep2 Alignments hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPapAlnRep1 HepG cyto pA+ A 1 HepG2 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001147 1147 Gingeras RIKEN J89 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageHepg2CytosolPapAlnRep1 Alignments hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHepg2CytosolPamAln HepG cyto pA- A 1 HepG2 Cage ENCODE June 2010 Freeze 2010-06-21 2010-01-13 2010-10-13 wgEncodeEH000343 343 Gingeras RIKEN I42 Delve version 0.9 cytosol longNonPolyA wgEncodeRikenCageHepg2CytosolPamAln Alignments hepatocellular carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CellPapAlnRep2 HeLa cell pA+ A 2 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001146 1146 Gingeras RIKEN J81 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CellPapAlnRep2 Alignments cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CellPapAlnRep1 HeLa cell pA+ A 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001146 1146 Gingeras RIKEN J80 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CellPapAlnRep1 Alignments cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPapAlnRep2 HeLa nucl pA+ A 2 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001145 1145 Gingeras RIKEN J97 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPapAlnRep2 Alignments cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPapAlnRep1 HeLa nucl pA+ A 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001145 1145 Gingeras RIKEN J96 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPapAlnRep1 Alignments cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleusPamAlnRep1 HeLa nucl pA- A 1 HeLa-S3 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-31 wgEncodeEH002775 2775 Gingeras RIKEN CTig10028 nucleus 1x36 1 longNonPolyA Illumina_GA2x wgEncodeRikenCageHelas3NucleusPamAlnRep1 Alignments cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 36 nt reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3NucleolusTotalAln HeLa nlus tot A 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-10-29 2011-07-29 wgEncodeEH001156 1156 Gingeras RIKEN J58 nucleolus total wgEncodeRikenCageHelas3NucleolusTotalAln Alignments cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleolus total CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPapAlnRep2 HeLa cyto pA+ A 2 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001144 1144 Gingeras RIKEN J88 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CytosolPapAlnRep2 Alignments cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPapAlnRep1 HeLa cyto pA+ A 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001144 1144 Gingeras RIKEN J87 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageHelas3CytosolPapAlnRep1 Alignments cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageHelas3CytosolPamAln HeLa cyto pA- A 1 HeLa-S3 Cage ENCODE Jan 2011 Freeze 2010-10-29 2011-07-29 wgEncodeEH001155 1155 Gingeras RIKEN J56 cytosol longNonPolyA wgEncodeRikenCageHelas3CytosolPamAln Alignments cervical carcinoma CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd20CellPapAlnRep2 CD20 cell pA+ A 2 CD20+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002738 2738 Gingeras RIKEN CThi10024 cell 1x50 2 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd20CellPapAlnRep2 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageCd20CellPapAlnRep1 CD20 cell pA+ A 1 CD20+ Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002738 2738 Gingeras RIKEN CThi10023 cell 1x50 1 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageCd20CellPapAlnRep1 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CellPapAlnRep2 A549 cell pA+ A 2 A549 Cage ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001158 1158 Gingeras RIKEN K17 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageA549CellPapAlnRep2 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CellPapAlnRep1 A549 cell pA+ A 1 A549 Cage ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001158 1158 Gingeras RIKEN K16 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageA549CellPapAlnRep1 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549NucleusPapAlnRep4 A549 nucl pA+ A 4 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002737 2737 Gingeras RIKEN CThi10060 nucleus 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549NucleusPapAlnRep4 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 nucleus polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549NucleusPapAlnRep3 A549 nucl pA+ A 3 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002737 2737 Gingeras RIKEN CThi10106 nucleus 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549NucleusPapAlnRep3 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 nucleus polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CytosolPapAlnRep4 A549 cyto pA+ A 4 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002736 2736 Gingeras RIKEN CThi10059 cytosol 1x50 4 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549CytosolPapAlnRep4 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 cytosol polyA+ CAGE Alignments Rep 4 from ENCODE/RIKEN Expression 
wgEncodeRikenCageA549CytosolPapAlnRep3 A549 cyto pA+ A 3 A549 Cage ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEH002736 2736 Gingeras RIKEN CThi10049 cytosol 1x50 3 longPolyA Illumina_HiSeq_2000 wgEncodeRikenCageA549CytosolPapAlnRep3 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Single 50 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 cytosol polyA+ CAGE Alignments Rep 3 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CellPapAlnRep2 K562 cell pA+ A 2 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001150 1150 Gingeras RIKEN J71 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageK562CellPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CellPapAlnRep1 K562 cell pA+ A 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001150 1150 Gingeras RIKEN J70 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageK562CellPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562PolysomePamAln K562 psom pA- A 1 K562 Cage ENCODE June 2010 Freeze 2010-06-21 2009-02-19 2009-11-19 wgEncodeEH000337 337 Gingeras RIKEN I32 Delve version 0.9 polysome longNonPolyA wgEncodeRikenCageK562PolysomePamAln Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Strand of mRNA with ribosomes attached Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polysome polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPapAlnRep2 K562 nucl pA+ A 2 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000333 333 Gingeras RIKEN J92 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageK562NucleusPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPapAlnRep1 K562 nucl pA+ A 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000333 333 Gingeras RIKEN J91 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageK562NucleusPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleusPamAln K562 nucl pA- A 1 K562 Cage ENCODE Jan 2011 Freeze 2010-08-26 2008-12-09 2009-09-09 wgEncodeEH000330 330 Gingeras RIKEN I23 nucleus longNonPolyA wgEncodeRikenCageK562NucleusPamAln Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleoplasmTotalAln K562 nplm tot A 1 K562 Cage ENCODE June 2010 Freeze 2010-06-21 2009-02-19 2009-11-19 wgEncodeEH000336 336 Gingeras RIKEN I34 Delve version 0.9 nucleoplasm total wgEncodeRikenCageK562NucleoplasmTotalAln Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center That part of the nuclear content other than the chromosomes or the nucleolus Total RNA extract (longer than 200 nt) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleoplasm total CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562NucleolusTotalAln K562 nlus tot A 1 K562 Cage ENCODE Jan 2011 Freeze 2010-11-09 2011-08-09 wgEncodeEH000335 335 Gingeras RIKEN I33 nucleolus total wgEncodeRikenCageK562NucleolusTotalAln Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleolus total CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPapAlnRep2 K562 cyto pA+ A 2 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000332 332 Gingeras RIKEN J83 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageK562CytosolPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPapAlnRep1 K562 cyto pA+ A 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000332 332 Gingeras RIKEN J82 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageK562CytosolPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562CytosolPamAln K562 cyto pA- A 1 K562 Cage ENCODE Jan 2011 Freeze 2010-09-22 2008-12-09 2009-09-09 wgEncodeEH000329 329 Gingeras RIKEN I22 cytosol longNonPolyA bowtie version 0.12.5 wgEncodeRikenCageK562CytosolPamAln Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageK562ChromatinTotalAln K562 chrm tot A 1 K562 Cage ENCODE June 2010 Freeze 2010-06-21 2009-02-19 2009-11-19 wgEncodeEH000334 334 Gingeras RIKEN I35 Delve version 0.9 chromatin total wgEncodeRikenCageK562ChromatinTotalAln Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Nuclear DNA and associated proteins Total RNA extract (longer than 200 nt) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 chromatin total CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPapAlnRep2 H1ES cell pA+ A 2 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001138 1138 Gingeras RIKEN J75 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCellPapAlnRep2 Alignments embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPapAlnRep1 H1ES cell pA+ A 1 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001138 1138 Gingeras RIKEN J74 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCellPapAlnRep1 Alignments embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCellPamAln H1ES cell pA- A 1 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-22 2010-01-13 2010-10-13 wgEncodeEH000341 341 Gingeras RIKEN I67 cell longNonPolyA Delve version 0.9 wgEncodeRikenCageH1hescCellPamAln Alignments embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescNucleusPapAlnRep2 H1ES nucl pA+ A 2 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001140 1140 Gingeras RIKEN J95 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescNucleusPapAlnRep2 Alignments embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC nucleus polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageH1hescCytosolPapAlnRep2 H1ES cyto pA+ A 2 H1-hESC Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001139 1139 Gingeras RIKEN J86 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageH1hescCytosolPapAlnRep2 Alignments embryonic stem cells CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC cytosol polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CellPapAlnRep2 GM78 cell pA+ A 2 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001680 1680 Gingeras RIKEN J73 cell 2 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CellPapAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CellPapAlnRep1 GM78 cell pA+ A 1 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001680 1680 Gingeras RIKEN J72 cell 1 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CellPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Whole cell Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPapAlnRep2 GM78 nucl pA+ A 2 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001678 1678 Gingeras RIKEN J94 nucleus 2 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878NucleusPapAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPapAlnRep1 GM78 nucl pA+ A 1 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001678 1678 Gingeras RIKEN J93 nucleus 1 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878NucleusPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleusPamAlnRep1 GM78 nucl pA- A 1 GM12878 Cage ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH000339 339 Gingeras RIKEN J59 nucleus longNonPolyA wgEncodeRikenCageGm12878NucleusPamAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878NucleolusTotalAln GM78 nlus tot A 1 GM12878 Cage ENCODE Jan 2011 Freeze 2010-08-23 2010-01-14 2010-10-13 wgEncodeEH000340 340 Gingeras RIKEN I69 nucleolus total wgEncodeRikenCageGm12878NucleolusTotalAln Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The part of the nucleus where ribosomal RNA is actively transcribed Total RNA extract (longer than 200 nt) Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleolus total CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPapAlnRep2 GM78 cyto pA+ A 2 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEH001679 1679 Gingeras RIKEN J85 cytosol 2 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CytosolPapAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA+ CAGE Alignments Rep 2 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPapAlnRep1 GM78 cyto pA+ A 1 GM12878 Cage ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEH001679 1679 Gingeras RIKEN J84 cytosol 1 longPolyA Illumina_GA2x wgEncodeRikenCageGm12878CytosolPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA+ CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
wgEncodeRikenCageGm12878CytosolPamAln GM78 cyto pA- A 1 GM12878 Cage ENCODE June 2010 Freeze 2010-06-21 2009-03-09 2009-12-09 wgEncodeEH000338 338 Gingeras RIKEN I27 Delve version 0.9 cytosol longNonPolyA wgEncodeRikenCageGm12878CytosolPamAln Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus CAGE 5' RNA Tags Gingeras Carninci - RIKEN Omics Science Center The fluid between the cells outer membrane and the nucleus Poly(A)- RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA- CAGE Alignments Rep 1 from ENCODE/RIKEN Expression 
ntSssSnps S SNPs SNPS Used for Selective Sweep Scan (S) Neandertal Assembly and Analysis Description This track shows single nucleotide polymorphisms (SNPs) used in a genome-wide scan for signals of positive selection in the human lineage since divergence from the Neandertal lineage. SNP labels represent the ancestral (A) or derived (D) status, determined by comparison with the chimpanzee reference genome, of alleles in the human reference assembly, five modern human genomes of diverse ancestry (see the Modern Human Seq track), and Neandertals. The first six characters of an item name show the status of the allele (A, D or _ if not known) in six genomes: human reference, San, Yoruba, Han, Papuan, and French, in that order. These characters are followed by a colon, the number of derived alleles found in Neandertals, a comma and the number of ancestral alleles found in Neandertals. For example, a SNP labeled AAADAA:0D,2A has the ancestral allele in the reference human genome and in all of the modern human genomes except Han. Among Neandertals, two instances of the ancestral allele were found, but no instances of the derived allele. SNPs are colored red when at least four of the six modern human genomes are derived while all observed Neandertal alleles are ancestral. An overrepresentation of such SNPs in a region would imply that the region had undergone positive selection in the modern human lineage since divergence from Neandertals; the Sel Swp Scan (S) track displays a signal calculated from these SNPs, and the 5% Lowest S track contains the regions in which the signal most strongly indicates selective pressure on the modern human lineage. Display Conventions and Configuration Red SNPs are those where at least four of the six modern human genomes are derived while all observed Neandertal alleles are ancestral. All other SNPs are black. Methods For the purposes of this analysis, SNPs were defined as single-base sites that are polymorphic among 5 modern human genomes of diverse ancestry (see the Modern Human Seq track) plus the human reference genome. SNPs at CpG sites were excluded because of the higher mutation rate at CpG sites. Ancestral or derived state was determined by comparison with the chimpanzee genome. Credits This track was produced at UCSC using data generated by Ed Green. Reference Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. PMID: 20448178 
genomicSuperDups Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence Repeats Description This track shows regions detected as putative genomic duplications within the golden path. The following display conventions are used to distinguish levels of similarity: Light to dark gray: 90 - 98% similarity Light to dark yellow: 98 - 99% similarity Light to dark orange: greater than 99% similarity Red: duplications of greater than 98% similarity that lack sufficient Segmental Duplication Database evidence (most likely missed overlaps) For a region to be included in the track, at least 1 Kb of the total sequence (containing at least 500 bp of non-RepeatMasked sequence) had to align and a sequence identity of at least 90% was required. Methods Segmental duplications play an important role in both genomic disease and gene evolution. This track displays an analysis of the global organization of these long-range segments of identity in genomic sequence. Large recent duplications (&gt;= 1 kb and &gt;= 90% identity) were detected by identifying high-copy repeats, removing these repeats from the genomic sequence ("fuguization") and searching all sequence for similarity. The repeats were then reinserted into the pairwise alignments, the ends of alignments trimmed, and global alignments were generated. For a full description of the "fuguization" detection method, see Bailey et al., 2001. This method has become known as WGAC (whole-genome assembly comparison); for example, see Bailey et al., 2002. Credits The data were provided by Saba Sajjadian, Arthur Ko and Evan Eichler at the University of Washington. References Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. Recent segmental duplications in the human genome. Science. 2002 Aug 9;297(5583):1003-7. PMID: 12169732 Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 2001 Jun;11(6):1005-17. PMID: 11381028; PMC: PMC311093 
ntSssZScorePMVar Sel Swp Scan (S) Selective Sweep Scan (S) on Neandertal vs. Human Polymorphisms (Z-Score +- Variance) Neandertal Assembly and Analysis Description This track shows the S score (Z-score +- variance) for positive selection in humans within a 100 kb window surrounding each polymorphic position in the five modern human sequences and the human reference genome as described in Green et al., Supplemental Online Material Text 13, Burbano et al.. A positive score indicates more derived alleles in Neandertal than expected, given the frequency of derived alleles in human. A negative score indicates fewer derived alleles in Neandertal, and may indicate an episode of positive selection in early humans. To view the polymorphic sites on which the S score was computed, open the S SNPs track. Methods Green et al. identified single-base sites that are polymorphic among five modern human genomes of diverse ancestry (in the Modern Human Seq track) plus the human reference genome. CpG sites were excluded because of the higher mutation rate at CpG sites. The ancestral or derived state of each single nucleotide polymorphism (SNP) was determined by comparison with the chimpanzee genome. The SNPs are displayed in the S SNPs track. The fact that SNPs with higher frequencies of the derived allele in modern humans were more likely to show the derived allele in Neandertals was used to calculate the expected number of derived alleles in Neandertal within a given region of the human genome. The observed numbers of derived alleles were compared to the expected numbers to identify regions where the Neandertals carry fewer derived alleles than expected given the human allelic states. The score assigned to each SNP is the z-score of the observed and expected counts relative to the variance in the number of the expected counts of derived alleles within the 100,000-base window around the SNP. Note: In order to display both the score and the variance within the same track in the UCSC Genome Browser, the scores were modified as follows: at the SNP position, the value displayed is the score plus the variance. At the position following the SNP position, the score minus the variance is displayed. When viewing large regions (at least 100,000 bases), the default mean+whiskers condensation of the scores provides an indication of the range covered by the variance. Reference Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. PMID: 20448178 
chainSelf Self Alignment Human Chained Self Alignments Repeats Description This track shows alignments of the human genome with itself, using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. The system can also tolerate gaps in both sets of sequence simultaneously. After filtering out the &quot;trivial&quot; alignments produced when identical locations of the genome map to one another (e.g. chrN mapping to chrN), the remaining alignments point out areas of duplication within the human genome. The pseudoautosomal regions of chrX and chrY are an exception: in this assembly, these regions have been copied from chrX into chrY, resulting in a large amount of self chains aligning in these positions on both chromosomes. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the query assembly or an insertion in the target assembly. Double lines represent more complex gaps that involve substantial sequence in both the query and target assemblies. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one of the assemblies. In cases where multiple chains align over a particular region of the human genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Display Conventions and Configuration By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Methods The genome was aligned to itself using blastz. Trivial alignments were filtered out, and the remaining alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single target chromosome and a single query chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A90-330-236-356 C-330100-318-236 G-236-318100-330 T-356-236-33090 Chains scoring below a minimum score of 2,000 were discarded; the remaining chains are displayed in this track. Credits Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains were generated by Robert Baertsch and Jim Kent. References Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002). Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. 
sestanBrainAtlas Sestan Brain Sestan Lab Human Brain Atlas Microarrays Expression Description This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually. Methods RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression). The probe set for this microarray track can be displayed by turning on the Affy HuEx 1.0 track. Core, extended, and full probe sets are shown. &quot;Bounded&quot; probe sets - exons that lie within the intron of more than one gene - and potentially cross-hybridizing probe sets were filtered from this dataset, leaving ~875K probe sets. Credits The data for this track were generated and analyzed by Matthew B. Johnson, Yuka Imamura Kawasawa, Christopher Mason, and the Yale Neuroscience Microarray Center. Links The raw microarray data are available via the NCBI Gene Expression Omnibus. More information is available at https://hbatlas.org/. 
sgpGene SGP Genes SGP Gene Predictions Using Mouse/Human Homology Genes and Gene Predictions Description This track shows gene predictions from the SGP2 homology-based gene prediction program developed by Roderic Guig&oacute;'s &quot;Computational Biology of RNA Processing&quot; group, which is part of the Centre de Regulaci&oacute; Gen&ograve;mica (CRG) in Barcelona, Catalunya, Spain. To predict genes in a genomic query, SGP2 combines geneid predictions with tblastx comparisons of the genome of the target species against genomic sequences of other species (reference genomes) deemed to be at an appropriate evolutionary distance from the target. Credits Thanks to the &quot;Computational Biology of RNA Processing&quot; group for providing these data. 
sibGene SIB Genes Swiss Institute of Bioinformatics Gene Predictions from mRNA and ESTs Genes and Gene Predictions Description The SIB Genes track is a transcript-based set of gene predictions based on data from RefSeq and EMBL/GenBank. Genes all have the support of at least one GenBank full length RNA sequence, one RefSeq RNA, or one spliced EST. The track includes both protein-coding and non-coding transcripts. The coding regions are predicted using ESTScan. Display Conventions and Configuration This track in general follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks while those for coding open reading frames are thicker. This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Go to the Coloring Gene Predictions and Annotations by Codon page for more information about this feature. Further information on the predicted transcripts can be found on the Transcriptome Web interface. Methods The SIB Genes are built using a multi-step pipeline: RefSeq and GenBank RNAs and ESTs are aligned to the genome with SIBsim4, keeping only the best alignments for each RNA. Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out. A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge. The graph is traversed to generate all unique transcripts. The traversal is guided by the initial RNAs to avoid a combinatorial explosion in alternative splicing. Protein predictions are generated. Credits The SIB Genes track was produced on the Vital-IT high-performance computing platform using a computational pipeline developed by Christian Iseli with help from colleagues at the Ludwig Institute for Cancer Research and the Swiss Institute of Bioinformatics. It is based on data from NCBI RefSeq and GenBank/EMBL. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them. References Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 
simpleRepeat Simple Repeats Simple Tandem Repeats by TRF Repeats Description This track displays simple tandem repeats (possibly imperfect repeats) located by Tandem Repeats Finder (TRF) which is specialized for this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases. Methods For more information about the TRF program, see Benson (1999). Credits TRF was written by Gary Benson. References Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217 
wgRna sno/miRNA C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase Genes and Gene Predictions Description This track displays positions of four different types of RNA in the human genome: precursor forms of microRNAs (pre-miRNAs) C/D box small nucleolar RNAs (C/D box snoRNAs) H/ACA box snoRNAs small Cajal body-specific RNAs (scaRNAs) C/D box and H/ACA box snoRNAs are guides for the 2'O-ribose methylation and the pseudouridilation, respectively, of rRNAs and snRNAs, although many of them have no documented target RNA. The scaRNAs guide modifications of the spliceosomal snRNAs transcribed by RNA polymerase II, and often contain both C/D and H/ACA domains. The pre-miRNA data are from the miRBase Sequence Database at the Wellcome Trust Sanger Institute. The snoRNA and scaRNA data are from snoRNABase, which is maintained at the Laboratoire de Biologie Mol&eacute;culaire Eucaryote. Display Conventions and Configuration This track follows the general display conventions for gene prediction tracks. At a zoomed-in resolution, arrows superimposed on the blocks indicate the sense orientation of the RNAs. The RNA types are represented by blocks of the following colors: red = pre-miRNA blue = C/D box snoRNA green = H/ACA box snoRNA magenta = scaRNA Methods Pre-miRNA genomic locations from miRBase were calculated using wublastn for sequence alignment with the requirement of 100% identity. The extents of the precursor sequences were not generally known and were predicted based on base-paired hairpin structure. The snoRNAs and scaRNAs genomic locations from snoRNABase were aligned to the hg18 human genome assembly using BLAT and were then lifted to the hg19 assembly. In a few cases, no exact match was found for the published sequences; these likely correspond to sequencing errors. In these cases, the best BLAT hit (which differed from the published sno/scaRNA sequence by 1-3 nucleotides) was adopted. Credits The genome coordinates for the pre-miRNAs were obtained from the miRBase Sequence Database FTP site, and the genome coordinates for the snoRNA and scaRNA were obtained from the snoRNABase coordinates download page. References When making use of these data, please cite the following articles and, if applicable, the primary sources of the RNA sequences: Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11. PMID: 14681370; PMC: PMC308757 Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4. PMID: 16381832; PMC: PMC1347474 Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8. PMID: 17991681; PMC: PMC2238936 Lestrade L, Weber MJ. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D158-62. PMID: 16381836; PMC: PMC1347365 Weber MJ. New human and mouse microRNA genes found by homology search. FEBS J. 2005 Jan;272(1):59-73. PMID: 15634332 For more information on BLAT, see Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 The following publication provides guidelines on miRNA annotation: Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M et al. A uniform system for microRNA annotation. RNA. 2003 Mar;9(3):277-9. PMID: 12592000; PMC: PMC1370393 
snpedia SNPedia SNPedia Phenotype and Literature Description SNPedia is a wiki investigating human genetics with information about the effects of variations in DNA, citing peer-reviewed scientific publications. SNPedia all: SNPedia all SNPs (including empty pages) The track &#34;SNPedia all&#34; shows all SNPs that exist as a page in SNPedia.com. As SNPedia's user collaboration grows, more detail will be added to SNPedia.com pages. For now, most of the pages are auto-generated by bots and have empty pages. According to Mike Carioso (SNPedia.com founder), SNPedia entries are mostly ClinVar entries marked as pathogenic with at least 4 stars as defined by the ClinVar review status. SNPedia with text: SNPedia pages with manually typed text The track &#34;SNPedia with text&#34; is a subset of the &#34;SNPedia all&#34; track. This track displays only SNPedia entries with a text page that was created manually by a user who typed in some text (approximately 5,000 entries). In the browser, click on the &#34;configure&#34; button and select &#34;next/previous item navigation&#34; to show clickable arrows in the browser which will jump to the next or previous item. Clicks on the features show the text from the SNPedia.com page and a link to the original page. Display Conventions and Configuration Genomic locations of SNPedia entries are labeled with the dbSNP ID. In the track &#34;SNPedia all SNPs&#34;, the features are colored based on the SNPedia microarray annotation: grey for SNPs that are on no microarray, dark blue for Affymetrix, dark purple for Illumina and black for features on both arrays. Methods The mappings displayed in this track were used as provided in the SNPedia GFF file. For the &#34;SNPedia with text&#34; track, all SNPedia pages were downloaded and their content checked with a script that tries to remove pages that were auto-generated and not created manually by a user. Credits Thanks to Mike Cariaso for help with the GFF download and Max Haeussler at UCSC for building this track. References Cariaso Michael; Lennon Greg. SNPedia: a wiki supporting personal genome annotation, interpretation and analysis. Nucleic acids research. 2012 40Database issue:D1308-12. PMID: 22140107; PMC: PMC3245045 
snpediaText SNPedia with text SNPedia pages with manually typed text Phenotype and Literature 
snpediaAll SNPedia all SNPedia all SNPs (including empty pages) Phenotype and Literature 
wgEncodeSydhNsome Stanf Nucleosome GSE35586 Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU Regulation Description Nucleosomes are part of the first level of chromatin packaging. They each consist of a histone heterooctamer around which DNA wraps 1.6 times. The histone heterooctomamer is made up of two copies of histones 2A, 2B, 3 and 5. The segment of DNA wrapped around the histones, the so-called &quot;core&quot; fragment, is 147 base pairs long. Neighboring nucleosomes are separated from one another by a stretch of DNA called the &quot;linker,&quot; whose size varies depending on organism, cell type, and even chromatin activity. Certain chromatin remodeling factors govern accessibility of DNA to regulatory proteins by repositioning nucleosomes to reveal regulatory sites that would otherwise be occluded by a nucleosome. In contrast to histone modifications such as methylation or acetylation, which are investigated by ChIP-seq, nucleosome positioning data are generated without immunoprecipitation (see Methods below). Instead, micrococcal nuclease is used to digest chromatin to apparent completion, the (well-defined and clearly visible) mononucleosomal core fragment fraction is isolated by gel purification, and one end is then sequenced. Mapping the sequence tag back to the genome reveals the precise position of one end of the core fragment that was protected by the nucleosome; the position of the other end can then simply be inferred by extending the read to a virtual length of 147 bases. Statistical analyses such as occupancy and positioning stringency can then be employed to analyze the local nucleosome landscape anywhere in the (mappable) genome or to infer global parameters of nucleosome organization. In the context of the ENCODE project, nucleosome positioning data are particularly valuable for analysis of the relationship between transcription factor binding, histone modifications, and gene activity. For a general primer on these types of data and analyses, refer to Valouev et al. (2008). Display Conventions and Configuration views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. --> To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. SignalDensity graph (wiggle) of signal enrichment based on processed data. Signals displayed in this track are the results of pooled replicates. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods To isolate mononucleosome core DNA fragments from the GM12878 and K562 ENCODE cell lines we followed the micrococcal nuclease (MNase) digestion and isolation protocol as described in Johnson et al. (2006), Valouev et al. (2008), and Valouev et al. (2011) with the following modifications. The precise concentrations of the two flash-frozen cell samples received from the Snyder Lab were not known so, per our standard procedure, we performed a series of digestions titrating the amount of MNase to determine the concentration of MNase for optimal digestion of each sample. Final concentrations of 25 U/&mu;L and 50 U/&mu;L of MNase were used to digest the GM12878 cells and K562 cells respectively at 20&deg;C for 12 min. All other steps in the digestion and isolation protocol were as described. Cells were grown according to the approved ENCODE cell culture protocols. K562 and GM12878 were each grown to &#126;2.5&times;108 cells. The cells were harvested, frozen and the nucleosome core isolation followed (Valouev et al. 2008). The SOLiD reads were mapped in color-space with the probabilistic mapper, DNAnexus. The DNAnexus mapper measures and propagates mapping uncertainty by including both quality values and mismatches in the alignment score calculation. The scores are then scaled across all possible mappings of the read to estimate the posterior probability for alignment to each genomic location. Reads corresponding to posterior probability of correct mapping &gt; 0.9 were reported. Nucleosome density signal maps (bedgraph and bigwig files) were generated by first shifting reads by 74 bp in the 5&acute; to 3&acute; direction and counting the total number of reads starting at each genomic coordinate on both strands. These counts are then smoothed using un-normalized kernel density smoothing with a triweight kernel. A bandwidth of 30 bp is used which is equivalent to a smoothing window of 60 bp. The smoothed counts at each position are then divided by the expected number of reads from an equivalent uniform distribution of reads in a &plusmn; 30 bp window around that position. If less than 25&#37; of the positions in a &plusmn; 30 bp window around a genomic location are uniquely mappable or if the location is part of an assembly gap, the signal value at that position is considered unreliable and not recorded in the signal files. Hence, genomic coordinates that do not have any associated signal value should be considered missing or unreliable data. Genomic coordinates associated with a signal value of 0 are reliably mapable but do not have any signal in the dataset. Verification The data were validated by pooling together separate runs to give sufficient sequencing depth for a reasonable signal to noise ratio. Verification that each replicate shows similar strand-cross correlation profiles with a strong peak at approximately 147 bp indicates that the predominant fragment length is equal to the typical size of a mononucleosome. Credits Michael Snyder (PI, Stanford University, California) Debasish Raha (Snyder lab) cell culture Steven Johnson (PI, Brigham Young University, Utah) Elliot Winters (Johnson lab) prepared the mononucleosome core fragments Arend Sidow (PI, Stanford University, California) Ziming Weng (Sidow lab) built the libraries Cheryl Smith (Sidow lab) sequenced the libraries Philippe Lacroute and Philipe Cayting (Stanford Center for Genomics and Personalized Medicine) managed the data submission Contact: Anshul Kundaje (Batzoglou and Sidow labs) mapped the data at DNAnexus and generated the signal tracks References Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 2006 Dec;16(12):1505-16. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Determinants of nucleosome organization in primary human cells. Nature. 2011 May 22;474(7352):516-20. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeSydhNsomeViewSignal Signal Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU Regulation 
wgEncodeSydhNsomeK562Sig K562 Sig K562 Nucleosome ENCODE Mar 2012 Freeze 2011-06-24 2011-01-22 2011-10-21 wgEncodeEH000921 921 GSM920557 Snyder Stanford hg19 AB_SOLiD_3.5 wgEncodeSydhNsomeK562Sig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Nucleosome Position Snyder Snyder - Stanford University Applied Biosystems SOLiD System 3.5 Signal K562 Nucleosome Signal from ENCODE/Stanford/BYU Regulation 
wgEncodeSydhNsomeGm12878Sig GM12878 Sig GM12878 Nucleosome ENCODE Mar 2012 Freeze 2011-06-24 2011-01-24 2011-10-24 wgEncodeEH000922 922 GSM920558 Snyder Stanford hg19 AB_SOLiD_3.5 wgEncodeSydhNsomeGm12878Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Nucleosome Position Snyder Snyder - Stanford University Applied Biosystems SOLiD System 3.5 Signal GM12878 Nucleosome Signal from ENCODE/Stanford/BYU Regulation 
stsMap STS Markers STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps Mapping and Sequencing Description This track shows locations of Sequence Tagged Site (STS) markers along the draft assembly. These markers have been mapped using either genetic mapping (Genethon, Marshfield, and deCODE maps), radiation hybridization mapping (Stanford, Whitehead RH, and GeneMap99 maps) or YAC mapping (the Whitehead YAC map) techniques. Since August 2001, this track no longer displays fluorescent in situ hybridization (FISH) clones, which are now displayed in a separate track. Genetic map markers are shown in blue; radiation hybrid map markers are shown in black. When a marker maps to multiple positions in the genome, it is shown in a lighter color. Methods Positions of STS markers are determined using both full sequences and primer information. Full sequences are aligned using blat, while isPCR (Jim Kent) and ePCR are used to find locations using primer information. Both sets of placements are combined to give final positions. In nearly all cases, full sequence and primer-based locations are in agreement, but in cases of disagreement, full sequence positions are used. Sequence and primer information for the markers were obtained from the primary sites for each of the maps, and from NCBI UniSTS (now part of NCBI Probe). Using the Filter The track filter can be used to change the color or include/exclude a set of map data within the track. This is helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: In the pulldown menu, select the map whose data you would like to highlight or exclude in the display. By default, the &quot;All Genetic&quot; option is selected. Choose the color or display characteristic that will be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display data from the map selected in the pulldown list. If &quot;include&quot; is selected, the browser will display only data from the selected map. When you have finished configuring the filter, click the Submit button. Credits This track was designed and implemented by Terry Furey. Many thanks to the researchers who worked on these maps, and to Greg Schuler, Arek Kasprzyk, Wonhee Jang, and Sanja Rogic for helping process the data. Additional data on the individual maps can be found at the following links: Genethon map Marshfield map deCODE map GeneMap99 GB4 and G3 maps Stanford TNG (Center has closed) Whitehead YAC and RH maps 
wgEncodeSunySwitchgear SUNY SwitchGear RNA Binding Protein Associated RNA by SwitchGear from ENCODE/SUNY Albany Regulation Description This track is produced as part of the Encyclopedia of DNA Elements (ENCODE) Project and displays 3&#39; UTR regions associated with RNA binding proteins in the HT-1080 cell line using reporters. In eukaryotic organisms gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show RNA binding protein associated (predicted via RIP-chip) mRNA 3&#39; UTRs whose attachment to a reporter gene led to a change of that reporter&#39;s expression when the associated RBP&#39;s level was altered. This experiment was proposed as a validation for the data found in SUNY RBP which is the precursor to the hg19 track SUNY GeneST. It was done on a small set of targets chosen from the earliest RIP arrays. Display Conventions and Configuration This is a composite track containing multiple subtracks that display individually in the browser. The subtracks within this track correspond to different mRNA 3&#39; UTRs attached to a reporter and tested for a response to a change in a particular RNA binding protein&#39;s level. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. Instructions for configuring multi-view tracks are here. --> Methods IGF2BP1 targets were identified by RIP-chip and cross referenced with Switchgear&#39;s 3&#39; UTR luciferase reporter clone inventory. 50 ng of putative IGF2BP1 target 3&#39;UTR reporter DNA was individually co-transfected with either 20 ng IGF2BP1(IMP1) cDNA (Origene, SC116030) or alone (untreated). Each transfection was performed in triplicate. The DNA was combined with FuGene transfection reagent (Roche) and allowed to complex for 30 minutes before being added to 7500 HT-1080 (ATCC) cells resuspended in warmed, complete media before being aliquotted into 96 well plates. Cells were returned to the incubator for 24 hours before 100 uL SteadyGlo Luciferase assay reagent was added to each well. The plate was incubated for 30 minutes before being read on a LmaxII-384 luminometer. Signals were normalized using controls and significance of treatment versus control was calculated via a two-tailed t-test. ELAVL1 targets were identified by RIP-chip and cross referenced with SwitchGear&#39;s 3&#39; UTR luciferase reporter clone inventory. We seeded 5,000 HT-1080 cells into 96-well plates the day before transfection and incubated overnight. 50 ng of putative ELAVL1 target 3&#39;UTR reporter DNA was individually co-transfected with either 10ng ELAVL1(HuR) cDNA ( Origene, SC119271) or alone (untreated). Each transfection was performed in triplicate. The DNA was combined with FuGene transfection reagent (Roche) and allowed to complex for 30 minutes before being added to 7500 HT-1080 (ATCC) cells resuspended in warmed, complete media before being aliquotted into 96 well plates. Cells were returned to the incubator for 24 hours before 100 uL SteadyGlo Luciferase assay reagent was added to each well. The plate was incubated for 30 minutes before being read on a LmaxII-384 luminometer. Signals were normalized using controls and significance of treatment versus control was calculated via a two-tailed t-test. For additional Switchgear 3&#39; UTR reporter assay information, see SwitchGear Genomics. Verification All experiments (including controls) performed in and analyzed as triplicates. Credits These data were produced and analyzed by a collaboration between the Tenenbaum lab at the University at Albany-SUNY, College of Nanoscale Science and Engineering, and SwitchGear Genomics. Contact: Scott Tenenbaum References SwitchGear Reporter Related: SwitchGear Publications RIP Related: Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol. 2008;419:93-108. George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006;3(2):57-9. Epub 2006 Apr 1. Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell. 2002;9(6):1161-7. Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes. Methods Mol Biol. 2004;257:125-34. Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods. 2002 Feb;26(2):191-8. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeSunySwitchgearHt1080Igf2bp1RbpAssocRna HT-1080 IGF2BP1 IGF2BP1 HT-1080 Switchgear ENCODE Jan 2011 Freeze 2010-12-10 2011-09-10 wgEncodeEH000610 610 Tenenbaum SunyAlbany wgEncodeSunySwitchgearHt1080Igf2bp1RbpAssocRna RbpAssocRna Insulin-like growth factor 2 mRNA binding protein 1 (Homo sapiens) epithelial cell line derived from a fibrosarcoma, (PMID: 4132053), pseudo-diploid male with a modal chromosome number of 46, numerous chromosome abnormalities RNA IP SwitchGear Validation Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HT-1080 IGF2BP1 RBP Associated RNA by Switchgear from ENCODE/SUNY Regulation 
wgEncodeSunySwitchgearHt1080Elavl1RbpAssocRna HT-1080 ELAVL1 ELAVL1 HT-1080 Switchgear ENCODE Jan 2011 Freeze 2010-12-10 2011-09-10 wgEncodeEH000609 609 Tenenbaum SunyAlbany wgEncodeSunySwitchgearHt1080Elavl1RbpAssocRna RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) epithelial cell line derived from a fibrosarcoma, (PMID: 4132053), pseudo-diploid male with a modal chromosome number of 46, numerous chromosome abnormalities RNA IP SwitchGear Validation Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HT-1080 ELAV1 RBP Associated RNA by Switchgear from ENCODE/SUNY Regulation 
switchDbTss SwitchGear TSS SwitchGear Genomics Transcription Start Sites Regulation Description This track describes the location of transcription start sites (TSS) throughout the human genome along with a confidence measure for each TSS based on experimental evidence. The TSSs of a gene are important landmarks that help define the promoter regions of a gene. These TSSs were determined by SwitchGear Genomics by integrating experimental data using an empirically derived scoring function. Each TSS has a unique identifier that associates it with a gene model (see details below), and each TSS is color-coded to reflect its confidence score. These TSSs are also available in a searchable format at SwitchDB, an open-access online database of human TSSs. Expermental tools are available through SwitchGear to study the function of the promoter regions associated with these TSSs. Methods The predicted TSSs are associated with a genome-wide set of gene models. SwitchGear gene models are defined as clusters of cDNA alignments that have overlapping exons on the same strand. These gene models were created from over 250,000 human cDNA alignments to construct a genome-wide set of ~37,000 gene models. Each gene model is identified by its chromosome number, strand, and unique identifier. For example, ID CHR7_P0362 indicates a cDNA cluster (0362) aligning to the plus strand (P) of chromosome 7 (CHR7). Existing gene annotation is mapped to the gene models through the NCBI annotation associated with Refseq accession numbers. The SwitchGear TSS prediction algorithm identifies the most likely sites of transcription initiation for each gene model. The algorithm employs a scoring metric to assign a confidence level to each TSS prediction based on existing experimental evidence. In addition to the ~250,000 human cDNAs listed in Genbank, more than 5 million additional 5' human cDNA sequence tags have been generated using a combination of approaches. While these short sequence reads do not reveal gene structure, they provide a significant amount of experimental evidence for identifying transcript start sites. For each gene model, the algorithm counts the number of TSSs (defined as the 5' end of a cDNA) within 200 bp of one another. The TSS score is based on the total number of TSSs identified within this window, with each TSS weighted according to several discriminating features: cDNA library source, relative location within the gene model, and exon structure of the transcript. Furthermore, the TSSs for each gene model are ranked to identify the TSS representing the most likely transcription initiation site for a gene model. Rankings are indicated in the TSS unique identifier by the addition of a suffix (i.e. CHR7_P0362_R1 or CHR7_P0362_R2). Using the Filter This track has a filter that can be used to change the TSS elements displayed by the browser. This filter is based on the score of the TSS element. The filter is located at the top of the track description page, which is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu. By default the track displays only those TSSs with a score of 10 or above. By default, the TSSs for predicted pseudogenes are not displayed. If you would like to display them, check the box next to the Include TSSs for predicted pseudogenes label. When you have finished configuring the filter, click the Submit button. Credits This track was created by Nathan Trinklein and Shelley Force Aldred of SwitchGear Genomics. 
tfbsConsSites TFBS Conserved HMR Conserved Transcription Factor Binding Sites Regulation Description This track contains the location and score of transcription factor binding sites conserved in the human/mouse/rat alignment. A binding site is considered to be conserved across the alignment if its score meets the threshold score for its binding matrix in all 3 species. The score and threshold are computed with the Transfac Matrix Database (v7.0) created by Biobase. The data are purely computational, and as such not all binding sites listed here are biologically functional binding sites. In the graphical display, each box represents one conserved putative tfbs. Clicking on a box brings up detailed information on the binding site, namely its Transfac I.D., a link to its Transfac Matrix (free registration with Transfac required), its location in the human genome (chromosome, start, end, and strand), its length in bases, its raw score, and its Z score. All binding factors that are known to bind to the particular binding matrix of the binding site are listed along with their species, SwissProt ID, and a link to that factor's page on the UCSC Protein Browser if such an entry exists. Methods The Transfac Matrix Database (v.7.0) contains position-weight matrices for 398 transcription factor binding sites, as characterized through experimental results in the scientific literature. Only binding matrices for known transcription factors in human, mouse, or rat were used for this track (258 of the 398). A typical (in this case ficticious) matrix (call it mat) will look something like: A C G T 01 15 15 15 15 N 02 20 10 15 15 N 03 0 0 60 0 G 04 60 0 0 0 A 05 0 0 0 60 T The above matrix specifies the results of 60 (the sum of each row) experiments. In the experiments, the first position of the binding site was A 15 times, C 15 times, G 15 times, and T 15 times (and so on for each position.) The consensus sequence of the above binding site as characterized by the matrix is NNGAT. The format of the consensus sequence is the deduced consensus in the IUPAC 15-letter code. In the general case, the goal is to find all matches to a matrix of length n that are conserved across ns sequences. For this example, n=5 and ns=3 (human, mouse, and rat.) Denote the multispecies alignment s, such that sji is the nucleotide at position j of species i. Also, define an ns x 4 background matrix (call it back) giving the background frequencies of each nucleotide in each species. A sliding window (of length n) calculates the "species score" for each species at each position: From this, a log-odds score is calculated for each species (normalizing by the length of the matrix and the number of species in the alignment): These scores are then summed for all species, yielding a final log-odds score for the current position: Note that the log-odds score of each species must exceed the threshold for that species. The threshold is calculated for each species such that the only hits that will be reported will have a Z score (to be discussed later) of 1.64 or higher in each species (corresponding to a p-value of 0.05). Next, the maximum and minimum possible log-odds scores are computed and summed across all species for the given binding matrix: These are then used to normalize the final, raw log-odds score so that its range is between 0 and 1: Next, the best raw score for each binding matrix is calculated for the 5,000 base upstream region of each human RefSeq gene (taken from the RefGene table for hg19.) The mean and standard deviation for each binding matrix are then calculated across all RefSeq genes. These are then used to create the threshold for each binding matrix, namely, 1.64 standard deviations above the mean. Tfloc is then run with this threshold on each chromosome for the 3-way multiz alignments. Finally, a Z score is calculated for each binding site hit h to matrix m according to the following formula: This final Z score can be interpreted as the number of standard deviations above the mean raw score for that binding matrix across the upstream regions of all RefSeq genes. The default Z score cutoff for display in the browser is 2.33 (corresponding to a p-value of 0.01.) This cutoff can be adjusted at the top of this page. After all hits have been recorded genome-wide, one final filtering step is performed. Due to the inherant redundancy of the Transfac database, several binding sites that all bind the same factor often appear together. For example, consider the following binding sites: 585 chr1 4021 4042 V$MEF2_02 875 - 2.83 585 chr1 4021 4042 V$MEF2_03 917 - 3.38 585 chr1 4021 4042 V$MEF2_04 844 - 3.45 585 chr1 4022 4037 V$HMEF2_Q6 810 - 2.34 585 chr1 4022 4037 V$MEF2_01 802 - 2.47 585 chr1 4022 4038 V$RSRFC4_Q2 875 - 2.65 585 chr1 4022 4039 V$AMEF2_Q6 823 - 2.44 585 chr1 4023 4038 V$RSRFC4_01 878 + 2.53 585 chr1 4024 4035 V$MEF2_Q6_01 913 + 2.41 585 chr1 4024 4039 V$MMEF2_Q6 861 - 2.39 These 10 overlapping binding sites bind a total of 19 factors. However, of these 19 factors, only 7 of them are unique. Many of the above binding sites are redundant (they add no additional factors). In fact, the first 3 binding sites all bind the same two factors (namely, aMEF-2 and MEF-2A). These ten binding sites can therefore be filtered down to the following four binding sites, without any loss of information (in terms of transcription factors). The final table entry then has the following four lines, since these four binding sites account for all 7 of the unique factors: 585 chr1 4021 4042 V$MEF2_04 844 - 3.45 585 chr1 4022 4038 V$RSRFC4_Q2 875 - 2.65 585 chr1 4024 4035 V$MEF2_Q6_01 913 + 2.41 585 chr1 4024 4039 V$MMEF2_Q6 861 - 2.39 In the event that multiple binding sites bind the same factors, the site with the highest Z score is chosen. Only binding sites which overlap each other and whose start positions are within 5 bases of each other are considered for merging. It should be noted that the positions of many of these conserved binding sites coincide with known exons and other highly conserved regions. Regions such as these are more likely to contain false positive matches, as the high sequence identity across the alignment increases the likelihood of a short motif that looks like a binding site to be conserved. Conversely, matches found in introns and intergenic regions are more likely to be real binding sites, since these regions are mostly poorly conserved. These data were obtained by running the program tfloc (Transcription Factor binding site LOCater) on multiz46way alignments, restricting only to the July 2007 (mm9) mouse genome assembly, the November 2004 rat assembly (rn4), and the February 2009 human genome assembly (hg19). Transcription factor information was culled from the Transfac Factor database, version 7.0. Table Format The format of the tfbsConsSites sql table is shown above. The columns are (from left to right): bin, chromosome, from, to, binding matrix ID, raw score, strand, and Z score. To get the corresponding transcription factor information for a given binding matrix, use the table tfbsConsFactors. The format of the tfbsConsFactors sql table is: V$MYOD_01 M00001 mouse MyoD P10085 V$E47_01 M00002 human E47 N V$CMYB_01 M00004 mouse c-Myb P06876 V$AP4_01 M00005 human AP-4 Q01664 V$MEF2_01 M00006 mouse aMEF-2 Q60929 V$MEF2_01 M00006 rat MEF-2 N V$MEF2_01 M00006 human MEF-2A Q02078 V$ELK1_01 M00007 human Elk-1 P19419 V$SP1_01 M00008 human Sp1 P08047 V$EVI1_06 M00011 mouse Evi-1 P14404 The columns are (from left to right): transfac binding matrix id, transfac binding matrix accession number, transcription factor species, transcription factor name, SwissProt accesssion number. When no factor species, name, or id information exists in the transfac factor database for a binding matrix, an 'N' appears in the corresponding column(s). Notice also that if more than one transcription factor is known for one binding matrix, each occurs on its own line, so multiple lines can exist for one binding matrix. Credits These data were generated using the Transfac Matrix and Factor databases created by Biobase. The tfloc program was developed at The Pennsylvania State University (with numerous updates done at UCSC) by Matt Weirauch. This track was created by Matt Weirauch and Brian Raney at The University of California at Santa Cruz. 
tRNAs tRNA Genes Transfer RNA Genes Identified with tRNAscan-SE Genes and Gene Predictions Description This track displays tRNA genes predicted by using tRNAscan-SE v.1.23. tRNAscan-SE is an integrated program that uses tRNAscan (Fichant) and an A/B box motif detection algorithm (Pavesi) as pre-filters to obtain an initial list of tRNA candidates. The program then filters these candidates with a covariance model-based search program COVE (Eddy) to obtain a highly specific set of primary sequence and secondary structure predictions that represent 99-100% of true tRNAs with a false positive rate of fewer than 1 per 15 gigabases. Detailed tRNA annotations for eukaryotes, bacteria, and archaea are available at Genomic tRNA Database (GtRNAdb). What does the tRNAscan-SE score mean? Anything with a score above 20 bits is likely to be derived from a tRNA, although this does not indicate whether the tRNA gene still encodes a functional tRNA molecule (i.e. tRNA-derived SINES probably do not function in the ribosome in translation). Vertebrate tRNAs with scores of &gt;60.0 (bits) are likely to encode functional tRNA genes, and those with scores below ~45 have sequence or structural features that indicate they probably are no longer involved in translation. tRNAs with scores between 45-60 bits are in the &quot;grey&quot; zone, and may or may not have all the required features to be functional. In these cases, tRNAs should be inspected carefully for loss of specific primary or secondary structure features (usually in alignments with other genes of the same isotype), in order to make a better educated guess. These rough score range guides are not exact, nor are they based on specific biochemical studies of atypical tRNA features, so please treat them accordingly. Please note that tRNA genes marked as &quot;Pseudo&quot; are low scoring predictions that are mostly pseudogenes or tRNA-derived elements. These genes do not usually fold into a typical cloverleaf tRNA secondary structure and the provided images of the predicted secondary structures may appear rotated. Credits Both tRNAscan-SE and GtRNAdb are maintained by the Lowe Lab at UCSC. Cove-predicted tRNA secondary structures were rendered by NAVIEW (c) 1988 Robert E. Bruccoleri. References When making use of these data, please cite the following articles: Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009 Jan;37(Database issue):D93-7. PMID: 18984615; PMC: PMC2686519 Eddy SR, Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res. 1994 Jun 11;22(11):2079-88. PMID: 8029015; PMC: PMC308124 Fichant GA, Burks C. Identifying potential tRNA genes in genomic DNA sequences. J Mol Biol. 1991 Aug 5;220(3):659-71. PMID: 1870126 Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955-64. PMID: 9023104; PMC: PMC146525 Pavesi A, Conterio F, Bolchi A, Dieci G, Ottonello S. Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucleic Acids Res. 1994 Apr 11;22(7):1247-56. PMID: 8165140; PMC: PMC523650 
targetScanS TS miRNA sites TargetScan miRNA Regulatory Sites (Release 5.1, April 2009) Regulation Description This track shows conserved mammalian microRNA regulatory target sites for conserved microRNA families in the 3' UTR regions of Refseq Genes, as predicted by TargetScanHuman 5.1. Method Putative miRNA binding sites in UTRs were identified using seven-nucleotide seed regions from all known miRNA families conserved across mammals. Using all human RefSeq transcripts and CDS annotation from NCBI, aligned vertebrate 3' UTRs were extracted from multiz alignments and masked for overlap with protein-coding sequences. These 3' UTRs were scanned to identify conserved matches to the miRNA seed region, as in Friedman et al., 2009. These sites were then assigned a percentile rank (0 to 100) based on their context score (Grimson et al., 2007). For further details of the methods used to generate this annotation, see the references and the TargetScan website. Credit Thanks to George Bell of Bioinformatics and Research Computing at the Whitehead Institute for providing this annotation, which was generated in collaboration with the labs of David Bartel and Chris Burge. Additional information on microRNA target prediction is available on the TargetScan website. References Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005 Jan 14;120(1):15-20. PMID: 15652477 Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007 Jul 6;27(1):91-105. PMID: 17612493; PMC: PMC3800283 Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009 Jan;19(1):92-105. PMID: 18955434; PMC: PMC2612969 
targetScanMiRnaSites TS miRNA Targets TargetScan predicted microRNA target sites Regulation Description TargetScan is a web resource that provides predictions of biological targets of microRNAs by searching for the presence of sites that match the seed region of each miRNA. The TargetScan browser tracks show conserved mammalian microRNA regulatory target sites for conserved microRNA families in the 3' UTR regions of human Refseq Genes. Credit Thanks to George Bell of Bioinformatics and Research Computing at the Whitehead Institute for providing this annotation, which was generated in collaboration with the labs of David Bartel and Chris Burge. Additional information on microRNA target prediction is available on the TargetScan website. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Data is also freely available on the TargetScan website. References Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015 Aug 12;4. PMID: 26267216; PMC: PMC4532895 Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol. 2011 Sep 11;18(10):1139-46. PMID: 21909094; PMC: PMC3190056 Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009 Jan;19(1):92-105. PMID: 18955434; PMC: PMC2612969 Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007 Jul 6;27(1):91-105. PMID: 17612493; PMC: PMC3800283 Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005 Jan 14;120(1):15-20. PMID: 15652477 
targetScanMiRnaSitesV72 TS miRNA v7.2 Predicted microRNA Target Sites from TargetScanHuman 7.2 (March 2018) Regulation Description This track shows conserved mammalian microRNA regulatory target sites for conserved microRNA families in the 3' UTR regions of Refseq Genes, as predicted by TargetScanHuman 7.2. Display Conventions The track items are colored based on the four classes of target sites identified in Agarwal et al., 2015. Purple 8mer Red 7mer-m8 Blue 7mer-A1 Green Non-canonical Method Putative miRNA binding sites in UTRs were found by searching for conserved 8mer, 7mer, and 6mer sites that match the seed regions from all known miRNA families in mammals. Using protein-coding human transcripts from GENCODE v19 and RefSeq, aligned vertebrate 3' UTRs were extracted from Multiz alignments to create 3' UTR profiles. These 3' UTRs were scanned to identify conserved matches to the miRNA seed region, as in Friedman et al., 2009. These sites were then assigned a percentile rank based on their context++ score (Agarwal et al., 2015). This field is set to -1 for some noncanonical sites where the context++ score model isn't applicable. For further details of the methods used to generate this annotation, see the references and the TargetScan website. Release Notes Compared to previous releases, Release 7 uses an improved method to predict targeting efficacy (the context++ model, Agarwal et al., 2015), uses 3' UTR profiles that indicate the fraction of mRNA containing each site (Nam et al., 2014), and uses updated miRNA families curated from Chiang et al., 2010 and Fromm et al., 2015. The previous version released by UCSC was 5.1. For further information on previous releases refer to TargetScan Releases. Credit Thanks to George Bell of Bioinformatics and Research Computing at the Whitehead Institute for providing this annotation, which was generated in collaboration with the labs of David Bartel and Chris Burge. Additional information on microRNA target prediction is available on the TargetScan website. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Data is also freely available on the Target Scan website TargetScanHuman V7.2 Data Download. References Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015 Aug 12;4. PMID: 26267216; PMC: PMC4532895 Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol. 2011 Sep 11;18(10):1139-46. PMID: 21909094; PMC: PMC3190056 Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009 Jan;19(1):92-105. PMID: 18955434; PMC: PMC2612969 Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007 Jul 6;27(1):91-105. PMID: 17612493; PMC: PMC3800283 Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005 Jan 14;120(1):15-20. PMID: 15652477 
knownAlt UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes Genes and Gene Predictions Description This track shows various types of alternative splicing and other events that result in more than a single transcript from the same gene. The label by an item describes the type of event. The events are: Alternate Promoter (altPromoter) - Transcription starts at multiple places. The altPromoter extends from 100 bases before to 50 bases after transcription start. Alternate Finish Site (altFinish) - Transcription ends at multiple places. Cassette Exon (cassetteExon) - Exon is present in some transcripts but not others. These are found by looking for exons that overlap an intron in the same transcript. Retained Intron (retainedIntron) - Introns are spliced out in some transcripts but not others. In some cases, particularly when the intron is near the 3' end, this can reflect an incompletely processed transcript rather than a true alt-splicing event. Overlapping Exon (bleedingExon) - Initial or terminal exons overlap in an intron in another transcript. These often are associated with incompletely processed transcripts. Alternate 3' End (altThreePrime) - Variations on the 3' end of an intron. Alternate 5' End (altFivePrime) - Variations on the 5' end of an intron. Intron Ends have AT/AC (atacIntron) - An intron with AT/AC ends rather than the usual GT/AG. These are associated with the minor spliceosome. Strange Intron Ends (strangeSplice) - An intron with ends that are not GT/AG, GC/AG, or AT/AC. These are usually artifacts of some sort due to sequencing error or polymorphism. Credits This track is based on an analysis by the txgAnalyse program of splicing graphs produced by the txGraph program. Both of these programs were written by Jim Kent at UCSC. 
ucsfBrainMethyl UCSF Brain Methyl UCSF Brain DNA Methylation Regulation Description Genome wide methylation (MeDIP-seq and MRE-seq), histone H3 lysine 4 trimethylation (H3K4me3) and gene expression (RNA-seq and RNA-seq (SMART)) data were generated from postmortem human frontal cortex gray matter of a 57 year-old male. This was done to investigate the role that intragenic, tissue-specific CpG island methylation plays in controlling gene expression (Maunakea, et al. 2010). Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. The following views are in this track: Raw Singal Density graph (wiggle) of signal enrichment. CpG score DNA methylation score on CpG sites. Methods DNA, RNA and native chromatin were extracted using standard methods; assay specific methods are described below. MRE-seq, MeDIP-seq, H3K4me3 ChIP-seq, RNA-seq and RNA-seq (SMART) libraries were sequenced using an Illumina Genome Analyzer II. Sequencing reads are available through the NCBI SRA (study accession number SRP002318). MeDIP-seq (Methylated DNA immunoprecipitation and sequencing) MeDIP-seq uses immunoprecipitation to extract the methylated fraction of the genome. Purified DNA was first sheared and processed following the Illumina Genomic DNA Library Kit protocol. These DNA fragments were then immunoprecipitated using an antibody raised against 5-methylcytosine, the methylated form of cytosine, before constructing a library, which was sequenced and mapped to the genome. MRE-seq (Methyl-sensitive restriction enzyme digest and sequencing) MRE-seq identifies unmethylated CpG sites by sequencing size-selected fragments from parallel DNA digestions with the MREs HpaII, Hin6I, and AciI. Since these enzymes require unmethylated CpG sites within their recognition sequences to cut DNA, identifying the end of each fragment generated allows inference of a single unmethylated cytosine. The 3 digests were combined and size-selected by gel electrophoresis to enrich for unmethylated CpG sites in close proximity. A library was constructed and sequenced; the sequence reads were then mapped to the genome with the additional requirement that they map to a known MRE recognition site. H3K4me3 ChIP-seq (Histone H3 lysine 4 trimethylation chromatin immunoprecipitation and sequencing) Chromatin immunoprecipitation was performed to enrich for histone H3 modified at lysine position 4 with trimethylation (H3K4me3), as this histone modification is associated with promoters. A ChIP-seq library was constructed as described in Robertson, et al. 2007, sequenced and mapped to the genome. RNA-seq and RNA-seq SMART (RNA sequencing and SMART-tagged RNA sequencing) Sheared RNA was used to synthesize full-length single-stranded cDNAs as described by Morin, et al. 2008. A library was constructed and sequenced, and sequence reads are mapped to the genome. The 5&#39; end of transcripts were tagged with a sequence tag, called a &quot;SMART tag&quot;, while making cDNA library for sequencing. SMART tagged reads were used to infer transcription initiation, while all reads together are used to infer gene expression level. Verification MeDIP-seq Each post-amplification library was QC&#39;d for quantity, quality and size distribution by spectrophotometry and Agilent DNA Bioanalyzer analysis. Four independent PCR reactions were performed to confirm enrichment for methylated and de-enrichment for unmethylated sequences, compared to input sonicated DNA. Visual inspection of extended coverage browser tracks confirmed expectations: lack of MeDIP signal in most 5&#39; CpG island promoters and in regions devoid of CpG sites, as well as high MeDIP signal at known methylated sites (i.e. some imprinted regions). MRE-seq Each post-amplification library was QC&#39;d for quantity, quality and size distribution by Nanodrop spectrophotometry and Agilent DNA Bioanalyzer analysis. Prior to high-throughput sequencing, a portion of each library was cloned into a sequencing vector and &#126;24 individual clones were Sanger sequenced to confirm the presence of MRE sites at the ends of each insert. Illumina sequencing reads were filtered to only include those that map to MRE sites in the reference. MRE reads occured frequently in 5&#39; CpG islands, which are often unmethylated and are enriched for the MRE recognition sequences relative to rest of the genome. H3K4me3 ChIP-seq Each post-amplification library was examined for quantity, quality and size distribution by Nanodrop spectrophotometry, Qubit fluoremetry and Agilent DNA Bioanalyzer. Fold H3K4me3 enrichment was confirmed by comparison to non-specific rabbit IgG enrichment. Visual inspection of the browser track of called peaks confirmed enrichment at a subset of annotated promoters. RNA-seq and RNA-seq (SMART) Each post-amplification library was examined for quantity, quality and size distribution by Nanodrop spectrophotometry, Qubit fluoremetry and Agilent DNA Bioanalyzer. Visual inspection of the browser track of extended reads confirmed enrichment at annotated exons and UTRs. SMART-tagged reads were enriched at known promoters, as expected. Credits UCSF: Joseph Costello, Raman Nagarajan, Shaun Fouse, Brett Johnson, Chibo Hong, Ksenya Shchors, Vivi M. Heine, David H. Rowitch Genome Sciences Centre, BC Cancer Agency: Mikhail Bilenky, Cletus D'Souza, Cydney Nielsen, Yongjun Zhao, Allen Delaney, Richard Varhol, Nina Thiessen, Steven S.J. Jones, Marco A. Marra, Martin Hirst Washington University, St. Louis, MO: Ting Wang, Xiaoyun Xing, Chris Fiore, Maximiliaan Schillebeeckx UCSC: Tracy J. Ballinger, David Haussler McGill: Gustavo Turecki References Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. PMID: 20613842 Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques. 2008 Jul;45(1):81-94. PMID: 18611170 Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug;4(8):651-7. PMID: 17558387 
ucsfBrainMethylViewCOV Raw Signal UCSF Brain DNA Methylation Regulation 
ucsfRnaSeqBrainSmartCoverage Smart RawSignal RNA-seq Smart-Tagged Raw Signal Regulation 
ucsfRnaSeqBrainAllCoverage RNA-seq RawSignal RNA-seq Raw Signal Regulation 
ucsfMedipSeqBrainCoverage MeDIP RawSignal MeDIP-seq Raw Signal Regulation 
ucsfChipSeqH3K4me3BrainCoverage H3K4me3 RawSignal H3K4me3 ChIP-seq Raw Signal Regulation 
ucsfBrainMethylViewCG CpG score UCSF Brain DNA Methylation Regulation 
ucsfMedipSeqBrainCpG MeDIP CpG MeDIP-seq CpG Score Regulation 
ucsfMreSeqBrainCpG MRE CpG MRE-seq CpG Score Regulation 
uMassBrainHistone UMMS Brain Hist Brain Histone H3K4me3 ChIP-Seq from Univ. Mass. Medical School (Akbarian/Weng) Regulation Description This track displays maps of histone H3K4me3 in human brain, identified by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). Measurements were made in neuronal and non-neuronal nuclei collected from prefrontal cortex (PFC) of 11 individuals ranging in age from 0.5 to 69 years. ChIP-Seq begins by using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. Methods Human prefrontal cortex samples used in this study were obtained from the Brain and Tissue Bank for Developmental Disorders, University of Maryland and a brain bank at the University of California, Irvine. Nuclei extraction, chromatin immunoprecipitation and sequencing were carried out as described in Cheung I, et al. (2010). Sequencing was performed on an Illumina Genome Analyzer (GA II). The length of sequence reads was 36 bp. Mapping was performed using Bowtie (version 0.11.3, Langmead B, Trapnell C, Pop M, Salzberg SL (2009)) allowing up to one mismatch to map all sequence reads to the gender appropriate human genome hg18 (NCBI36), and 67-87% of the reads in the neuronal samples mapped to one unique location in the genome. The mapped reads were analyzed using the MACS software package (version 1.3.5, Zhang Y, et al. (2008)) to identify peaks, with bw = 230 bp, as defined experimentally by PCR, tSize = 36 bp, and other parameters set at default. The scored peaks were then lifted to the hg19 (GRCh37) assembly. Signal tracks were generated directly from a remapping of the reads to hg19. Verification Experimental testing was performed on a subset of the peaks that were positioned more than 10 kb from annotated genes for RNA expression in PFC neurons by qRT-PCR and in situ hybridization. These results suggest that H3K4me3 mapping can serve as a guide to uncover potentially hundreds of unannotated novel and cell-specific transcripts in the brain. Credits Chromatin immunoprecipitation experiments were carried out by Iris Cheung, Yan Jiang and Schahram Akbarian; analyses were performed by Hennady Shulha, Jie Wang and Zhiping Weng at the University of Massachusetts Medical School. References Cheung I, Shulha HP, Jiang Y, Matevossian A, Wang J, Weng Z, Akbarian S. Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proc Natl Acad Sci U S A. 2010 May 11;107(19):8824-9. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. 
uMassBrainHistoneViewSignal View Signal Brain Histone H3K4me3 ChIP-Seq from Univ. Mass. Medical School (Akbarian/Weng) Regulation 
uMassBrainHistoneSignalS11NeuM69yrsF NeuN- 69yrs F UMMS Brain Histone H3K4me3 (NeuN- D11) Gender-female Age-69 Regulation 
uMassBrainHistoneSignalS6NeuM4pt7yrsM NeuN- 4.7yrs M UMMS Brain Histone H3K4me3 (NeuN- D6) Gender-male Age-4.7 Regulation 
uMassBrainHistoneSignalS11NeuP69yrsF NeuN+ 69yrs F UMMS Brain Histone H3K4me3 (NeuN+ D11) Gender-female Age-69 Regulation 
uMassBrainHistoneSignalS10NeuP69yrsF NeuN+ 69yrs F UMMS Brain Histone H3K4me3 (NeuN+ D10) Gender-female Age-69 Regulation 
uMassBrainHistoneSignalS9NeuP68yrsF NeuN+ 68yrs F UMMS Brain Histone H3K4me3 (NeuN+ D9) Gender-female Age-68 Regulation 
uMassBrainHistoneSignalS8NeuP14yrsM NeuN+ 14yrs M UMMS Brain Histone H3K4me3 (NeuN+ D8) Gender-male Age-14 Regulation 
uMassBrainHistoneSignalS7NeuP8pt8yrsM NeuN+ 8yrs M UMMS Brain Histone H3K4me3 (NeuN+ D7) Gender-male Age-8.8 Regulation 
uMassBrainHistoneSignalS6NeuP4pt7yrsM NeuN+ 4.7yrs M UMMS Brain Histone H3K4me3 (NeuN+ D6) Gender-male Age-4.7 Regulation 
uMassBrainHistoneSignalS5NeuP2pt8yrsF NeuN+ 2.8yrs F UMMS Brain Histone H3K4me3 (NeuN+ D5) Gender-female Age-2.8 Regulation 
uMassBrainHistoneSignalS4NeuP1pt3yrsM NeuN+ 1.3yrs M UMMS Brain Histone H3K4me3 (NeuN+ D4) Gender-male Age-1.3 Regulation 
uMassBrainHistoneSignalS3NeuP0pt75yrsF NeuN+ 0.75yrs F UMMS Brain Histone H3K4me3 (NeuN+ D3) Gender-female Age-0.75 Regulation 
uMassBrainHistoneSignalS2NeuP0pt58yrsM NeuN+ 0.58yrs M UMMS Brain Histone H3K4me3 (NeuN+ D2) Gender-male Age-0.58 Regulation 
uMassBrainHistoneSignalS1NeuP0pt5yrsM NeuN+ 0.50yrs M UMMS Brain Histone H3K4me3 (NeuN+ D1) Gender-male Age-0.5 Regulation 
uMassBrainHistoneViewPeaks View Peaks Brain Histone H3K4me3 ChIP-Seq from Univ. Mass. Medical School (Akbarian/Weng) Regulation 
uMassBrainHistonePeaksSample Sample-specific Sample-specific Brain Histone H3K4me3 from UMMS Regulation 
uMassBrainHistonePeaksNeuron Neuron-specific Neuron-specific Brain Histone H3K4me3 from UMMS Regulation 
uMassBrainHistonePeaksInfant Developmental Developmental Brain Histone H3K4me3 from UMMS Regulation 
wgEncodeOpenChromFaire UNC FAIRE GSE35239 Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill) Regulation Description These tracks display Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) evidence as part of the four Open Chromatin track sets (see below). FAIRE is a method to isolate and identify nucleosome-depleted regions of the genome. FAIRE was initially discovered in yeast and subsequently shown to identify active regulatory elements in human cells (Giresi et al., 2007). Similar to DNaseI HS, FAIRE appears to identify functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions and novel elements. Together with DNaseI HS and ChIP-seq experiments, these tracks display the locations of active regulatory elements identified as open chromatin in multiple cell types from the Duke, UNC-Chapel Hill, UT-Austin, and EBI ENCODE group. Within this project, open chromatin was identified using two independent and complementary methods: DNaseI hypersensitivity (HS) and these FAIRE assays, combined with chromatin immunoprecipitation (ChIP) for select regulatory factors. DNaseI HS and FAIRE provide assay cross-validation with commonly identified regions delineating the highest confidence areas of open chromatin. ChIP assays provide functional validation and preliminary annotation of a subset of open chromatin sites. Each method employed Illumina (formerly Solexa) sequencing by synthesis as the detection platform. The Tier 1 and Tier 2 cell types were additionally verified by a second platform, high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen. Other Open Chromatin track sets: Data for the DNase experiments can be found in Duke DNaseI HS. Data for the ChIP experiments can be found in UTA TFBS. A synthesis of all the open chromatin assays for select cell lines can be found in Open Chrom Synth. Display Conventions and Configuration This track is a multi-view composite track that contains a single data type with multiple levels of annotation (views). For each view, there are multiple subtracks representing different cell types that display individually on the browser. Instructions for configuring multi-view tracks are here. Chromatin data displayed here represents a continuum of signal intensities. The Leib lab recommends setting the &quot;Data view scaling: auto-scale&quot; option when viewing signal data in full mode to see the full dynamic range of the data. Note that in regions that do not have open chromatin sites, autoscale will rescale the data and inflate the background signal, making the regions appear noisy. Changing back to fixed scale will alleviate this issue. In general, for each experiment in each of the cell types, the UNC FAIRE tracks contain the following views: Peaks Peaks are regions of enriched signal in FAIRE experiments. Peaks were called based on signals created using F-Seq, a software program developed at Duke (Boyle et al., 2008b). Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. The solid vertical line in the peak represents the point with highest signal. F-Seq Density Signal F-Seq Density Signal is a graph (wiggle) of signal enrichment calculated using F-Seq for the combined set of sequences from all replicates. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). This method does not look at fixed-length windows, but rather weights contributions of nearby sequences in proportion to their distance from that base. It only considers sequences aligned four or less times in the genome, and uses an alignability background model to try to correct for regions where sequences cannot be aligned. A model based on control input data was also used for each cell type to try to correct for amplifications and deletions, especially important for cells with an abnormal karyotype. Base Overlap Signal Base Overlap Signal is an alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Tracks displayed in this track are the results of pooled replicates. The raw sequence and alignment files for each replicate are available for download. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. FAIRE was performed (Giresi et al., 2007) by cross-linking proteins to DNA using 1% formaldehyde solution, and the complex was sheared using sonication. Phenol/chloroform extractions were performed to remove DNA fragments cross-linked to protein. The DNA recovered in the aqueous phase was sequenced using an Illumina (Solexa) sequencing system. FAIRE-seq data for Tier 1 and Tier 2 cell lines were verified by comparing multiple independent growths (replicates) and determining the reproducibility of the data. For some cell types additional verification was performed using the same material, but hybridized to NimbleGen Human ENCODE tiling arrays (1&#37; of the genome) along with the input DNA as reference (FAIRE-chip). A more detailed protocol is available here and in the references below (Giresi et al., 2009). DNA fragments isolated by FAIRE are 100-200 bp in length, with the average length being 134 bp. Sequences from each experiment were aligned to the genome using Burrows-Wheeler Aligner (BWA) (Li et al., 2010) for the NCBI 36 (hg19) assembly. The command used for these alignments was: &gt; bwa aln -t 8 genome.fa s_1.sequence.txt.bfq &gt; s_1.sequence.txt.sai Where genome.fa is the whole genome sequence and s_1.sequence.txt.bfq is one lane of sequences converted into the required bfq format. Sequences from multiple lanes are combined for a single replicate using the bwa samse command, and converted in the sam/bam format using SAMtools. Only those that aligned to four or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes - see supplemental materials). The mappings of these short reads to the genome are available for download. The resulting digital signal was converted to a continuous wiggle track using F-Seq that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Input data has been generated for several cell lines. These are used directly to create a control/background model used for F-Seq when generating signal annotations for these cell lines. These models are meant to correct for sequencing biases, alignment artifacts, and copy number changes in these cell lines. Input data is not being generated directly for other cell lines. For cell lines for which there is no input experiment available, the peaks were generated using the control of generic_male or generic_female, as an attempt to create a general background based on input data from several cell types. These files are in &quot;iff&quot; format, which is used when calling peaks with F-seq software, and can be downloaded from the production lab directly from under the section titled &quot;Copy number / karyotype correction.&quot Using a general background model derived from the available Input data sets provided corrections for sequencing biases and alignment artifacts, but will not correct for cell-type-specific copy number changes. The exact command used for this step is: &gt; fseq -l 800 -v -b &lt;bff files&gt; -p &lt;iff files&gt; aligments.bed Where the (bff files) are the background files based on alignability, the (iff files) are the background files based on the input experiments, and alignments.bed are a bed file of filtered sequence alignments. Discrete FAIRE sites (peaks) were identified from FAIRE-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. Data from the high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen were normalized using the Tukey biweight normalization, and peaks were called using ChIPOTle (Buck et al., 2005) at multiple levels of significance. Regions matched on size to these peaks that were devoid of any significant signal were also created as a null model. These data were used for additional verification of Tier 1 and Tier 2 cell lines by ROC analysis. Files labeled Validation view containing this data are available for download. Release Notes Release 2 (September 2012) of this track consists of 12 new experiments, including 11 new cell lines. A synthesis of open chromatin evidence from the three assay types was compiled for Tier 1 and 2 cell lines can be found in: Open Chromatin Synthesis. Enhancer and Insulator Functional assays: A subset of DNase and FAIRE regions were cloned into functional tissue culture reporter assays to test for enhancer and insulator activity. Coordinates and results from these experiments can be found here. Credits These data and annotations were created by a collaboration of multiple institutions (contact: Terry Furey): Duke University's Institute for Genome Sciences & Policy (IGSP): Alan Boyle, Lingyun Song, Terry Furey, and Greg Crawford University of North Carolina at Chapel Hill: Paul Giresi and Jason Lieb Universty of Texas at Austin: Zheng Liu, Ryan McDaniell, Bum-Kyu Lee, and Vishy Iyer European Bioinformatics Insitute: Paul Flicek, Damian Keefe, and Ewan Birney University of Cambridge, Department of Oncology and CR-UK Cambridge Research Institute (CRI) : Stefan Graf We thank NHGRI for ENCODE funding support. References Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res. 2007 Jun;17(6):910-6. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008 Jan 25;132(2):311-22. Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8. Buck MJ, Nobel AB, Lieb JD. ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 2005;6(11):R97. Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods. 2006 Jul;3(7):503-9. Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123-31. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guig&#243; R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007 Jun;17(6):877-85. Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods. 2009 Jul;48(3):233-9. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Nov;18(11):1851-8. Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeOpenChromFaireViewPeaks Peaks Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill) Regulation 
wgEncodeOpenChromFaireUrotsaUt189Pk Urothl ec FAIR Pk Urothelia FaireSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001123 1123 GSM864342 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireUrotsaUt189Pk UT189 Peaks primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina UT189 E.Coli treatment 1 hour, followed by 24 hour incubation Regions of enriched signal in experiment Urothelia UT189 E.coli FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireUrotsaPk Urothl FAIRE Pk Urothelia FaireSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001122 1122 GSM864353 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireUrotsaPk Peaks primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment Urothelia FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireSmallintestineocPk Smll int FAIRE Pk Small_intestine_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003502 3502 GSM1011130 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireSmallintestineocPk Peaks Primary frozen small intestine tissue from NCTC donor IDs 10-0063A (Rep B1) and 09-0143A (Rep B2) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment Small intestine FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireRcc7860Pk RCC7860 FAIR Pk RCC_7860 FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003498 3498 GSM1011120 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireRcc7860Pk Peaks renal cell adenocarcinmoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment RCC 7860 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFairePanisletsPk PanIslet FAIRE Pk PanIslets FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-14 2010-07-14 wgEncodeEH000573 573 GSM864346 Crawford UNC Lieb Lab peaks hg18 wgEncodeOpenChromFairePanisletsPk Peaks pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment PanIslets FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFairePancreasocPk Pancreas FAIRE Pk Pancreas_OC FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003497 3497 GSM1011129 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFairePancreasocPk Peaks Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment Pancreas FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireNhekPk NHEK FAIRE Pk NHEK FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000558 558 GSM864338 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireNhekPk Peaks epidermal keratinocytes FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment NHEK FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireNhbePk NHBE FAIRE Pk NHBE FaireSeq ENCODE Mar 2012 Freeze 2011-02-11 2010-01-09 2010-10-09 wgEncodeEH000604 604 GSM864337 Crawford UNC p-value cutoff: 0.1 hg18 wgEncodeOpenChromFaireNhbePk Peaks bronchial epithelial cells FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment NHBE FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireNhaPk NH-A FAIRE Pk NH-A FaireSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001115 1115 GSM864347 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireNhaPk Peaks astrocytes (also called Astrocy) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment NH-A FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMrtttc549Pk MRT TTC549 F Pk MRT_TTC549 FaireSeq ENCODE Jul 2012 Freeze 2012-04-20 2013-01-20 wgEncodeEH003494 3494 GSM1011124 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireMrtttc549Pk Peaks Malignant Hepatic Rhabdoid tumor line FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment MRT TTC549 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMrtg4016Pk MRT G401.6 F Pk MRT_G401 FaireSeq ENCODE Jul 2012 Freeze 2012-04-20 2013-01-20 wgEncodeEH003493 3493 GSM1011127 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireMrtg4016Pk Peaks Malignant renal rhabdoid tumor line FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment MRT G401.6 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMrta2041Pk MRT A204.1 F Pk MRT_A204 FaireSeq ENCODE Jul 2012 Freeze 2012-04-20 2013-01-20 wgEncodeEH003492 3492 GSM1011126 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireMrta2041Pk Peaks Malignant rhabdoid tumor (MRT) line, rhabdomyosarcoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment MRT A204.1 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMedulloPk Medullo FAIRE Pk Medullo FaireSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001118 1118 GSM864351 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireMedulloPk Peaks medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment Medullo FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireKidneyocPk Kidney FAIRE Pk Kidney_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003501 3501 GSM1011123 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireKidneyocPk Peaks Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment Kidney FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHtr8Pk HTR8svn FAIRE Pk HTR8svn FaireSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001124 1124 GSM864343 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireHtr8Pk Peaks trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment HTR8svn FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm19239Pk GM19239 FAIRE Pk GM19239 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-18 2010-09-18 wgEncodeEH000580 580 GSM864358 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireGm19239Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment GM19239 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm18507Pk GM18507 FAIRE Pk GM18507 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-20 2010-09-19 wgEncodeEH000586 586 GSM864355 Crawford UNC p-value cutoff: 0.1 hg18 wgEncodeOpenChromFaireGm18507Pk Peaks lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment GM18507 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm12892Pk GM12892 FAIRE Pk GM12892 FaireSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001117 1117 GSM864357 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireGm12892Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment GM12892 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm12891Pk GM12891 FAIRE Pk GM12891 FaireSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001116 1116 GSM864349 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireGm12891Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment GM12891 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGlioblaPk Gliobla FAIRE Pk Gliobla FaireSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001119 1119 GSM864350 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireGlioblaPk Peaks glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment Gliobla FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireFrontalcortexocPk Frntl crtx FAI Pk Frontal_cortex_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-04 2013-04-04 wgEncodeEH003500 3500 GSM1011122 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireFrontalcortexocPk Peaks Primary ventromedial prefrontal cortex, from KPBBB donor IDs 673 (Rep B1) and 913 (Rep B2) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment Frontal cortex FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireEndometriumocPk Endometr FAIRE Pk Endometrium_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003503 3503 GSM1011119 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireEndometriumocPk Peaks Endometrium isolated from uterine lining FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment Endometrium FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireColonocPk Colon FAIRE Pk Colon_OC FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003495 3495 GSM1011125 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireColonocPk Peaks Primary frozen colon tissue from NCTC donor IDs 10-0005A (Rep B1) and 10-0170A (Rep B2), African American and caucasian FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment Colon FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMcf7VehPk MCF-7 Veh FAIR Pk MCF-7 FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003496 3496 GSM1011128 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireMcf7VehPk vehicle Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Charcoal stripped hormone-free FBS for 72 hours (Crawford) Regions of enriched signal in experiment MCF-7 Vehicle FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMcf7HypoxlacPk MCF7 hypox FAI Pk MCF-7 FaireSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001125 1125 GSM864344 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireMcf7HypoxlacPk Hypoxia_LacAcid Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) Regions of enriched signal in experiment MCF-7 Hypoxia LacAcid FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMcf7Est10nm30mPk MCF-7 Est FAIR Pk MCF-7 FaireSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003499 3499 GSM1011121 Crawford UNC p-value cutoff: 0.1 wgEncodeOpenChromFaireMcf7Est10nm30mPk Estradiol_10nM_30m Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 30 min with 10nM 7b-Estradiol (Crawford) Regions of enriched signal in experiment MCF-7 Estradiol 10nM 30m FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHuvecPk HUVEC FAIRE Pk HUVEC FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-24 2010-06-24 wgEncodeEH000549 549 GSM864352 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireHuvecPk Peaks umbilical vein endothelial cells FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment HUVEC FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHepg2Pk HepG2 FAIRE Pk HepG2 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-04-17 2010-01-17 wgEncodeEH000546 546 GSM864354 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireHepg2Pk Peaks hepatocellular carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment HepG2 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHelas3Ifng4hPk HeLa IFg FAIRE Pk HeLa-S3 FaireSeq ENCODE June 2010 Freeze 2010-06-18 2009-12-20 2010-09-20 wgEncodeEH000588 588 GSM864359 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireHelas3Ifng4hPk IFNg4h Peaks cervical carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Interferon gamma treatment - 4 hours with 5 ng/ml (Crawford) Regions of enriched signal in experiment HeLa-S3 IFNg 4hr FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHelas3Ifna4hPk HeLa IFa FAIRE Pk HeLa-S3 FaireSeq ENCODE June 2010 Freeze 2010-06-18 2009-12-20 2010-09-20 wgEncodeEH000587 587 GSM864356 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireHelas3Ifna4hPk IFNa4h Peaks cervical carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 4 hours of 500 U/ml Interferon alpha (Crawford) Regions of enriched signal in experiment HeLa-S3 IFNa 4hr FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHelas3Pk HeLa-S3 FAIRE Pk HeLa-S3 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-22 2009-12-22 wgEncodeEH000544 544 GSM864348 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireHelas3Pk Peaks cervical carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment HeLa-S3 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireA549Pk A549 FAIRE Pk A549 FaireSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001126 1126 GSM864345 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireA549Pk Peaks epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment A549 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireK562NabutPk K562 NaBu FAIR Pk K562 FaireSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001120 1120 GSM864339 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireK562NabutPk NaBut Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 0.5 mM Sodium Butyrate for 72 hours Regions of enriched signal in experiment K562 Sodium Butyrate FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireK562OhureaPk K562 urea FAIR Pk K562 FaireSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001121 1121 GSM864340 Crawford UNC p-value cutoff: 0.1 hg19 wgEncodeOpenChromFaireK562OhureaPk OHUrea Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 100 uM Hydroxyurea for 72 hours Regions of enriched signal in experiment K562 Hydroxyurea FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireK562Pk K562 FAIRE Pk K562 FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-04-20 2010-01-20 wgEncodeEH000531 531 GSM864361 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireK562Pk Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment K562 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireH1hescPk H1-hESC FAIRE Pk H1-hESC FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-30 2010-06-30 wgEncodeEH000557 557 GSM864341 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireH1hescPk Peaks embryonic stem cells FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment H1-hESC FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm12878Pk GM12878 FAIRE Pk GM12878 FaireSeq ENCODE June 2010 Freeze 2010-06-15 2009-04-20 2010-01-20 wgEncodeEH000533 533 GSM864360 Crawford UNC p-value cutoff: 0.05 hg18 wgEncodeOpenChromFaireGm12878Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Regions of enriched signal in experiment GM12878 FAIRE Peaks from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireViewSignal FAIRE F-Seq Density Signal Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill) Regulation 
wgEncodeOpenChromFaireUrotsaUt189Sig Urothl ec FAIR DS Urothelia FaireSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001123 1123 GSM864342 Crawford UNC fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromFaireUrotsaUt189Sig UT189 Signal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina UT189 E.Coli treatment 1 hour, followed by 24 hour incubation Signal Urothelia UT189 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireUrotsaSig Urothl FAIRE DS Urothelia FaireSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001122 1122 GSM864353 Crawford UNC fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromFaireUrotsaSig Signal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal Urothelia FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireSmallintestineocSig Smll int FAIRE DS Small_intestine_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003502 3502 GSM1011130 Crawford UNC fseq v 1.84, iff_generic_male wgEncodeOpenChromFaireSmallintestineocSig Signal Primary frozen small intestine tissue from NCTC donor IDs 10-0063A (Rep B1) and 09-0143A (Rep B2) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal Small intestine FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireRcc7860Sig RCC7860 FAIR DS RCC_7860 FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003498 3498 GSM1011120 Crawford UNC fseq v 1.84, iff_generic_male wgEncodeOpenChromFaireRcc7860Sig Signal renal cell adenocarcinmoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal RCC 7860 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFairePanisletsSig PanIslet FAIRE DS PanIslets FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-14 2010-07-14 wgEncodeEH000573 573 GSM864346 Crawford UNC fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromFairePanisletsSig Signal pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal PanIslets FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFairePancreasocSig Pancreas FAIRE DS Pancreas_OC FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003497 3497 GSM1011129 Crawford UNC fseq v 1.84, iff_generic_male wgEncodeOpenChromFairePancreasocSig Signal Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal Pancreas FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireNhekSig NHEK FAIRE DS NHEK FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000558 558 GSM864338 Crawford UNC fseq v 1.84, iff_generic_female hg18 wgEncodeOpenChromFaireNhekSig Signal epidermal keratinocytes FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal NHEK FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireNhbeSig NHBE FAIRE DS NHBE FaireSeq ENCODE Mar 2012 Freeze 2011-02-11 2010-01-09 2010-10-09 wgEncodeEH000604 604 GSM864337 Crawford UNC fseq v 1.84, iff_generic_female hg18 wgEncodeOpenChromFaireNhbeSig Signal bronchial epithelial cells FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal NHBE FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireNhaSig NH-A FAIRE DS NH-A FaireSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001115 1115 GSM864347 Crawford UNC fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromFaireNhaSig Signal astrocytes (also called Astrocy) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal NH-A FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMrtttc549Sig MRT TTC549 F DS MRT_TTC549 FaireSeq ENCODE Jul 2012 Freeze 2012-04-20 2013-01-20 wgEncodeEH003494 3494 GSM1011124 Crawford UNC fseq v 1.84, iff_generic_female wgEncodeOpenChromFaireMrtttc549Sig Signal Malignant Hepatic Rhabdoid tumor line FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal MRT TTC549 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMrtg4016Sig MRT G401.6 F DS MRT_G401 FaireSeq ENCODE Jul 2012 Freeze 2012-04-20 2013-01-20 wgEncodeEH003493 3493 GSM1011127 Crawford UNC fseq v 1.84, iff_generic_male wgEncodeOpenChromFaireMrtg4016Sig Signal Malignant renal rhabdoid tumor line FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal MRT G401.6 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMrta2041Sig MRT A204.1 F DS MRT_A204 FaireSeq ENCODE Jul 2012 Freeze 2012-04-20 2013-01-20 wgEncodeEH003492 3492 GSM1011126 Crawford UNC fseq v 1.84, iff_generic_female wgEncodeOpenChromFaireMrta2041Sig Signal Malignant rhabdoid tumor (MRT) line, rhabdomyosarcoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal MRT A204.1 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMedulloSig Medullo FAIRE DS Medullo FaireSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001118 1118 GSM864351 Crawford UNC fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromFaireMedulloSig Signal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal Medullo FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireKidneyocSig Kidney FAIRE DS Kidney_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003501 3501 GSM1011123 Crawford UNC fseq v 1.84, iff_generic_male wgEncodeOpenChromFaireKidneyocSig Signal Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal Kidney FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHtr8Sig HTR8svn FAIRE DS HTR8svn FaireSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001124 1124 GSM864343 Crawford UNC fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromFaireHtr8Sig Signal trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal HTR8svn FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm19239Sig GM19239 FAIRE DS GM19239 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-18 2010-09-18 wgEncodeEH000580 580 GSM864358 Crawford UNC fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromFaireGm19239Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal GM19239 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm18507Sig GM18507 FAIRE DS GM18507 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-20 2010-09-19 wgEncodeEH000586 586 GSM864355 Crawford UNC fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromFaireGm18507Sig Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal GM18507 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm12892Sig GM12892 FAIRE DS GM12892 FaireSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001117 1117 GSM864357 Crawford UNC fseq v 1.84, iff_generic_female hg19 wgEncodeOpenChromFaireGm12892Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal GM12892 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm12891Sig GM12891 FAIRE DS GM12891 FaireSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001116 1116 GSM864349 Crawford UNC fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromFaireGm12891Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal GM12891 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGlioblaSig Gliobla FAIRE DS Gliobla FaireSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001119 1119 GSM864350 Crawford UNC fseq v 1.84, iff_H54 hg19 wgEncodeOpenChromFaireGlioblaSig Signal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal Gliobla FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireFrontalcortexocSig Frntl crtx FAI DS Frontal_cortex_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-04 2013-04-04 wgEncodeEH003500 3500 GSM1011122 Crawford UNC fseq v 1.84, iff_generic_female wgEncodeOpenChromFaireFrontalcortexocSig Signal Primary ventromedial prefrontal cortex, from KPBBB donor IDs 673 (Rep B1) and 913 (Rep B2) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal Frontal cortex FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireEndometriumocSig Endometr FAIRE DS Endometrium_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003503 3503 GSM1011119 Crawford UNC fseq v 1.84, iff_generic_female wgEncodeOpenChromFaireEndometriumocSig Signal Endometrium isolated from uterine lining FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal Endometrium FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireColonocSig Colon FAIRE DS Colon_OC FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003495 3495 GSM1011125 Crawford UNC fseq v 1.84, iff_generic_male wgEncodeOpenChromFaireColonocSig Signal Primary frozen colon tissue from NCTC donor IDs 10-0005A (Rep B1) and 10-0170A (Rep B2), African American and caucasian FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal Colon FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMcf7VehSig MCF-7 Veh FAIR DS MCF-7 FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003496 3496 GSM1011128 Crawford UNC fseq v 1.84, iff_MCF7 wgEncodeOpenChromFaireMcf7VehSig vehicle Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Charcoal stripped hormone-free FBS for 72 hours (Crawford) Signal MCF-7 Vehicle FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMcf7HypoxlacSig MCF7 hypox FAI DS MCF-7 FaireSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001125 1125 GSM864344 Crawford UNC fseq v 1.84, iff_MCF7 hg19 wgEncodeOpenChromFaireMcf7HypoxlacSig Hypoxia_LacAcid Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) Signal MCF-7 Hypoxia FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMcf7Est10nm30mSig MCF-7 Est FAIR DS MCF-7 FaireSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003499 3499 GSM1011121 Crawford UNC fseq v 1.84, iff_MCF7 wgEncodeOpenChromFaireMcf7Est10nm30mSig Estradiol_10nM_30m Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 30 min with 10nM 7b-Estradiol (Crawford) Signal MCF-7 Estradiol 10nM 30m FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHuvecSig HUVEC FAIRE DS HUVEC FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-24 2010-06-24 wgEncodeEH000549 549 GSM864352 Crawford UNC fseq v 1.84, iff_HUVEC hg18 wgEncodeOpenChromFaireHuvecSig Signal umbilical vein endothelial cells FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal HUVEC FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHepg2Sig HepG2 FAIRE DS HepG2 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-04-17 2010-01-17 wgEncodeEH000546 546 GSM864354 Crawford UNC fseq v 1.84, iff_HepG2 hg18 wgEncodeOpenChromFaireHepg2Sig Signal hepatocellular carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal HepG2 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHelas3Ifng4hSig HeLa IFg FAIRE DS HeLa-S3 FaireSeq ENCODE June 2010 Freeze 2010-06-18 2009-03-22 2009-12-22 wgEncodeEH000588 588 GSM864359 Crawford UNC fseq v 1.84, iff_HelaS3 hg18 wgEncodeOpenChromFaireHelas3Ifng4hSig IFNg4h Signal cervical carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Interferon gamma treatment - 4 hours with 5 ng/ml (Crawford) Signal HeLa-S3 IFNg 4hr FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHelas3Ifna4hSig HeLa IFa FAIRE DS HeLa-S3 FaireSeq ENCODE June 2010 Freeze 2010-06-18 2009-03-22 2009-12-22 wgEncodeEH000587 587 GSM864356 Crawford UNC fseq v 1.84, iff_HelaS3 hg18 wgEncodeOpenChromFaireHelas3Ifna4hSig IFNa4h Signal cervical carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 4 hours of 500 U/ml Interferon alpha (Crawford) Signal HeLa-S3 IFNa 4hr FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHelas3Sig HeLa-S3 FAIRE DS HeLa-S3 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-22 2009-12-22 wgEncodeEH000544 544 GSM864348 Crawford UNC fseq v 1.84, iff_HelaS3 hg18 wgEncodeOpenChromFaireHelas3Sig Signal cervical carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal HeLa-S3 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireA549Sig A549 FAIRE DS A549 FaireSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001126 1126 GSM864345 Crawford UNC fseq v 1.84, iff_generic_male hg19 wgEncodeOpenChromFaireA549Sig Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal A549 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireK562NabutSig K562 NaBu FAIR DS K562 FaireSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001120 1120 GSM864339 Crawford UNC fseq v 1.84, iff_K562 hg19 wgEncodeOpenChromFaireK562NabutSig NaBut Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 0.5 mM Sodium Butyrate for 72 hours Signal K562 Na Butyrate FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireK562OhureaSig K562 urea FAIR DS K562 FaireSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001121 1121 GSM864340 Crawford UNC fseq v 1.84, iff_K562 hg19 wgEncodeOpenChromFaireK562OhureaSig OHUrea Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 100 uM Hydroxyurea for 72 hours Signal K562 Hydroxyurea FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireK562Sig K562 FAIRE DS K562 FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-02-26 2009-11-26 wgEncodeEH000531 531 GSM864361 Crawford UNC fseq v 1.84, iff_K562 hg18 wgEncodeOpenChromFaireK562Sig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal K562 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireH1hescSig H1-hESC FAIRE DS H1-hESC FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-30 2010-06-30 wgEncodeEH000557 557 GSM864341 Crawford UNC fseq v 1.84, iff_generic_male hg18 wgEncodeOpenChromFaireH1hescSig Signal embryonic stem cells FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal H1-hESC FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm12878Sig GM12878 FAIRE DS GM12878 FaireSeq ENCODE June 2010 Freeze 2010-06-15 2009-02-25 2009-11-25 wgEncodeEH000533 533 GSM864360 Crawford UNC fseq v 1.84, iff_GM12878 hg18 wgEncodeOpenChromFaireGm12878Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Signal GM12878 FAIRE Density Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireViewSigBo Base Overlap Signal Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill) Regulation 
wgEncodeOpenChromFaireUrotsaUt189BaseOverlapSignal Urothl ec FAIR OS Urothelia FaireSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001123 1123 GSM864342 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireUrotsaUt189BaseOverlapSignal UT189 Base_Overlap_Signal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina UT189 E.Coli treatment 1 hour, followed by 24 hour incubation An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Urothelia UT189 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireUrotsaBaseOverlapSignal Urothl FAIRE OS Urothelia FaireSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001122 1122 GSM864353 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireUrotsaBaseOverlapSignal Base_Overlap_Signal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Urothelia FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireSmallintestineocBaseOverlapSignal Smll int FAIRE OS Small_intestine_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003502 3502 GSM1011130 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireSmallintestineocBaseOverlapSignal Base_Overlap_Signal Primary frozen small intestine tissue from NCTC donor IDs 10-0063A (Rep B1) and 09-0143A (Rep B2) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Small intestine FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireRcc7860BaseOverlapSignal RCC7860 FAIR OS RCC_7860 FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003498 3498 GSM1011120 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireRcc7860BaseOverlapSignal Base_Overlap_Signal renal cell adenocarcinmoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. RCC 7860 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFairePanisletsBaseOverlapSignal PanIslet FAIRE OS PanIslets FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-14 2010-07-14 wgEncodeEH000573 573 GSM864346 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFairePanisletsBaseOverlapSignal Base_Overlap_Signal pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. PanIslets FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFairePancreasocBaseOverlapSignal Pancreas FAIRE OS Pancreas_OC FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003497 3497 GSM1011129 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFairePancreasocBaseOverlapSignal Base_Overlap_Signal Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Pancreas FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireNhekBaseOverlapSignal NHEK FAIRE OS NHEK FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000558 558 GSM864338 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireNhekBaseOverlapSignal Base_Overlap_Signal epidermal keratinocytes FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. NHEK FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireNhbeBaseOverlapSignal NHBE FAIRE OS NHBE FaireSeq ENCODE Mar 2012 Freeze 2011-02-11 2010-01-09 2010-10-09 wgEncodeEH000604 604 GSM864337 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireNhbeBaseOverlapSignal Base_Overlap_Signal bronchial epithelial cells FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. NHBE FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireNhaBaseOverlapSignal NH-A FAIRE OS NH-A FaireSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001115 1115 GSM864347 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireNhaBaseOverlapSignal Base_Overlap_Signal astrocytes (also called Astrocy) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. NH-A FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMrtttc549BaseOverlapSignal MRT TTC549 F OS MRT_TTC549 FaireSeq ENCODE Jul 2012 Freeze 2012-04-20 2013-01-20 wgEncodeEH003494 3494 GSM1011124 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireMrtttc549BaseOverlapSignal Base_Overlap_Signal Malignant Hepatic Rhabdoid tumor line FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MRT TTC549 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMrtg4016BaseOverlapSignal MRT G401.6 F OS MRT_G401 FaireSeq ENCODE Jul 2012 Freeze 2012-04-20 2013-01-20 wgEncodeEH003493 3493 GSM1011127 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireMrtg4016BaseOverlapSignal Base_Overlap_Signal Malignant renal rhabdoid tumor line FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MRT G401.6 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMrta2041BaseOverlapSignal MRT A204.1 F OS MRT_A204 FaireSeq ENCODE Jul 2012 Freeze 2012-04-20 2013-01-20 wgEncodeEH003492 3492 GSM1011126 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireMrta2041BaseOverlapSignal Base_Overlap_Signal Malignant rhabdoid tumor (MRT) line, rhabdomyosarcoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MRT A204.1 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMedulloBaseOverlapSignal Medullo FAIRE OS Medullo FaireSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001118 1118 GSM864351 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireMedulloBaseOverlapSignal Base_Overlap_Signal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Medullo FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireKidneyocBaseOverlapSignal Kidney FAIRE OS Kidney_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003501 3501 GSM1011123 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireKidneyocBaseOverlapSignal Base_Overlap_Signal Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Kidney FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHtr8BaseOverlapSignal HTR8svn FAIRE OS HTR8svn FaireSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001124 1124 GSM864343 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireHtr8BaseOverlapSignal Base_Overlap_Signal trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HTR8svn FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm19239BaseOverlapSignal GM19239 FAIRE OS GM19239 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-18 2010-09-18 wgEncodeEH000580 580 GSM864358 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireGm19239BaseOverlapSignal Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19239 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm18507BaseOverlapSignal GM18507 FAIRE OS GM18507 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-20 2010-09-19 wgEncodeEH000586 586 GSM864355 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireGm18507BaseOverlapSignal Base_Overlap_Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM18507 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm12892BaseOverlapSignal GM12892 FAIRE OS GM12892 FaireSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001117 1117 GSM864357 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireGm12892BaseOverlapSignal Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12892 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm12891BaseOverlapSignal GM12891 FAIRE OS GM12891 FaireSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001116 1116 GSM864349 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireGm12891BaseOverlapSignal Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12891 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGlioblaBaseOverlapSignal Gliobla FAIRE OS Gliobla FaireSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001119 1119 GSM864350 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireGlioblaBaseOverlapSignal Base_Overlap_Signal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Gliobla FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireFrontalcortexocBaseOverlapSignal Frntl crtx FAI OS Frontal_cortex_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-04 2013-04-04 wgEncodeEH003500 3500 GSM1011122 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireFrontalcortexocBaseOverlapSignal Base_Overlap_Signal Primary ventromedial prefrontal cortex, from KPBBB donor IDs 673 (Rep B1) and 913 (Rep B2) FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Frontal cortex FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireEndometriumocBaseOverlapSignal Endometr FAIRE OS Endometrium_OC FaireSeq ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003503 3503 GSM1011119 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireEndometriumocBaseOverlapSignal Base_Overlap_Signal Endometrium isolated from uterine lining FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Endometrium FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireColonocBaseOverlapSignal Colon FAIRE OS Colon_OC FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003495 3495 GSM1011125 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireColonocBaseOverlapSignal Base_Overlap_Signal Primary frozen colon tissue from NCTC donor IDs 10-0005A (Rep B1) and 10-0170A (Rep B2), African American and caucasian FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Colon FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMcf7VehBaseOverlapSignal MCF-7 Veh FAIR OS MCF-7 FaireSeq ENCODE Jul 2012 Freeze 2012-06-19 2013-03-19 wgEncodeEH003496 3496 GSM1011128 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireMcf7VehBaseOverlapSignal vehicle Base_Overlap_Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Charcoal stripped hormone-free FBS for 72 hours (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 Vehicle FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal MCF7 hypox FAI OS MCF-7 FaireSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001125 1125 GSM864344 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal Hypoxia_LacAcid Base_Overlap_Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 Hypoxia FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireMcf7Est10nm30mBaseOverlapSignal MCF-7 Est FAIR OS MCF-7 FaireSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003499 3499 GSM1011121 Crawford UNC baseAlignCounts.pl v 1 wgEncodeOpenChromFaireMcf7Est10nm30mBaseOverlapSignal Estradiol_10nM_30m Base_Overlap_Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 30 min with 10nM 7b-Estradiol (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 Estradiol 10nM 30m FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHuvecBaseOverlapSignal HUVEC FAIRE OS HUVEC FaireSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-24 2010-06-24 wgEncodeEH000549 549 GSM864352 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireHuvecBaseOverlapSignal Base_Overlap_Signal umbilical vein endothelial cells FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HUVEC FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHepg2BaseOverlapSignal HepG2 FAIRE OS HepG2 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-04-17 2010-01-17 wgEncodeEH000546 546 GSM864354 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireHepg2BaseOverlapSignal Base_Overlap_Signal hepatocellular carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HepG2 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHelas3Ifng4hBaseOverlapSignal HeLa IFg FAIRE OS HeLa-S3 FaireSeq ENCODE June 2010 Freeze 2010-06-18 2009-03-22 2009-12-22 wgEncodeEH000588 588 GSM864359 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireHelas3Ifng4hBaseOverlapSignal IFNg4h Base_Overlap_Signal cervical carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina Interferon gamma treatment - 4 hours with 5 ng/ml (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 IFNg 4hr FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHelas3Ifna4hBaseOverlapSignal HeLa IFa FAIRE OS HeLa-S3 FaireSeq ENCODE June 2010 Freeze 2010-06-18 2009-03-22 2009-12-22 wgEncodeEH000587 587 GSM864356 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireHelas3Ifna4hBaseOverlapSignal IFNa4h Base_Overlap_Signal cervical carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 4 hours of 500 U/ml Interferon alpha (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 IFNa 4hr FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireHelas3BaseOverlapSignal HeLa-S3 FAIRE OS HeLa-S3 FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-22 2009-12-22 wgEncodeEH000544 544 GSM864348 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireHelas3BaseOverlapSignal Base_Overlap_Signal cervical carcinoma FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireA549BaseOverlapSignal A549 FAIRE OS A549 FaireSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001126 1126 GSM864345 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireA549BaseOverlapSignal Base_Overlap_Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. A549 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireK562NabutBaseOverlapSignal K562 NaBu FAIR OS K562 FaireSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001120 1120 GSM864339 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireK562NabutBaseOverlapSignal NaBut Base_Overlap_Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 0.5 mM Sodium Butyrate for 72 hours An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 Na Butyrate FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireK562OhureaBaseOverlapSignal K562 urea FAIR OS K562 FaireSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001121 1121 GSM864340 Crawford UNC baseAlignCounts.pl v 1 hg19 wgEncodeOpenChromFaireK562OhureaBaseOverlapSignal OHUrea Base_Overlap_Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina 100 uM Hydroxyurea for 72 hours An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 Hydroxyurea FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireK562BaseOverlapSignal K562 FAIRE OS K562 FaireSeq ENCODE June 2010 Freeze 2010-06-17 2008-12-09 2009-08-09 wgEncodeEH000531 531 GSM864361 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireK562BaseOverlapSignal Base_Overlap_Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireH1hescBaseOverlapSignal H1-hESC FAIRE OS H1-hESC FaireSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-30 2010-06-30 wgEncodeEH000557 557 GSM864341 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireH1hescBaseOverlapSignal Base_Overlap_Signal embryonic stem cells FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H1-hESC FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
wgEncodeOpenChromFaireGm12878BaseOverlapSignal GM12878 FAIRE OS GM12878 FaireSeq ENCODE June 2010 Freeze 2010-06-15 2009-02-25 2009-11-25 wgEncodeEH000533 533 GSM864360 Crawford UNC baseAlignCounts.pl v 1 hg18 wgEncodeOpenChromFaireGm12878BaseOverlapSignal Base_Overlap_Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus FAIRE-seq Open Chromatin Crawford Lieb - University of North Carolina An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12878 FAIRE Overlap Signal from ENCODE/OpenChrom(UNC) Regulation 
uniprot UniProt UniProt SwissProt/TrEMBL Protein Annotations Genes and Gene Predictions Description This track shows protein sequences and annotations on them from the UniProt/SwissProt database, mapped to genomic coordinates. UniProt/SwissProt data has been curated from scientific publications by the UniProt staff, UniProt/TrEMBL data has been predicted by various computational algorithms. The annotations are divided into multiple subtracks, based on their &quot;feature type&quot; in UniProt. The first two subtracks below - one for SwissProt, one for TrEMBL - show the alignments of protein sequences to the genome, all other tracks below are the protein annotations mapped through these alignments to the genome. Track Name Description UCSC Alignment, SwissProt = curated protein sequences Protein sequences from SwissProt mapped to the genome. All other tracks are (start,end) SwissProt annotations on these sequences mapped through this alignment. Even protein sequences without a single curated annotation (splice isoforms) are visible in this track. Each UniProt protein has one main isoform, which is colored in dark. Alternative isoforms are sequences that do not have annotations on them and are colored in light-blue. They can be hidden with the TrEMBL/Isoform filter (see below). UCSC Alignment, TrEMBL = predicted protein sequences Protein sequences from TrEMBL mapped to the genome. All other tracks below are (start,end) TrEMBL annotations mapped to the genome using this track. This track is hidden by default. To show it, click its checkbox on the track configuration page. UniProt Signal Peptides Regions found in proteins destined to be secreted, generally cleaved from mature protein. UniProt Extracellular Domains Protein domains with the comment &quot;Extracellular&quot;. UniProt Transmembrane Domains Protein domains of the type &quot;Transmembrane&quot;. UniProt Cytoplasmic Domains Protein domains with the comment &quot;Cytoplasmic&quot;. UniProt Polypeptide Chains Polypeptide chain in mature protein after post-processing. UniProt Regions of Interest Regions that have been experimentally defined, such as the role of a region in mediating protein-protein interactions or some other biological process. UniProt Domains Protein domains, zinc finger regions and topological domains. UniProt Disulfide Bonds Disulfide bonds. UniProt Amino Acid Modifications Glycosylation sites, modified residues and lipid moiety-binding regions. UniProt Amino Acid Mutations Mutagenesis sites and sequence variants. UniProt Protein Primary/Secondary Structure Annotations Beta strands, helices, coiled-coil regions and turns. UniProt Sequence Conflicts Differences between Genbank sequences and the UniProt sequence. UniProt Repeats Regions of repeated sequence motifs or repeated domains. UniProt Other Annotations All other annotations, e.g. compositional bias For consistency and convenience for users of mutation-related tracks, the subtrack &quot;UniProt/SwissProt Variants&quot; is a copy of the track &quot;UniProt Variants&quot; in the track group &quot;Phenotype and Literature&quot;, or &quot;Variation and Repeats&quot;, depending on the assembly. Display Conventions and Configuration Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. &quot;glyco&quot;, &quot;disulf bond&quot;, &quot;Signal peptide&quot; etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt record for more details. TrEMBL annotations are always shown in light blue, except in the Signal Peptides, Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks. Mouse over a feature to see the full UniProt annotation comment. For variants, the mouse over will show the full name of the UniProt disease acronym. The subtracks for domains related to subcellular location are sorted from outside to inside of the cell: Signal peptide, extracellular, transmembrane, and cytoplasmic. Features in the &quot;UniProt Modifications&quot; (modified residues) track are drawn in light green. Disulfide bonds are shown in dark grey. Topological domains in maroon and zinc finger regions in olive green. Duplicate annotations are removed as far as possible: if a TrEMBL annotation has the same genome position and same feature type, comment, disease and mutated amino acids as a SwissProt annotation, it is not shown again. Two annotations mapped through different protein sequence alignments but with the same genome coordinates are only shown once. On the configuration page of this track, you can choose to hide any TrEMBL annotations. This filter will also hide the UniProt alternative isoform protein sequences because both types of information are less relevant to most users. Please contact us if you want more detailed filtering features. Note that for the human hg38 assembly and SwissProt annotations, there also is a public track hub prepared by UniProt itself, with genome annotations maintained by UniProt using their own mapping method based on those Gencode/Ensembl gene models that are annotated in UniProt for a given protein. For proteins that differ from the genome, UniProt's mapping method will, in most cases, map a protein and its annotations to an unexpected location (see below for details on UCSC's mapping method). Methods Briefly, UniProt protein sequences were aligned to the transcripts associated with the protein, the top-scoring alignments were retained, and the result was projected to the genome through a transcript-to-genome alignment. Depending on the genome, the transcript-genome alignments was either provided by the source database (NBCI RefSeq), created at UCSC (UCSC RefSeq) or derived from the transcripts (Ensembl/Augustus). The transcript set is NCBI RefSeq for hg38, UCSC RefSeq for hg19 (due to alt/fix haplotype misplacements in the NCBI RefSeq set on hg19). For other genomes, RefSeq, Ensembl and Augustus are tried, in this order. The resulting protein-genome alignments of this process are available in the file formats for liftOver or pslMap from our data archive (see "Data Access" section below). An important step of the mapping process protein -&gt; transcript -&gt; genome is filtering the alignment from protein to transcript. Due to differences between the UniProt proteins and the transcripts (proteins were made many years before the transcripts were made, and human genomes have variants), the transcript with the highest BLAST score when aligning the protein to all transcripts is not always the correct transcript for a protein sequence. Therefore, the protein sequence is aligned to only a very short list of one or sometimes more transcripts, selected by a three-step procedure: Use transcripts directly annotated by UniProt: for organisms that have a RefSeq transcript track, proteins are aligned to the RefSeq transcripts that are annotated by UniProt for this particular protein. Use transcripts for NCBI Gene ID annotated by UniProt: If no transcripts are annotated on the protein, or the annotated ones have been deprecated by NCBI, but a NCBI Gene ID is annotated, the RefSeq transcripts for this Gene ID are used. This can result in multiple matching transcripts for a protein. Use best matching transcript: If no NCBI Gene is annotated, then BLAST scores are used to pick the transcripts. There can be multiple transcripts for one protein, as their coding sequences can be identical. All transcripts within 1% of the highest observed BLAST score are used. For strategy 2 and 3, many of the transcripts found do not differ in coding sequence, so the resulting alignments on the genome will be identical. Therefore, any identical alignments are removed in a final filtering step. The details page of these alignments will contain a list of all transcripts that result in the same protein-genome alignment. On hg38, only a handful of edge cases (pseudogenes, very recently added proteins) remain in 2023 where strategy 3 has to be used. In other words, when an NCBI or UCSC RefSeq track is used for the mapping and to align a protein sequence to the correct transcript, we use a three stage process: If UniProt has annotated a given RefSeq transcript for a given protein sequence, the protein is aligned to this transcript. Any difference in the version suffix is tolerated in this comparison. If no transcript is annotated or the transcript cannot be found in the NCBI/UCSC RefSeq track, the UniProt-annotated NCBI Gene ID is resolved to a set of NCBI RefSeq transcript IDs via the most current version of NCBI genes tables. Only the top match of the resulting alignments and all others within 1% of its score are used for the mapping. If no transcript can be found after step (2), the protein is aligned to all transcripts, the top match, and all others within 1% of its score are used. This system was designed to resolve the problem of incorrect mappings of proteins, mostly on hg38, due to differences between the SwissProt sequences and the genome reference sequence, which has changed since the proteins were defined. The problem is most pronounced for gene families composed of either very repetitive or very similar proteins. To make sure that the alignments always go to the best chromosome location, all _alt and _fix reference patch sequences are ignored for the alignment, so the patches are entirely free of UniProt annotations. Please contact us if you have feedback on this process or example edge cases. We are not aware of a way to evaluate the results completely and in an automated manner. Proteins were aligned to transcripts with TBLASTN, converted to PSL, filtered with pslReps (93% query coverage, keep alignments within top 1% score), lifted to genome positions with pslMap and filtered again with pslReps. UniProt annotations were obtained from the UniProt XML file. The UniProt annotations were then mapped to the genome through the alignment described above using the pslMap program. This approach draws heavily on the LS-SNP pipeline by Mark Diekhans. Like all Genome Browser source code, the main script used to build this track can be found on Github. Older releases This track is automatically updated on an ongoing basis, every 2-3 months. The current version name is always shown on the track details page, it includes the release of UniProt, the version of the transcript set and a unique MD5 that is based on the protein sequences, the transcript sequences, the mapping file between both and the transcript-genome alignment. The exact transcript that was used for the alignment is shown when clicking a protein alignment in one of the two alignment tracks. For reproducibility of older analysis results and for manual inspection, previous versions of this track are available for browsing in the form of the UCSC UniProt Archive Track Hub (click this link to connect the hub now). The underlying data of all releases of this track (past and current) can be obtained from our downloads server, including the UniProt protein-to-genome alignment. Data Access The raw data of the current track can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server. The exact filenames can be found in the track configuration file. Annotations can be converted to ASCII text by our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/uniprot/unipStruct.bb -chrom=chr6 -start=0 -end=1000000 stdout Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Lifting from UniProt to genome coordinates in pipelines To facilitate mapping protein coordinates to the genome, we provide the alignment files in formats that are suitable for our command line tools. Our command line programs liftOver or pslMap can be used to map coordinates on protein sequences to genome coordinates. The filenames are unipToGenome.over.chain.gz (liftOver) and unipToGenomeLift.psl.gz (pslMap). Example commands: wget -q https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/uniprot/2022_03/unipToGenome.over.chain.gz wget -q https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver chmod a+x liftOver echo 'Q99697 1 10 annotationOnProtein' &gt; prot.bed liftOver prot.bed unipToGenome.over.chain.gz genome.bed cat genome.bed Credits This track was created by Maximilian Haeussler at UCSC, with a lot of input from Chris Lee, Mark Diekhans and Brian Raney, feedback from the UniProt staff, Alejo Mujica, Regeneron Pharmaceuticals and Pia Riestra, GeneDx. Thanks to UniProt for making all data available for download. References UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. PMID: 22102590; PMC: PMC3245120 Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat. 2004 May;23(5):464-70. PMID: 15108278 
unipConflict Seq. Conflicts UniProt Sequence Conflicts Genes and Gene Predictions 
unipRepeat Repeats UniProt Repeats Genes and Gene Predictions 
unipStruct Structure UniProt Protein Primary/Secondary Structure Annotations Genes and Gene Predictions 
unipOther Other Annot. UniProt Other Annotations Genes and Gene Predictions 
unipMut Mutations UniProt Amino Acid Mutations Genes and Gene Predictions 
unipModif AA Modifications UniProt Amino Acid Modifications Genes and Gene Predictions 
unipDomain Domains UniProt Domains Genes and Gene Predictions 
unipDisulfBond Disulf. Bonds UniProt Disulfide Bonds Genes and Gene Predictions 
unipChain Chains UniProt Mature Protein Products (Polypeptide Chains) Genes and Gene Predictions 
unipLocCytopl Cytoplasmic UniProt Cytoplasmic Domains Genes and Gene Predictions 
unipLocTransMemb Transmembrane UniProt Transmembrane Domains Genes and Gene Predictions 
unipInterest Interest UniProt Regions of Interest Genes and Gene Predictions 
unipLocExtra Extracellular UniProt Extracellular Domain Genes and Gene Predictions 
unipLocSignal Signal Peptide UniProt Signal Peptides Genes and Gene Predictions 
unipAliTrembl TrEMBL Aln. UCSC alignment of TrEMBL proteins to genome Genes and Gene Predictions 
unipAliSwissprot SwissProt Aln. UCSC alignment of SwissProt proteins to genome (dark blue: main isoform, light blue: alternative isoforms) Genes and Gene Predictions 
spMut UniProt Variants UniProt/SwissProt Amino Acid Substitutions Phenotype and Literature Description NOTE: This track is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the genome browser database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. This track shows the genomic positions of natural and artifical amino acid variants in the UniProt/SwissProt database. The data has been curated from scientific publications by the UniProt staff. Display Conventions and Configuration Genomic locations of UniProt/SwissProt variants are labeled with the amino acid change at a given position and, if known, the abbreviated disease name. A &quot;?&quot; is used if there is no disease annotated at this location, but the protein is described as being linked to only a single disease in UniProt. Mouse over a mutation to see the UniProt comments. Artificially-introduced mutations are colored green and naturally-occurring variants are colored red. For full information about a particular variant, click the &quot;UniProt variant&quot; linkout. The &quot;UniProt record&quot; linkout lists all variants of a particular protein sequence. The &quot;Source articles&quot; linkout lists the articles in PubMed that originally described the variant(s) and were used as evidence by the UniProt curators. Methods UniProt sequences were aligned to RefSeq sequences first with BLAT, then lifted to genome positions with pslMap. UniProt variants were parsed from the UniProt XML file. The variants were then mapped to the genome through the alignment using the pslMap program. This mapping approach draws heavily on the LS-SNP pipeline by Mark Diekhans. The complete script is part of the kent source tree and is located in src/hg/utils/uniprotMutations. Data Access The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server. The underlying data file for this track is called spMut.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/uniprot/spMut.bb -chrom=chr6 -start=0 -end=1000000 stdout Please refer to our mailing list archives for questions, or our Data Access FAQ for more information. Credits This track was created by Maximilian Haeussler, with advice from Mark Diekhans and Brian Raney. References UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. PMID: 22102590; PMC: PMC3245120 Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat. 2004 May;23(5):464-70. PMID: 15108278 
wgEncodeUw5C UW 5C GSE39505 Chromatin Interactions by 5C from ENCODE/University of Washington Regulation Description This track contains chromatin interaction data from the University of Washington ENCODE group generated using 5C (Chromatin Conformation Capture Carbon Copy). The 5C method is used here to define short and long-range range interactions between transcription start sites (TSS) and DNaseI hypersensitive sites (DHS) or other genomic features. The 5C method is summarized below. Transcription factors bind to promoter-associated proteins, bringing the associated DNA sequences in close proximity to each other. Cross linking the DNA and proteins immobilizes these interactions and thus maintains their close proximity. Cleavage of the sample with restriction endonuclease followed by ligation results in hybrid molecules where a fragment with a regulatory element is physically associated with a fragment containing a TSS. The interactions are then detected by oligonucleotide-dependent, ligation-mediated assays, where one set of primers is complementary to the end of fragments with a TSS and the second set of primers are complementary to fragments with a feature. Primers are designed to the forward strand of the feature and the reverse strand of the TSS so that ligation only occurs between TSS and feature, not between different features. Specific interactions are detected by massively parallel sequencing. The data in this track comprises two different experiment types focusing on targeted regions: Gene-targeted project Analysis of DNase I hypersensitive sites reveals many genes where there are multiple sites restricted to the cell type where a protein is observed to be expressed. These sites potentially identify regulatory sites for the gene. This set of experiments attempts to observe interactions between these DHS sites and transcription starts in 25 regions selected based on genes expressed in GM06990 (B-lymphocyte), BJ (foreskin fibroblast), HepG2 (liver cancer cell line), or SK-N-SH_RA (neuroblastoma cell line, SKNSH, differentiated with retinoic acid). Myc project Genome wide association studies have identified SNPs linked to prostate, colon, and breast cancer in the gene desert region upstream of the myc gene. 5C of HindIII fragments interacting with those containing refSeq txStarts in this region were performed in 5 cell types: GM12878 (B-lymphocyte), CaCo2 (colon cancer cell line), LNCaP (prostate cancer cell line), MCF7 (breast cancer cell line), and K562 (erythroleukemia cell line). File Conventions The following types of data are available for download: Matrix Interaction files are in a matrix format indicating interaction strength, with "reverse primer name | genome version | reverse HindIII fragment coordinates" in the top row and "forward primer name | genome version | forward primer fragment coordinates" in the first column. The number of sequences mapped to each interaction fills the matrix. In order to understand the Matrix data, you must download the associated primer data file. Primer Primer data files include the sequences of the primers used in the experiments and sequences for control sites in the ENCODE pilot ENr313 gene desert region on chr16. These files are available for download in the supplemental materials. Raw Data Sequencing files are provided in fastQ format. Methods Cells were grown according to the approved ENCODE cell culture protocols. The isolated nuclei were formaldehyde cross-linked. The DNA isolated from the nuclei was cleaved with restriction enzyme, ligated, and cross-links removed to create a 3C library (Dekker et al., 2002). Primers complementary to the TSS and feature were added, annealed and ligated to produce a 5C library (Dostie et al., 2006). The DNA fragments generated in the ligation mediated-reactions were partially digested with DNaseI, end-repaired and ligated to adapters, before sequencing. The sequencing reads generated were mapped to the predicted ligation products. The number of sequences mapping to predicted junction fragments were tabulated from sequencing runs. The number of times a sequence was detected for a given interaction between a TSS and feature indicates the relative strength of the interation. Gene-targeted project Forward primers were designed to HindIII sites in a 230-415 kb sequence centered on the DNase I hypersensitive sites of interest. Reverse primers were designed to HindIII sites for all transcription starts extending 1 Mb on either side of the region targeted by the forward primer set. Matrix files are labeled by the coordinates of the region covered by the forward primer set. These experiments were done in a multiplex manner with the forward and reverse primers for all 25 regions mixed together in a single reaction. Two replicates were performed for 4 cell lines for 25 regions. High-throughput sequencing was performed on an ABI SOLiD instrument collecting 50 bp reads. The interaction files provided map all the reads in the output sequence without a mismatch threshold. Myc project Forward primers were designed to HindIII fragments of 4.29 Mb section of human chromosome 8 centered on the gene desert 5~R of the myc gene. Reverse primers were designed to all HindIII fragments containing refseq txStarts in a 7.6 Mb region extending &gt; 2 Mb on either side of the forward primer set. High-throughput sequencing was performed on an ABI SOLiD instrument collecting 50 bp reads. The interaction files provided map all the reads in the output sequence without a mismatch threshold. Verification Data were verified by sequencing biological replicates displaying correlation coefficient &gt; 0.9. Credits These data were generated by the University of Washington ENCODE Group. Contact: Richard Sandstrom References Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 2002 Feb 15;295(5558):1306-11. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 2006 Oct;16(10):1299-309. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwDgf UW DNaseI DGF GSE26328 DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Regulation Description This track, produced as part of the ENCODE Project, contains deep sequencing DNase data that will be used to identify sites where regulatory factors bind to the genome (footprints). Footprinting is a technique used to define the DNA sequences that interact with and bind DNA-binding proteins, such as transcription factors, zinc-finger proteins, hormone-receptor complexes, and other chromatin-modulating factors like CTCF. The technique depends upon the strength and tight nature of protein-DNA interactions. In their native chromatin state, DNA sequences that interact directly with DNA-binding proteins are relatively protected from DNA-degrading endonucleases, while the exposed/unbound portions are readily degraded by such endonucleases. A massively parallel next-generation sequencing technique to define the DNase hypersensitive sites in the genome was adopted. The DNase samples were sequenced using next-generation sequencing machines to significantly higher depths of 300-fold or greater. This produces a base-pair level resolution of the DNase susceptibility maps of the native chromatin state. These base-pair resolution maps represent and are dependent upon the nature and the specificity of interaction of the DNA with the regulatory/modulatory proteins binding at specific loci in the genome; thus they represent the native chromatin state of the genome under investigation. The deep sequencing approach has been used to define the footprint landscape of the genome by identifying DNA motifs that interact with known or novel DNA-binding proteins. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: HotSpots DNaseI hypersensitive zones identified using the HotSpot algorithm. Peaks DNaseI hypersensitive sites (DHSs) identified as signal peaks within FDR 1.0% hypersensitive zones. Footprint While the HotSpots algorithm identifies genomic regions of elevated tag counts relative to random expectation, the FP-DETECTOR algorithm (developed in our center) searches for smaller locations where proteins are most likely bound within the identified HotSpot regions. --> Signal Per-base count of sequence reads whose 5' end (corresponding to a DNaseI-induced DNA cut) coincides with the given position. Raw Signal The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). NOTE: The names of the signal views in this track are reversed from conventions used in other ENCODE tracks, where the less processed signal is termed 'Raw'. DNaseI sensitivity is shown as the absolute density of in vivo cleavage sites across the genome mapped using the Digital DNaseI methodology (see below). Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. --> Methods Cells were grown according to the approved ENCODE cell culture protocols. Digital DNaseI was performed by DNaseI digestion of intact nuclei, followed by isolation of DNaseI 'double-hit' fragments as described in Sabo et al. (2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Solexa platform (27 bp reads). High-quality reads were mapped to the GRCh37/hg19 human genome using Bowtie 0.12.5 (Eland was used to map to NCBI36/hg18); only unique mappings were kept. DNaseI sensitivity is directly reflected in raw tag density (Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). DNaseI hypersensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). False discovery rate thresholds of 1.0% (FDR 1.0%) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36-mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within 1.0% (FDR 1.0%) hypersensitive zones using a peak-finding algorithm. Only DNase Solexa libraries from unique cell types producing the highest quality data, as defined by Percent Tags in Hotspots (PTIH ~40%), were designated for deep sequencing to a depth of over 200 million tags. FP-DETECTOR algorithm (developed by the UW ENCODE group) searches for smaller locations where proteins are most likely bound within the identified HotSpot regions. The reported regions marked as footprints are disjoint, 6 to 40 base-pairs in length, and show a marked depletion of tag counts relative to their respective, local backgrounds. --> Verification Results were validated by conventional DNaseI hypersensitivity assays using end-labeling/Southern blotting methods. Images and their associated mappings can be found in the supplemental data. Release Notes This is Release 4 (August 2012) of this track, which includes 10 new experiments across 8 cell lines. A number of previously released Peaks have been replaced by updated versions. The affected database tables and files include 'V2' in the name, and metadata is marked with "submittedDataVersion=V2", followed by the reason for replacement, "Fixed bug in peak calls that artificially reduced the number of peaks". Previous versions of files are available for download from the FTP site. Credits These data were generated by the UW ENCODE group. Contact: Richard Sandstrom References Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods. 2006 Jul;3(7):511-8. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwDgfViewSignal Signal DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Regulation 
wgEncodeUwDgfTregwb78495824Sig Treg Sig Treg_Wb78495824 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003161 3161 GSM1014523 Stam UW DS14702 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTregwb78495824Sig None Signal T regulatory cells in vivo isolation DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal Treg Wb78495824 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh17Sig Th17 Sig Th17 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003158 3158 GSM1014541 Stam UW DS11039 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh17Sig None Signal T helper cells expressing IL-17, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal Th17 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh2wb54553204Sig Th2 54553204 Sig Th2_Wb54553204 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003160 3160 GSM1014522 Stam UW DS17597 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh2wb54553204Sig None Signal Th2 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal Th2 Wb54553204 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh2Sig Th2 Sig Th2 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003162 3162 GSM1014521 Stam UW DS17603 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh2Sig None Signal primary Th2 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal Th2 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh1wb33676984Sig Th1 33676984 Sig Th1_Wb33676984 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003159 3159 GSM1014540 Stam UW DS18015 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh1wb33676984Sig None Signal Th1 cells in vivo isolation DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal Th1 Wb33676984 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh1SigRep2 Th1 Sig 2 Th1 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH000478 478 GSM646569 Stam UW DS18018 hg19 2 Illumina_HiSeq_2000 wgEncodeUwDgfTh1SigRep2 None Signal primary Th1 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal Th1 DNaseI DGF Per-base Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDgfTh1Sig Th1 Sig 1 Th1 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-05 2010-07-05 wgEncodeEH000478 478 GSM646569 Stam UW DS7840 hg18 wgEncodeUwDgfTh1Sig Signal primary Th1 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal Th1 DNaseI DGF Per-base Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDgfT47dSig T-47D Sig T-47D DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003157 3157 GSM1014536 Stam UW DS19794 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfT47dSig None Signal epithelial cell line derived from a mammary ductal carcinoma. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal T-47D DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfSkmcSig SKMC Sig SKMC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000840 840 GSM646562 Stam UW DS11949 hg19 wgEncodeUwDgfSkmcSig Signal skeletal muscle cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal SKMC DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfSknshraSig SK-N-SH_RA Sig SK-N-SH_RA DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-02 2010-07-02 wgEncodeEH000477 477 GSM646566 Stam UW DS8482 hg18 wgEncodeUwDgfSknshraSig Signal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal SK-N-SH_RA DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfSaecSig SAEC Sig SAEC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000847 847 GSM849025 Stam UW DS10518 hg19 wgEncodeUwDgfSaecSig Signal small airway epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal SAEC DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfRpmi7951Sig RPMI-7951 Sig RPMI-7951 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003150 3150 GSM1014535 Stam UW DS20909 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfRpmi7951Sig Signal Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal RPMI-7951 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNhlfSig NHLF Sig NHLF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002458 2458 GSM1014509 Stam UW DS12829 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNhlfSig Signal lung fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal NHLF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNhdfneoSig NHDF-neo Sig NHDF-neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002457 2457 GSM1014512 Stam UW DS11923 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNhdfneoSig Signal neonatal dermal fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal NHDF-neo DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNhdfadSig NHDF-Ad Sig NHDF-Ad DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000839 839 GSM646564 Stam UW DS12863 hg19 wgEncodeUwDgfNhdfadSig Signal adult dermal fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal NHDF-Ad DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNhaSig NH-A Sig NH-A DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000846 846 GSM849026 Stam UW DS12800 hg19 wgEncodeUwDgfNhaSig Signal astrocytes (also called Astrocy) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal NH-A DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNb4Sig NB4 Sig NB4 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002451 2451 GSM1014513 Stam UW DS12543 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNb4Sig Signal acute promyelocytic leukemia cell line. (PMID: 1995093) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal NB4 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfM059jSig M059J Sig M059J DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003155 3155 GSM1014538 Stam UW DS20493 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfM059jSig Signal malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal M059J DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHvmfSig HVMF Sig HVMF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002455 2455 GSM1014510 Stam UW DS13981 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHvmfSig Signal villous mesenchymal fibroblast cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HVMF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHsmmSig HSMM Sig HSMM DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002450 2450 GSM1014514 Stam UW DS14426 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHsmmSig Signal skeletal muscle myoblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HSMM DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHrceSig HRCEpiC Sig HRCEpiC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000845 845 GSM849027 Stam UW DS10666 hg19 wgEncodeUwDgfHrceSig Signal renal cortical epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal HRCEpiC DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHpfSig HPF Sig HPF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000844 844 GSM849028 Stam UW DS13390 hg19 wgEncodeUwDgfHpfSig Signal pulmonary fibroblasts isolated from lung tissue DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal HPF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHpdlfSig HPdLF Sig HPdLF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000843 843 GSM849030 Stam UW DS13573 hg19 wgEncodeUwDgfHpdlfSig Signal periodontal ligament fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal HPdLF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHpafSig HPAF Sig HPAF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000842 842 GSM849031 Stam UW DS13411 hg19 wgEncodeUwDgfHpafSig Signal pulmonary artery fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal HPAF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecbSig HMVEC-LLy Sig HMVEC-LLy DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002447 2447 GSM1014529 Stam UW DS13185 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecbSig Signal lymphatic microvascular endothelial cells, lung-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HMVEC-LLy DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvechSig HMVEC-LBl Sig HMVEC-LBl DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003148 3148 GSM1014519 Stam UW DS13372 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvechSig Signal blood microvascular endothelial cells, lung-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HMVEC-LBl DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecfSig HMVEC-dLy-Neo Sig HMVEC-dLy-Neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002449 2449 GSM1014533 Stam UW DS13150 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecfSig Signal neonatal lymphatic microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HMVEC-dLy-Neo DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecdSig HMVEC-dBl-Neo Sig HMVEC-dBl-Neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002448 2448 GSM1014532 Stam UW DS13242 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecdSig Signal neonatal blood microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HMVEC-dBl-Neo DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecdbladSig HMVEC-dBl-Ad Sig HMVEC-dBl-Ad DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-25 wgEncodeEH000838 838 GSM646570 Stam UW DS13337 hg19 wgEncodeUwDgfHmvecdbladSig Signal adult blood microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal HMVEC-dBl-Ad DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmfSig HMF Sig HMF DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-25 wgEncodeEH000837 837 GSM646561 Stam UW DS13368 hg19 wgEncodeUwDgfHmfSig Signal mammary fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal HMF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHipeSig HIPEpiC Sig HIPEpiC DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002446 2446 GSM1014520 Stam UW DS12684 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHipeSig Signal iris pigment epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HIPEpiC DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHgfSig HGF Sig HGF DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003151 3151 GSM1014534 Stam UW DS11752 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHgfSig Signal gingival fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HGF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHffSig HFF Sig HFF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002445 2445 GSM1014531 Stam UW DS15115 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHffSig Signal foreskin fibroblast DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HFF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHeeSig HEEpiC Sig HEEpiC DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002454 2454 GSM1014511 Stam UW DS12763 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHeeSig Signal esophageal epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HEEpiC DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHcpeSig HCPEpiC Sig HCPEpiC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-25 wgEncodeEH000836 836 GSM646565 Stam UW DS12447 hg19 wgEncodeUwDgfHcpeSig Signal choroid plexus epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal HCPEpiC DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHcmSig HCM Sig HCM DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002453 2453 GSM1014515 Stam UW DS12599 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcmSig Signal cardiac myocytes DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HCM DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHcfaaSig HCFaa Sig HCFaa DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003147 3147 GSM1014518 Stam UW DS13480 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcfaaSig Signal cardiac fibroblasts- adult atrial DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HCFaa DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHcfSig HCF Sig HCF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002444 2444 GSM1014530 Stam UW DS12501 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcfSig Signal cardiac fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HCF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHaeSig HAEpiC Sig HAEpiC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000835 835 GSM646560 Stam UW DS12663 hg19 wgEncodeUwDgfHaeSig Signal amniotic epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal HAEpiC DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHaspSig HA-sp Sig HA-sp DnaseDgf ENCODE Mar 2012 Freeze 2011-12-16 2012-09-15 wgEncodeEH002459 2459 GSM1014508 Stam UW DS14790 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHaspSig Signal astrocytes spinal cord DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HA-sp DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHahSig HA-h Sig HA-h DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002452 2452 GSM1014516 Stam UW DS15192 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHahSig Signal astrocytes-hippocampal DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HA-h DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfH7esSig H7-hESC Sig H7-hESC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000834 834 GSM646563 Stam UW DS11909 hg19 wgEncodeUwDgfH7esSig Signal undifferentiated embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal H7-hESC DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfGm12865Sig GM12865 Sig GM12865 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002443 2443 GSM1014526 Stam UW DS12436 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfGm12865Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal GM12865 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfGm06990Sig GM06990 Sig GM06990 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-14 wgEncodeEH000479 479 GSM646568 Stam UW DS7748 hg18 wgEncodeUwDgfGm06990Sig Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal GM06990 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfCd4naivewb11970640Sig CD4+_Naive Sig CD4+_Naive_Wb11970640 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003156 3156 GSM1014537 Stam UW DS14108 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfCd4naivewb11970640Sig None Signal CD4+ naive sorted cells, donor is Caucasian, male 26 year old, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal CD4+ Naive Wb11970640 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfAoafSig AoAF Sig AoAF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000841 841 GSM849029 Stam UW DS13513 hg19 wgEncodeUwDgfAoafSig Signal aortic adventitial fibroblast cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal AoAF DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfAg10803Sig AG10803 Sig AG10803 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002441 2441 GSM1014527 Stam UW DS12374 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfAg10803Sig Signal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal AG10803 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfLhcnm2Sig LHCNM2 Sig LHCN-M2 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003149 3149 GSM1014524 Stam UW DS20548 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfLhcnm2Sig Signal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal LHCN-M2 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfLhcnm2Diff4dSig LHCNM2 DIFF4d Sig LHCN-M2 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003154 3154 GSM1014539 Stam UW DS20534 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfLhcnm2Diff4dSig DIFF_4d Signal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) Signal LHCN-M2 DIFF 4 d DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHuvecSig HUVEC Sig HUVEC DnaseDgf ENCODE Mar 2012 Freeze 2011-12-16 2012-09-15 wgEncodeEH002460 2460 GSM1014528 Stam UW DS10060 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHuvecSig Signal umbilical vein endothelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal HUVEC DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHepg2Sig HepG2 Sig HepG2 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-02 2010-07-02 wgEncodeEH000476 476 GSM646559 Stam UW DS7764 hg18 wgEncodeUwDgfHepg2Sig Signal hepatocellular carcinoma DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal HepG2 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfCd20ro01778Sig CD20+ Sig CD20+_RO01778 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002442 2442 GSM1014525 Stam UW DS18208 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfCd20ro01778Sig Signal B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal B cells CD20+ RO01778 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfA549Sig A549 Sig A549 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003146 3146 GSM1014517 Stam UW DS14289 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfA549Sig Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Signal A549 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfK562Sig K562 Sig K562 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000480 480 GSM646567 Stam UW DS9767 hg18 wgEncodeUwDgfK562Sig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal K562 DNaseI DGF Per-base Signal from ENCODE/UW Regulation 
wgEncodeUwDgfViewzRaw RawSignal DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Regulation 
wgEncodeUwDgfTregwb78495824Raw Treg Raw Treg_Wb78495824 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003161 3161 GSM1014523 Stam UW DS14702 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTregwb78495824Raw None RawSignal T regulatory cells in vivo isolation DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) Treg Wb78495824 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh17Raw Th17 Raw Th17 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003158 3158 GSM1014541 Stam UW DS11039 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh17Raw None RawSignal T helper cells expressing IL-17, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) Th17 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh2wb54553204Raw Th2 54553204 Raw Th2_Wb54553204 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003160 3160 GSM1014522 Stam UW DS17597 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh2wb54553204Raw None RawSignal Th2 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) Th2 Wb54553204 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh2Raw Th2 Raw Th2 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003162 3162 GSM1014521 Stam UW DS17603 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh2Raw None RawSignal primary Th2 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) Th2 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh1wb33676984Raw Th1 33676984 Raw Th1_Wb33676984 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003159 3159 GSM1014540 Stam UW DS18015 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh1wb33676984Raw None RawSignal Th1 cells in vivo isolation DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) Th1 Wb33676984 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfTh1RawRep2 Th1 Raw 2 Th1 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH000478 478 GSM646569 Stam UW DS18018 WindowDensity-bin20-win+/-75 hg19 2 Illumina_HiSeq_2000 wgEncodeUwDgfTh1RawRep2 None RawSignal primary Th1 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) Th1 DNaseI DGF Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDgfTh1Raw Th1 Raw 1 Th1 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-05 2010-07-05 wgEncodeEH000478 478 GSM646569 Stam UW DS7840 WindowDensity-bin20-win+/-75 hg18 wgEncodeUwDgfTh1Raw RawSignal primary Th1 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th1 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDgfT47dRaw T-47D Raw T-47D DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003157 3157 GSM1014536 Stam UW DS19794 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfT47dRaw None RawSignal epithelial cell line derived from a mammary ductal carcinoma. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfSkmcRaw SKMC Raw SKMC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000840 840 GSM646562 Stam UW DS11949 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfSkmcRaw RawSignal skeletal muscle cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SKMC DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfSknshraRaw SK-N-SH_RA Raw SK-N-SH_RA DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-02 2010-07-02 wgEncodeEH000477 477 GSM646566 Stam UW DS8482 WindowDensity-bin20-win+/-75 hg18 wgEncodeUwDgfSknshraRaw RawSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfSaecRaw SAEC Raw SAEC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000847 847 GSM849025 Stam UW DS10518 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfSaecRaw RawSignal small airway epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfRpmi7951Raw RPMI-7951 Raw RPMI-7951 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003150 3150 GSM1014535 Stam UW DS20909 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfRpmi7951Raw RawSignal Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) RPMI-7951 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNhlfRaw NHLF Raw NHLF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002458 2458 GSM1014509 Stam UW DS12829 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNhlfRaw RawSignal lung fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNhdfneoRaw NHDF-neo Raw NHDF-neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002457 2457 GSM1014512 Stam UW DS11923 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNhdfneoRaw RawSignal neonatal dermal fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNhdfadRaw NHDF-Ad Raw NHDF-Ad DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000839 839 GSM646564 Stam UW DS12863 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfNhdfadRaw RawSignal adult dermal fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-Ad DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNhaRaw NH-A Raw NH-A DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000846 846 GSM849026 Stam UW DS12800 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfNhaRaw RawSignal astrocytes (also called Astrocy) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NH-A DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfNb4Raw NB4 Raw NB4 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002451 2451 GSM1014513 Stam UW DS12543 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNb4Raw RawSignal acute promyelocytic leukemia cell line. (PMID: 1995093) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfM059jRaw M059J Raw M059J DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003155 3155 GSM1014538 Stam UW DS20493 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfM059jRaw RawSignal malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) M059J DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHvmfRaw HVMF Raw HVMF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002455 2455 GSM1014510 Stam UW DS13981 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHvmfRaw RawSignal villous mesenchymal fibroblast cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHsmmRaw HSMM Raw HSMM DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002450 2450 GSM1014514 Stam UW DS14426 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHsmmRaw RawSignal skeletal muscle myoblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HSMM DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHrceRaw HRCEpiC Raw HRCEpiC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000845 845 GSM849027 Stam UW DS10666 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfHrceRaw RawSignal renal cortical epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRCEpiC DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHpfRaw HPF Raw HPF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000844 844 GSM849028 Stam UW DS13390 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfHpfRaw RawSignal pulmonary fibroblasts isolated from lung tissue DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHpdlfRaw HPdLF Raw HPdLF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000843 843 GSM849030 Stam UW DS13573 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfHpdlfRaw RawSignal periodontal ligament fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPdLF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHpafRaw HPAF Raw HPAF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000842 842 GSM849031 Stam UW DS13411 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfHpafRaw RawSignal pulmonary artery fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecbRaw HMVEC-LLy Raw HMVEC-LLy DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002447 2447 GSM1014529 Stam UW DS13185 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecbRaw RawSignal lymphatic microvascular endothelial cells, lung-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-LLy DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvechRaw HMVEC-LBl Raw HMVEC-LBl DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003148 3148 GSM1014519 Stam UW DS13372 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvechRaw RawSignal blood microvascular endothelial cells, lung-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-LBl DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecfRaw HMVEC-dLy-Neo Raw HMVEC-dLy-Neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002449 2449 GSM1014533 Stam UW DS13150 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecfRaw RawSignal neonatal lymphatic microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dLy-Neo DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecdRaw HMVEC-dBl-Neo Raw HMVEC-dBl-Neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002448 2448 GSM1014532 Stam UW DS13242 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecdRaw RawSignal neonatal blood microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dBl-Neo DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecdbladRaw HMVEC-dBl-Ad Raw HMVEC-dBl-Ad DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-25 wgEncodeEH000838 838 GSM646570 Stam UW DS13337 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfHmvecdbladRaw RawSignal adult blood microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dBl-Ad DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHmfRaw HMF Raw HMF DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-25 wgEncodeEH000837 837 GSM646561 Stam UW DS13368 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfHmfRaw RawSignal mammary fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHipeRaw HIPEpiC Raw HIPEpiC DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002446 2446 GSM1014520 Stam UW DS12684 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHipeRaw RawSignal iris pigment epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HIPEpiC DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHgfRaw HGF Raw HGF DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003151 3151 GSM1014534 Stam UW DS11752 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHgfRaw RawSignal gingival fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HGF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHffRaw HFF Raw HFF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002445 2445 GSM1014531 Stam UW DS15115 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHffRaw RawSignal foreskin fibroblast DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHeeRaw HEEpiC Raw HEEpiC DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002454 2454 GSM1014511 Stam UW DS12763 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHeeRaw RawSignal esophageal epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpiC DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHcpeRaw HCPEpiC Raw HCPEpiC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-25 wgEncodeEH000836 836 GSM646565 Stam UW DS12447 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfHcpeRaw RawSignal choroid plexus epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpiC DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHcmRaw HCM Raw HCM DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002453 2453 GSM1014515 Stam UW DS12599 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcmRaw RawSignal cardiac myocytes DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHcfaaRaw HCFaa Raw HCFaa DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003147 3147 GSM1014518 Stam UW DS13480 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcfaaRaw RawSignal cardiac fibroblasts- adult atrial DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHcfRaw HCF Raw HCF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002444 2444 GSM1014530 Stam UW DS12501 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcfRaw RawSignal cardiac fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHaeRaw HAEpiC Raw HAEpiC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000835 835 GSM646560 Stam UW DS12663 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfHaeRaw RawSignal amniotic epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAEpiC DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHaspRaw HA-sp Raw HA-sp DnaseDgf ENCODE Mar 2012 Freeze 2011-12-16 2012-09-15 wgEncodeEH002459 2459 GSM1014508 Stam UW DS14790 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHaspRaw RawSignal astrocytes spinal cord DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHahRaw HA-h Raw HA-h DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002452 2452 GSM1014516 Stam UW DS15192 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHahRaw RawSignal astrocytes-hippocampal DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-h DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfH7esRaw H7-hESC Raw H7-hESC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000834 834 GSM646563 Stam UW DS11909 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfH7esRaw RawSignal undifferentiated embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfGm12865Raw GM12865 Raw GM12865 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002443 2443 GSM1014526 Stam UW DS12436 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfGm12865Raw RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfGm06990Raw GM06990 Raw GM06990 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-14 wgEncodeEH000479 479 GSM646568 Stam UW DS7748 WindowDensity-bin20-win+/-75 hg18 wgEncodeUwDgfGm06990Raw RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfCd4naivewb11970640Raw CD4+_Naive Raw CD4+_Naive_Wb11970640 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003156 3156 GSM1014537 Stam UW DS14108 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfCd4naivewb11970640Raw None RawSignal CD4+ naive sorted cells, donor is Caucasian, male 26 year old, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) CD4+ Naive Wb11970640 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfAoafRaw AoAF Raw AoAF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000841 841 GSM849029 Stam UW DS13513 WindowDensity-bin20-win+/-75 hg19 wgEncodeUwDgfAoafRaw RawSignal aortic adventitial fibroblast cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfAg10803Raw AG10803 Raw AG10803 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002441 2441 GSM1014527 Stam UW DS12374 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfAg10803Raw RawSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfLhcnm2Raw LHCNM2 Raw LHCN-M2 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003149 3149 GSM1014524 Stam UW DS20548 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfLhcnm2Raw RawSignal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) LHCN-M2 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfLhcnm2Diff4dRaw LHCNM2 DIFF4d Raw LHCN-M2 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003154 3154 GSM1014539 Stam UW DS20534 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfLhcnm2Diff4dRaw DIFF_4d RawSignal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) LHCN-M2 DIFF 4 d DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHuvecRaw HUVEC Raw HUVEC DnaseDgf ENCODE Mar 2012 Freeze 2011-12-16 2012-09-15 wgEncodeEH002460 2460 GSM1014528 Stam UW DS10060 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHuvecRaw RawSignal umbilical vein endothelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfHepg2Raw HepG2 Raw HepG2 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-02 2010-07-02 wgEncodeEH000476 476 GSM646559 Stam UW DS7764 WindowDensity-bin20-win+/-75 hg18 wgEncodeUwDgfHepg2Raw RawSignal hepatocellular carcinoma DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfCd20ro01778Raw CD20+ Raw CD20+_RO01778 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002442 2442 GSM1014525 Stam UW DS18208 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfCd20ro01778Raw RawSignal B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) B cells CD20+ RO01778 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfA549Raw A549 Raw A549 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003146 3146 GSM1014517 Stam UW DS14289 WindowDensity-bin20-win+/-75 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfA549Raw RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfK562Raw K562 Raw K562 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000480 480 GSM646567 Stam UW DS9767 WindowDensity-bin20-win+/-75 hg18 wgEncodeUwDgfK562Raw RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 DNaseI DGF Raw Signal from ENCODE/UW Regulation 
wgEncodeUwDgfViewPeaks Peaks DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Regulation 
wgEncodeUwDgfTregwb78495824Pk Treg Pk Treg_Wb78495824 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003161 3161 GSM1014523 Stam UW DS14702 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTregwb78495824Pk None Peaks T regulatory cells in vivo isolation DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment Treg Wb78495824 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfTh17Pk Th17 Pk Th17 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003158 3158 GSM1014541 Stam UW DS11039 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh17Pk None Peaks T helper cells expressing IL-17, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment Th17 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfTh2wb54553204Pk Th2 54553204 Pk Th2_Wb54553204 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003160 3160 GSM1014522 Stam UW DS17597 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh2wb54553204Pk None Peaks Th2 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment Th2 Wb54553204 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfTh2Pk Th2 Pk Th2 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003162 3162 GSM1014521 Stam UW DS17603 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh2Pk None Peaks primary Th2 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment Th2 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfTh1wb33676984Pk Th1 33676984 Pk Th1_Wb33676984 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003159 3159 GSM1014540 Stam UW DS18015 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh1wb33676984Pk None Peaks Th1 cells in vivo isolation DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment Th1 Wb33676984 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfTh1PkRep2 Th1 Pk 2 Th1 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH000478 478 GSM646569 Stam UW DS18018 lmax-v1.0 hg19 2 Illumina_HiSeq_2000 wgEncodeUwDgfTh1PkRep2 None Peaks primary Th1 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment Th1 DNaseI DGF Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDgfTh1Pk Th1 Pk 1 Th1 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-05 2010-07-05 wgEncodeEH000478 478 GSM646569 Stam UW DS7840 lmax-v1.0 hg18 wgEncodeUwDgfTh1Pk Peaks primary Th1 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th1 DNaseI DGF Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDgfT47dPk T-47D Pk T-47D DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003157 3157 GSM1014536 Stam UW DS19794 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfT47dPk None Peaks epithelial cell line derived from a mammary ductal carcinoma. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment T-47D DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfSkmcPkV2 SKMC Pk SKMC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000840 840 GSM646562 Stam UW DS11949 lmax-v1.0 hg19 wgEncodeUwDgfSkmcPkV2 Peaks skeletal muscle cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SKMC DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfSknshraPk SK-N-SH_RA Pk SK-N-SH_RA DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-02 2010-07-02 wgEncodeEH000477 477 GSM646566 Stam UW DS8482 lmax-v1.0 hg18 wgEncodeUwDgfSknshraPk Peaks neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfSaecPk SAEC Pk SAEC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000847 847 GSM849025 Stam UW DS10518 lmax-v1.0 hg19 wgEncodeUwDgfSaecPk Peaks small airway epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfRpmi7951Pk RPMI-7951 Pk RPMI-7951 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003150 3150 GSM1014535 Stam UW DS20909 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfRpmi7951Pk Peaks Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment RPMI-7951 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfNhlfPk NHLF Pk NHLF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002458 2458 GSM1014509 Stam UW DS12829 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNhlfPk Peaks lung fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment NHLF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfNhdfneoPk NHDF-neo Pk NHDF-neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002457 2457 GSM1014512 Stam UW DS11923 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNhdfneoPk Peaks neonatal dermal fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment NHDF-neo DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfNhdfadPkV2 NHDF-Ad Pk NHDF-Ad DnaseDgf ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000839 839 GSM646564 Stam UW DS12863 lmax-v1.0 hg19 wgEncodeUwDgfNhdfadPkV2 Peaks adult dermal fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-Ad DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfNhaPk NH-A Pk NH-A DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000846 846 GSM849026 Stam UW DS12800 lmax-v1.0 hg19 wgEncodeUwDgfNhaPk Peaks astrocytes (also called Astrocy) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NH-A DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfNb4Pk NB4 Pk NB4 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002451 2451 GSM1014513 Stam UW DS12543 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNb4Pk Peaks acute promyelocytic leukemia cell line. (PMID: 1995093) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment NB4 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfM059jPk M059J Pk M059J DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003155 3155 GSM1014538 Stam UW DS20493 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfM059jPk Peaks malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment M059J DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHvmfPk HVMF Pk HVMF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002455 2455 GSM1014510 Stam UW DS13981 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHvmfPk Peaks villous mesenchymal fibroblast cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HVMF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHsmmPk HSMM Pk HSMM DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002450 2450 GSM1014514 Stam UW DS14426 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHsmmPk Peaks skeletal muscle myoblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HSMM DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHrcePk HRCEpiC Pk HRCEpiC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000845 845 GSM849027 Stam UW DS10666 lmax-v1.0 hg19 wgEncodeUwDgfHrcePk Peaks renal cortical epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRCEpiC DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHpfPk HPF Pk HPF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000844 844 GSM849028 Stam UW DS13390 lmax-v1.0 hg19 wgEncodeUwDgfHpfPk Peaks pulmonary fibroblasts isolated from lung tissue DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHpdlfPk HPdLF Pk HPdLF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000843 843 GSM849030 Stam UW DS13573 lmax-v1.0 hg19 wgEncodeUwDgfHpdlfPk Peaks periodontal ligament fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPdLF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHpafPk HPAF Pk HPAF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000842 842 GSM849031 Stam UW DS13411 lmax-v1.0 hg19 wgEncodeUwDgfHpafPk Peaks pulmonary artery fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecbPk HMVEC-LLy Pk HMVEC-LLy DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002447 2447 GSM1014529 Stam UW DS13185 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecbPk Peaks lymphatic microvascular endothelial cells, lung-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HMVEC-LLy DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHmvechPk HMVEC-LBl Pk HMVEC-LBl DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003148 3148 GSM1014519 Stam UW DS13372 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvechPk Peaks blood microvascular endothelial cells, lung-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HMVEC-LBl DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecfPk HMVEC-dLy-Neo Pk HMVEC-dLy-Neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002449 2449 GSM1014533 Stam UW DS13150 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecfPk Peaks neonatal lymphatic microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HMVEC-dLy-Neo DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecdPk HMVEC-dBl-Neo Pk HMVEC-dBl-Neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002448 2448 GSM1014532 Stam UW DS13242 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecdPk Peaks neonatal blood microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HMVEC-dBl-Neo DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecdbladPkV2 HMVEC-dBl-Ad Pk HMVEC-dBl-Ad DnaseDgf ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000838 838 GSM646570 Stam UW DS13337 lmax-v1.0 hg19 wgEncodeUwDgfHmvecdbladPkV2 Peaks adult blood microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dBl-Ad DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHmfPkV2 HMF Pk HMF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000837 837 GSM646561 Stam UW DS13368 lmax-v1.0 hg19 wgEncodeUwDgfHmfPkV2 Peaks mammary fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHipePk HIPEpiC Pk HIPEpiC DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002446 2446 GSM1014520 Stam UW DS12684 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHipePk Peaks iris pigment epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HIPEpiC DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHgfPk HGF Pk HGF DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003151 3151 GSM1014534 Stam UW DS11752 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHgfPk Peaks gingival fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HGF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHffPk HFF Pk HFF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002445 2445 GSM1014531 Stam UW DS15115 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHffPk Peaks foreskin fibroblast DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HFF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHeePk HEEpiC Pk HEEpiC DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002454 2454 GSM1014511 Stam UW DS12763 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHeePk Peaks esophageal epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HEEpiC DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHcpePkV2 HCPEpiC Pk HCPEpiC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000836 836 GSM646565 Stam UW DS12447 lmax-v1.0 hg19 wgEncodeUwDgfHcpePkV2 Peaks choroid plexus epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpiC DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHcmPk HCM Pk HCM DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002453 2453 GSM1014515 Stam UW DS12599 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcmPk Peaks cardiac myocytes DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HCM DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHcfaaPk HCFaa Pk HCFaa DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003147 3147 GSM1014518 Stam UW DS13480 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcfaaPk Peaks cardiac fibroblasts- adult atrial DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HCFaa DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHcfPk HCF Pk HCF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002444 2444 GSM1014530 Stam UW DS12501 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcfPk Peaks cardiac fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HCF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHaePkV2 HAEpiC Pk HAEpiC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000835 835 GSM646560 Stam UW DS12663 lmax-v1.0 hg19 wgEncodeUwDgfHaePkV2 Peaks amniotic epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAEpiC DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHaspPk HA-sp Pk HA-sp DnaseDgf ENCODE Mar 2012 Freeze 2011-12-16 2012-09-15 wgEncodeEH002459 2459 GSM1014508 Stam UW DS14790 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHaspPk Peaks astrocytes spinal cord DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HA-sp DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHahPk HA-h Pk HA-h DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002452 2452 GSM1014516 Stam UW DS15192 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHahPk Peaks astrocytes-hippocampal DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HA-h DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfH7esPkV2 H7-hESC Pk H7-hESC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000834 834 GSM646563 Stam UW DS11909 lmax-v1.0 hg19 wgEncodeUwDgfH7esPkV2 Peaks undifferentiated embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfGm12865Pk GM12865 Pk GM12865 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002443 2443 GSM1014526 Stam UW DS12436 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfGm12865Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment GM12865 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfGm06990Pk GM06990 Pk GM06990 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-14 wgEncodeEH000479 479 GSM646568 Stam UW DS7748 lmax-v1.0 hg18 wgEncodeUwDgfGm06990Pk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfCd4naivewb11970640Pk CD4+_Naive Pk CD4+_Naive_Wb11970640 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003156 3156 GSM1014537 Stam UW DS14108 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfCd4naivewb11970640Pk None Peaks CD4+ naive sorted cells, donor is Caucasian, male 26 year old, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment CD4+ Naive Wb11970640 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfAoafPk AoAF Pk AoAF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000841 841 GSM849029 Stam UW DS13513 lmax-v1.0 hg19 wgEncodeUwDgfAoafPk Peaks aortic adventitial fibroblast cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfAg10803Pk AG10803 Pk AG10803 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002441 2441 GSM1014527 Stam UW DS12374 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfAg10803Pk Peaks abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment AG10803 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfLhcnm2Pk LHCNM2 Pk LHCN-M2 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003149 3149 GSM1014524 Stam UW DS20548 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfLhcnm2Pk Peaks skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment LHCN-M2 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfLhcnm2Diff4dPk LHCNM2 DIFF4d Pk LHCN-M2 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003154 3154 GSM1014539 Stam UW DS20534 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfLhcnm2Diff4dPk DIFF_4d Peaks skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) Regions of enriched signal in experiment LHCN-M2 DIFF 4 d DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHuvecPk HUVEC Pk HUVEC DnaseDgf ENCODE Mar 2012 Freeze 2011-12-16 2012-09-15 wgEncodeEH002460 2460 GSM1014528 Stam UW DS10060 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHuvecPk Peaks umbilical vein endothelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment HUVEC DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfHepg2Pk HepG2 Pk HepG2 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-02 2010-07-02 wgEncodeEH000476 476 GSM646559 Stam UW DS7764 lmax-v1.0 hg18 wgEncodeUwDgfHepg2Pk Peaks hepatocellular carcinoma DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfCd20ro01778Pk CD20+ Pk CD20+_RO01778 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002442 2442 GSM1014525 Stam UW DS18208 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfCd20ro01778Pk Peaks B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment B cells CD20+ RO01778 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfA549Pk A549 Pk A549 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003146 3146 GSM1014517 Stam UW DS14289 lmax-v1.0 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfA549Pk Peaks epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Regions of enriched signal in experiment A549 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfK562Pk K562 Pk K562 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000480 480 GSM646567 Stam UW DS9767 lmax-v1.0 hg18 wgEncodeUwDgfK562Pk Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 DNaseI DGF Peaks from ENCODE/UW Regulation 
wgEncodeUwDgfViewHotspots Hotspots DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Regulation 
wgEncodeUwDgfTregwb78495824Hotspots Treg Hot Treg_Wb78495824 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003161 3161 GSM1014523 Stam UW DS14702 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTregwb78495824Hotspots None Hotspots T regulatory cells in vivo isolation DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm Treg Wb78495824 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfTh17Hotspots Th17 Hot Th17 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003158 3158 GSM1014541 Stam UW DS11039 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh17Hotspots None Hotspots T helper cells expressing IL-17, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm Th17 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfTh2wb54553204Hotspots Th2 54553204 Hot Th2_Wb54553204 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003160 3160 GSM1014522 Stam UW DS17597 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh2wb54553204Hotspots None Hotspots Th2 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm Th2 Wb54553204 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfTh2Hotspots Th2 Hot Th2 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003162 3162 GSM1014521 Stam UW DS17603 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh2Hotspots None Hotspots primary Th2 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm Th2 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfTh1wb33676984Hotspots Th1 33676984 Hot Th1_Wb33676984 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003159 3159 GSM1014540 Stam UW DS18015 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfTh1wb33676984Hotspots None Hotspots Th1 cells in vivo isolation DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm Th1 Wb33676984 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfTh1HotspotsRep2 Th1 Hot 2 Th1 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH000478 478 GSM646569 Stam UW DS18018 Hotspot-v5.2 hg19 2 Illumina_HiSeq_2000 wgEncodeUwDgfTh1HotspotsRep2 None Hotspots primary Th1 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm Th1 DNaseI DGF Hotspots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDgfTh1Hotspots Th1 Hot 1 Th1 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-05 2010-07-05 wgEncodeEH000478 478 GSM646569 Stam UW DS7840 Hotspot-v5.1 hg18 wgEncodeUwDgfTh1Hotspots Hotspots primary Th1 T cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th1 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDgfT47dHotspots T-47D Hot T-47D DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003157 3157 GSM1014536 Stam UW DS19794 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfT47dHotspots None Hotspots epithelial cell line derived from a mammary ductal carcinoma. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm T-47D DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfSkmcHotspots SKMC Hot SKMC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000840 840 GSM646562 Stam UW DS11949 Hotspot-v5.1 hg19 wgEncodeUwDgfSkmcHotspots Hotspots skeletal muscle cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SKMC DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfSknshraHotspots SK-N-SH_RA Hot SK-N-SH_RA DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-02 2010-07-02 wgEncodeEH000477 477 GSM646566 Stam UW DS8482 Hotspot-v5.1 hg18 wgEncodeUwDgfSknshraHotspots Hotspots neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfSaecHotspots SAEC Hot SAEC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000847 847 GSM849025 Stam UW DS10518 Hotspot-v5.1 hg19 wgEncodeUwDgfSaecHotspots Hotspots small airway epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfRpmi7951Hotspots RPMI-7951 Hot RPMI-7951 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003150 3150 GSM1014535 Stam UW DS20909 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfRpmi7951Hotspots Hotspots Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm RPMI-7951 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfNhlfHotspots NHLF Hot NHLF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002458 2458 GSM1014509 Stam UW DS12829 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNhlfHotspots Hotspots lung fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm NHLF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfNhdfneoHotspots NHDF-neo Hot NHDF-neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002457 2457 GSM1014512 Stam UW DS11923 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNhdfneoHotspots Hotspots neonatal dermal fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfNhdfadHotspots NHDF-Ad Hot NHDF-Ad DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000839 839 GSM646564 Stam UW DS12863 Hotspot-v5.1 hg19 wgEncodeUwDgfNhdfadHotspots Hotspots adult dermal fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-Ad DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfNhaHotspots NH-A Hot NH-A DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000846 846 GSM849026 Stam UW DS12800 Hotspot-v5.1 hg19 wgEncodeUwDgfNhaHotspots Hotspots astrocytes (also called Astrocy) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NH-A DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfNb4Hotspots NB4 Hot NB4 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002451 2451 GSM1014513 Stam UW DS12543 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfNb4Hotspots Hotspots acute promyelocytic leukemia cell line. (PMID: 1995093) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm NB4 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfM059jHotspots M059J Hot M059J DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003155 3155 GSM1014538 Stam UW DS20493 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfM059jHotspots Hotspots malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm M059J DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHvmfHotspots HVMF Hot HVMF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002455 2455 GSM1014510 Stam UW DS13981 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHvmfHotspots Hotspots villous mesenchymal fibroblast cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HVMF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHsmmHotspots HSMM Hot HSMM DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002450 2450 GSM1014514 Stam UW DS14426 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHsmmHotspots Hotspots skeletal muscle myoblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HSMM DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHrceHotspots HRCEpiC Hot HRCEpiC DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000845 845 GSM849027 Stam UW DS10666 Hotspot-v5.1 hg19 wgEncodeUwDgfHrceHotspots Hotspots renal cortical epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRCEpiC DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHpfHotspots HPF Hot HPF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-08 2011-10-07 wgEncodeEH000844 844 GSM849028 Stam UW DS13390 Hotspot-v5.1 hg19 wgEncodeUwDgfHpfHotspots Hotspots pulmonary fibroblasts isolated from lung tissue DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHpdlfHotspots HPdLF Hot HPdLF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000843 843 GSM849030 Stam UW DS13573 Hotspot-v5.1 hg19 wgEncodeUwDgfHpdlfHotspots Hotspots periodontal ligament fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPdLF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHpafHotspots HPAF Hot HPAF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000842 842 GSM849031 Stam UW DS13411 Hotspot-v5.1 hg19 wgEncodeUwDgfHpafHotspots Hotspots pulmonary artery fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecbHotspots HMVEC-LLy Hot HMVEC-LLy DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002447 2447 GSM1014529 Stam UW DS13185 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecbHotspots Hotspots lymphatic microvascular endothelial cells, lung-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-LLy DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHmvechHotspots HMVEC-LBl Hot HMVEC-LBl DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003148 3148 GSM1014519 Stam UW DS13372 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvechHotspots Hotspots blood microvascular endothelial cells, lung-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-LBl DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecfHotspots HMVEC-dLy-Neo Hot HMVEC-dLy-Neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002449 2449 GSM1014533 Stam UW DS13150 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecfHotspots Hotspots neonatal lymphatic microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dLy-Neo DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecdHotspots HMVEC-dBl-Neo Hot HMVEC-dBl-Neo DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002448 2448 GSM1014532 Stam UW DS13242 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHmvecdHotspots Hotspots neonatal blood microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dBl-Neo DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHmvecdbladHotspots HMVEC-dBl-Ad Hot HMVEC-dBl-Ad DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-25 wgEncodeEH000838 838 GSM646570 Stam UW DS13337 Hotspot-v5.1 hg19 wgEncodeUwDgfHmvecdbladHotspots Hotspots adult blood microvascular endothelial cells, dermal-derived DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dBl-Ad DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHmfHotspots HMF Hot HMF DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-25 wgEncodeEH000837 837 GSM646561 Stam UW DS13368 Hotspot-v5.1 hg19 wgEncodeUwDgfHmfHotspots Hotspots mammary fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHipeHotspots HIPEpiC Hot HIPEpiC DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002446 2446 GSM1014520 Stam UW DS12684 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHipeHotspots Hotspots iris pigment epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HIPEpiC DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHgfHotspots HGF Hot HGF DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003151 3151 GSM1014534 Stam UW DS11752 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHgfHotspots Hotspots gingival fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HGF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHffHotspots HFF Hot HFF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002445 2445 GSM1014531 Stam UW DS15115 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHffHotspots Hotspots foreskin fibroblast DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HFF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHeeHotspots HEEpiC Hot HEEpiC DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002454 2454 GSM1014511 Stam UW DS12763 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHeeHotspots Hotspots esophageal epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HEEpiC DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHcpeHotspots HCPEpiC Hot HCPEpiC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-25 wgEncodeEH000836 836 GSM646565 Stam UW DS12447 Hotspot-v5.1 hg19 wgEncodeUwDgfHcpeHotspots Hotspots choroid plexus epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpiC DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHcmHotspots HCM Hot HCM DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002453 2453 GSM1014515 Stam UW DS12599 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcmHotspots Hotspots cardiac myocytes DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HCM DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHcfaaHotspots HCFaa Hot HCFaa DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003147 3147 GSM1014518 Stam UW DS13480 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcfaaHotspots Hotspots cardiac fibroblasts- adult atrial DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HCFaa DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHcfHotspots HCF Hot HCF DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002444 2444 GSM1014530 Stam UW DS12501 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHcfHotspots Hotspots cardiac fibroblasts DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HCF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHaeHotspots HAEpiC Hot HAEpiC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000835 835 GSM646560 Stam UW DS12663 Hotspot-v5.1 hg19 wgEncodeUwDgfHaeHotspots Hotspots amniotic epithelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAEpiC DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHaspHotspots HA-sp Hot HA-sp DnaseDgf ENCODE Mar 2012 Freeze 2011-12-16 2012-09-15 wgEncodeEH002459 2459 GSM1014508 Stam UW DS14790 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHaspHotspots Hotspots astrocytes spinal cord DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHahHotspots HA-h Hot HA-h DnaseDgf ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002452 2452 GSM1014516 Stam UW DS15192 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHahHotspots Hotspots astrocytes-hippocampal DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HA-h DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfH7esHotspots H7-hESC Hot H7-hESC DnaseDgf ENCODE Jan 2011 Freeze 2010-07-25 2011-04-24 wgEncodeEH000834 834 GSM646563 Stam UW DS11909 Hotspot-v5.1 hg19 wgEncodeUwDgfH7esHotspots Hotspots undifferentiated embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfGm12865Hotspots GM12865 Hot GM12865 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002443 2443 GSM1014526 Stam UW DS12436 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfGm12865Hotspots Hotspots B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfGm06990Hotspots GM06990 Hot GM06990 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-14 wgEncodeEH000479 479 GSM646568 Stam UW DS7748 Hotspot-v5.1 hg18 wgEncodeUwDgfGm06990Hotspots Hotspots B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfCd4naivewb11970640Hotspots CD4+_Naive Hot CD4+_Naive_Wb11970640 DnaseDgf ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEH003156 3156 GSM1014537 Stam UW DS14108 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfCd4naivewb11970640Hotspots None Hotspots CD4+ naive sorted cells, donor is Caucasian, male 26 year old, primary pheresis of single normal subject DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm CD4+ Naive Wb11970640 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfAoafHotspots AoAF Hot AoAF DnaseDgf ENCODE Jan 2011 Freeze 2011-01-07 2011-10-07 wgEncodeEH000841 841 GSM849029 Stam UW DS13513 Hotspot-v5.1 hg19 wgEncodeUwDgfAoafHotspots Hotspots aortic adventitial fibroblast cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfAg10803Hotspots AG10803 Hot AG10803 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002441 2441 GSM1014527 Stam UW DS12374 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfAg10803Hotspots Hotspots abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfLhcnm2Hotspots LHCNM2 Hot LHCN-M2 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003149 3149 GSM1014524 Stam UW DS20548 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfLhcnm2Hotspots Hotspots skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm LHCN-M2 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfLhcnm2Diff4dHotspots LHCNM2 DIFF4d Hot LHCN-M2 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-28 2012-12-27 wgEncodeEH003154 3154 GSM1014539 Stam UW DS20534 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfLhcnm2Diff4dHotspots DIFF_4d Hotspots skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm LHCN-M2 DIFF 4 d DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHuvecHotspots HUVEC Hot HUVEC DnaseDgf ENCODE Mar 2012 Freeze 2011-12-16 2012-09-15 wgEncodeEH002460 2460 GSM1014528 Stam UW DS10060 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfHuvecHotspots Hotspots umbilical vein endothelial cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfHepg2Hotspots HepG2 Hot HepG2 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2009-10-02 2010-07-02 wgEncodeEH000476 476 GSM646559 Stam UW DS7764 Hotspot-v5.1 hg18 wgEncodeUwDgfHepg2Hotspots Hotspots hepatocellular carcinoma DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfCd20ro01778Hotspots CD20+ Hot CD20+_RO01778 DnaseDgf ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002442 2442 GSM1014525 Stam UW DS18208 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfCd20ro01778Hotspots Hotspots B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm B cells CD20+ RO01778 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfA549Hotspots A549 Hot A549 DnaseDgf ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH003146 3146 GSM1014517 Stam UW DS14289 Hotspot-v5.2 hg19 Illumina_HiSeq_2000 wgEncodeUwDgfA549Hotspots Hotspots epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 ChIP-seq affinity zones identified using the HotSpot algorithm A549 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDgfK562Hotspots K562 Hot K562 DnaseDgf ENCODE June 2010 Freeze 2010-06-21 2010-01-14 2010-10-13 wgEncodeEH000480 480 GSM646567 Stam UW DS9767 Hotspot-v5.1 hg18 wgEncodeUwDgfK562Hotspots Hotspots leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 DNaseI DGF Hotspots from ENCODE/UW Regulation 
wgEncodeUwDnase UW DNaseI HS GSE29692 DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington Regulation Description This track was produced as part of the ENCODE Project. This track shows DNaseI sensitivity measured genome-wide in different cell lines using the Digital DNaseI methodology (see below) and DNaseI hypersensitive sites. DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promoters, locus control regions and novel elements. For each experiment (cell type), this track shows DNaseI sensitivity as a continuous function using sequencing tag density (Raw Signal) and discrete loci of DNaseI sensitive zones (HotSpots) and hypersensitive sites (Peaks). Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: HotSpots DNaseI sensitive zones identified using the HotSpot algorithm. Peaks DNaseI hypersensitive sites (DHSs) identified as signal peaks within FDR 1.0% hypersensitive zones. Raw Signal The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). DNaseI sensitivity is shown as the absolute density of in vivo cleavage sites across the genome mapped using the Digital DNaseI methodology (see below). Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Digital DNaseI was performed by DNaseI digestion of intact nuclei, isolation of DNaseI 'double-hit' fragments as described in Sabo et al. (2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Illumina Geneome Analyzer II platform (36 bp reads). Uniquely mapping high-quality reads were mapped to the genome. DNaseI sensitivity is directly reflected in raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). DNaseI sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). False discovery rate thresholds of 1.0% (FDR 1.0%) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm. Verification Data were verified by sequencing biological replicates displaying a correlation coefficient &gt; 0.9. Results were extensively validated by conventional DNaseI hypersensitivity assays using end-labeling/Southern blotting methods. Release Notes This is release 6 (July 2012) of this track. It includes 11 new experiments across 12 new cell lines: bone marrow HS27a, bone marrow HS5, bone marrow MSC, CD4+ Naive Wb11970640, CD4+ Naive Wb78495824, Th17, Th1 Wb33676984, Th1 Wb54553204, Th2 Wb33676984, Th2 Wb54553204, Treg Wb78495824, Treg Wb83319432. This release also removes previously release K562 zinc-finger experiments. There are questions concerning the data due to a merging issue. Credits These data were generated by the UW ENCODE group. Contact: Richard Sandstrom References Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods. 2006 Jul;3(7):511-8. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwDnaseViewzRaw Raw Signal DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington Regulation 
wgEncodeUwDnaseWi38RawRep2 WI-38 Sg 2 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001197 1197 GSM736526 Stam UW DS14320 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseWi38RawRep2 None RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseWi38OhtamRawRep2 WI-38 OHTM Sg 2 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001198 1198 GSM736526 Stam UW DS14328 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseWi38OhtamRawRep2 4OHTAM_20nM_72hr RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 4-OHTAM 20 nM 72 hr DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseWi38RawRep1 WI-38 Sg 1 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001197 1197 GSM736613 Stam UW DS14315 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseWi38RawRep1 None RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseWi38OhtamRawRep1 WI-38 OHTM Sg 1 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001198 1198 GSM736613 Stam UW DS14323 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseWi38OhtamRawRep1 4OHTAM_20nM_72hr RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 4-OHTAM 20 nM 72 hr DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseWerirb1RawRep2 WERI-Rb-1 Sg 2 WERI-Rb-1 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001190 1190 GSM736636 Stam UW DS13670 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseWerirb1RawRep2 None RawSignal retinoblastoma (PMID: 844036) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseWerirb1RawRep1 WERI-Rb-1 Sg 1 WERI-Rb-1 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001190 1190 GSM736495 Stam UW DS13681 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseWerirb1RawRep1 None RawSignal retinoblastoma (PMID: 844036) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTregwb83319432RawRep1 Treg Wb432 Sg 1 Treg_Wb83319432 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003026 3026 GSM1024741 Stam UW DS17589 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseTregwb83319432RawRep1 None RawSignal T regulatory cells in vivo isolation, donor is Caucasian, male 28 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Treg Wb83319432 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTregwb78495824RawRep1 Treg Wb824 Sg 1 Treg_Wb78495824 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003025 3025 GSM1024744 Stam UW DS14702 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseTregwb78495824RawRep1 None RawSignal T regulatory cells in vivo isolation DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Treg Wb78495824 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh17RawRep1 Th17 Sg 1 Th17 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003020 3020 GSM1024790 Stam UW DS11039 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseTh17RawRep1 None RawSignal T helper cells expressing IL-17, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th17 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2wb54553204RawRep1 Th2 Wb204 Sg 1 Th2_Wb54553204 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003024 3024 GSM1024739 Stam UW DS17597 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseTh2wb54553204RawRep1 None RawSignal Th2 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th2 Wb54553204 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2wb33676984RawRep1 Th2 Wb984 Sg 1 Th2_Wb33676984 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003023 3023 GSM1024740 Stam UW DS18057 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseTh2wb33676984RawRep1 None RawSignal Th2 cells in vivo isolation, donor is Asian, female 26 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th2 Wb33676984 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2RawRep2 Th2 Sg 2 Th2 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH000491 491 GSM1024792 Stam UW DS17603 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseTh2RawRep2 None RawSignal primary Th2 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th2 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2RawRep1 Th2 Sg 1 Th2 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-04-29 2010-01-29 wgEncodeEH000491 491 GSM736502 Stam UW DS7842 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseTh2RawRep1 None RawSignal primary Th2 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th2 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1wb54553204RawRep2 Th1 Wb204 Sg 2 Th1_Wb54553204 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003022 3022 GSM1024752 Stam UW DS17592 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseTh1wb54553204RawRep2 None RawSignal Th1 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th1 Wb54553204 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1wb54553204RawRep1 Th1 Wb204 Sg 1 Th1_Wb54553204 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003022 3022 GSM1024753 Stam UW DS17593 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseTh1wb54553204RawRep1 None RawSignal Th1 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th1 Wb54553204 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1wb33676984RawRep1 Th1 Wb984 Sg 1 Th1_Wb33676984 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003021 3021 GSM1024749 Stam UW DS18015 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseTh1wb33676984RawRep1 None RawSignal Th1 cells in vivo isolation DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th1 Wb33676984 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1RawRep2 Th1 Sg 2 Th1 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH000483 483 GSM1024760 Stam UW DS18018 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseTh1RawRep2 None RawSignal primary Th1 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th1 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1RawRep1 Th1 Sg 1 Th1 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2008-11-20 2009-08-20 wgEncodeEH000483 483 GSM736592 Stam UW DS7840 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseTh1RawRep1 None RawSignal primary Th1 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Th1 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseT47dRawRep2 T-47D Sg 2 T-47D DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002583 2583 GSM1024761 Stam UW DS19790 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseT47dRawRep2 None RawSignal epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseT47dRawRep1 T-47D Sg 1 T-47D DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002583 2583 GSM1024762 Stam UW DS19794 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseT47dRawRep1 None RawSignal epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSkmcRawRep2 SkMC Sg 2 SKMC DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-10-27 2010-07-26 wgEncodeEH000490 490 GSM736497 Stam UW DS11939 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseSkmcRawRep2 None RawSignal skeletal muscle cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SkMC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSkmcRawRep1 SkMC Sg 1 SKMC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-04-29 2010-01-29 wgEncodeEH000490 490 GSM736593 Stam UW DS11949 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseSkmcRawRep1 None RawSignal skeletal muscle cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SkMC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknshraRawRep2 SKNSHRA Sg 2 SK-N-SH_RA DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-17 2010-04-17 wgEncodeEH000485 485 GSM736578 Stam UW DS8476 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseSknshraRawRep2 None RawSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknshraRawRep1 SKNSHRA Sg 1 SK-N-SH_RA DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-04-17 2010-01-17 wgEncodeEH000485 485 GSM736559 Stam UW DS8482 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseSknshraRawRep1 None RawSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknmcRawRep2 SKNMC Sg 2 SK-N-MC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001189 1189 GSM736570 Stam UW DS14413 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseSknmcRawRep2 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknmcRawRep1 SKNMC Sg 1 SK-N-MC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001189 1189 GSM736522 Stam UW DS14408 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseSknmcRawRep1 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSaecRawRep2 SAEC Sg 2 SAEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000501 501 GSM736617 Stam UW DS10514 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseSaecRawRep2 None RawSignal small airway epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSaecRawRep1 SAEC Sg 1 SAEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000501 501 GSM736608 Stam UW DS10518 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseSaecRawRep1 None RawSignal small airway epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseRptecRawRep2 RPTEC Sg 2 RPTEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001188 1188 GSM736539 Stam UW DS14065 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseRptecRawRep2 None RawSignal renal proximal tubule epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseRptecRawRep1 RPTEC Sg 1 RPTEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001188 1188 GSM736543 Stam UW DS14061 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseRptecRawRep1 None RawSignal renal proximal tubule epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseRpmi7951RawRep2 RPMI7951 Sg 2 RPMI-7951 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-22 2012-12-22 wgEncodeEH003007 3007 GSM1024793 Stam UW DS20904 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseRpmi7951RawRep2 None RawSignal Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPMI-7951 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseRpmi7951RawRep1 RPMI7951 Sg 1 RPMI-7951 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-22 2012-12-22 wgEncodeEH003007 3007 GSM1024779 Stam UW DS20909 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseRpmi7951RawRep1 None RawSignal Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPMI-7951 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnasePrecRawRep2 PrEC Sg 2 PrEC DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001888 1888 GSM1024743 Stam UW DS12088 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnasePrecRawRep2 None RawSignal prostate epithelial cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PrEC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnasePrecRawRep1 PrEC Sg 1 PrEC DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001888 1888 GSM1024742 Stam UW DS12098 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnasePrecRawRep1 None RawSignal prostate epithelial cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PrEC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnasePanc1RawRep2 PANC1 Sg 2 PANC-1 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000500 500 GSM736519 Stam UW DS9873 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnasePanc1RawRep2 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnasePanc1RawRep1 PANC1 Sg 1 PANC-1 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-09-19 2010-06-19 wgEncodeEH000500 500 GSM736517 Stam UW DS9955 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnasePanc1RawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNt2d1RawRep2 NT2D1 Sg 2 NT2-D1 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001887 1887 GSM1024795 Stam UW DS14564 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseNt2d1RawRep2 None RawSignal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NT2-D1 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNt2d1RawRep1 NT2D1 Sg 1 NT2-D1 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001887 1887 GSM1024751 Stam UW DS14575 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseNt2d1RawRep1 None RawSignal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NT2-D1 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhlfRawRep2 NHLF Sg 2 NHLF DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000521 521 GSM736536 Stam UW DS12834 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseNhlfRawRep2 None RawSignal lung fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhlfRawRep1 NHLF Sg 1 NHLF DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000521 521 GSM736612 Stam UW DS12829 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseNhlfRawRep1 None RawSignal lung fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhekRawRep2 NHEK Sg 2 NHEK DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000499 499 GSM736556 Stam UW DS11476 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseNhekRawRep2 None RawSignal epidermal keratinocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhekRawRep1 NHEK Sg 1 NHEK DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-09-19 2010-06-19 wgEncodeEH000499 499 GSM736545 Stam UW DS11474 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseNhekRawRep1 None RawSignal epidermal keratinocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfneoRawRep2 NHDFneo Sg 2 NHDF-neo DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-09 2010-10-08 wgEncodeEH000518 518 GSM736546 Stam UW DS11918 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseNhdfneoRawRep2 None RawSignal neonatal dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfneoRawRep1 NHDFneo Sg 1 NHDF-neo DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-08 2010-10-08 wgEncodeEH000518 518 GSM736498 Stam UW DS11923 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseNhdfneoRawRep1 None RawSignal neonatal dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfadRawRep2 NHDFAd Sg 2 NHDF-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001177 1177 GSM736520 Stam UW DS12855 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseNhdfadRawRep2 None RawSignal adult dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-Ad DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfadRawRep1 NHDFAd Sg 1 NHDF-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001177 1177 GSM736567 Stam UW DS12863 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseNhdfadRawRep1 None RawSignal adult dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-Ad DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhberaRawRep2 NHBE RA Sg 2 NHBE_RA DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002582 2582 GSM1024756 Stam UW DS11959 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseNhberaRawRep2 None RawSignal bronchial epithelial cells with retinoic acid DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHBE RA DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhberaRawRep1 NHBE RA Sg 1 NHBE_RA DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002582 2582 GSM1024781 Stam UW DS11969 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseNhberaRawRep1 None RawSignal bronchial epithelial cells with retinoic acid DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHBE RA DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhaRawRep2 NH-A Sg 2 NH-A DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001179 1179 GSM736584 Stam UW DS12805 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseNhaRawRep2 None RawSignal astrocytes (also called Astrocy) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NH-A DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhaRawRep1 NH-A Sg 1 NH-A DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001179 1179 GSM736544 Stam UW DS12800 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseNhaRawRep1 None RawSignal astrocytes (also called Astrocy) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NH-A DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNb4RawRep2 NB4 Sg 2 NB4 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-08 wgEncodeEH000498 498 GSM736529 Stam UW DS12538 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseNb4RawRep2 None RawSignal acute promyelocytic leukemia cell line. (PMID: 1995093) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNb4RawRep1 NB4 Sg 1 NB4 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000498 498 GSM736604 Stam UW DS12543 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseNb4RawRep1 None RawSignal acute promyelocytic leukemia cell line. (PMID: 1995093) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseM059jRawRep2 M059J Sg 2 M059J DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002581 2581 GSM1024794 Stam UW DS20497 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseM059jRawRep2 None RawSignal malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) M059J DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseM059jRawRep1 M059J Sg 1 M059J DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002581 2581 GSM1024773 Stam UW DS20493 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseM059jRawRep1 None RawSignal malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) M059J DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseLncapRawRep2 LNCaP Sg 2 LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001187 1187 GSM736603 Stam UW DS14680 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseLncapRawRep2 None RawSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseLncapRawRep1 LNCaP Sg 1 LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001187 1187 GSM736565 Stam UW DS14684 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseLncapRawRep1 None RawSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseJurkatRawRep2 Jurkat Sg 2 Jurkat DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000497 497 GSM736492 Stam UW DS10681 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseJurkatRawRep2 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseJurkatRawRep1 Jurkat Sg 1 Jurkat DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000497 497 GSM736501 Stam UW DS12659 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseJurkatRawRep1 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHvmfRawRep2 HVMF Sg 2 HVMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001176 1176 GSM736491 Stam UW DS13977 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHvmfRawRep2 None RawSignal villous mesenchymal fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHvmfRawRep1 HVMF Sg 1 HVMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001176 1176 GSM736534 Stam UW DS13981 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHvmfRawRep1 None RawSignal villous mesenchymal fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmtRawRep2 HSMMtube Sg 2 HSMMtube DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001186 1186 GSM1024788 Stam UW DS15538 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHsmmtRawRep2 None RawSignal skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HSMMtube DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmtRawRep1 HSMMtube Sg 1 HSMMtube DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001186 1186 GSM736530 Stam UW DS15542 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHsmmtRawRep1 None RawSignal skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HSMMtube DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmRawRep2 HSMM Sg 2 HSMM DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001185 1185 GSM736553 Stam UW DS14430 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHsmmRawRep2 None RawSignal skeletal muscle myoblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HSMM DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmRawRep1 HSMM Sg 1 HSMM DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001185 1185 GSM736560 Stam UW DS14426 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHsmmRawRep1 None RawSignal skeletal muscle myoblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HSMM DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrpeRawRep2 HRPEpiC Sg 2 HRPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-08 wgEncodeEH000517 517 GSM736623 Stam UW DS12568 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHrpeRawRep2 None RawSignal retinal pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpiC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrpeRawRep1 HRPEpiC Sg 1 HRPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-08 wgEncodeEH000517 517 GSM736630 Stam UW DS12583 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHrpeRawRep1 None RawSignal retinal pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpiC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrgecRawRep2 HRGEC Sg 2 HRGEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001195 1195 GSM736618 Stam UW DS13716 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHrgecRawRep2 None RawSignal renal glomerular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRGEC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrgecRawRep1 HRGEC Sg 1 HRGEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001195 1195 GSM736499 Stam UW DS13705 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHrgecRawRep1 None RawSignal renal glomerular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRGEC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHreRawRep2 HRE Sg 2 HRE DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000494 494 GSM736548 Stam UW DS10631 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHreRawRep2 None RawSignal renal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHreRawRep1 HRE Sg 1 HRE DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000494 494 GSM736527 Stam UW DS10641 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHreRawRep1 None RawSignal renal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrceRawRep2 HRCEpiC Sg 2 HRCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000493 493 GSM736557 Stam UW DS10662 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHrceRawRep2 None RawSignal renal cortical epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRCEpiC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrceRawRep1 HRCEpiC Sg 1 HRCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000493 493 GSM736549 Stam UW DS10666 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHrceRawRep1 None RawSignal renal cortical epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRCEpiC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpfRawRep2 HPF Sg 2 HPF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001174 1174 GSM736503 Stam UW DS13380 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHpfRawRep2 None RawSignal pulmonary fibroblasts isolated from lung tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpfRawRep1 HPF Sg 1 HPF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001174 1174 GSM736574 Stam UW DS13390 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHpfRawRep1 None RawSignal pulmonary fibroblasts isolated from lung tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpdlfRawRep2 HPdLF Sg 2 HPdLF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001175 1175 GSM736528 Stam UW DS13569 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHpdlfRawRep2 None RawSignal periodontal ligament fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPdLF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpdlfRawRep1 HPdLF Sg 1 HPdLF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001175 1175 GSM736632 Stam UW DS13573 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHpdlfRawRep1 None RawSignal periodontal ligament fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPdLF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpafRawRep2 HPAF Sg 2 HPAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001173 1173 GSM736614 Stam UW DS13416 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHpafRawRep2 None RawSignal pulmonary artery fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpafRawRep1 HPAF Sg 1 HPAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001173 1173 GSM736555 Stam UW DS13411 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHpafRawRep1 None RawSignal pulmonary artery fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpaecRawRep1 HPAEC Sg 1 HPAEC DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001886 1886 GSM1024763 Stam UW DS12916 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHpaecRawRep1 None RawSignal pulmonary artery endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAEC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHnpceRawRep2 HNPCEpiC Sg 2 HNPCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000516 516 GSM736550 Stam UW DS12471 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHnpceRawRep2 None RawSignal non-pigment ciliary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HNPCEpiC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHnpceRawRep1 HNPCEpiC Sg 1 HNPCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000516 516 GSM736621 Stam UW DS12467 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHnpceRawRep1 None RawSignal non-pigment ciliary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HNPCEpiC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecllyRawRep2 HMVECLLy Sg 2 HMVEC-LLy DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001167 1167 GSM736627 Stam UW DS13193 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmvecllyRawRep2 None RawSignal lymphatic microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-LLy DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecllyRawRep1 HMVECLLy Sg 1 HMVEC-LLy DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001167 1167 GSM736507 Stam UW DS13185 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHmvecllyRawRep1 None RawSignal lymphatic microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-LLy DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmveclblRawRep2 HMVECLBl Sg 2 HMVEC-LBl DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001163 1163 GSM736511 Stam UW DS13375 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmveclblRawRep2 None RawSignal blood microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-LBl DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmveclblRawRep1 HMVECLBl Sg 1 HMVEC-LBl DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH001163 1163 GSM736542 Stam UW DS13372 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHmveclblRawRep1 None RawSignal blood microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-LBl DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdneoRawRep2 HMVECdNeo Sg 2 HMVEC-dNeo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001172 1172 GSM736624 Stam UW DS12929 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmvecdneoRawRep2 None RawSignal neonatal microvascular endothelial cells (single donor), dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dNeo DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdneoRawRep1 HMVECdNeo Sg 1 HMVEC-dNeo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001172 1172 GSM736611 Stam UW DS12937 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHmvecdneoRawRep1 None RawSignal neonatal microvascular endothelial cells (single donor), dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dNeo DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyneoRawRep2 HMVECdLyNeo Sg 2 HMVEC-dLy-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001171 1171 GSM736573 Stam UW DS13146 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmvecdlyneoRawRep2 None RawSignal neonatal lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dLy-Neo DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyneoRawRep1 HMVECdLyNeo Sg 1 HMVEC-dLy-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001171 1171 GSM736577 Stam UW DS13150 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHmvecdlyneoRawRep1 None RawSignal neonatal lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dLy-Neo DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyadRawRep2 HMVECdLyAd Sg 2 HMVEC-dLy-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001170 1170 GSM736591 Stam UW DS13256 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmvecdlyadRawRep2 None RawSignal adult lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dLy-Ad DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyadRawRep1 HMVECdLyAd Sg 1 HMVEC-dLy-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001170 1170 GSM736599 Stam UW DS13261 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHmvecdlyadRawRep1 None RawSignal adult lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dLy-Ad DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdblneoRawRep2 HMVECdBlNeo Sg 2 HMVEC-dBl-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001169 1169 GSM736521 Stam UW DS13233 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmvecdblneoRawRep2 None RawSignal neonatal blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dBl-Neo DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdblneoRawRep1 HMVECdBlNeo Sg 1 HMVEC-dBl-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001169 1169 GSM736571 Stam UW DS13242 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHmvecdblneoRawRep1 None RawSignal neonatal blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dBl-Neo DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdbladRawRep2 HMVECdBlAd Sg 2 HMVEC-dBl-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001168 1168 GSM736523 Stam UW DS13329 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmvecdbladRawRep2 None RawSignal adult blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dBl-Ad DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdbladRawRep1 HMVECdBlAd Sg 1 HMVEC-dBl-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001168 1168 GSM736609 Stam UW DS13337 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHmvecdbladRawRep1 None RawSignal adult blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dBl-Ad DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdadRawRep2 HMVECdAd Sg 2 HMVEC-dAd DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-28 wgEncodeEH001889 1889 GSM1024747 Stam UW DS12952 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmvecdadRawRep2 None RawSignal adult dermal microvascular endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dAd DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdadRawRep1 HMVECdAd Sg 1 HMVEC-dAd DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-28 wgEncodeEH001889 1889 GSM1024745 Stam UW DS12957 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHmvecdadRawRep1 None RawSignal adult dermal microvascular endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMVEC-dAd DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmfRawRep2 HMF Sg 2 HMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001166 1166 GSM736541 Stam UW DS13368 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmfRawRep2 None RawSignal mammary fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmfRawRep1 HMF Sg 1 HMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001166 1166 GSM736628 Stam UW DS13363 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHmfRawRep1 None RawSignal mammary fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmecRawRep2 HMEC Sg 2 HMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH000503 503 GSM736552 Stam UW DS13921 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHmecRawRep2 None RawSignal mammary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmecRawRep1 HMEC Sg 1 HMEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000503 503 GSM736634 Stam UW DS8680 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHmecRawRep1 None RawSignal mammary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHl60RawRep2 HL60 Sg 2 HL-60 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000489 489 GSM736595 Stam UW DS11733 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHl60RawRep2 None RawSignal promyelocytic leukemia cells, (PMID: 276884) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHl60RawRep1 HL60 Sg 1 HL-60 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-04-29 2010-01-29 wgEncodeEH000489 489 GSM736626 Stam UW DS11809 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHl60RawRep1 None RawSignal promyelocytic leukemia cells, (PMID: 276884) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHipeRawRep2 HIPEpiC Sg 2 HIPEpiC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001184 1184 GSM736615 Stam UW DS12689 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHipeRawRep2 None RawSignal iris pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HIPEpiC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHipeRawRep1 HIPEpiC Sg 1 HIPEpiC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001184 1184 GSM736589 Stam UW DS12684 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHipeRawRep1 None RawSignal iris pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HIPEpiC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHgfRawRep2 HGF Sg 2 HGF DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-10-20 2010-07-20 wgEncodeEH000504 504 GSM736576 Stam UW DS11738 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHgfRawRep2 None RawSignal gingival fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HGF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHgfRawRep1 HGF Sg 1 HGF DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-20 2010-07-20 wgEncodeEH000504 504 GSM736579 Stam UW DS11752 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHgfRawRep1 None RawSignal gingival fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HGF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffmycRawRep2 HFFMyc Sg 2 HFF-Myc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001194 1194 GSM736605 Stam UW DS15073 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHffmycRawRep2 None RawSignal foreskin fibroblast cells expressing canine cMyc DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF-Myc DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffmycRawRep1 HFFMyc Sg 1 HFF-Myc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001194 1194 GSM736524 Stam UW DS15079 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHffmycRawRep1 None RawSignal foreskin fibroblast cells expressing canine cMyc DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF-Myc DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffRawRep2 HFF Sg 2 HFF DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001193 1193 GSM736572 Stam UW DS15119 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHffRawRep2 None RawSignal foreskin fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffRawRep1 HFF Sg 1 HFF DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001193 1193 GSM736602 Stam UW DS15115 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHffRawRep1 None RawSignal foreskin fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHeeRawRep2 HEEpiC Sg 2 HEEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000515 515 GSM736532 Stam UW DS12768 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHeeRawRep2 None RawSignal esophageal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpiC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHeeRawRep1 HEEpiC Sg 1 HEEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-10 2010-10-09 wgEncodeEH000515 515 GSM736585 Stam UW DS12763 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHeeRawRep1 None RawSignal esophageal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpiC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHct116RawRep2 HCT-116 Sg 2 HCT-116 DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH001162 1162 GSM736493 Stam UW DS13547 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHct116RawRep2 None RawSignal colorectal carcinoma (PMID: 7214343) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHct116RawRep1 HCT-116 Sg 1 HCT-116 DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH001162 1162 GSM736600 Stam UW DS13551 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHct116RawRep1 None RawSignal colorectal carcinoma (PMID: 7214343) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcpeRawRep2 HCPEpiC Sg 2 HCPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000514 514 GSM736597 Stam UW DS12457 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHcpeRawRep2 None RawSignal choroid plexus epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpiC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcpeRawRep1 HCPEpiC Sg 1 HCPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000514 514 GSM736569 Stam UW DS12447 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHcpeRawRep1 None RawSignal choroid plexus epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpiC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHconfRawRep2 HConF Sg 2 HConF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001165 1165 GSM736515 Stam UW DS11637 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHconfRawRep2 None RawSignal conjunctival fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HConF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHconfRawRep1 HConF Sg 1 HConF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001165 1165 GSM736547 Stam UW DS11642 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHconfRawRep1 None RawSignal conjunctival fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HConF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcmRawRep2 HCM Sg 2 HCM DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-09 2010-10-08 wgEncodeEH000519 519 GSM736504 Stam UW DS12589 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHcmRawRep2 None RawSignal cardiac myocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcmRawRep1 HCM Sg 1 HCM DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-09 2010-10-08 wgEncodeEH000519 519 GSM736516 Stam UW DS12599 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHcmRawRep1 None RawSignal cardiac myocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfaaRawRep2 HCFaa Sg 2 HCFaa DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001164 1164 GSM736601 Stam UW DS13484 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHcfaaRawRep2 None RawSignal cardiac fibroblasts- adult atrial DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfaaRawRep1 HCFaa Sg 1 HCFaa DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001164 1164 GSM736494 Stam UW DS13480 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHcfaaRawRep1 None RawSignal cardiac fibroblasts- adult atrial DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfRawRep2 HCF Sg 2 HCF DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000513 513 GSM736540 Stam UW DS12491 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHcfRawRep2 None RawSignal cardiac fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfRawRep1 HCF Sg 1 HCF DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-09 2010-10-08 wgEncodeEH000513 513 GSM736568 Stam UW DS12501 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHcfRawRep1 None RawSignal cardiac fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbvsmcRawRep2 HBVSCM Sg 2 HBVSMC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002580 2580 GSM1024769 Stam UW DS14845 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHbvsmcRawRep2 None RawSignal brain vascular smooth muscle cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBVSCM DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbvsmcRawRep1 HBVSCM Sg 1 HBVSMC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002580 2580 GSM1024768 Stam UW DS14860 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHbvsmcRawRep1 None RawSignal brain vascular smooth muscle cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBVSCM DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbvpRawRep1 HBVP Sg 1 HBVP DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002579 2579 GSM1024750 Stam UW DS14834 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHbvpRawRep1 None RawSignal brain vascular pericytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBVP DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbmecRawRep2 HBMEC Sg 2 HBMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001178 1178 GSM736554 Stam UW DS13806 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHbmecRawRep2 None RawSignal brain microvascular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbmecRawRep1 HBMEC Sg 1 HBMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001178 1178 GSM736509 Stam UW DS13817 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHbmecRawRep1 None RawSignal brain microvascular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaeRawRep2 HAEpiC Sg 2 HAEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-07 wgEncodeEH000512 512 GSM736606 Stam UW DS12673 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHaeRawRep2 None RawSignal amniotic epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAEpiC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaeRawRep1 HAEpiC Sg 1 HAEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-07 wgEncodeEH000512 512 GSM736631 Stam UW DS12663 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHaeRawRep1 None RawSignal amniotic epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAEpiC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHacRawRep2 HAc Sg 2 HAc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001192 1192 GSM736538 Stam UW DS14770 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHacRawRep2 None RawSignal astrocytes-cerebellar DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHacRawRep1 HAc Sg 1 HAc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001192 1192 GSM736586 Stam UW DS14765 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHacRawRep1 None RawSignal astrocytes-cerebellar DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaspRawRep2 HAsp Sg 2 HA-sp DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001183 1183 GSM736625 Stam UW DS14794 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHaspRawRep2 None RawSignal astrocytes spinal cord DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaspRawRep1 HAsp Sg 1 HA-sp DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001183 1183 GSM736537 Stam UW DS14790 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHaspRawRep1 None RawSignal astrocytes spinal cord DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHahRawRep2 HAh Sg 2 HA-h DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001191 1191 GSM736535 Stam UW DS15202 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHahRawRep2 None RawSignal astrocytes-hippocampal DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-h DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHahRawRep1 HAh Sg 1 HA-h DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001191 1191 GSM736594 Stam UW DS15192 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHahRawRep1 None RawSignal astrocytes-hippocampal DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-h DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esRawRep2 H7h Sg 2 H7-hESC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000511 511 GSM736610 Stam UW DS13133 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseH7esRawRep2 None RawSignal undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa5dRawRep2 H7h difPA5 Sg 2 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002578 2578 GSM1024755 Stam UW DS11953 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseH7esDiffa5dRawRep2 diffProtA_5d RawSignal undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC diffProtA 5 d DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa14dRawRep2 H7h difPA14 Sg 2 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002576 2576 GSM1024758 Stam UW DS11814 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseH7esDiffa14dRawRep2 diffProtA_14d RawSignal undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC diffProtA 14 d DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esRawRep1 H7h Sg 1 H7-hESC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-08 wgEncodeEH000511 511 GSM736638 Stam UW DS11909 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseH7esRawRep1 None RawSignal undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa9dRawRep1 H7h difPA9 Sg 1 H7-hESC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003019 3019 GSM1024778 Stam UW DS15809 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseH7esDiffa9dRawRep1 diffProtA_9d RawSignal undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC diffProtA 9 d DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa5dRawRep1 H7h difPA5 Sg 1 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002578 2578 GSM1024754 Stam UW DS15665 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseH7esDiffa5dRawRep1 diffProtA_5d RawSignal undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC diffProtA 5 d DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa2dRawRep1 H7h difPA2 Sg 1 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002577 2577 GSM1024774 Stam UW DS14732 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseH7esDiffa2dRawRep1 diffProtA_2d RawSignal undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC diffProtA 2 d DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa14dRawRep1 H7h difPA14 Sg 1 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002576 2576 GSM1024759 Stam UW DS12147 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseH7esDiffa14dRawRep1 diffProtA_14d RawSignal undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC diffProtA 14 d DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12865RawRep2 GM12865 Sg 2 GM12865 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000520 520 GSM736561 Stam UW DS12442 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseGm12865RawRep2 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12865RawRep1 GM12865 Sg 1 GM12865 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000520 520 GSM736512 Stam UW DS12436 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseGm12865RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12864RawRep1 GM12864 Sg 1 GM12864 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001182 1182 GSM736525 Stam UW DS12431 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseGm12864RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm06990RawRep2 GM06990 Sg 2 GM06990 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-01 2010-04-01 wgEncodeEH000481 481 GSM736635 Stam UW DS7784 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseGm06990RawRep2 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm06990RawRep1 GM06990 Sg 1 GM06990 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2008-11-19 2009-08-18 wgEncodeEH000481 481 GSM736558 Stam UW DS7748 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseGm06990RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04504RawRep2 GM04504 Sg 2 GM04504 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002575 2575 GSM1024776 Stam UW DS18975 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseGm04504RawRep2 None RawSignal adult twin pair fibroblasts, monozygotic twin of GM04503, 13% of the cells examined show random chromosome loss DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM04504 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04504RawRep1 GM04504 Sg 1 GM04504 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002575 2575 GSM1024775 Stam UW DS18973 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseGm04504RawRep1 None RawSignal adult twin pair fibroblasts, monozygotic twin of GM04503, 13% of the cells examined show random chromosome loss DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM04504 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04503RawRep2 GM04503 Sg 2 GM04503 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002574 2574 GSM1024780 Stam UW DS18640 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseGm04503RawRep2 None RawSignal adult twin pair fibroblasts, monozygotic twin of GM04504 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM04503 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04503RawRep1 GM04503 Sg 1 GM04503 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002574 2574 GSM1024777 Stam UW DS18637 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseGm04503RawRep1 None RawSignal adult twin pair fibroblasts, monozygotic twin of GM04504 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM04503 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCmkRawRep1 CMK Sg 1 CMK DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-07 wgEncodeEH000510 510 GSM736607 Stam UW DS12393 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseCmkRawRep1 None RawSignal acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CMK DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd34mobilizedRawRep1 CD34+ Mob Sg 1 CD34+_Mobilized DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001885 1885 GSM1024770 Stam UW DS16814 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseCd34mobilizedRawRep1 None RawSignal hematopoietic progenitor cells- mobilized, from donor RO01679. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD34+ Mobilized DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd4naivewb78495824RawRep1 CD4 NveWb824 Sg 1 CD4+_Naive_Wb78495824 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-09 2013-04-09 wgEncodeEH003028 3028 GSM1024782 Stam UW DS15241 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseCd4naivewb78495824RawRep1 None RawSignal CD4+ naive sorted cells, donor is Causasian, female 35 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD4+ Naive Wb78495824 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd4naivewb11970640RawRep1 CD4 NveWb640 Sg 1 CD4+_Naive_Wb11970640 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-09 2013-04-09 wgEncodeEH003027 3027 GSM1024789 Stam UW DS14108 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseCd4naivewb11970640RawRep1 None RawSignal CD4+ naive sorted cells, donor is Caucasian, male 26 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD4+ Naive Wb11970640 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCaco2RawRep2 Caco2 Sg 2 Caco-2 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-01 2010-03-30 wgEncodeEH000486 486 GSM736587 Stam UW DS8416 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseCaco2RawRep2 None RawSignal colorectal adenocarcinoma. (PMID: 1939345) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseCaco2RawRep1 Caco2 Sg 1 Caco-2 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-04-24 2010-01-24 wgEncodeEH000486 486 GSM736500 Stam UW DS8235 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseCaco2RawRep1 None RawSignal colorectal adenocarcinoma. (PMID: 1939345) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMscRawRep2 Bon MarMSC Sg 2 bone_marrow_MSC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003031 3031 GSM1024748 Stam UW DS20518 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseMscRawRep2 None RawSignal These cells are primary fibroblastoid cells obtained from human bone marrow of normal donors as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Bone Marrow MSC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMscRawRep1 Bon MarMSC Sg 1 bone_marrow_MSC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003031 3031 GSM1024757 Stam UW DS20514 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseMscRawRep1 None RawSignal These cells are primary fibroblastoid cells obtained from human bone marrow of normal donors as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Bone Marrow MSC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHs5RawRep1 Bon MarHS5 Sg 1 bone_marrow_HS5 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003030 3030 GSM1024746 Stam UW DS16597 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHs5RawRep1 None RawSignal HS5 Human Marrow Stromal Cells are fibroblastoid cells immortalized with HPV16 E6/E7 genes as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005, insert DNA is LXSN-16 E6E7 packaged in PA31. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Bone Marrow HS5 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHs27aRawRep1 Bon MarHS27a Sg 1 bone_marrow_HS27a DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003029 3029 GSM1024785 Stam UW DS16602 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseHs27aRawRep1 None RawSignal HS27a Human Marrow Stromal Cells are fibroblastoid cells immortalized with HPV16 E6/E7 genes as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005, insert DNA is LXSN-16 E6E7 packaged in PA31. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Bone Marrow HS27a DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseBjRawRep2 BJ Sg 2 BJ DnaseSeq ENCODE June 2010 Freeze 2010-06-06 2010-06-06 2011-03-06 wgEncodeEH000487 487 GSM736596 Stam UW DS10018 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseBjRawRep2 None RawSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseBjRawRep1 BJ Sg 1 BJ DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-06-19 2011-03-19 wgEncodeEH000487 487 GSM736518 Stam UW DS10081 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseBjRawRep1 None RawSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseBe2cRawRep2 BE2 C Sg 2 BE2_C DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001181 1181 GSM736622 Stam UW DS14635 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseBe2cRawRep2 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2 C DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseBe2cRawRep1 BE2 C Sg 1 BE2_C DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001181 1181 GSM736508 Stam UW DS14625 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseBe2cRawRep1 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2 C DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAoafRawRep2 AoAF Sg 2 AoAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH001161 1161 GSM736505 Stam UW DS13513 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseAoafRawRep2 None RawSignal aortic adventitial fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAoafRawRep1 AoAF Sg 1 AoAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001161 1161 GSM736583 Stam UW DS13523 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseAoafRawRep1 None RawSignal aortic adventitial fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg10803RawRep2 AG10803 Sg 2 AG10803 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-08 wgEncodeEH000509 509 GSM736633 Stam UW DS12374 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseAg10803RawRep2 None RawSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg10803RawRep1 AG10803 Sg 1 AG10803 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-08 wgEncodeEH000509 509 GSM736598 Stam UW DS12384 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseAg10803RawRep1 None RawSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09319RawRep2 AG09319 Sg 2 AG09319 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000508 508 GSM736619 Stam UW DS12286 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseAg09319RawRep2 None RawSignal gum tissue fibroblasts from apparently heathly 24 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09319RawRep1 AG09319 Sg 1 AG09319 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000508 508 GSM736531 Stam UW DS12291 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseAg09319RawRep1 None RawSignal gum tissue fibroblasts from apparently heathly 24 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09309RawRep2 AG09309 Sg 2 AG09309 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000507 507 GSM736616 Stam UW DS12357 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseAg09309RawRep2 None RawSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09309RawRep1 AG09309 Sg 1 AG09309 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000507 507 GSM736551 Stam UW DS12352 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseAg09309RawRep1 None RawSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04450RawRep2 AG04450 Sg 2 AG04450 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000506 506 GSM736563 Stam UW DS12255 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseAg04450RawRep2 None RawSignal fetal lung fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04450RawRep1 AG04450 Sg 1 AG04450 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000506 506 GSM736514 Stam UW DS12270 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseAg04450RawRep1 None RawSignal fetal lung fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04449RawRep2 AG04449 Sg 2 AG04449 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000505 505 GSM736590 Stam UW DS12329 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseAg04449RawRep2 None RawSignal fetal buttock/thigh fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04449RawRep1 AG04449 Sg 1 AG04449 DnaseSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-06 2010-10-05 wgEncodeEH000505 505 GSM736562 Stam UW DS12319 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseAg04449RawRep1 None RawSignal fetal buttock/thigh fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMonocd14ro1746RawRep2 CD14+ Mono Sg 2 Monocytes-CD14+_RO01746 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001196 1196 GSM1024791 Stam UW DS18065 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseMonocd14ro1746RawRep2 None RawSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Monocytes CD14+ RO01746 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7RawRep2 MCF7 Sg 2 MCF-7 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000502 502 GSM736588 Stam UW DS12619 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseMcf7RawRep2 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Estctrl0hRawRep2 MCF7 EstCtrl Sg 2 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003018 3018 GSM1024767 Stam UW DS18021 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseMcf7Estctrl0hRawRep2 Estradiol_ctrl_0hr RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Estradiol Control 0 hr DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Est100nm1hRawRep2 MCF7 Est1h Sg 2 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003017 3017 GSM1024783 Stam UW DS18025 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseMcf7Est100nm1hRawRep2 Estradiol_100nM_1hr RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 1 h with 100 nM Estradiol, hormone treatment (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Estradiol 100 nM 1 hr DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7RawRep1 MCF7 Sg 1 MCF-7 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-09-29 2010-06-29 wgEncodeEH000502 502 GSM736581 Stam UW DS9445 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseMcf7RawRep1 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Estctrl0hRawRep1 MCF7 EstCtrl Sg 1 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003018 3018 GSM1024764 Stam UW DS18267 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseMcf7Estctrl0hRawRep1 Estradiol_ctrl_0hr RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Estradiol Control 0 hr DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Est100nm1hRawRep1 MCF7 Est1h Sg 1 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003017 3017 GSM1024784 Stam UW DS18271 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseMcf7Est100nm1hRawRep1 Estradiol_100nM_1hr RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 1 h with 100 nM Estradiol, hormone treatment (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Estradiol 100 nM 1 hr DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2RawRep2 LHCNM2 Sg 2 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003005 3005 GSM1024786 Stam UW DS20485 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseLhcnm2RawRep2 None RawSignal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LHCN-M2 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2Diff4dRawRep2 LHCNM2 dif4d Sg 2 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003006 3006 GSM1024772 Stam UW DS20534 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseLhcnm2Diff4dRawRep2 DIFF_4d RawSignal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) LHCN-M2 DIFF 4 d DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2RawRep1 LHCNM2 Sg 1 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003005 3005 GSM1024787 Stam UW DS20548 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseLhcnm2RawRep1 None RawSignal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LHCN-M2 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2Diff4dRawRep1 LHCNM2 dif4d Sg 1 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003006 3006 GSM1024771 Stam UW DS20647 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseLhcnm2Diff4dRawRep1 DIFF_4d RawSignal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) LHCN-M2 DIFF 4 d DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHuvecRawRep2 HUVEC Sg 2 HUVEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000488 488 GSM736533 Stam UW DS13475 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseHuvecRawRep2 None RawSignal umbilical vein endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHuvecRawRep1 HUVEC Sg 1 HUVEC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-04-27 2010-01-27 wgEncodeEH000488 488 GSM736575 Stam UW DS10060 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHuvecRawRep1 None RawSignal umbilical vein endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHepg2RawRep2 HepG2 Sg 2 HepG2 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-01 2010-04-01 wgEncodeEH000482 482 GSM736639 Stam UW DS7768 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHepg2RawRep2 None RawSignal hepatocellular carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHepg2RawRep1 HepG2 Sg 1 HepG2 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2008-11-19 2009-08-18 wgEncodeEH000482 482 GSM736637 Stam UW DS7764 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHepg2RawRep1 None RawSignal hepatocellular carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHelas3RawRep2 HeLaS3 Sg 2 HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-02 2010-04-01 wgEncodeEH000495 495 GSM736510 Stam UW DS8200 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseHelas3RawRep2 None RawSignal cervical carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHelas3RawRep1 HeLaS3 Sg 1 HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-02 2010-04-01 wgEncodeEH000495 495 GSM736564 Stam UW DS10011 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseHelas3RawRep1 None RawSignal cervical carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd20ro01778RawRep2 CD20+ Sg 2 CD20+_RO01778 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001884 1884 GSM1024766 Stam UW DS17541 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseCd20ro01778RawRep2 None RawSignal B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) B cells CD20+ RO01778 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd20ro01778RawRep1 CD20+ Sg 1 CD20+_RO01778 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-13 wgEncodeEH001884 1884 GSM1024765 Stam UW DS18208 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseCd20ro01778RawRep1 None RawSignal B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) B cells CD20+ RO01778 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseA549RawRep2 A549 Sg 2 A549 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-04 wgEncodeEH001180 1180 GSM736506 Stam UW DS14285 WindowDensity-bin20-win+/-75 hg19 2 wgEncodeUwDnaseA549RawRep2 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseA549RawRep1 A549 Sg 1 A549 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-04 2011-10-04 wgEncodeEH001180 1180 GSM736580 Stam UW DS14289 WindowDensity-bin20-win+/-75 hg19 1 wgEncodeUwDnaseA549RawRep1 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseK562RawRep2 K562 Sg 2 K562 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2008-12-09 2009-09-09 wgEncodeEH000484 484 GSM736566 Stam UW DS9764 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseK562RawRep2 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseK562RawRep1 K562 Sg 1 K562 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2008-12-09 2009-09-09 wgEncodeEH000484 484 GSM736629 Stam UW DS9767 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseK562RawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH1hescRawRep1 H1hESC Sg 1 H1-hESC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-18 wgEncodeEH000496 496 GSM736582 Stam UW DS10167 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseH1hescRawRep1 None RawSignal embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12878RawRep2 GM12878 Sg 2 GM12878 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-01 2010-04-01 wgEncodeEH000492 492 GSM736620 Stam UW DS9432 WindowDensity-bin20-win+/-75 hg18 2 wgEncodeUwDnaseGm12878RawRep2 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 DNaseI HS Raw Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12878RawRep1 GM12878 Sg 1 GM12878 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000492 492 GSM736496 Stam UW DS10671 WindowDensity-bin20-win+/-75 hg18 1 wgEncodeUwDnaseGm12878RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 DNaseI HS Raw Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseViewaPeaks Peaks DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington Regulation 
wgEncodeUwDnaseWi38PkRep2 WI-38 Pk 2 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001197 1197 GSM736526 Stam UW DS14320 lmax-v1.0 hg19 2 wgEncodeUwDnaseWi38PkRep2 None Peaks embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseWi38OhtamPkRep2 WI-38 OHTM Pk 2 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001198 1198 GSM736526 Stam UW DS14328 lmax-v1.0 hg19 2 wgEncodeUwDnaseWi38OhtamPkRep2 4OHTAM_20nM_72hr Peaks embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Regions of enriched signal in experiment WI-38 4-OHTAM 20 nM 72 hr DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseWi38PkRep1 WI-38 Pk 1 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001197 1197 GSM736613 Stam UW DS14315 lmax-v1.0 hg19 1 wgEncodeUwDnaseWi38PkRep1 None Peaks embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseWi38OhtamPkRep1 WI-38 OHTM Pk 1 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001198 1198 GSM736613 Stam UW DS14323 lmax-v1.0 hg19 1 wgEncodeUwDnaseWi38OhtamPkRep1 4OHTAM_20nM_72hr Peaks embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Regions of enriched signal in experiment WI-38 4-OHTAM 20 nM 72 hr DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseWerirb1PkRep2 WERI-Rb-1 Pk 2 WERI-Rb-1 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001190 1190 GSM736636 Stam UW DS13670 lmax-v1.0 hg19 2 wgEncodeUwDnaseWerirb1PkRep2 None Peaks retinoblastoma (PMID: 844036) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseWerirb1PkRep1 WERI-Rb-1 Pk 1 WERI-Rb-1 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001190 1190 GSM736495 Stam UW DS13681 lmax-v1.0 hg19 1 wgEncodeUwDnaseWerirb1PkRep1 None Peaks retinoblastoma (PMID: 844036) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTregwb83319432PkRep1 Treg Wb432 Pk 1 Treg_Wb83319432 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003026 3026 GSM1024741 Stam UW DS17589 lmax-v1.0 hg19 1 wgEncodeUwDnaseTregwb83319432PkRep1 None Peaks T regulatory cells in vivo isolation, donor is Caucasian, male 28 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Treg Wb83319432 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTregwb78495824PkRep1 Treg Wb824 Pk 1 Treg_Wb78495824 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003025 3025 GSM1024744 Stam UW DS14702 lmax-v1.0 hg19 1 wgEncodeUwDnaseTregwb78495824PkRep1 None Peaks T regulatory cells in vivo isolation DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Treg Wb78495824 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh17PkRep1 Th17 Pk 1 Th17 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003020 3020 GSM1024790 Stam UW DS11039 lmax-v1.0 hg19 1 wgEncodeUwDnaseTh17PkRep1 None Peaks T helper cells expressing IL-17, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th17 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2wb54553204PkRep1 Th2 Wb204 Pk 1 Th2_Wb54553204 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003024 3024 GSM1024739 Stam UW DS17597 lmax-v1.0 hg19 1 wgEncodeUwDnaseTh2wb54553204PkRep1 None Peaks Th2 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th2 Wb54553204 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2wb33676984PkRep1 Th2 Wb984 Pk 1 Th2_Wb33676984 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003023 3023 GSM1024740 Stam UW DS18057 lmax-v1.0 hg19 1 wgEncodeUwDnaseTh2wb33676984PkRep1 None Peaks Th2 cells in vivo isolation, donor is Asian, female 26 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th2 Wb33676984 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2PkRep2 Th2 Pk 2 Th2 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH000491 491 GSM1024792 Stam UW DS17603 lmax-v1.0 hg19 2 wgEncodeUwDnaseTh2PkRep2 None Peaks primary Th2 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th2 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2PkRep1 Th2 Pk 1 Th2 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-04-29 2010-01-29 wgEncodeEH000491 491 GSM736502 Stam UW DS7842 lmax-v1.0 hg18 1 wgEncodeUwDnaseTh2PkRep1 None Peaks primary Th2 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th2 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1wb54553204PkRep2 Th1 Wb204 Pk 2 Th1_Wb54553204 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003022 3022 GSM1024752 Stam UW DS17592 lmax-v1.0 hg19 2 wgEncodeUwDnaseTh1wb54553204PkRep2 None Peaks Th1 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th1 Wb54553204 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1wb54553204PkRep1 Th1 Wb204 Pk 1 Th1_Wb54553204 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003022 3022 GSM1024753 Stam UW DS17593 lmax-v1.0 hg19 1 wgEncodeUwDnaseTh1wb54553204PkRep1 None Peaks Th1 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th1 Wb54553204 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1wb33676984PkRep1 Th1 Wb984 Pk 1 Th1_Wb33676984 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003021 3021 GSM1024749 Stam UW DS18015 lmax-v1.0 hg19 1 wgEncodeUwDnaseTh1wb33676984PkRep1 None Peaks Th1 cells in vivo isolation DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th1 Wb33676984 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1PkRep2 Th1 Pk 2 Th1 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH000483 483 GSM1024760 Stam UW DS18018 lmax-v1.0 hg19 2 wgEncodeUwDnaseTh1PkRep2 None Peaks primary Th1 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th1 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1PkRep1 Th1 Pk 1 Th1 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2008-11-20 2009-08-20 wgEncodeEH000483 483 GSM736592 Stam UW DS7840 lmax-v1.0 hg18 1 wgEncodeUwDnaseTh1PkRep1 None Peaks primary Th1 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Th1 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseT47dPkRep2 T-47D Pk 2 T-47D DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002583 2583 GSM1024761 Stam UW DS19790 lmax-v1.0 hg19 2 wgEncodeUwDnaseT47dPkRep2 None Peaks epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment T-47D DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseT47dPkRep1 T-47D Pk 1 T-47D DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002583 2583 GSM1024762 Stam UW DS19794 lmax-v1.0 hg19 1 wgEncodeUwDnaseT47dPkRep1 None Peaks epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment T-47D DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSkmcPkRep2 SkMC Pk 2 SKMC DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-10-27 2010-07-26 wgEncodeEH000490 490 GSM736497 Stam UW DS11939 lmax-v1.0 hg18 2 wgEncodeUwDnaseSkmcPkRep2 None Peaks skeletal muscle cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SkMC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSkmcPkRep1 SkMC Pk 1 SKMC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-04-29 2010-01-29 wgEncodeEH000490 490 GSM736593 Stam UW DS11949 lmax-v1.0 hg18 1 wgEncodeUwDnaseSkmcPkRep1 None Peaks skeletal muscle cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SkMC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknshraPkRep2 SKNSHRA Pk 2 SK-N-SH_RA DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-17 2010-04-17 wgEncodeEH000485 485 GSM736578 Stam UW DS8476 lmax-v1.0 hg18 2 wgEncodeUwDnaseSknshraPkRep2 None Peaks neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH RA DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknshraPkRep1 SKNSHRA Pk 1 SK-N-SH_RA DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-04-17 2010-01-17 wgEncodeEH000485 485 GSM736559 Stam UW DS8482 lmax-v1.0 hg18 1 wgEncodeUwDnaseSknshraPkRep1 None Peaks neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH RA DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknmcPkRep2 SKNMC Pk 2 SK-N-MC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001189 1189 GSM736570 Stam UW DS14413 lmax-v1.0 hg19 2 wgEncodeUwDnaseSknmcPkRep2 None Peaks neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-MC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknmcPkRep1 SKNMC Pk 1 SK-N-MC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001189 1189 GSM736522 Stam UW DS14408 lmax-v1.0 hg19 1 wgEncodeUwDnaseSknmcPkRep1 None Peaks neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-MC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSaecPkRep2 SAEC Pk 2 SAEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000501 501 GSM736617 Stam UW DS10514 lmax-v1.0 hg18 2 wgEncodeUwDnaseSaecPkRep2 None Peaks small airway epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSaecPkRep1 SAEC Pk 1 SAEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000501 501 GSM736608 Stam UW DS10518 lmax-v1.0 hg18 1 wgEncodeUwDnaseSaecPkRep1 None Peaks small airway epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseRptecPkRep2 RPTEC Pk 2 RPTEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001188 1188 GSM736539 Stam UW DS14065 lmax-v1.0 hg19 2 wgEncodeUwDnaseRptecPkRep2 None Peaks renal proximal tubule epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseRptecPkRep1 RPTEC Pk 1 RPTEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001188 1188 GSM736543 Stam UW DS14061 lmax-v1.0 hg19 1 wgEncodeUwDnaseRptecPkRep1 None Peaks renal proximal tubule epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseRpmi7951PkRep2 RPMI7951 Pk 2 RPMI-7951 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-22 2012-12-22 wgEncodeEH003007 3007 GSM1024793 Stam UW DS20904 lmax-v1.0 hg19 2 wgEncodeUwDnaseRpmi7951PkRep2 None Peaks Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPMI-7951 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseRpmi7951PkRep1 RPMI7951 Pk 1 RPMI-7951 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-22 2012-12-22 wgEncodeEH003007 3007 GSM1024779 Stam UW DS20909 lmax-v1.0 hg19 1 wgEncodeUwDnaseRpmi7951PkRep1 None Peaks Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPMI-7951 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnasePrecPkRep2 PrEC Pk 2 PrEC DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001888 1888 GSM1024743 Stam UW DS12088 lmax-v1.0 hg19 2 wgEncodeUwDnasePrecPkRep2 None Peaks prostate epithelial cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PrEC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnasePrecPkRep1 PrEC Pk 1 PrEC DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001888 1888 GSM1024742 Stam UW DS12098 lmax-v1.0 hg19 1 wgEncodeUwDnasePrecPkRep1 None Peaks prostate epithelial cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PrEC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnasePanc1PkRep2 PANC1 Pk 2 PANC-1 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000500 500 GSM736519 Stam UW DS9873 lmax-v1.0 hg18 2 wgEncodeUwDnasePanc1PkRep2 None Peaks pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PANC-1 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnasePanc1PkRep1 PANC1 Pk 1 PANC-1 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-09-19 2010-06-19 wgEncodeEH000500 500 GSM736517 Stam UW DS9955 lmax-v1.0 hg18 1 wgEncodeUwDnasePanc1PkRep1 None Peaks pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PANC-1 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNt2d1PkRep2 NT2D1 Pk 2 NT2-D1 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001887 1887 GSM1024795 Stam UW DS14564 lmax-v1.0 hg19 2 wgEncodeUwDnaseNt2d1PkRep2 None Peaks malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NT2-D1 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNt2d1PkRep1 NT2D1 Pk 1 NT2-D1 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001887 1887 GSM1024751 Stam UW DS14575 lmax-v1.0 hg19 1 wgEncodeUwDnaseNt2d1PkRep1 None Peaks malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NT2-D1 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhlfPkRep2 NHLF Pk 2 NHLF DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000521 521 GSM736536 Stam UW DS12834 lmax-v1.0 hg18 2 wgEncodeUwDnaseNhlfPkRep2 None Peaks lung fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhlfPkRep1 NHLF Pk 1 NHLF DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000521 521 GSM736612 Stam UW DS12829 lmax-v1.0 hg18 1 wgEncodeUwDnaseNhlfPkRep1 None Peaks lung fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhekPkRep2 NHEK Pk 2 NHEK DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000499 499 GSM736556 Stam UW DS11476 lmax-v1.0 hg19 2 wgEncodeUwDnaseNhekPkRep2 None Peaks epidermal keratinocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhekPkRep1 NHEK Pk 1 NHEK DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-09-19 2010-06-19 wgEncodeEH000499 499 GSM736545 Stam UW DS11474 lmax-v1.0 hg18 1 wgEncodeUwDnaseNhekPkRep1 None Peaks epidermal keratinocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfneoPkRep2 NHDFneo Pk 2 NHDF-neo DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-09 2010-10-08 wgEncodeEH000518 518 GSM736546 Stam UW DS11918 lmax-v1.0 hg18 2 wgEncodeUwDnaseNhdfneoPkRep2 None Peaks neonatal dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfneoPkRep1 NHDFneo Pk 1 NHDF-neo DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-08 2010-10-08 wgEncodeEH000518 518 GSM736498 Stam UW DS11923 lmax-v1.0 hg18 1 wgEncodeUwDnaseNhdfneoPkRep1 None Peaks neonatal dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfadPkRep2 NHDFAd Pk 2 NHDF-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001177 1177 GSM736520 Stam UW DS12855 lmax-v1.0 hg19 2 wgEncodeUwDnaseNhdfadPkRep2 None Peaks adult dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-Ad DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfadPkRep1 NHDFAd Pk 1 NHDF-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001177 1177 GSM736567 Stam UW DS12863 lmax-v1.0 hg19 1 wgEncodeUwDnaseNhdfadPkRep1 None Peaks adult dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-Ad DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhberaPkRep2 NHBE RA Pk 2 NHBE_RA DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002582 2582 GSM1024756 Stam UW DS11959 lmax-v1.0 hg19 2 wgEncodeUwDnaseNhberaPkRep2 None Peaks bronchial epithelial cells with retinoic acid DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHBE RA DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhberaPkRep1 NHBE RA Pk 1 NHBE_RA DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002582 2582 GSM1024781 Stam UW DS11969 lmax-v1.0 hg19 1 wgEncodeUwDnaseNhberaPkRep1 None Peaks bronchial epithelial cells with retinoic acid DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHBE RA DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhaPkRep2 NH-A Pk 2 NH-A DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001179 1179 GSM736584 Stam UW DS12805 lmax-v1.0 hg19 2 wgEncodeUwDnaseNhaPkRep2 None Peaks astrocytes (also called Astrocy) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NH-A DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhaPkRep1 NH-A Pk 1 NH-A DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001179 1179 GSM736544 Stam UW DS12800 lmax-v1.0 hg19 1 wgEncodeUwDnaseNhaPkRep1 None Peaks astrocytes (also called Astrocy) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NH-A DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNb4PkRep2 NB4 Pk 2 NB4 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-08 wgEncodeEH000498 498 GSM736529 Stam UW DS12538 lmax-v1.0 hg18 2 wgEncodeUwDnaseNb4PkRep2 None Peaks acute promyelocytic leukemia cell line. (PMID: 1995093) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NB4 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNb4PkRep1 NB4 Pk 1 NB4 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000498 498 GSM736604 Stam UW DS12543 lmax-v1.0 hg18 1 wgEncodeUwDnaseNb4PkRep1 None Peaks acute promyelocytic leukemia cell line. (PMID: 1995093) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NB4 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseM059jPkRep2 M059J Pk 2 M059J DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002581 2581 GSM1024794 Stam UW DS20497 lmax-v1.0 hg19 2 wgEncodeUwDnaseM059jPkRep2 None Peaks malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment M059J DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseM059jPkRep1 M059J Pk 1 M059J DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002581 2581 GSM1024773 Stam UW DS20493 lmax-v1.0 hg19 1 wgEncodeUwDnaseM059jPkRep1 None Peaks malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment M059J DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseLncapPkRep2 LNCaP Pk 2 LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001187 1187 GSM736603 Stam UW DS14680 lmax-v1.0 hg19 2 wgEncodeUwDnaseLncapPkRep2 None Peaks prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment LNCaP DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseLncapPkRep1 LNCaP Pk 1 LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001187 1187 GSM736565 Stam UW DS14684 lmax-v1.0 hg19 1 wgEncodeUwDnaseLncapPkRep1 None Peaks prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment LNCaP DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseJurkatPkRep2 Jurkat Pk 2 Jurkat DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000497 497 GSM736492 Stam UW DS10681 lmax-v1.0 hg19 2 wgEncodeUwDnaseJurkatPkRep2 None Peaks T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Jurkat DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseJurkatPkRep1 Jurkat Pk 1 Jurkat DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000497 497 GSM736501 Stam UW DS12659 lmax-v1.0 hg19 1 wgEncodeUwDnaseJurkatPkRep1 None Peaks T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Jurkat DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHvmfPkRep2 HVMF Pk 2 HVMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001176 1176 GSM736491 Stam UW DS13977 lmax-v1.0 hg19 2 wgEncodeUwDnaseHvmfPkRep2 None Peaks villous mesenchymal fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHvmfPkRep1 HVMF Pk 1 HVMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001176 1176 GSM736534 Stam UW DS13981 lmax-v1.0 hg19 1 wgEncodeUwDnaseHvmfPkRep1 None Peaks villous mesenchymal fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmtPkRep2 HSMMtube Pk 2 HSMMtube DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001186 1186 GSM1024788 Stam UW DS15538 lmax-v1.0 hg19 2 wgEncodeUwDnaseHsmmtPkRep2 None Peaks skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HSMMtube DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmtPkRep1 HSMMtube Pk 1 HSMMtube DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001186 1186 GSM736530 Stam UW DS15542 lmax-v1.0 hg19 1 wgEncodeUwDnaseHsmmtPkRep1 None Peaks skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HSMMtube DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmPkRep2 HSMM Pk 2 HSMM DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001185 1185 GSM736553 Stam UW DS14430 lmax-v1.0 hg19 2 wgEncodeUwDnaseHsmmPkRep2 None Peaks skeletal muscle myoblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HSMM DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmPkRep1 HSMM Pk 1 HSMM DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001185 1185 GSM736560 Stam UW DS14426 lmax-v1.0 hg19 1 wgEncodeUwDnaseHsmmPkRep1 None Peaks skeletal muscle myoblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HSMM DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrpePkRep2V2 HRPEpiC Pk 2 HRPEpiC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000517 517 GSM736623 Stam UW DS12568 lmax-v1.0 hg18 2 wgEncodeUwDnaseHrpePkRep2V2 None Peaks retinal pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpiC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrpePkRep1V2 HRPEpiC Pk 1 HRPEpiC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000517 517 GSM736630 Stam UW DS12583 lmax-v1.0 hg18 1 wgEncodeUwDnaseHrpePkRep1V2 None Peaks retinal pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpiC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrgecPkRep2 HRGEC Pk 2 HRGEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001195 1195 GSM736618 Stam UW DS13716 lmax-v1.0 hg19 2 wgEncodeUwDnaseHrgecPkRep2 None Peaks renal glomerular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRGEC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrgecPkRep1 HRGEC Pk 1 HRGEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001195 1195 GSM736499 Stam UW DS13705 lmax-v1.0 hg19 1 wgEncodeUwDnaseHrgecPkRep1 None Peaks renal glomerular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRGEC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrePkRep2V2 HRE Pk 2 HRE DnaseSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000494 494 GSM736548 Stam UW DS10631 lmax-v1.0 hg18 2 wgEncodeUwDnaseHrePkRep2V2 None Peaks renal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrePkRep1V2 HRE Pk 1 HRE DnaseSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000494 494 GSM736527 Stam UW DS10641 lmax-v1.0 hg18 1 wgEncodeUwDnaseHrePkRep1V2 None Peaks renal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrcePkRep2 HRCEpiC Pk 2 HRCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000493 493 GSM736557 Stam UW DS10662 lmax-v1.0 hg18 2 wgEncodeUwDnaseHrcePkRep2 None Peaks renal cortical epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRCEpiC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrcePkRep1 HRCEpiC Pk 1 HRCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000493 493 GSM736549 Stam UW DS10666 lmax-v1.0 hg18 1 wgEncodeUwDnaseHrcePkRep1 None Peaks renal cortical epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRCEpiC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpfPkRep2 HPF Pk 2 HPF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001174 1174 GSM736503 Stam UW DS13380 lmax-v1.0 hg19 2 wgEncodeUwDnaseHpfPkRep2 None Peaks pulmonary fibroblasts isolated from lung tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpfPkRep1 HPF Pk 1 HPF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001174 1174 GSM736574 Stam UW DS13390 lmax-v1.0 hg19 1 wgEncodeUwDnaseHpfPkRep1 None Peaks pulmonary fibroblasts isolated from lung tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpdlfPkRep2 HPdLF Pk 2 HPdLF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001175 1175 GSM736528 Stam UW DS13569 lmax-v1.0 hg19 2 wgEncodeUwDnaseHpdlfPkRep2 None Peaks periodontal ligament fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPdLF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpdlfPkRep1 HPdLF Pk 1 HPdLF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001175 1175 GSM736632 Stam UW DS13573 lmax-v1.0 hg19 1 wgEncodeUwDnaseHpdlfPkRep1 None Peaks periodontal ligament fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPdLF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpafPkRep2 HPAF Pk 2 HPAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001173 1173 GSM736614 Stam UW DS13416 lmax-v1.0 hg19 2 wgEncodeUwDnaseHpafPkRep2 None Peaks pulmonary artery fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpafPkRep1 HPAF Pk 1 HPAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001173 1173 GSM736555 Stam UW DS13411 lmax-v1.0 hg19 1 wgEncodeUwDnaseHpafPkRep1 None Peaks pulmonary artery fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpaecPkRep1 HPAEC Pk 1 HPAEC DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001886 1886 GSM1024763 Stam UW DS12916 lmax-v1.0 hg19 1 wgEncodeUwDnaseHpaecPkRep1 None Peaks pulmonary artery endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAEC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHnpcePkRep2V2 HNPCEpiC Pk 2 HNPCEpiC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000516 516 GSM736550 Stam UW DS12471 lmax-v1.0 hg18 2 wgEncodeUwDnaseHnpcePkRep2V2 None Peaks non-pigment ciliary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HNPCEpiC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHnpcePkRep1 HNPCEpiC Pk 1 HNPCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000516 516 GSM736621 Stam UW DS12467 lmax-v1.0 hg18 1 wgEncodeUwDnaseHnpcePkRep1 None Peaks non-pigment ciliary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HNPCEpiC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecllyPkRep2 HMVECLLy Pk 2 HMVEC-LLy DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001167 1167 GSM736627 Stam UW DS13193 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmvecllyPkRep2 None Peaks lymphatic microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-LLy DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecllyPkRep1 HMVECLLy Pk 1 HMVEC-LLy DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001167 1167 GSM736507 Stam UW DS13185 lmax-v1.0 hg19 1 wgEncodeUwDnaseHmvecllyPkRep1 None Peaks lymphatic microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-LLy DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmveclblPkRep2 HMVECLBl Pk 2 HMVEC-LBl DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001163 1163 GSM736511 Stam UW DS13375 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmveclblPkRep2 None Peaks blood microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-LBl DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmveclblPkRep1 HMVECLBl Pk 1 HMVEC-LBl DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH001163 1163 GSM736542 Stam UW DS13372 lmax-v1.0 hg19 1 wgEncodeUwDnaseHmveclblPkRep1 None Peaks blood microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-LBl DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdneoPkRep2 HMVECdNeo Pk 2 HMVEC-dNeo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001172 1172 GSM736624 Stam UW DS12929 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmvecdneoPkRep2 None Peaks neonatal microvascular endothelial cells (single donor), dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dNeo DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdneoPkRep1 HMVECdNeo Pk 1 HMVEC-dNeo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001172 1172 GSM736611 Stam UW DS12937 lmax-v1.0 hg19 1 wgEncodeUwDnaseHmvecdneoPkRep1 None Peaks neonatal microvascular endothelial cells (single donor), dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dNeo DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyneoPkRep2 HMVECdLyNeo Pk 2 HMVEC-dLy-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001171 1171 GSM736573 Stam UW DS13146 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmvecdlyneoPkRep2 None Peaks neonatal lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dLy-Neo DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyneoPkRep1 HMVECdLyNeo Pk 1 HMVEC-dLy-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001171 1171 GSM736577 Stam UW DS13150 lmax-v1.0 hg19 1 wgEncodeUwDnaseHmvecdlyneoPkRep1 None Peaks neonatal lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dLy-Neo DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyadPkRep2 HMVECdLyAd Pk 2 HMVEC-dLy-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001170 1170 GSM736591 Stam UW DS13256 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmvecdlyadPkRep2 None Peaks adult lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dLy-Ad DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyadPkRep1 HMVECdLyAd Pk 1 HMVEC-dLy-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001170 1170 GSM736599 Stam UW DS13261 lmax-v1.0 hg19 1 wgEncodeUwDnaseHmvecdlyadPkRep1 None Peaks adult lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dLy-Ad DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdblneoPkRep2 HMVECdBlNeo Pk 2 HMVEC-dBl-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001169 1169 GSM736521 Stam UW DS13233 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmvecdblneoPkRep2 None Peaks neonatal blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dBl-Neo DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdblneoPkRep1 HMVECdBlNeo Pk 1 HMVEC-dBl-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001169 1169 GSM736571 Stam UW DS13242 lmax-v1.0 hg19 1 wgEncodeUwDnaseHmvecdblneoPkRep1 None Peaks neonatal blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dBl-Neo DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdbladPkRep2 HMVECdBlAd Pk 2 HMVEC-dBl-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001168 1168 GSM736523 Stam UW DS13329 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmvecdbladPkRep2 None Peaks adult blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dBl-Ad DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdbladPkRep1 HMVECdBlAd Pk 1 HMVEC-dBl-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001168 1168 GSM736609 Stam UW DS13337 lmax-v1.0 hg19 1 wgEncodeUwDnaseHmvecdbladPkRep1 None Peaks adult blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dBl-Ad DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdadPkRep2 HMVECdAd Pk 2 HMVEC-dAd DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-28 wgEncodeEH001889 1889 GSM1024747 Stam UW DS12952 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmvecdadPkRep2 None Peaks adult dermal microvascular endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dAd DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdadPkRep1 HMVECdAd Pk 1 HMVEC-dAd DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-28 wgEncodeEH001889 1889 GSM1024745 Stam UW DS12957 lmax-v1.0 hg19 1 wgEncodeUwDnaseHmvecdadPkRep1 None Peaks adult dermal microvascular endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMVEC-dAd DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmfPkRep2 HMF Pk 2 HMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001166 1166 GSM736541 Stam UW DS13368 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmfPkRep2 None Peaks mammary fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmfPkRep1 HMF Pk 1 HMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001166 1166 GSM736628 Stam UW DS13363 lmax-v1.0 hg19 1 wgEncodeUwDnaseHmfPkRep1 None Peaks mammary fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmecPkRep2 HMEC Pk 2 HMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH000503 503 GSM736552 Stam UW DS13921 lmax-v1.0 hg19 2 wgEncodeUwDnaseHmecPkRep2 None Peaks mammary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmecPkRep1 HMEC Pk 1 HMEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000503 503 GSM736634 Stam UW DS8680 lmax-v1.0 hg18 1 wgEncodeUwDnaseHmecPkRep1 None Peaks mammary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHl60PkRep2 HL60 Pk 2 HL-60 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000489 489 GSM736595 Stam UW DS11733 lmax-v1.0 hg18 2 wgEncodeUwDnaseHl60PkRep2 None Peaks promyelocytic leukemia cells, (PMID: 276884) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHl60PkRep1 HL60 Pk 1 HL-60 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-04-29 2010-01-29 wgEncodeEH000489 489 GSM736626 Stam UW DS11809 lmax-v1.0 hg18 1 wgEncodeUwDnaseHl60PkRep1 None Peaks promyelocytic leukemia cells, (PMID: 276884) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHipePkRep2 HIPEpiC Pk 2 HIPEpiC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001184 1184 GSM736615 Stam UW DS12689 lmax-v1.0 hg19 2 wgEncodeUwDnaseHipePkRep2 None Peaks iris pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HIPEpiC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHipePkRep1 HIPEpiC Pk 1 HIPEpiC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001184 1184 GSM736589 Stam UW DS12684 lmax-v1.0 hg19 1 wgEncodeUwDnaseHipePkRep1 None Peaks iris pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HIPEpiC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHgfPkRep2 HGF Pk 2 HGF DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-10-20 2010-07-20 wgEncodeEH000504 504 GSM736576 Stam UW DS11738 lmax-v1.0 hg18 2 wgEncodeUwDnaseHgfPkRep2 None Peaks gingival fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HGF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHgfPkRep1 HGF Pk 1 HGF DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-20 2010-07-20 wgEncodeEH000504 504 GSM736579 Stam UW DS11752 lmax-v1.0 hg18 1 wgEncodeUwDnaseHgfPkRep1 None Peaks gingival fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HGF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffmycPkRep2 HFFMyc Pk 2 HFF-Myc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001194 1194 GSM736605 Stam UW DS15073 lmax-v1.0 hg19 2 wgEncodeUwDnaseHffmycPkRep2 None Peaks foreskin fibroblast cells expressing canine cMyc DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF-Myc DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffmycPkRep1 HFFMyc Pk 1 HFF-Myc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001194 1194 GSM736524 Stam UW DS15079 lmax-v1.0 hg19 1 wgEncodeUwDnaseHffmycPkRep1 None Peaks foreskin fibroblast cells expressing canine cMyc DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF-Myc DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffPkRep2 HFF Pk 2 HFF DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001193 1193 GSM736572 Stam UW DS15119 lmax-v1.0 hg19 2 wgEncodeUwDnaseHffPkRep2 None Peaks foreskin fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffPkRep1 HFF Pk 1 HFF DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001193 1193 GSM736602 Stam UW DS15115 lmax-v1.0 hg19 1 wgEncodeUwDnaseHffPkRep1 None Peaks foreskin fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHeePkRep2 HEEpiC Pk 2 HEEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000515 515 GSM736532 Stam UW DS12768 lmax-v1.0 hg18 2 wgEncodeUwDnaseHeePkRep2 None Peaks esophageal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpiC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHeePkRep1 HEEpiC Pk 1 HEEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-10 2010-10-09 wgEncodeEH000515 515 GSM736585 Stam UW DS12763 lmax-v1.0 hg18 1 wgEncodeUwDnaseHeePkRep1 None Peaks esophageal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpiC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHct116PkRep2 HCT-116 Pk 2 HCT-116 DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH001162 1162 GSM736493 Stam UW DS13547 lmax-v1.0 hg19 2 wgEncodeUwDnaseHct116PkRep2 None Peaks colorectal carcinoma (PMID: 7214343) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHct116PkRep1 HCT-116 Pk 1 HCT-116 DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH001162 1162 GSM736600 Stam UW DS13551 lmax-v1.0 hg19 1 wgEncodeUwDnaseHct116PkRep1 None Peaks colorectal carcinoma (PMID: 7214343) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcpePkRep2 HCPEpiC Pk 2 HCPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000514 514 GSM736597 Stam UW DS12457 lmax-v1.0 hg18 2 wgEncodeUwDnaseHcpePkRep2 None Peaks choroid plexus epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpiC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcpePkRep1 HCPEpiC Pk 1 HCPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000514 514 GSM736569 Stam UW DS12447 lmax-v1.0 hg18 1 wgEncodeUwDnaseHcpePkRep1 None Peaks choroid plexus epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpiC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHconfPkRep2 HConF Pk 2 HConF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001165 1165 GSM736515 Stam UW DS11637 lmax-v1.0 hg19 2 wgEncodeUwDnaseHconfPkRep2 None Peaks conjunctival fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HConF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHconfPkRep1 HConF Pk 1 HConF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001165 1165 GSM736547 Stam UW DS11642 lmax-v1.0 hg19 1 wgEncodeUwDnaseHconfPkRep1 None Peaks conjunctival fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HConF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcmPkRep2 HCM Pk 2 HCM DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-09 2010-10-08 wgEncodeEH000519 519 GSM736504 Stam UW DS12589 lmax-v1.0 hg18 2 wgEncodeUwDnaseHcmPkRep2 None Peaks cardiac myocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcmPkRep1 HCM Pk 1 HCM DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-09 2010-10-08 wgEncodeEH000519 519 GSM736516 Stam UW DS12599 lmax-v1.0 hg18 1 wgEncodeUwDnaseHcmPkRep1 None Peaks cardiac myocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfaaPkRep2 HCFaa Pk 2 HCFaa DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001164 1164 GSM736601 Stam UW DS13484 lmax-v1.0 hg19 2 wgEncodeUwDnaseHcfaaPkRep2 None Peaks cardiac fibroblasts- adult atrial DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCFaa DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfaaPkRep1 HCFaa Pk 1 HCFaa DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001164 1164 GSM736494 Stam UW DS13480 lmax-v1.0 hg19 1 wgEncodeUwDnaseHcfaaPkRep1 None Peaks cardiac fibroblasts- adult atrial DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCFaa DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfPkRep2 HCF Pk 2 HCF DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000513 513 GSM736540 Stam UW DS12491 lmax-v1.0 hg18 2 wgEncodeUwDnaseHcfPkRep2 None Peaks cardiac fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfPkRep1 HCF Pk 1 HCF DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-09 2010-10-08 wgEncodeEH000513 513 GSM736568 Stam UW DS12501 lmax-v1.0 hg18 1 wgEncodeUwDnaseHcfPkRep1 None Peaks cardiac fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbvsmcPkRep2 HBVSCM Pk 2 HBVSMC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002580 2580 GSM1024769 Stam UW DS14845 lmax-v1.0 hg19 2 wgEncodeUwDnaseHbvsmcPkRep2 None Peaks brain vascular smooth muscle cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBVSCM DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbvsmcPkRep1 HBVSCM Pk 1 HBVSMC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002580 2580 GSM1024768 Stam UW DS14860 lmax-v1.0 hg19 1 wgEncodeUwDnaseHbvsmcPkRep1 None Peaks brain vascular smooth muscle cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBVSCM DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbvpPkRep1 HBVP Pk 1 HBVP DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002579 2579 GSM1024750 Stam UW DS14834 lmax-v1.0 hg19 1 wgEncodeUwDnaseHbvpPkRep1 None Peaks brain vascular pericytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBVP DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbmecPkRep2 HBMEC Pk 2 HBMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001178 1178 GSM736554 Stam UW DS13806 lmax-v1.0 hg19 2 wgEncodeUwDnaseHbmecPkRep2 None Peaks brain microvascular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbmecPkRep1 HBMEC Pk 1 HBMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001178 1178 GSM736509 Stam UW DS13817 lmax-v1.0 hg19 1 wgEncodeUwDnaseHbmecPkRep1 None Peaks brain microvascular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaePkRep2 HAEpiC Pk 2 HAEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-07 wgEncodeEH000512 512 GSM736606 Stam UW DS12673 lmax-v1.0 hg18 2 wgEncodeUwDnaseHaePkRep2 None Peaks amniotic epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAEpiC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaePkRep1 HAEpiC Pk 1 HAEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-07 wgEncodeEH000512 512 GSM736631 Stam UW DS12663 lmax-v1.0 hg18 1 wgEncodeUwDnaseHaePkRep1 None Peaks amniotic epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAEpiC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHacPkRep2 HAc Pk 2 HAc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001192 1192 GSM736538 Stam UW DS14770 lmax-v1.0 hg19 2 wgEncodeUwDnaseHacPkRep2 None Peaks astrocytes-cerebellar DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHacPkRep1 HAc Pk 1 HAc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001192 1192 GSM736586 Stam UW DS14765 lmax-v1.0 hg19 1 wgEncodeUwDnaseHacPkRep1 None Peaks astrocytes-cerebellar DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaspPkRep2 HAsp Pk 2 HA-sp DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001183 1183 GSM736625 Stam UW DS14794 lmax-v1.0 hg19 2 wgEncodeUwDnaseHaspPkRep2 None Peaks astrocytes spinal cord DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaspPkRep1 HAsp Pk 1 HA-sp DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001183 1183 GSM736537 Stam UW DS14790 lmax-v1.0 hg19 1 wgEncodeUwDnaseHaspPkRep1 None Peaks astrocytes spinal cord DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHahPkRep2 HAh Pk 2 HA-h DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001191 1191 GSM736535 Stam UW DS15202 lmax-v1.0 hg19 2 wgEncodeUwDnaseHahPkRep2 None Peaks astrocytes-hippocampal DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-h DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHahPkRep1 HAh Pk 1 HA-h DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001191 1191 GSM736594 Stam UW DS15192 lmax-v1.0 hg19 1 wgEncodeUwDnaseHahPkRep1 None Peaks astrocytes-hippocampal DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-h DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esPkRep2 H7h Pk 2 H7-hESC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000511 511 GSM736610 Stam UW DS13133 lmax-v1.0 hg19 2 wgEncodeUwDnaseH7esPkRep2 None Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa5dPkRep2 H7h difPA5 Pk 2 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002578 2578 GSM1024755 Stam UW DS11953 lmax-v1.0 hg19 2 wgEncodeUwDnaseH7esDiffa5dPkRep2 diffProtA_5d Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC diffProtA 5 d DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa14dPkRep2 H7h difPA14 Pk 2 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002576 2576 GSM1024758 Stam UW DS11814 lmax-v1.0 hg19 2 wgEncodeUwDnaseH7esDiffa14dPkRep2 diffProtA_14d Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC diffProtA 14 d DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esPkRep1V2 H7h Pk 1 H7-hESC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000511 511 GSM736638 Stam UW DS11909 lmax-v1.0 hg18 1 wgEncodeUwDnaseH7esPkRep1V2 None Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa9dPkRep1 H7h difPA9 Pk 1 H7-hESC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003019 3019 GSM1024778 Stam UW DS15809 lmax-v1.0 hg19 1 wgEncodeUwDnaseH7esDiffa9dPkRep1 diffProtA_9d Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC diffProtA 9 d DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa5dPkRep1 H7h difPA5 Pk 1 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002578 2578 GSM1024754 Stam UW DS15665 lmax-v1.0 hg19 1 wgEncodeUwDnaseH7esDiffa5dPkRep1 diffProtA_5d Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC diffProtA 5 d DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa2dPkRep1 H7h difPA2 Pk 1 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002577 2577 GSM1024774 Stam UW DS14732 lmax-v1.0 hg19 1 wgEncodeUwDnaseH7esDiffa2dPkRep1 diffProtA_2d Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC diffProtA 2 d DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa14dPkRep1 H7h difPA14 Pk 1 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002576 2576 GSM1024759 Stam UW DS12147 lmax-v1.0 hg19 1 wgEncodeUwDnaseH7esDiffa14dPkRep1 diffProtA_14d Peaks undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC diffProtA 14 d DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12865PkRep2 GM12865 Pk 2 GM12865 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000520 520 GSM736561 Stam UW DS12442 lmax-v1.0 hg18 2 wgEncodeUwDnaseGm12865PkRep2 None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12865PkRep1 GM12865 Pk 1 GM12865 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000520 520 GSM736512 Stam UW DS12436 lmax-v1.0 hg18 1 wgEncodeUwDnaseGm12865PkRep1 None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12864PkRep1 GM12864 Pk 1 GM12864 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001182 1182 GSM736525 Stam UW DS12431 lmax-v1.0 hg19 1 wgEncodeUwDnaseGm12864PkRep1 None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm06990PkRep2 GM06990 Pk 2 GM06990 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-01 2010-04-01 wgEncodeEH000481 481 GSM736635 Stam UW DS7784 lmax-v1.0 hg18 2 wgEncodeUwDnaseGm06990PkRep2 None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm06990PkRep1 GM06990 Pk 1 GM06990 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2008-11-19 2009-08-18 wgEncodeEH000481 481 GSM736558 Stam UW DS7748 lmax-v1.0 hg18 1 wgEncodeUwDnaseGm06990PkRep1 None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04504PkRep2 GM04504 Pk 2 GM04504 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002575 2575 GSM1024776 Stam UW DS18975 lmax-v1.0 hg19 2 wgEncodeUwDnaseGm04504PkRep2 None Peaks adult twin pair fibroblasts, monozygotic twin of GM04503, 13% of the cells examined show random chromosome loss DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM04504 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04504PkRep1 GM04504 Pk 1 GM04504 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002575 2575 GSM1024775 Stam UW DS18973 lmax-v1.0 hg19 1 wgEncodeUwDnaseGm04504PkRep1 None Peaks adult twin pair fibroblasts, monozygotic twin of GM04503, 13% of the cells examined show random chromosome loss DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM04504 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04503PkRep2 GM04503 Pk 2 GM04503 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002574 2574 GSM1024780 Stam UW DS18640 lmax-v1.0 hg19 2 wgEncodeUwDnaseGm04503PkRep2 None Peaks adult twin pair fibroblasts, monozygotic twin of GM04504 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM04503 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04503PkRep1 GM04503 Pk 1 GM04503 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002574 2574 GSM1024777 Stam UW DS18637 lmax-v1.0 hg19 1 wgEncodeUwDnaseGm04503PkRep1 None Peaks adult twin pair fibroblasts, monozygotic twin of GM04504 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM04503 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCmkPkRep1 CMK Pk 1 CMK DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-07 wgEncodeEH000510 510 GSM736607 Stam UW DS12393 lmax-v1.0 hg18 1 wgEncodeUwDnaseCmkPkRep1 None Peaks acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CMK DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd34mobilizedPkRep1 CD34+ Mob Pk 1 CD34+_Mobilized DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001885 1885 GSM1024770 Stam UW DS16814 lmax-v1.0 hg19 1 wgEncodeUwDnaseCd34mobilizedPkRep1 None Peaks hematopoietic progenitor cells- mobilized, from donor RO01679. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD34+ Mobilized DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd4naivewb78495824PkRep1 CD4 NveWb824 Pk 1 CD4+_Naive_Wb78495824 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-09 2013-04-09 wgEncodeEH003028 3028 GSM1024782 Stam UW DS15241 lmax-v1.0 hg19 1 wgEncodeUwDnaseCd4naivewb78495824PkRep1 None Peaks CD4+ naive sorted cells, donor is Causasian, female 35 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD4+ Naive Wb78495824 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd4naivewb11970640PkRep1 CD4 NveWb640 Pk 1 CD4+_Naive_Wb11970640 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-09 2013-04-09 wgEncodeEH003027 3027 GSM1024789 Stam UW DS14108 lmax-v1.0 hg19 1 wgEncodeUwDnaseCd4naivewb11970640PkRep1 None Peaks CD4+ naive sorted cells, donor is Caucasian, male 26 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD4+ Naive Wb11970640 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCaco2PkRep2 Caco2 Pk 2 Caco-2 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-01 2010-03-30 wgEncodeEH000486 486 GSM736587 Stam UW DS8416 lmax-v1.0 hg18 2 wgEncodeUwDnaseCaco2PkRep2 None Peaks colorectal adenocarcinoma. (PMID: 1939345) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseCaco2PkRep1 Caco2 Pk 1 Caco-2 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-04-24 2010-01-24 wgEncodeEH000486 486 GSM736500 Stam UW DS8235 lmax-v1.0 hg18 1 wgEncodeUwDnaseCaco2PkRep1 None Peaks colorectal adenocarcinoma. (PMID: 1939345) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMscPkRep2 Bon MarMSC Pk 2 bone_marrow_MSC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003031 3031 GSM1024748 Stam UW DS20518 lmax-v1.0 hg19 2 wgEncodeUwDnaseMscPkRep2 None Peaks These cells are primary fibroblastoid cells obtained from human bone marrow of normal donors as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Bone Marrow MSC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMscPkRep1 Bon MarMSC Pk 1 bone_marrow_MSC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003031 3031 GSM1024757 Stam UW DS20514 lmax-v1.0 hg19 1 wgEncodeUwDnaseMscPkRep1 None Peaks These cells are primary fibroblastoid cells obtained from human bone marrow of normal donors as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Bone Marrow MSC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHs5PkRep1 Bon MarHS5 Pk 1 bone_marrow_HS5 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003030 3030 GSM1024746 Stam UW DS16597 lmax-v1.0 hg19 1 wgEncodeUwDnaseHs5PkRep1 None Peaks HS5 Human Marrow Stromal Cells are fibroblastoid cells immortalized with HPV16 E6/E7 genes as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005, insert DNA is LXSN-16 E6E7 packaged in PA31. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Bone Marrow HS5 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHs27aPkRep1 Bon MarHS27a Pk 1 bone_marrow_HS27a DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003029 3029 GSM1024785 Stam UW DS16602 lmax-v1.0 hg19 1 wgEncodeUwDnaseHs27aPkRep1 None Peaks HS27a Human Marrow Stromal Cells are fibroblastoid cells immortalized with HPV16 E6/E7 genes as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005, insert DNA is LXSN-16 E6E7 packaged in PA31. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Bone Marrow HS27a DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseBjPkRep2 BJ Pk 2 BJ DnaseSeq ENCODE June 2010 Freeze 2010-06-06 2010-06-06 2011-03-06 wgEncodeEH000487 487 GSM736596 Stam UW DS10018 lmax-v1.0 hg18 2 wgEncodeUwDnaseBjPkRep2 None Peaks skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseBjPkRep1 BJ Pk 1 BJ DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-06-19 2011-03-19 wgEncodeEH000487 487 GSM736518 Stam UW DS10081 lmax-v1.0 hg18 1 wgEncodeUwDnaseBjPkRep1 None Peaks skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseBe2cPkRep2 BE2 C Pk 2 BE2_C DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001181 1181 GSM736622 Stam UW DS14635 lmax-v1.0 hg19 2 wgEncodeUwDnaseBe2cPkRep2 None Peaks neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2 C DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseBe2cPkRep1 BE2 C Pk 1 BE2_C DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001181 1181 GSM736508 Stam UW DS14625 lmax-v1.0 hg19 1 wgEncodeUwDnaseBe2cPkRep1 None Peaks neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2 C DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAoafPkRep2 AoAF Pk 2 AoAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH001161 1161 GSM736505 Stam UW DS13513 lmax-v1.0 hg19 2 wgEncodeUwDnaseAoafPkRep2 None Peaks aortic adventitial fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAoafPkRep1 AoAF Pk 1 AoAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001161 1161 GSM736583 Stam UW DS13523 lmax-v1.0 hg19 1 wgEncodeUwDnaseAoafPkRep1 None Peaks aortic adventitial fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg10803PkRep2 AG10803 Pk 2 AG10803 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-08 wgEncodeEH000509 509 GSM736633 Stam UW DS12374 lmax-v1.0 hg18 2 wgEncodeUwDnaseAg10803PkRep2 None Peaks abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg10803PkRep1 AG10803 Pk 1 AG10803 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-08 wgEncodeEH000509 509 GSM736598 Stam UW DS12384 lmax-v1.0 hg18 1 wgEncodeUwDnaseAg10803PkRep1 None Peaks abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09319PkRep2 AG09319 Pk 2 AG09319 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000508 508 GSM736619 Stam UW DS12286 lmax-v1.0 hg18 2 wgEncodeUwDnaseAg09319PkRep2 None Peaks gum tissue fibroblasts from apparently heathly 24 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09319PkRep1V2 AG09319 Pk 1 AG09319 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000508 508 GSM736531 Stam UW DS12291 lmax-v1.0 hg18 1 wgEncodeUwDnaseAg09319PkRep1V2 None Peaks gum tissue fibroblasts from apparently heathly 24 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09309PkRep2 AG09309 Pk 2 AG09309 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000507 507 GSM736616 Stam UW DS12357 lmax-v1.0 hg18 2 wgEncodeUwDnaseAg09309PkRep2 None Peaks adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09309PkRep1 AG09309 Pk 1 AG09309 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000507 507 GSM736551 Stam UW DS12352 lmax-v1.0 hg18 1 wgEncodeUwDnaseAg09309PkRep1 None Peaks adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04450PkRep2 AG04450 Pk 2 AG04450 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000506 506 GSM736563 Stam UW DS12255 lmax-v1.0 hg18 2 wgEncodeUwDnaseAg04450PkRep2 None Peaks fetal lung fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04450PkRep1 AG04450 Pk 1 AG04450 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000506 506 GSM736514 Stam UW DS12270 lmax-v1.0 hg18 1 wgEncodeUwDnaseAg04450PkRep1 None Peaks fetal lung fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04449PkRep2 AG04449 Pk 2 AG04449 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000505 505 GSM736590 Stam UW DS12329 lmax-v1.0 hg18 2 wgEncodeUwDnaseAg04449PkRep2 None Peaks fetal buttock/thigh fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04449PkRep1 AG04449 Pk 1 AG04449 DnaseSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-06 2010-10-05 wgEncodeEH000505 505 GSM736562 Stam UW DS12319 lmax-v1.0 hg18 1 wgEncodeUwDnaseAg04449PkRep1 None Peaks fetal buttock/thigh fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMonocd14ro1746PkRep2 CD14+ Mono Pk 2 Monocytes-CD14+_RO01746 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001196 1196 GSM1024791 Stam UW DS18065 lmax-v1.0 hg19 2 wgEncodeUwDnaseMonocd14ro1746PkRep2 None Peaks Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Monocytes CD14+ RO01746 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7PkRep2 MCF7 Pk 2 MCF-7 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000502 502 GSM736588 Stam UW DS12619 lmax-v1.0 hg18 2 wgEncodeUwDnaseMcf7PkRep2 None Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Estctrl0hPkRep2 MCF7 EstCtrl Pk 2 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003018 3018 GSM1024767 Stam UW DS18021 lmax-v1.0 hg19 2 wgEncodeUwDnaseMcf7Estctrl0hPkRep2 Estradiol_ctrl_0hr Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam) Regions of enriched signal in experiment MCF-7 Estradiol Control 0 hr DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Est100nm1hPkRep2 MCF7 Est1h Pk 2 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003017 3017 GSM1024783 Stam UW DS18025 lmax-v1.0 hg19 2 wgEncodeUwDnaseMcf7Est100nm1hPkRep2 Estradiol_100nM_1hr Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 1 h with 100 nM Estradiol, hormone treatment (Stam) Regions of enriched signal in experiment MCF-7 Estradiol 100 nM 1 hr DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7PkRep1 MCF7 Pk 1 MCF-7 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-09-29 2010-06-29 wgEncodeEH000502 502 GSM736581 Stam UW DS9445 lmax-v1.0 hg18 1 wgEncodeUwDnaseMcf7PkRep1 None Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Estctrl0hPkRep1 MCF7 EstCtrl Pk 1 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003018 3018 GSM1024764 Stam UW DS18267 lmax-v1.0 hg19 1 wgEncodeUwDnaseMcf7Estctrl0hPkRep1 Estradiol_ctrl_0hr Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam) Regions of enriched signal in experiment MCF-7 Estradiol Control 0 hr DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Est100nm1hPkRep1 MCF7 Est1h Pk 1 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003017 3017 GSM1024784 Stam UW DS18271 lmax-v1.0 hg19 1 wgEncodeUwDnaseMcf7Est100nm1hPkRep1 Estradiol_100nM_1hr Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 1 h with 100 nM Estradiol, hormone treatment (Stam) Regions of enriched signal in experiment MCF-7 Estradiol 100 nM 1 hr DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2PkRep2 LHCNM2 Pk 2 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003005 3005 GSM1024786 Stam UW DS20485 lmax-v1.0 hg19 2 wgEncodeUwDnaseLhcnm2PkRep2 None Peaks skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment LHCN-M2 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2Diff4dPkRep2 LHCNM2 dif4d Pk 2 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003006 3006 GSM1024772 Stam UW DS20534 lmax-v1.0 hg19 2 wgEncodeUwDnaseLhcnm2Diff4dPkRep2 DIFF_4d Peaks skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) Regions of enriched signal in experiment LHCN-M2 DIFF 4 d DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2PkRep1 LHCNM2 Pk 1 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003005 3005 GSM1024787 Stam UW DS20548 lmax-v1.0 hg19 1 wgEncodeUwDnaseLhcnm2PkRep1 None Peaks skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment LHCN-M2 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2Diff4dPkRep1 LHCNM2 dif4d Pk 1 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003006 3006 GSM1024771 Stam UW DS20647 lmax-v1.0 hg19 1 wgEncodeUwDnaseLhcnm2Diff4dPkRep1 DIFF_4d Peaks skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) Regions of enriched signal in experiment LHCN-M2 DIFF 4 d DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHuvecPkRep2 HUVEC Pk 2 HUVEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000488 488 GSM736533 Stam UW DS13475 lmax-v1.0 hg19 2 wgEncodeUwDnaseHuvecPkRep2 None Peaks umbilical vein endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHuvecPkRep1V2 HUVEC Pk 1 HUVEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH000488 488 GSM736575 Stam UW DS10060 lmax-v1.0 hg18 1 wgEncodeUwDnaseHuvecPkRep1V2 None Peaks umbilical vein endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHepg2PkRep2 HepG2 Pk 2 HepG2 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-01 2010-04-01 wgEncodeEH000482 482 GSM736639 Stam UW DS7768 lmax-v1.0 hg18 2 wgEncodeUwDnaseHepg2PkRep2 None Peaks hepatocellular carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHepg2PkRep1 HepG2 Pk 1 HepG2 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2008-11-19 2009-08-18 wgEncodeEH000482 482 GSM736637 Stam UW DS7764 lmax-v1.0 hg18 1 wgEncodeUwDnaseHepg2PkRep1 None Peaks hepatocellular carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHelas3PkRep2 HeLaS3 Pk 2 HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-02 2010-04-01 wgEncodeEH000495 495 GSM736510 Stam UW DS8200 lmax-v1.0 hg18 2 wgEncodeUwDnaseHelas3PkRep2 None Peaks cervical carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHelas3PkRep1 HeLaS3 Pk 1 HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-02 2010-04-01 wgEncodeEH000495 495 GSM736564 Stam UW DS10011 lmax-v1.0 hg18 1 wgEncodeUwDnaseHelas3PkRep1 None Peaks cervical carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd20ro01778PkRep2 CD20+ Pk 2 CD20+_RO01778 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001884 1884 GSM1024766 Stam UW DS17541 lmax-v1.0 hg19 2 wgEncodeUwDnaseCd20ro01778PkRep2 None Peaks B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment B cells CD20+ RO01778 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd20ro01778PkRep1 CD20+ Pk 1 CD20+_RO01778 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-13 wgEncodeEH001884 1884 GSM1024765 Stam UW DS18208 lmax-v1.0 hg19 1 wgEncodeUwDnaseCd20ro01778PkRep1 None Peaks B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment B cells CD20+ RO01778 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseA549PkRep2 A549 Pk 2 A549 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-04 wgEncodeEH001180 1180 GSM736506 Stam UW DS14285 lmax-v1.0 hg19 2 wgEncodeUwDnaseA549PkRep2 None Peaks epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseA549PkRep1 A549 Pk 1 A549 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-04 2011-10-04 wgEncodeEH001180 1180 GSM736580 Stam UW DS14289 lmax-v1.0 hg19 1 wgEncodeUwDnaseA549PkRep1 None Peaks epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseK562PkRep2 K562 Pk 2 K562 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-02 2010-04-01 wgEncodeEH000484 484 GSM736566 Stam UW DS9764 lmax-v1.0 hg18 2 wgEncodeUwDnaseK562PkRep2 None Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseK562PkRep1 K562 Pk 1 K562 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2008-12-09 2009-09-09 wgEncodeEH000484 484 GSM736629 Stam UW DS9767 lmax-v1.0 hg18 1 wgEncodeUwDnaseK562PkRep1 None Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH1hescPkRep1 H1hESC Pk 1 H1-hESC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-18 wgEncodeEH000496 496 GSM736582 Stam UW DS10167 lmax-v1.0 hg18 1 wgEncodeUwDnaseH1hescPkRep1 None Peaks embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H1-hESC DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12878PkRep2 GM12878 Pk 2 GM12878 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-01 2010-04-01 wgEncodeEH000492 492 GSM736620 Stam UW DS9432 lmax-v1.0 hg18 2 wgEncodeUwDnaseGm12878PkRep2 None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 DNaseI HS Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12878PkRep1 GM12878 Pk 1 GM12878 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000492 492 GSM736496 Stam UW DS10671 lmax-v1.0 hg18 1 wgEncodeUwDnaseGm12878PkRep1 None Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 DNaseI HS Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseViewHot Hot Spots DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington Regulation 
wgEncodeUwDnaseWi38OhtamHotspotsRep2 WI-38 OHTM Ht 2 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001198 1198 GSM736526 Stam UW DS14328 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseWi38OhtamHotspotsRep2 4OHTAM_20nM_72hr Hotspots embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 4-OHTAM 20 nM 72 hr DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseWi38HotspotsRep2 WI-38 Ht 2 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001197 1197 GSM736526 Stam UW DS14320 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseWi38HotspotsRep2 None Hotspots embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseWi38OhtamHotspotsRep1 WI-38 OHTM Ht 1 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001198 1198 GSM736613 Stam UW DS14323 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseWi38OhtamHotspotsRep1 4OHTAM_20nM_72hr Hotspots embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 4-OHTAM 20 nM 72 hr DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseWi38HotspotsRep1 WI-38 Ht 1 WI-38 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001197 1197 GSM736613 Stam UW DS14315 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseWi38HotspotsRep1 None Hotspots embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseWerirb1HotspotsRep2 WERI-Rb-1 Ht 2 WERI-Rb-1 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001190 1190 GSM736636 Stam UW DS13670 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseWerirb1HotspotsRep2 None Hotspots retinoblastoma (PMID: 844036) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseWerirb1HotspotsRep1 WERI-Rb-1 Ht 1 WERI-Rb-1 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001190 1190 GSM736495 Stam UW DS13681 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseWerirb1HotspotsRep1 None Hotspots retinoblastoma (PMID: 844036) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTregwb83319432HotspotsRep1 Treg Wb432 Ht 1 Treg_Wb83319432 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003026 3026 GSM1024741 Stam UW DS17589 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseTregwb83319432HotspotsRep1 None Hotspots T regulatory cells in vivo isolation, donor is Caucasian, male 28 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Treg Wb83319432 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTregwb78495824HotspotsRep1 Treg Wb824 Ht 1 Treg_Wb78495824 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003025 3025 GSM1024744 Stam UW DS14702 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseTregwb78495824HotspotsRep1 None Hotspots T regulatory cells in vivo isolation DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Treg Wb78495824 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh17HotspotsRep1 Th17 Ht 1 Th17 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003020 3020 GSM1024790 Stam UW DS11039 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseTh17HotspotsRep1 None Hotspots T helper cells expressing IL-17, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th17 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2wb54553204HotspotsRep1 Th2 Wb204 Ht 1 Th2_Wb54553204 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003024 3024 GSM1024739 Stam UW DS17597 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseTh2wb54553204HotspotsRep1 None Hotspots Th2 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th2 Wb54553204 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2wb33676984HotspotsRep1 Th2 Wb984 Ht 1 Th2_Wb33676984 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003023 3023 GSM1024740 Stam UW DS18057 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseTh2wb33676984HotspotsRep1 None Hotspots Th2 cells in vivo isolation, donor is Asian, female 26 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th2 Wb33676984 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2HotspotsRep2 Th2 Ht 2 Th2 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH000491 491 GSM1024792 Stam UW DS17603 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseTh2HotspotsRep2 None Hotspots primary Th2 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th2 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh2HotspotsRep1 Th2 Ht 1 Th2 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-04-29 2010-01-29 wgEncodeEH000491 491 GSM736502 Stam UW DS7842 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseTh2HotspotsRep1 None Hotspots primary Th2 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th2 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1wb54553204HotspotsRep2 Th1 Wb204 Ht 2 Th1_Wb54553204 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003022 3022 GSM1024752 Stam UW DS17592 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseTh1wb54553204HotspotsRep2 None Hotspots Th1 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th1 Wb54553204 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1wb54553204HotspotsRep1 Th1 Wb204 Ht 1 Th1_Wb54553204 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003022 3022 GSM1024753 Stam UW DS17593 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseTh1wb54553204HotspotsRep1 None Hotspots Th1 cells in vivo isolation, donor is Caucasian, male 33 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th1 Wb54553204 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1wb33676984HotspotsRep1 Th1 Wb984 Ht 1 Th1_Wb33676984 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003021 3021 GSM1024749 Stam UW DS18015 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseTh1wb33676984HotspotsRep1 None Hotspots Th1 cells in vivo isolation DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th1 Wb33676984 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1HotspotsRep2 Th1 Ht 2 Th1 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH000483 483 GSM1024760 Stam UW DS18018 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseTh1HotspotsRep2 None Hotspots primary Th1 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th1 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseTh1HotspotsRep1 Th1 Ht 1 Th1 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2008-11-20 2009-08-20 wgEncodeEH000483 483 GSM736592 Stam UW DS7840 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseTh1HotspotsRep1 None Hotspots primary Th1 T cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Th1 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseT47dHotspotsRep2 T-47D Ht 2 T-47D DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002583 2583 GSM1024761 Stam UW DS19790 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseT47dHotspotsRep2 None Hotspots epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm T-47D DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseT47dHotspotsRep1 T-47D Ht 1 T-47D DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002583 2583 GSM1024762 Stam UW DS19794 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseT47dHotspotsRep1 None Hotspots epithelial cell line derived from a mammary ductal carcinoma. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm T-47D DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSkmcHotspotsRep2 SkMC Ht 2 SKMC DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-10-27 2010-07-26 wgEncodeEH000490 490 GSM736497 Stam UW DS11939 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseSkmcHotspotsRep2 None Hotspots skeletal muscle cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SkMC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSkmcHotspotsRep1 SkMC Ht 1 SKMC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-04-29 2010-01-29 wgEncodeEH000490 490 GSM736593 Stam UW DS11949 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseSkmcHotspotsRep1 None Hotspots skeletal muscle cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SkMC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknshraHotspotsRep2 SKNSHRA Ht 2 SK-N-SH_RA DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-17 2010-04-17 wgEncodeEH000485 485 GSM736578 Stam UW DS8476 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseSknshraHotspotsRep2 None Hotspots neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH RA DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknshraHotspotsRep1 SKNSHRA Ht 1 SK-N-SH_RA DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-04-17 2010-01-17 wgEncodeEH000485 485 GSM736559 Stam UW DS8482 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseSknshraHotspotsRep1 None Hotspots neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH RA DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknmcHotspotsRep2 SKNMC Ht 2 SK-N-MC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001189 1189 GSM736570 Stam UW DS14413 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseSknmcHotspotsRep2 None Hotspots neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-MC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSknmcHotspotsRep1 SKNMC Ht 1 SK-N-MC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001189 1189 GSM736522 Stam UW DS14408 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseSknmcHotspotsRep1 None Hotspots neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-MC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseSaecHotspotsRep2 SAEC Ht 2 SAEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000501 501 GSM736617 Stam UW DS10514 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseSaecHotspotsRep2 None Hotspots small airway epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseSaecHotspotsRep1 SAEC Ht 1 SAEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000501 501 GSM736608 Stam UW DS10518 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseSaecHotspotsRep1 None Hotspots small airway epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseRptecHotspotsRep2 RPTEC Ht 2 RPTEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001188 1188 GSM736539 Stam UW DS14065 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseRptecHotspotsRep2 None Hotspots renal proximal tubule epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseRptecHotspotsRep1 RPTEC Ht 1 RPTEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001188 1188 GSM736543 Stam UW DS14061 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseRptecHotspotsRep1 None Hotspots renal proximal tubule epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseRpmi7951HotspotsRep2 RPMI7951 Ht 2 RPMI-7951 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-22 2012-12-22 wgEncodeEH003007 3007 GSM1024793 Stam UW DS20904 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseRpmi7951HotspotsRep2 None Hotspots Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPMI-7951 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseRpmi7951HotspotsRep1 RPMI7951 Ht 1 RPMI-7951 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-22 2012-12-22 wgEncodeEH003007 3007 GSM1024779 Stam UW DS20909 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseRpmi7951HotspotsRep1 None Hotspots Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPMI-7951 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnasePrecHotspotsRep2 PrEC Ht 2 PrEC DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001888 1888 GSM1024743 Stam UW DS12088 Hotspot-v5.2 hg19 2 wgEncodeUwDnasePrecHotspotsRep2 None Hotspots prostate epithelial cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm PrEC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnasePrecHotspotsRep1 PrEC Ht 1 PrEC DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001888 1888 GSM1024742 Stam UW DS12098 Hotspot-v5.2 hg19 1 wgEncodeUwDnasePrecHotspotsRep1 None Hotspots prostate epithelial cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm PrEC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnasePanc1HotspotsRep2 PANC1 Ht 2 PANC-1 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000500 500 GSM736519 Stam UW DS9873 Hotspot-v5.1 hg18 2 wgEncodeUwDnasePanc1HotspotsRep2 None Hotspots pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm PANC-1 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnasePanc1HotspotsRep1 PANC1 Ht 1 PANC-1 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-09-19 2010-06-19 wgEncodeEH000500 500 GSM736517 Stam UW DS9955 Hotspot-v5.1 hg18 1 wgEncodeUwDnasePanc1HotspotsRep1 None Hotspots pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm PANC-1 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNt2d1HotspotsRep2 NT2D1 Ht 2 NT2-D1 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001887 1887 GSM1024795 Stam UW DS14564 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseNt2d1HotspotsRep2 None Hotspots malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NT2-D1 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNt2d1HotspotsRep1 NT2D1 Ht 1 NT2-D1 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001887 1887 GSM1024751 Stam UW DS14575 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseNt2d1HotspotsRep1 None Hotspots malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NT2-D1 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhlfHotspotsRep2 NHLF Ht 2 NHLF DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000521 521 GSM736536 Stam UW DS12834 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseNhlfHotspotsRep2 None Hotspots lung fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHLF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhlfHotspotsRep1 NHLF Ht 1 NHLF DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000521 521 GSM736612 Stam UW DS12829 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseNhlfHotspotsRep1 None Hotspots lung fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHLF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhekHotspotsRep2 NHEK Ht 2 NHEK DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000499 499 GSM736556 Stam UW DS11476 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseNhekHotspotsRep2 None Hotspots epidermal keratinocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhekHotspotsRep1 NHEK Ht 1 NHEK DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-09-19 2010-06-19 wgEncodeEH000499 499 GSM736545 Stam UW DS11474 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseNhekHotspotsRep1 None Hotspots epidermal keratinocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfneoHotspotsRep2 NHDFneo Ht 2 NHDF-neo DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-09 2010-10-08 wgEncodeEH000518 518 GSM736546 Stam UW DS11918 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseNhdfneoHotspotsRep2 None Hotspots neonatal dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfneoHotspotsRep1 NHDFneo Ht 1 NHDF-neo DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-08 2010-10-08 wgEncodeEH000518 518 GSM736498 Stam UW DS11923 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseNhdfneoHotspotsRep1 None Hotspots neonatal dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfadHotspotsRep2 NHDFAd Ht 2 NHDF-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001177 1177 GSM736520 Stam UW DS12855 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseNhdfadHotspotsRep2 None Hotspots adult dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-Ad DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhdfadHotspotsRep1 NHDFAd Ht 1 NHDF-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001177 1177 GSM736567 Stam UW DS12863 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseNhdfadHotspotsRep1 None Hotspots adult dermal fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-Ad DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhberaHotspotsRep2 NHBE RA Ht 2 NHBE_RA DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002582 2582 GSM1024756 Stam UW DS11959 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseNhberaHotspotsRep2 None Hotspots bronchial epithelial cells with retinoic acid DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHBE RA DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhberaHotspotsRep1 NHBE RA Ht 1 NHBE_RA DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002582 2582 GSM1024781 Stam UW DS11969 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseNhberaHotspotsRep1 None Hotspots bronchial epithelial cells with retinoic acid DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHBE RA DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhaHotspotsRep2 NH-A Ht 2 NH-A DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001179 1179 GSM736584 Stam UW DS12805 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseNhaHotspotsRep2 None Hotspots astrocytes (also called Astrocy) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NH-A DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNhaHotspotsRep1 NH-A Ht 1 NH-A DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001179 1179 GSM736544 Stam UW DS12800 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseNhaHotspotsRep1 None Hotspots astrocytes (also called Astrocy) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NH-A DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseNb4HotspotsRep2 NB4 Ht 2 NB4 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-08 wgEncodeEH000498 498 GSM736529 Stam UW DS12538 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseNb4HotspotsRep2 None Hotspots acute promyelocytic leukemia cell line. (PMID: 1995093) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NB4 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseNb4HotspotsRep1 NB4 Ht 1 NB4 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000498 498 GSM736604 Stam UW DS12543 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseNb4HotspotsRep1 None Hotspots acute promyelocytic leukemia cell line. (PMID: 1995093) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NB4 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseM059jHotspotsRep2 M059J Ht 2 M059J DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002581 2581 GSM1024794 Stam UW DS20497 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseM059jHotspotsRep2 None Hotspots malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm M059J DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseM059jHotspotsRep1 M059J Ht 1 M059J DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH002581 2581 GSM1024773 Stam UW DS20493 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseM059jHotspotsRep1 None Hotspots malignant glioblastoma, glioma, lack DNA-dependent protein kinase activity, deficient in repair of DNA double strand breaks, the cells are negative for glial fibrillary acidic protein (GFAP), tumor specimen taken from a 33 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm M059J DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseLncapHotspotsRep2 LNCaP Ht 2 LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001187 1187 GSM736603 Stam UW DS14680 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseLncapHotspotsRep2 None Hotspots prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm LNCaP DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseLncapHotspotsRep1 LNCaP Ht 1 LNCaP DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001187 1187 GSM736565 Stam UW DS14684 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseLncapHotspotsRep1 None Hotspots prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm LNCaP DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseJurkatHotspotsRep2 Jurkat Ht 2 Jurkat DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000497 497 GSM736492 Stam UW DS10681 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseJurkatHotspotsRep2 None Hotspots T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Jurkat DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseJurkatHotspotsRep1 Jurkat Ht 1 Jurkat DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000497 497 GSM736501 Stam UW DS12659 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseJurkatHotspotsRep1 None Hotspots T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Jurkat DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHvmfHotspotsRep2 HVMF Ht 2 HVMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001176 1176 GSM736491 Stam UW DS13977 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHvmfHotspotsRep2 None Hotspots villous mesenchymal fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHvmfHotspotsRep1 HVMF Ht 1 HVMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001176 1176 GSM736534 Stam UW DS13981 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHvmfHotspotsRep1 None Hotspots villous mesenchymal fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmtHotspotsRep2 HSMMtube Ht 2 HSMMtube DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001186 1186 GSM1024788 Stam UW DS15538 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseHsmmtHotspotsRep2 None Hotspots skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HSMMtube DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmtHotspotsRep1 HSMMtube Ht 1 HSMMtube DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001186 1186 GSM736530 Stam UW DS15542 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHsmmtHotspotsRep1 None Hotspots skeletal muscle myotubes differentiated from the HSMM cell line DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HSMMtube DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmHotspotsRep2 HSMM Ht 2 HSMM DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001185 1185 GSM736553 Stam UW DS14430 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHsmmHotspotsRep2 None Hotspots skeletal muscle myoblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HSMM DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHsmmHotspotsRep1 HSMM Ht 1 HSMM DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001185 1185 GSM736560 Stam UW DS14426 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHsmmHotspotsRep1 None Hotspots skeletal muscle myoblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HSMM DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrpeHotspotsRep2 HRPEpiC Ht 2 HRPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-08 wgEncodeEH000517 517 GSM736623 Stam UW DS12568 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHrpeHotspotsRep2 None Hotspots retinal pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpiC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrpeHotspotsRep1 HRPEpiC Ht 1 HRPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-08 wgEncodeEH000517 517 GSM736630 Stam UW DS12583 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHrpeHotspotsRep1 None Hotspots retinal pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpiC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrgecHotspotsRep2 HRGEC Ht 2 HRGEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001195 1195 GSM736618 Stam UW DS13716 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHrgecHotspotsRep2 None Hotspots renal glomerular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRGEC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrgecHotspotsRep1 HRGEC Ht 1 HRGEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001195 1195 GSM736499 Stam UW DS13705 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHrgecHotspotsRep1 None Hotspots renal glomerular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRGEC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHreHotspotsRep2 HRE Ht 2 HRE DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000494 494 GSM736548 Stam UW DS10631 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHreHotspotsRep2 None Hotspots renal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHreHotspotsRep1 HRE Ht 1 HRE DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000494 494 GSM736527 Stam UW DS10641 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHreHotspotsRep1 None Hotspots renal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrceHotspotsRep2 HRCEpiC Ht 2 HRCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000493 493 GSM736557 Stam UW DS10662 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHrceHotspotsRep2 None Hotspots renal cortical epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRCEpiC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHrceHotspotsRep1 HRCEpiC Ht 1 HRCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000493 493 GSM736549 Stam UW DS10666 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHrceHotspotsRep1 None Hotspots renal cortical epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRCEpiC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpfHotspotsRep2 HPF Ht 2 HPF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001174 1174 GSM736503 Stam UW DS13380 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHpfHotspotsRep2 None Hotspots pulmonary fibroblasts isolated from lung tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpfHotspotsRep1 HPF Ht 1 HPF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001174 1174 GSM736574 Stam UW DS13390 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHpfHotspotsRep1 None Hotspots pulmonary fibroblasts isolated from lung tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpdlfHotspotsRep2 HPdLF Ht 2 HPdLF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001175 1175 GSM736528 Stam UW DS13569 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHpdlfHotspotsRep2 None Hotspots periodontal ligament fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPdLF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpdlfHotspotsRep1 HPdLF Ht 1 HPdLF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001175 1175 GSM736632 Stam UW DS13573 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHpdlfHotspotsRep1 None Hotspots periodontal ligament fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPdLF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpafHotspotsRep2 HPAF Ht 2 HPAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001173 1173 GSM736614 Stam UW DS13416 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHpafHotspotsRep2 None Hotspots pulmonary artery fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpafHotspotsRep1 HPAF Ht 1 HPAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001173 1173 GSM736555 Stam UW DS13411 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHpafHotspotsRep1 None Hotspots pulmonary artery fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHpaecHotspotsRep1 HPAEC Ht 1 HPAEC DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001886 1886 GSM1024763 Stam UW DS12916 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseHpaecHotspotsRep1 None Hotspots pulmonary artery endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAEC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHnpceHotspotsRep2 HNPCEpiC Ht 2 HNPCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000516 516 GSM736550 Stam UW DS12471 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHnpceHotspotsRep2 None Hotspots non-pigment ciliary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HNPCEpiC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHnpceHotspotsRep1 HNPCEpiC Ht 1 HNPCEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000516 516 GSM736621 Stam UW DS12467 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHnpceHotspotsRep1 None Hotspots non-pigment ciliary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HNPCEpiC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecllyHotspotsRep2 HMVECLLy Ht 2 HMVEC-LLy DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001167 1167 GSM736627 Stam UW DS13193 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHmvecllyHotspotsRep2 None Hotspots lymphatic microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-LLy DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecllyHotspotsRep1 HMVECLLy Ht 1 HMVEC-LLy DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001167 1167 GSM736507 Stam UW DS13185 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHmvecllyHotspotsRep1 None Hotspots lymphatic microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-LLy DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmveclblHotspotsRep2 HMVECLBl Ht 2 HMVEC-LBl DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001163 1163 GSM736511 Stam UW DS13375 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHmveclblHotspotsRep2 None Hotspots blood microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-LBl DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmveclblHotspotsRep1 HMVECLBl Ht 1 HMVEC-LBl DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH001163 1163 GSM736542 Stam UW DS13372 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHmveclblHotspotsRep1 None Hotspots blood microvascular endothelial cells, lung-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-LBl DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdneoHotspotsRep2 HMVECdNeo Ht 2 HMVEC-dNeo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001172 1172 GSM736624 Stam UW DS12929 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHmvecdneoHotspotsRep2 None Hotspots neonatal microvascular endothelial cells (single donor), dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dNeo DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdneoHotspotsRep1 HMVECdNeo Ht 1 HMVEC-dNeo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001172 1172 GSM736611 Stam UW DS12937 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHmvecdneoHotspotsRep1 None Hotspots neonatal microvascular endothelial cells (single donor), dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dNeo DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyneoHotspotsRep2 HMVECdLyNeo Ht 2 HMVEC-dLy-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001171 1171 GSM736573 Stam UW DS13146 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHmvecdlyneoHotspotsRep2 None Hotspots neonatal lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dLy-Neo DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyneoHotspotsRep1 HMVECdLyNeo Ht 1 HMVEC-dLy-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001171 1171 GSM736577 Stam UW DS13150 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHmvecdlyneoHotspotsRep1 None Hotspots neonatal lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dLy-Neo DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyadHotspotsRep2 HMVECdLyAd Ht 2 HMVEC-dLy-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001170 1170 GSM736591 Stam UW DS13256 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHmvecdlyadHotspotsRep2 None Hotspots adult lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dLy-Ad DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdlyadHotspotsRep1 HMVECdLyAd Ht 1 HMVEC-dLy-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001170 1170 GSM736599 Stam UW DS13261 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHmvecdlyadHotspotsRep1 None Hotspots adult lymphatic microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dLy-Ad DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdblneoHotspotsRep2 HMVECdBlNeo Ht 2 HMVEC-dBl-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001169 1169 GSM736521 Stam UW DS13233 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHmvecdblneoHotspotsRep2 None Hotspots neonatal blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dBl-Neo DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdblneoHotspotsRep1 HMVECdBlNeo Ht 1 HMVEC-dBl-Neo DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001169 1169 GSM736571 Stam UW DS13242 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHmvecdblneoHotspotsRep1 None Hotspots neonatal blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dBl-Neo DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdbladHotspotsRep2 HMVECdBlAd Ht 2 HMVEC-dBl-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001168 1168 GSM736523 Stam UW DS13329 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHmvecdbladHotspotsRep2 None Hotspots adult blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dBl-Ad DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdbladHotspotsRep1 HMVECdBlAd Ht 1 HMVEC-dBl-Ad DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001168 1168 GSM736609 Stam UW DS13337 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHmvecdbladHotspotsRep1 None Hotspots adult blood microvascular endothelial cells, dermal-derived DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dBl-Ad DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdadHotspotsRep2 HMVECdAd Ht 2 HMVEC-dAd DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-28 wgEncodeEH001889 1889 GSM1024747 Stam UW DS12952 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseHmvecdadHotspotsRep2 None Hotspots adult dermal microvascular endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dAd DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmvecdadHotspotsRep1 HMVECdAd Ht 1 HMVEC-dAd DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-28 wgEncodeEH001889 1889 GSM1024745 Stam UW DS12957 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseHmvecdadHotspotsRep1 None Hotspots adult dermal microvascular endothelial cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMVEC-dAd DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmfHotspotsRep2 HMF Ht 2 HMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001166 1166 GSM736541 Stam UW DS13368 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHmfHotspotsRep2 None Hotspots mammary fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmfHotspotsRep1 HMF Ht 1 HMF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001166 1166 GSM736628 Stam UW DS13363 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHmfHotspotsRep1 None Hotspots mammary fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmecHotspotsRep2 HMEC Ht 2 HMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH000503 503 GSM736552 Stam UW DS13921 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHmecHotspotsRep2 None Hotspots mammary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHmecHotspotsRep1 HMEC Ht 1 HMEC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000503 503 GSM736634 Stam UW DS8680 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHmecHotspotsRep1 None Hotspots mammary epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHl60HotspotsRep2 HL60 Ht 2 HL-60 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-19 wgEncodeEH000489 489 GSM736595 Stam UW DS11733 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHl60HotspotsRep2 None Hotspots promyelocytic leukemia cells, (PMID: 276884) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HL-60 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHl60HotspotsRep1 HL60 Ht 1 HL-60 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-04-29 2010-01-29 wgEncodeEH000489 489 GSM736626 Stam UW DS11809 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHl60HotspotsRep1 None Hotspots promyelocytic leukemia cells, (PMID: 276884) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HL-60 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHipeHotspotsRep2 HIPEpiC Ht 2 HIPEpiC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001184 1184 GSM736615 Stam UW DS12689 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHipeHotspotsRep2 None Hotspots iris pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HIPEpiC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHipeHotspotsRep1 HIPEpiC Ht 1 HIPEpiC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001184 1184 GSM736589 Stam UW DS12684 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHipeHotspotsRep1 None Hotspots iris pigment epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HIPEpiC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHgfHotspotsRep2 HGF Ht 2 HGF DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-10-20 2010-07-20 wgEncodeEH000504 504 GSM736576 Stam UW DS11738 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHgfHotspotsRep2 None Hotspots gingival fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HGF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHgfHotspotsRep1 HGF Ht 1 HGF DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-20 2010-07-20 wgEncodeEH000504 504 GSM736579 Stam UW DS11752 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHgfHotspotsRep1 None Hotspots gingival fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HGF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffmycHotspotsRep2 HFFMyc Ht 2 HFF-Myc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001194 1194 GSM736605 Stam UW DS15073 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHffmycHotspotsRep2 None Hotspots foreskin fibroblast cells expressing canine cMyc DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF-Myc DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffmycHotspotsRep1 HFFMyc Ht 1 HFF-Myc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001194 1194 GSM736524 Stam UW DS15079 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHffmycHotspotsRep1 None Hotspots foreskin fibroblast cells expressing canine cMyc DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF-Myc DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffHotspotsRep2 HFF Ht 2 HFF DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001193 1193 GSM736572 Stam UW DS15119 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHffHotspotsRep2 None Hotspots foreskin fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHffHotspotsRep1 HFF Ht 1 HFF DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001193 1193 GSM736602 Stam UW DS15115 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHffHotspotsRep1 None Hotspots foreskin fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHeeHotspotsRep2 HEEpiC Ht 2 HEEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000515 515 GSM736532 Stam UW DS12768 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHeeHotspotsRep2 None Hotspots esophageal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpiC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHeeHotspotsRep1 HEEpiC Ht 1 HEEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-10 2010-10-09 wgEncodeEH000515 515 GSM736585 Stam UW DS12763 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHeeHotspotsRep1 None Hotspots esophageal epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpiC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHct116HotspotsRep2 HCT-116 Ht 2 HCT-116 DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH001162 1162 GSM736493 Stam UW DS13547 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHct116HotspotsRep2 None Hotspots colorectal carcinoma (PMID: 7214343) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHct116HotspotsRep1 HCT-116 Ht 1 HCT-116 DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-24 wgEncodeEH001162 1162 GSM736600 Stam UW DS13551 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHct116HotspotsRep1 None Hotspots colorectal carcinoma (PMID: 7214343) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcpeHotspotsRep2 HCPEpiC Ht 2 HCPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000514 514 GSM736597 Stam UW DS12457 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHcpeHotspotsRep2 None Hotspots choroid plexus epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpiC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcpeHotspotsRep1 HCPEpiC Ht 1 HCPEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000514 514 GSM736569 Stam UW DS12447 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHcpeHotspotsRep1 None Hotspots choroid plexus epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpiC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHconfHotspotsRep2 HConF Ht 2 HConF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001165 1165 GSM736515 Stam UW DS11637 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHconfHotspotsRep2 None Hotspots conjunctival fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HConF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHconfHotspotsRep1 HConF Ht 1 HConF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001165 1165 GSM736547 Stam UW DS11642 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHconfHotspotsRep1 None Hotspots conjunctival fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HConF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcmHotspotsRep2 HCM Ht 2 HCM DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-09 2010-10-08 wgEncodeEH000519 519 GSM736504 Stam UW DS12589 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHcmHotspotsRep2 None Hotspots cardiac myocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcmHotspotsRep1 HCM Ht 1 HCM DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-09 2010-10-08 wgEncodeEH000519 519 GSM736516 Stam UW DS12599 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHcmHotspotsRep1 None Hotspots cardiac myocytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfaaHotspotsRep2 HCFaa Ht 2 HCFaa DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001164 1164 GSM736601 Stam UW DS13484 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHcfaaHotspotsRep2 None Hotspots cardiac fibroblasts- adult atrial DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCFaa DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfaaHotspotsRep1 HCFaa Ht 1 HCFaa DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001164 1164 GSM736494 Stam UW DS13480 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHcfaaHotspotsRep1 None Hotspots cardiac fibroblasts- adult atrial DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCFaa DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfHotspotsRep2 HCF Ht 2 HCF DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-07 wgEncodeEH000513 513 GSM736540 Stam UW DS12491 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHcfHotspotsRep2 None Hotspots cardiac fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHcfHotspotsRep1 HCF Ht 1 HCF DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-09 2010-10-08 wgEncodeEH000513 513 GSM736568 Stam UW DS12501 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHcfHotspotsRep1 None Hotspots cardiac fibroblasts DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbvsmcHotspotsRep2 HBVSCM Ht 2 HBVSMC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002580 2580 GSM1024769 Stam UW DS14845 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseHbvsmcHotspotsRep2 None Hotspots brain vascular smooth muscle cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBVSCM DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbvsmcHotspotsRep1 HBVSCM Ht 1 HBVSMC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002580 2580 GSM1024768 Stam UW DS14860 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseHbvsmcHotspotsRep1 None Hotspots brain vascular smooth muscle cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBVSCM DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbvpHotspotsRep1 HBVP Ht 1 HBVP DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002579 2579 GSM1024750 Stam UW DS14834 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseHbvpHotspotsRep1 None Hotspots brain vascular pericytes DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBVP DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbmecHotspotsRep2 HBMEC Ht 2 HBMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001178 1178 GSM736554 Stam UW DS13806 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHbmecHotspotsRep2 None Hotspots brain microvascular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHbmecHotspotsRep1 HBMEC Ht 1 HBMEC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-31 2011-05-01 wgEncodeEH001178 1178 GSM736509 Stam UW DS13817 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHbmecHotspotsRep1 None Hotspots brain microvascular endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaeHotspotsRep2 HAEpiC Ht 2 HAEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-07 wgEncodeEH000512 512 GSM736606 Stam UW DS12673 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHaeHotspotsRep2 None Hotspots amniotic epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAEpiC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaeHotspotsRep1 HAEpiC Ht 1 HAEpiC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-07 wgEncodeEH000512 512 GSM736631 Stam UW DS12663 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHaeHotspotsRep1 None Hotspots amniotic epithelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAEpiC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHacHotspotsRep2 HAc Ht 2 HAc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001192 1192 GSM736538 Stam UW DS14770 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHacHotspotsRep2 None Hotspots astrocytes-cerebellar DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHacHotspotsRep1 HAc Ht 1 HAc DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001192 1192 GSM736586 Stam UW DS14765 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHacHotspotsRep1 None Hotspots astrocytes-cerebellar DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaspHotspotsRep2 HAsp Ht 2 HA-sp DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001183 1183 GSM736625 Stam UW DS14794 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHaspHotspotsRep2 None Hotspots astrocytes spinal cord DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHaspHotspotsRep1 HAsp Ht 1 HA-sp DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001183 1183 GSM736537 Stam UW DS14790 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHaspHotspotsRep1 None Hotspots astrocytes spinal cord DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHahHotspotsRep2 HAh Ht 2 HA-h DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001191 1191 GSM736535 Stam UW DS15202 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHahHotspotsRep2 None Hotspots astrocytes-hippocampal DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-h DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHahHotspotsRep1 HAh Ht 1 HA-h DnaseSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH001191 1191 GSM736594 Stam UW DS15192 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseHahHotspotsRep1 None Hotspots astrocytes-hippocampal DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-h DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esHotspotsRep2 H7h Ht 2 H7-hESC DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000511 511 GSM736610 Stam UW DS13133 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseH7esHotspotsRep2 None Hotspots undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa5dHotspotsRep2 H7h difPA5 Ht 2 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002578 2578 GSM1024755 Stam UW DS11953 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseH7esDiffa5dHotspotsRep2 diffProtA_5d Hotspots undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC diffProtA 5 d DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa14dHotspotsRep2 H7h difPA14 Ht 2 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002576 2576 GSM1024758 Stam UW DS11814 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseH7esDiffa14dHotspotsRep2 diffProtA_14d Hotspots undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC diffProtA 14 d DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esHotspotsRep1 H7h Ht 1 H7-hESC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2010-01-08 2010-10-08 wgEncodeEH000511 511 GSM736638 Stam UW DS11909 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseH7esHotspotsRep1 None Hotspots undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa9dHotspotsRep1 H7h difPA9 Ht 1 H7-hESC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-07 2013-04-06 wgEncodeEH003019 3019 GSM1024778 Stam UW DS15809 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseH7esDiffa9dHotspotsRep1 diffProtA_9d Hotspots undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC diffProtA 9 d DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa5dHotspotsRep1 H7h difPA5 Ht 1 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002578 2578 GSM1024754 Stam UW DS15665 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseH7esDiffa5dHotspotsRep1 diffProtA_5d Hotspots undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC diffProtA 5 d DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa2dHotspotsRep1 H7h difPA2 Ht 1 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002577 2577 GSM1024774 Stam UW DS14732 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseH7esDiffa2dHotspotsRep1 diffProtA_2d Hotspots undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC diffProtA 2 d DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH7esDiffa14dHotspotsRep1 H7h difPA14 Ht 1 H7-hESC DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002576 2576 GSM1024759 Stam UW DS12147 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseH7esDiffa14dHotspotsRep1 diffProtA_14d Hotspots undifferentiated embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC diffProtA 14 d DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12865HotspotsRep2 GM12865 Ht 2 GM12865 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000520 520 GSM736561 Stam UW DS12442 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseGm12865HotspotsRep2 None Hotspots B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12865HotspotsRep1 GM12865 Ht 1 GM12865 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000520 520 GSM736512 Stam UW DS12436 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseGm12865HotspotsRep1 None Hotspots B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12864HotspotsRep1 GM12864 Ht 1 GM12864 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001182 1182 GSM736525 Stam UW DS12431 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseGm12864HotspotsRep1 None Hotspots B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm06990HotspotsRep2 GM06990 Ht 2 GM06990 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-01 2010-04-01 wgEncodeEH000481 481 GSM736635 Stam UW DS7784 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseGm06990HotspotsRep2 None Hotspots B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm06990HotspotsRep1 GM06990 Ht 1 GM06990 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2008-11-19 2009-08-18 wgEncodeEH000481 481 GSM736558 Stam UW DS7748 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseGm06990HotspotsRep1 None Hotspots B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04504HotspotsRep2 GM04504 Ht 2 GM04504 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002575 2575 GSM1024776 Stam UW DS18975 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseGm04504HotspotsRep2 None Hotspots adult twin pair fibroblasts, monozygotic twin of GM04503, 13% of the cells examined show random chromosome loss DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM04504 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04504HotspotsRep1 GM04504 Ht 1 GM04504 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002575 2575 GSM1024775 Stam UW DS18973 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseGm04504HotspotsRep1 None Hotspots adult twin pair fibroblasts, monozygotic twin of GM04503, 13% of the cells examined show random chromosome loss DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM04504 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04503HotspotsRep2 GM04503 Ht 2 GM04503 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002574 2574 GSM1024780 Stam UW DS18640 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseGm04503HotspotsRep2 None Hotspots adult twin pair fibroblasts, monozygotic twin of GM04504 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM04503 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm04503HotspotsRep1 GM04503 Ht 1 GM04503 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEH002574 2574 GSM1024777 Stam UW DS18637 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseGm04503HotspotsRep1 None Hotspots adult twin pair fibroblasts, monozygotic twin of GM04504 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM04503 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCmkHotspotsRep1 CMK Ht 1 CMK DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-07 wgEncodeEH000510 510 GSM736607 Stam UW DS12393 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseCmkHotspotsRep1 None Hotspots acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CMK DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd34mobilizedHotspotsRep1 CD34+ Mob Ht 1 CD34+_Mobilized DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001885 1885 GSM1024770 Stam UW DS16814 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseCd34mobilizedHotspotsRep1 None Hotspots hematopoietic progenitor cells- mobilized, from donor RO01679. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CD34+ Mobilized DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd4naivewb78495824HotspotsRep1 CD4 NveWb824 Ht 1 CD4+_Naive_Wb78495824 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-09 2013-04-09 wgEncodeEH003028 3028 GSM1024782 Stam UW DS15241 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseCd4naivewb78495824HotspotsRep1 None Hotspots CD4+ naive sorted cells, donor is Causasian, female 35 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CD4+ Naive Wb78495824 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd4naivewb11970640HotspotsRep1 CD4 NveWb640 Ht 1 CD4+_Naive_Wb11970640 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-09 2013-04-09 wgEncodeEH003027 3027 GSM1024789 Stam UW DS14108 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseCd4naivewb11970640HotspotsRep1 None Hotspots CD4+ naive sorted cells, donor is Caucasian, male 26 year old, primary pheresis of single normal subject DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CD4+ Naive Wb11970640 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCaco2HotspotsRep2 Caco2 Ht 2 Caco-2 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-01 2010-03-30 wgEncodeEH000486 486 GSM736587 Stam UW DS8416 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseCaco2HotspotsRep2 None Hotspots colorectal adenocarcinoma. (PMID: 1939345) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseCaco2HotspotsRep1 Caco2 Ht 1 Caco-2 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-04-24 2010-01-24 wgEncodeEH000486 486 GSM736500 Stam UW DS8235 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseCaco2HotspotsRep1 None Hotspots colorectal adenocarcinoma. (PMID: 1939345) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMscHotspotsRep2 Bon MarMSC Ht 2 bone_marrow_MSC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003031 3031 GSM1024748 Stam UW DS20518 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseMscHotspotsRep2 None Hotspots These cells are primary fibroblastoid cells obtained from human bone marrow of normal donors as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Bone Marrow MSC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMscHotspotsRep1 Bon MarMSC Ht 1 bone_marrow_MSC DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003031 3031 GSM1024757 Stam UW DS20514 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseMscHotspotsRep1 None Hotspots These cells are primary fibroblastoid cells obtained from human bone marrow of normal donors as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Bone Marrow MSC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHs5HotspotsRep1 Bon MarHS5 Ht 1 bone_marrow_HS5 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003030 3030 GSM1024746 Stam UW DS16597 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseHs5HotspotsRep1 None Hotspots HS5 Human Marrow Stromal Cells are fibroblastoid cells immortalized with HPV16 E6/E7 genes as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005, insert DNA is LXSN-16 E6E7 packaged in PA31. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Bone Marrow HS5 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHs27aHotspotsRep1 Bon MarHS27a Ht 1 bone_marrow_HS27a DnaseSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-12 wgEncodeEH003029 3029 GSM1024785 Stam UW DS16602 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseHs27aHotspotsRep1 None Hotspots HS27a Human Marrow Stromal Cells are fibroblastoid cells immortalized with HPV16 E6/E7 genes as described in Roecklein and Torok-Storb, 1995 Blood 85:997-1005, insert DNA is LXSN-16 E6E7 packaged in PA31. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Bone Marrow HS27a DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseBjHotspotsRep2 BJ Ht 2 BJ DnaseSeq ENCODE June 2010 Freeze 2010-06-06 2010-06-06 2011-03-06 wgEncodeEH000487 487 GSM736596 Stam UW DS10018 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseBjHotspotsRep2 None Hotspots skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseBjHotspotsRep1 BJ Ht 1 BJ DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2010-06-19 2011-03-19 wgEncodeEH000487 487 GSM736518 Stam UW DS10081 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseBjHotspotsRep1 None Hotspots skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseBe2cHotspotsRep2 BE2 C Ht 2 BE2_C DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001181 1181 GSM736622 Stam UW DS14635 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseBe2cHotspotsRep2 None Hotspots neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2 C DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseBe2cHotspotsRep1 BE2 C Ht 1 BE2_C DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001181 1181 GSM736508 Stam UW DS14625 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseBe2cHotspotsRep1 None Hotspots neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2 C DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAoafHotspotsRep2 AoAF Ht 2 AoAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH001161 1161 GSM736505 Stam UW DS13513 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseAoafHotspotsRep2 None Hotspots aortic adventitial fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAoafHotspotsRep1 AoAF Ht 1 AoAF DnaseSeq ENCODE Jan 2011 Freeze 2010-07-26 2011-04-26 wgEncodeEH001161 1161 GSM736583 Stam UW DS13523 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseAoafHotspotsRep1 None Hotspots aortic adventitial fibroblast cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg10803HotspotsRep2 AG10803 Ht 2 AG10803 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-08 wgEncodeEH000509 509 GSM736633 Stam UW DS12374 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseAg10803HotspotsRep2 None Hotspots abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg10803HotspotsRep1 AG10803 Ht 1 AG10803 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-08 2010-10-08 wgEncodeEH000509 509 GSM736598 Stam UW DS12384 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseAg10803HotspotsRep1 None Hotspots abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09319HotspotsRep2 AG09319 Ht 2 AG09319 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000508 508 GSM736619 Stam UW DS12286 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseAg09319HotspotsRep2 None Hotspots gum tissue fibroblasts from apparently heathly 24 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09319HotspotsRep1 AG09319 Ht 1 AG09319 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000508 508 GSM736531 Stam UW DS12291 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseAg09319HotspotsRep1 None Hotspots gum tissue fibroblasts from apparently heathly 24 year old DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09309HotspotsRep2 AG09309 Ht 2 AG09309 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000507 507 GSM736616 Stam UW DS12357 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseAg09309HotspotsRep2 None Hotspots adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg09309HotspotsRep1 AG09309 Ht 1 AG09309 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000507 507 GSM736551 Stam UW DS12352 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseAg09309HotspotsRep1 None Hotspots adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04450HotspotsRep2 AG04450 Ht 2 AG04450 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000506 506 GSM736563 Stam UW DS12255 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseAg04450HotspotsRep2 None Hotspots fetal lung fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04450HotspotsRep1 AG04450 Ht 1 AG04450 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000506 506 GSM736514 Stam UW DS12270 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseAg04450HotspotsRep1 None Hotspots fetal lung fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04449HotspotsRep2 AG04449 Ht 2 AG04449 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-07 2010-10-07 wgEncodeEH000505 505 GSM736590 Stam UW DS12329 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseAg04449HotspotsRep2 None Hotspots fetal buttock/thigh fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseAg04449HotspotsRep1 AG04449 Ht 1 AG04449 DnaseSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-06 2010-10-05 wgEncodeEH000505 505 GSM736562 Stam UW DS12319 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseAg04449HotspotsRep1 None Hotspots fetal buttock/thigh fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMonocd14ro1746HotspotsRep2 CD14+ Mono Ht 2 Monocytes-CD14+_RO01746 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001196 1196 GSM1024791 Stam UW DS18065 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseMonocd14ro1746HotspotsRep2 None Hotspots Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Monocytes CD14+ RO01746 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7HotspotsRep2 MCF7 Ht 2 MCF-7 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2010-01-10 2010-10-09 wgEncodeEH000502 502 GSM736588 Stam UW DS12619 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseMcf7HotspotsRep2 None Hotspots mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Estctrl0hHotspotsRep2 MCF7 EstCtrl Ht 2 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003018 3018 GSM1024767 Stam UW DS18021 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseMcf7Estctrl0hHotspotsRep2 Estradiol_ctrl_0hr Hotspots mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 Estradiol Control 0 hr DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Est100nm1hHotspotsRep2 MCF7 Est1h Ht 2 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003017 3017 GSM1024783 Stam UW DS18025 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseMcf7Est100nm1hHotspotsRep2 Estradiol_100nM_1hr Hotspots mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 1 h with 100 nM Estradiol, hormone treatment (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 Estradiol 100 nM 1 hr DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7HotspotsRep1 MCF7 Ht 1 MCF-7 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-09-29 2010-06-29 wgEncodeEH000502 502 GSM736581 Stam UW DS9445 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseMcf7HotspotsRep1 None Hotspots mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Estctrl0hHotspotsRep1 MCF7 EstCtrl Ht 1 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003018 3018 GSM1024764 Stam UW DS18267 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseMcf7Estctrl0hHotspotsRep1 Estradiol_ctrl_0hr Hotspots mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 Estradiol Control 0 hr DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseMcf7Est100nm1hHotspotsRep1 MCF7 Est1h Ht 1 MCF-7 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003017 3017 GSM1024784 Stam UW DS18271 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseMcf7Est100nm1hHotspotsRep1 Estradiol_100nM_1hr Hotspots mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 1 h with 100 nM Estradiol, hormone treatment (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 Estradiol 100 nM 1 hr DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2HotspotsRep2 LHCNM2 Ht 2 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003005 3005 GSM1024786 Stam UW DS20485 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseLhcnm2HotspotsRep2 None Hotspots skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm LHCN-M2 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2Diff4dHotspotsRep2 LHCNM2 dif4d Ht 2 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003006 3006 GSM1024772 Stam UW DS20534 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseLhcnm2Diff4dHotspotsRep2 DIFF_4d Hotspots skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm LHCN-M2 DIFF 4 d DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2HotspotsRep1 LHCNM2 Ht 1 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003005 3005 GSM1024787 Stam UW DS20548 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseLhcnm2HotspotsRep1 None Hotspots skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm LHCN-M2 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseLhcnm2Diff4dHotspotsRep1 LHCNM2 dif4d Ht 1 LHCN-M2 DnaseSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-20 wgEncodeEH003006 3006 GSM1024771 Stam UW DS20647 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseLhcnm2Diff4dHotspotsRep1 DIFF_4d Hotspots skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Myocytes differentiated from myoblasts for 4 days. See specific cell protocol for treatment details. (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm LHCN-M2 DIFF 4 d DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHuvecHotspotsRep2 HUVEC Ht 2 HUVEC DnaseSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH000488 488 GSM736533 Stam UW DS13475 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseHuvecHotspotsRep2 None Hotspots umbilical vein endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHuvecHotspotsRep1 HUVEC Ht 1 HUVEC DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-04-27 2010-01-27 wgEncodeEH000488 488 GSM736575 Stam UW DS10060 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHuvecHotspotsRep1 None Hotspots umbilical vein endothelial cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHepg2HotspotsRep2 HepG2 Ht 2 HepG2 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-01 2010-04-01 wgEncodeEH000482 482 GSM736639 Stam UW DS7768 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHepg2HotspotsRep2 None Hotspots hepatocellular carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHepg2HotspotsRep1 HepG2 Ht 1 HepG2 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2008-11-19 2009-08-18 wgEncodeEH000482 482 GSM736637 Stam UW DS7764 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHepg2HotspotsRep1 None Hotspots hepatocellular carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseHelas3HotspotsRep2 HeLaS3 Ht 2 HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-02 2010-04-01 wgEncodeEH000495 495 GSM736510 Stam UW DS8200 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseHelas3HotspotsRep2 None Hotspots cervical carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseHelas3HotspotsRep1 HeLaS3 Ht 1 HeLa-S3 DnaseSeq ENCODE June 2010 Freeze 2010-06-18 2009-07-02 2010-04-01 wgEncodeEH000495 495 GSM736564 Stam UW DS10011 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseHelas3HotspotsRep1 None Hotspots cervical carcinoma DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd20ro01778HotspotsRep2 CD20+ Ht 2 CD20+_RO01778 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-25 wgEncodeEH001884 1884 GSM1024766 Stam UW DS17541 Hotspot-v5.2 hg19 2 wgEncodeUwDnaseCd20ro01778HotspotsRep2 None Hotspots B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm B cells CD20+ RO01778 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseCd20ro01778HotspotsRep1 CD20+ Ht 1 CD20+_RO01778 DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-13 wgEncodeEH001884 1884 GSM1024765 Stam UW DS18208 Hotspot-v5.2 hg19 1 wgEncodeUwDnaseCd20ro01778HotspotsRep1 None Hotspots B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm B cells CD20+ RO01778 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseA549HotspotsRep2 A549 Ht 2 A549 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-04 wgEncodeEH001180 1180 GSM736506 Stam UW DS14285 Hotspot-v5.1 hg19 2 wgEncodeUwDnaseA549HotspotsRep2 None Hotspots epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseA549HotspotsRep1 A549 Ht 1 A549 DnaseSeq ENCODE Jan 2011 Freeze 2011-01-04 2011-10-04 wgEncodeEH001180 1180 GSM736580 Stam UW DS14289 Hotspot-v5.1 hg19 1 wgEncodeUwDnaseA549HotspotsRep1 None Hotspots epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseK562HotspotsRep2 K562 Ht 2 K562 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2008-12-09 2009-09-09 wgEncodeEH000484 484 GSM736566 Stam UW DS9764 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseK562HotspotsRep2 None Hotspots leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseK562HotspotsRep1 K562 Ht 1 K562 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2008-12-09 2009-09-09 wgEncodeEH000484 484 GSM736629 Stam UW DS9767 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseK562HotspotsRep1 None Hotspots leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseH1hescHotspotsRep1 H1hESC Ht 1 H1-hESC DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-19 2010-06-18 wgEncodeEH000496 496 GSM736582 Stam UW DS10167 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseH1hescHotspotsRep1 None Hotspots embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H1-hESC DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12878HotspotsRep2 GM12878 Ht 2 GM12878 DnaseSeq ENCODE June 2010 Freeze 2010-06-19 2009-07-01 2010-04-01 wgEncodeEH000492 492 GSM736620 Stam UW DS9432 Hotspot-v5.1 hg18 2 wgEncodeUwDnaseGm12878HotspotsRep2 None Hotspots B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 DNaseI HS HotSpots Rep 2 from ENCODE/UW Regulation 
wgEncodeUwDnaseGm12878HotspotsRep1 GM12878 Ht 1 GM12878 DnaseSeq ENCODE June 2010 Freeze 2010-06-17 2009-07-02 2010-04-01 wgEncodeEH000492 492 GSM736496 Stam UW DS10671 Hotspot-v5.1 hg18 1 wgEncodeUwDnaseGm12878HotspotsRep1 None Hotspots B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 DNaseI HS HotSpots Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeq UW Repli-seq GSE34399 Replication Timing by Repli-seq from ENCODE/University of Washington Regulation Description This track is produced as part of the ENCODE Project. This track shows genome-wide assessment of DNA replication timing in cell lines using the sequencing-based "Repli-seq" methodology (see below). Replication timing is known to be an important feature for epigenetic control of gene expression that usually operates at a higher-order level than at the level of specific genes. For each experiment (cell line, replicate), replication timing was ascertained by the isolation and sequencing of newly replicated DNA from six cell cycle fractions: G1/G1b, S1, S2, S3, S4, G2 (six fraction profile). Replication patterns are visualized as a continuous function based on sequencing tag density (Percentage-normalized Signal) and as a wavelet-smoothed transform of the six fraction profile (Wavelet-smoothed Signal). Replication peaks corresponding to replication initiation zones (Peaks) and valleys corresponding to replication termination zones (Valleys) were determined from local maxima and minima, respectively, in the wavelet-smoothed signal data. A measure of relative copy number at each genomic location (Summed Densities) was determined by summing the normalized tag density values of each cell cycle fraction at that location (equals one replicated genome equivalent). Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: Percentage-normalized Signal Replication signal at 1 kb intervals as a percentage of normalized +/-25 kb tag densities for all cell cycle fractions (G1/G1b, S1, S2, S3, S4, G2). Wavelet-smoothed Signal Wavelet-smoothed transform of the six fraction profile that is a weighted average of the percentage-normalized signals such that earlier replication has higher values. Peaks Local maxima in the wavelet-smoothed signal data corresponding to replication initiation (replication origin) zones. Valleys Local minima in the wavelet-smoothed signal data corresponding to replication termination zones. Summed Densities A measure of relative copy number at each genomic location that is the sum of normalized tag densities for each cell cycle fraction. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Repli-seq was performed as described by Hansen et al. (2010). Briefly, newly replicated DNA was labeled in vivo with a pulse of 5-bromo-2-deoxyuridine (BrdU), cells were fractionated into six different parts of the cell cycle by flow cytometry according to DNA content, cell cycle fractionated DNA was sonicated and an anti-BrdU monoclonal antibody was used to isolate the newly replicating DNA. Fragment ends were sequenced using the Illumina Genome Analyzer II or HiSeq platforms (36 bp reads). Some experiments (BJ, K562, BG02ES, GM06990) were originally performed and mapped to an earlier version of the human reference genome NCBI36/hg18 (Hansen et al., 2010) and were remapped to the more recent reference genome GRCh37/hg19. Uniquely mapping high-quality reads were mapped to the genome minus the Y chromosome. Replication signals within each six cell cycle fraction were derived from the density of sequence tags mapping within a 50 kb sliding window (stepped 1 kb across the genome); these densities were normalized to 4 million tags per genome. To avoid variation due to copy number or sequence bias, cell cycle-specific replication signals at each location were determined as a percentage of the sum of the six normalized tag density signals (Percentage-normalized Signal). To transform the six fraction replication signals into one track (Wavelet-smoothed Signal), the percentage-normalized signals at each location were used to calculate a weighted average value based on the average DNA content of each fraction according to flow cytometry [higher values correspond to earlier replication; formula=(0.917*G1b)+(0.750*S1)+(0.583*S2)+(0.417*S3)+(0.250*S4)+(0*G2)]. These weighted average data were smoothed by wavelet transformation [J7 level, corresponding to a scale of 128 kb; see Thurman et al. (2007)]. Replication initiation zones were flagged by determining local maxima in the wavelet-smoothed data (Peaks) and, similarly, replication termination zones were flagged by local minima (Valleys). The sum of the 4 million normalized replication tag densities correspond to replication of one genome and can, therefore, be used as a measure of relative genomic copy number (Summed Densities). This is useful for evaluation of unusual replication patterns, such as "biphasic" ones where replication has both early and late components [as described by Hansen et al. (2010)]. Verification Data were verified by determining replication time with a PCR-based examination of replication for particular loci in addition to sequencing biological replicates, as described by Hansen et al. (2010). Credits These data were generated by the UW ENCODE group. Contact: Richard Sandstrom References Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44. Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA. Identification of higher-order functional domains in the human ENCODE regions. Genome Res. 2007 Jun;17(6):917-27. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwRepliSeqViewWaveSignal Wavelet-smoothed Signal Replication Timing by Repli-seq from ENCODE/University of Washington Regulation 
wgEncodeUwRepliSeqNhekWaveSignalRep1 NHEK Ws 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW NHEK-1 hg19 1 F wgEncodeUwRepliSeqNhekWaveSignalRep1 WaveSignal epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Shows smoothed wavelet over all phases NHEK Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813WaveSignalRep1 GM12813 Ws 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW GM12813-1 hg19 1 wgEncodeUwRepliSeqGm12813WaveSignalRep1 WaveSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases GM12813 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812WaveSignalRep1 GM12812 Ws 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW GM12812-1 hg19 1 wgEncodeUwRepliSeqGm12812WaveSignalRep1 WaveSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases GM12812 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801WaveSignalRep1 GM12801 Ws 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW GM12801-1 hg19 1 wgEncodeUwRepliSeqGm12801WaveSignalRep1 WaveSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases GM12801 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990WaveSignalRep1 GM06990 Ws 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW GM06990-1 hg19 1 wgEncodeUwRepliSeqGm06990WaveSignalRep1 WaveSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases GM06990 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjWaveSignalRep2 BJ Ws 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW BJ-2 hg19 2 wgEncodeUwRepliSeqBjWaveSignalRep2 WaveSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases BJ Repli-seq Wavelet-smoothed Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjWaveSignalRep1 BJ Ws 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW BJ-1 hg19 1 wgEncodeUwRepliSeqBjWaveSignalRep1 WaveSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases BJ Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esWaveSignalRep1 BG02ES Ws 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW BG02ES-1 hg19 1 wgEncodeUwRepliSeqBg02esWaveSignalRep1 WaveSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases BG02ES Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshWaveSignalRep1 SK-N-SH Ws 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW SK-N-SH_RA-1 hg19 1 wgEncodeUwRepliSeqSknshWaveSignalRep1 WaveSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases SK-N-SH Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7WaveSignalRep1 MCF-7 Ws 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW MCF-7-1 hg19 1 wgEncodeUwRepliSeqMcf7WaveSignalRep1 WaveSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases MCF-7 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90WaveSignalRep1 IMR90 Ws 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW IMR90-1 hg19 1 wgEncodeUwRepliSeqImr90WaveSignalRep1 WaveSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases IMR90 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecWaveSignalRep1 HUVEC Ws 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW HUVEC-1 hg19 1 wgEncodeUwRepliSeqHuvecWaveSignalRep1 WaveSignal umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases HUVEC Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2WaveSignalRep1 HepG2 Ws 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW HepG2-1 hg19 1 wgEncodeUwRepliSeqHepg2WaveSignalRep1 WaveSignal hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases HepG2 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3WaveSignalRep1 HeLa-S3 Ws 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW HeLa-S3-1 hg19 1 wgEncodeUwRepliSeqHelas3WaveSignalRep1 WaveSignal cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases HeLa-S3 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562WaveSignalRep1 K562 Ws 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW K562-1 hg19 1 wgEncodeUwRepliSeqK562WaveSignalRep1 WaveSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases K562 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878WaveSignalRep1 GM12878 Ws 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW GM12878-1 hg19 1 wgEncodeUwRepliSeqGm12878WaveSignalRep1 WaveSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows smoothed wavelet over all phases GM12878 Repli-seq Wavelet-smoothed Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqViewValleys Valleys Replication Timing by Repli-seq from ENCODE/University of Washington Regulation 
wgEncodeUwRepliSeqNhekValleysRep1 NHEK Vly 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW NHEK-1 hg19 1 F wgEncodeUwRepliSeqNhekValleysRep1 Valleys epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Regions of enriched signal in experiment NHEK Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813ValleysRep1 GM12813 Vly 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW GM12813-1 hg19 1 wgEncodeUwRepliSeqGm12813ValleysRep1 Valleys B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12813 Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812ValleysRep1 GM12812 Vly 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW GM12812-1 hg19 1 wgEncodeUwRepliSeqGm12812ValleysRep1 Valleys B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12812 Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801ValleysRep1 GM12801 Vly 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW GM12801-1 hg19 1 wgEncodeUwRepliSeqGm12801ValleysRep1 Valleys B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12801 Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990ValleysRep1 GM06990 Vly 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW GM06990-1 hg19 1 wgEncodeUwRepliSeqGm06990ValleysRep1 Valleys B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjValleysRep2 BJ Vly 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW BJ-2 hg19 2 wgEncodeUwRepliSeqBjValleysRep2 Valleys skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ Repli-seq Valleys Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjValleysRep1 BJ Vly 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW BJ-1 hg19 1 wgEncodeUwRepliSeqBjValleysRep1 Valleys skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esValleysRep1 BG02ES Vly 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW BG02ES-1 hg19 1 wgEncodeUwRepliSeqBg02esValleysRep1 Valleys embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BG02ES Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshValleysRep1 SK-N-SH Vly 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW SK-N-SH_RA-1 hg19 1 wgEncodeUwRepliSeqSknshValleysRep1 Valleys neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7ValleysRep1 MCF-7 Vly 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW MCF-7-1 hg19 1 wgEncodeUwRepliSeqMcf7ValleysRep1 Valleys mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90ValleysRep1 IMR90 Vly 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW IMR90-1 hg19 1 wgEncodeUwRepliSeqImr90ValleysRep1 Valleys fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment IMR90 Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecValleysRep1 HUVEC Vly 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW HUVEC-1 hg19 1 wgEncodeUwRepliSeqHuvecValleysRep1 Valleys umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2ValleysRep1 HepG2 Vly 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW HepG2-1 hg19 1 wgEncodeUwRepliSeqHepg2ValleysRep1 Valleys hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2-Phase Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3ValleysRep1 HeLa-S3 Vly 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW HeLa-S3-1 hg19 1 wgEncodeUwRepliSeqHelas3ValleysRep1 Valleys cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3-Phase Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562ValleysRep1 K562 Vly 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW K562-1 hg19 1 wgEncodeUwRepliSeqK562ValleysRep1 Valleys leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878ValleysRep1 GM12878 Vly 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW GM12878-1 hg19 1 wgEncodeUwRepliSeqGm12878ValleysRep1 Valleys B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 Repli-seq Valleys Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqViewSumSignal Summed Densities Replication Timing by Repli-seq from ENCODE/University of Washington Regulation 
wgEncodeUwRepliSeqNhekSumSignalRep1 NHEK Sd 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW NHEK-1 hg19 1 F wgEncodeUwRepliSeqNhekSumSignalRep1 SumSignal epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Shows summed densities of all phases combined NHEK Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813SumSignalRep1 GM12813 Sd 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW GM12813-1 hg19 1 wgEncodeUwRepliSeqGm12813SumSignalRep1 SumSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined GM12813 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812SumSignalRep1 GM12812 Sd 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW GM12812-1 hg19 1 wgEncodeUwRepliSeqGm12812SumSignalRep1 SumSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined GM12812 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801SumSignalRep1 GM12801 Sd 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW GM12801-1 hg19 1 wgEncodeUwRepliSeqGm12801SumSignalRep1 SumSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined GM12801 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990SumSignalRep1 GM06990 Sd 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW GM06990-1 hg19 1 wgEncodeUwRepliSeqGm06990SumSignalRep1 SumSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined GM06990 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjSumSignalRep2 BJ Sd 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW BJ-2 hg19 2 wgEncodeUwRepliSeqBjSumSignalRep2 SumSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined BJ Repli-seq Summed Densities Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjSumSignalRep1 BJ Sd 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW BJ-1 hg19 1 wgEncodeUwRepliSeqBjSumSignalRep1 SumSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined BJ Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esSumSignalRep1 BG02ES Sd 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW BG02ES-1 hg19 1 wgEncodeUwRepliSeqBg02esSumSignalRep1 SumSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined BG02ES Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshSumSignalRep1 SK-N-SH Sd 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW SK-N-SH_RA-1 hg19 1 wgEncodeUwRepliSeqSknshSumSignalRep1 SumSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined SK-N-SH Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7SumSignalRep1 MCF-7 Sd 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW MCF-7-1 hg19 1 wgEncodeUwRepliSeqMcf7SumSignalRep1 SumSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined MCF-7 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90SumSignalRep1 IMR90 Sd 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW IMR90-1 hg19 1 wgEncodeUwRepliSeqImr90SumSignalRep1 SumSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined IMR90 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecSumSignalRep1 HUVEC Sd 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW HUVEC-1 hg19 1 wgEncodeUwRepliSeqHuvecSumSignalRep1 SumSignal umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined HUVEC Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2SumSignalRep1 HepG2 Sd 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW HepG2-1 hg19 1 wgEncodeUwRepliSeqHepg2SumSignalRep1 SumSignal hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined HepG2 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3SumSignalRep1 HeLa-S3 Sd 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW HeLa-S3-1 hg19 1 wgEncodeUwRepliSeqHelas3SumSignalRep1 SumSignal cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined HeLa-S3 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562SumSignalRep1 K562 Sd 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW K562-1 hg19 1 wgEncodeUwRepliSeqK562SumSignalRep1 SumSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined K562 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878SumSignalRep1 GM12878 Sd 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW GM12878-1 hg19 1 wgEncodeUwRepliSeqGm12878SumSignalRep1 SumSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows summed densities of all phases combined GM12878 Repli-seq Summed Densities Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqViewPctSignal Percentile Normalized Signal Replication Timing by Repli-seq from ENCODE/University of Washington Regulation 
wgEncodeUwRepliSeqNhekG2PctSignalRep1 NHEK G2 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW DS9948 hg19 1 F wgEncodeUwRepliSeqNhekG2PctSignalRep1 PctSignal epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Signal over an interval as a percentage of normalized tag densities over all phases NHEK G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqNhekS4PctSignalRep1 NHEK S4 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW DS9952 hg19 1 F wgEncodeUwRepliSeqNhekS4PctSignalRep1 PctSignal epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Signal over an interval as a percentage of normalized tag densities over all phases NHEK S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqNhekS3PctSignalRep1 NHEK S3 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW DS9951 hg19 1 F wgEncodeUwRepliSeqNhekS3PctSignalRep1 PctSignal epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Signal over an interval as a percentage of normalized tag densities over all phases NHEK S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqNhekS2PctSignalRep1 NHEK S2 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW DS9950 hg19 1 F wgEncodeUwRepliSeqNhekS2PctSignalRep1 PctSignal epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Signal over an interval as a percentage of normalized tag densities over all phases NHEK S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqNhekS1PctSignalRep1 NHEK S1 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW DS9949 hg19 1 F wgEncodeUwRepliSeqNhekS1PctSignalRep1 PctSignal epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Signal over an interval as a percentage of normalized tag densities over all phases NHEK S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqNhekG1bPctSignalRep1 NHEK G1b 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW DS9947 hg19 1 F wgEncodeUwRepliSeqNhekG1bPctSignalRep1 PctSignal epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Signal over an interval as a percentage of normalized tag densities over all phases NHEK G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813G2PctSignalRep1 GM12813 G2 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW DS9828 hg19 1 wgEncodeUwRepliSeqGm12813G2PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12813 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813S4PctSignalRep1 GM12813 S4 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW DS9832 hg19 1 wgEncodeUwRepliSeqGm12813S4PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12813 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813S3PctSignalRep1 GM12813 S3 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW DS9831 hg19 1 wgEncodeUwRepliSeqGm12813S3PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12813 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813S2PctSignalRep1 GM12813 S2 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW DS9830 hg19 1 wgEncodeUwRepliSeqGm12813S2PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12813 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813S1PctSignalRep1 GM12813 S1 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW DS9829 hg19 1 wgEncodeUwRepliSeqGm12813S1PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12813 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813G1bPctSignalRep1 GM12813 G1b 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW DS9827 hg19 1 wgEncodeUwRepliSeqGm12813G1bPctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12813 G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812G2PctSignalRep1 GM12812 G2 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW DS9821 hg19 1 wgEncodeUwRepliSeqGm12812G2PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12812 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812S4PctSignalRep1 GM12812 S4 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW DS9825 hg19 1 wgEncodeUwRepliSeqGm12812S4PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12812 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812S3PctSignalRep1 GM12812 S3 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW DS9824 hg19 1 wgEncodeUwRepliSeqGm12812S3PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12812 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812S2PctSignalRep1 GM12812 S2 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW DS9823 hg19 1 wgEncodeUwRepliSeqGm12812S2PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12812 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812S1PctSignalRep1 GM12812 S1 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW DS9822 hg19 1 wgEncodeUwRepliSeqGm12812S1PctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12812 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812G1bPctSignalRep1 GM12812 G1b 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW DS9820 hg19 1 wgEncodeUwRepliSeqGm12812G1bPctSignalRep1 PctSignal B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12812 G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801G2PctSignalRep1 GM12801 G2 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW DS9814 hg19 1 wgEncodeUwRepliSeqGm12801G2PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12801 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801S4PctSignalRep1 GM12801 S4 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW DS9818 hg19 1 wgEncodeUwRepliSeqGm12801S4PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12801 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801S3PctSignalRep1 GM12801 S3 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW DS9817 hg19 1 wgEncodeUwRepliSeqGm12801S3PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12801 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801S2PctSignalRep1 GM12801 S2 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW DS9816 hg19 1 wgEncodeUwRepliSeqGm12801S2PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12801 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801S1PctSignalRep1 GM12801 S1 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW DS9815 hg19 1 wgEncodeUwRepliSeqGm12801S1PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12801 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801G1bPctSignalRep1 GM12801 G1b 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW DS9813 hg19 1 wgEncodeUwRepliSeqGm12801G1bPctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12801 G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990G2PctSignalRep1 GM06990 G2 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW DS9016 hg19 1 wgEncodeUwRepliSeqGm06990G2PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM06990 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990S4PctSignalRep1 GM06990 S4 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW DS9020 hg19 1 wgEncodeUwRepliSeqGm06990S4PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM06990 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990S3PctSignalRep1 GM06990 S3 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW DS9019 hg19 1 wgEncodeUwRepliSeqGm06990S3PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM06990 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990S2PctSignalRep1 GM06990 S2 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW DS9018 hg19 1 wgEncodeUwRepliSeqGm06990S2PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM06990 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990S1PctSignalRep1 GM06990 S1 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW DS9017 hg19 1 wgEncodeUwRepliSeqGm06990S1PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM06990 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990G1bPctSignalRep1 GM06990 G1b 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW DS9015 hg19 1 wgEncodeUwRepliSeqGm06990G1bPctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM06990 G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjG2PctSignalRep2 BJ G2 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS10030 hg19 2 wgEncodeUwRepliSeqBjG2PctSignalRep2 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ G2-Phase Repli-seq Percentage-normalized Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjS4PctSignalRep2 BJ S4 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS10034 hg19 2 wgEncodeUwRepliSeqBjS4PctSignalRep2 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ S4-Phase Repli-seq Percentage-normalized Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjS3PctSignalRep2 BJ S3 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS10033 hg19 2 wgEncodeUwRepliSeqBjS3PctSignalRep2 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ S3-Phase Repli-seq Percentage-normalized Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjS2PctSignalRep2 BJ S2 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS10032 hg19 2 wgEncodeUwRepliSeqBjS2PctSignalRep2 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ S2-Phase Repli-seq Percentage-normalized Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjS1PctSignalRep2 BJ S1 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS10031 hg19 2 wgEncodeUwRepliSeqBjS1PctSignalRep2 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ S1-Phase Repli-seq Percentage-normalized Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjG1bPctSignalRep2 BJ G1b 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS10029 hg19 2 wgEncodeUwRepliSeqBjG1bPctSignalRep2 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ G1b-Phase Repli-seq Percentage-normalized Signal Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjG2PctSignalRep1 BJ G2 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS9022 hg19 1 wgEncodeUwRepliSeqBjG2PctSignalRep1 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjS4PctSignalRep1 BJ S4 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS9026 hg19 1 wgEncodeUwRepliSeqBjS4PctSignalRep1 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjS3PctSignalRep1 BJ S3 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS9025 hg19 1 wgEncodeUwRepliSeqBjS3PctSignalRep1 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjS2PctSignalRep1 BJ S2 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS9024 hg19 1 wgEncodeUwRepliSeqBjS2PctSignalRep1 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjS1PctSignalRep1 BJ S1 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS9023 hg19 1 wgEncodeUwRepliSeqBjS1PctSignalRep1 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjG1bPctSignalRep1 BJ G1b 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW DS9021 hg19 1 wgEncodeUwRepliSeqBjG1bPctSignalRep1 PctSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BJ G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esG2PctSignalRep1 BG02ES G2 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW DS9028 hg19 1 wgEncodeUwRepliSeqBg02esG2PctSignalRep1 PctSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BG02ES G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esS4PctSignalRep1 BG02ES S4 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW DS9032 hg19 1 wgEncodeUwRepliSeqBg02esS4PctSignalRep1 PctSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BG02ES S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esS3PctSignalRep1 BG02ES S3 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW DS9031 hg19 1 wgEncodeUwRepliSeqBg02esS3PctSignalRep1 PctSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BG02ES S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esS2PctSignalRep1 BG02ES S2 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW DS9030 hg19 1 wgEncodeUwRepliSeqBg02esS2PctSignalRep1 PctSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BG02ES S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esS1PctSignalRep1 BG02ES S1 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW DS9029 hg19 1 wgEncodeUwRepliSeqBg02esS1PctSignalRep1 PctSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BG02ES S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esG1bPctSignalRep1 BG02ES G1b 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW DS9027 hg19 1 wgEncodeUwRepliSeqBg02esG1bPctSignalRep1 PctSignal embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases BG02ES G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshG2PctSignalRep1 SK-N-SH G2 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW DS9914 hg19 1 wgEncodeUwRepliSeqSknshG2PctSignalRep1 PctSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases SK-N-SH G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshS4PctSignalRep1 SK-N-SH S4 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW DS9918 hg19 1 wgEncodeUwRepliSeqSknshS4PctSignalRep1 PctSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases SK-N-SH S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshS3PctSignalRep1 SK-N-SH S3 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW DS9917 hg19 1 wgEncodeUwRepliSeqSknshS3PctSignalRep1 PctSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases SK-N-SH S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshS2PctSignalRep1 SK-N-SH S2 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW DS9916 hg19 1 wgEncodeUwRepliSeqSknshS2PctSignalRep1 PctSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases SK-N-SH S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshS1PctSignalRep1 SK-N-SH S1 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW DS9915 hg19 1 wgEncodeUwRepliSeqSknshS1PctSignalRep1 PctSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases SK-N-SH S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshG1bPctSignalRep1 SK-N-SH G1b 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW DS9913 hg19 1 wgEncodeUwRepliSeqSknshG1bPctSignalRep1 PctSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases SK-N-SH G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7G2PctSignalRep1 MCF-7 G2 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW DS9796 hg19 1 wgEncodeUwRepliSeqMcf7G2PctSignalRep1 PctSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases MCF-7 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7S4PctSignalRep1 MCF-7 S4 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW DS9800 hg19 1 wgEncodeUwRepliSeqMcf7S4PctSignalRep1 PctSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases MCF-7 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7S3PctSignalRep1 MCF-7 S3 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW DS9799 hg19 1 wgEncodeUwRepliSeqMcf7S3PctSignalRep1 PctSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases MCF-7 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7S2PctSignalRep1 MCF-7 S2 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW DS9798 hg19 1 wgEncodeUwRepliSeqMcf7S2PctSignalRep1 PctSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases MCF-7 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7S1PctSignalRep1 MCF-7 S1 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW DS9797 hg19 1 wgEncodeUwRepliSeqMcf7S1PctSignalRep1 PctSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases MCF-7 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7G1bPctSignalRep1 MCF-7 G1b 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW DS9795 hg19 1 wgEncodeUwRepliSeqMcf7G1bPctSignalRep1 PctSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases MCF-7 G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90G2PctSignalRep1 IMR90 G2 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW DS17626 hg19 1 wgEncodeUwRepliSeqImr90G2PctSignalRep1 PctSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases IMR90 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90S4PctSignalRep1 IMR90 S4 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW DS17630 hg19 1 wgEncodeUwRepliSeqImr90S4PctSignalRep1 PctSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases IMR90 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90S3PctSignalRep1 IMR90 S3 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW DS17629 hg19 1 wgEncodeUwRepliSeqImr90S3PctSignalRep1 PctSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases IMR90 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90S2PctSignalRep1 IMR90 S2 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW DS17628 hg19 1 wgEncodeUwRepliSeqImr90S2PctSignalRep1 PctSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases IMR90 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90S1PctSignalRep1 IMR90 S1 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW DS17627 hg19 1 wgEncodeUwRepliSeqImr90S1PctSignalRep1 PctSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases IMR90 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90G1bPctSignalRep1 IMR90 G1b 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW DS17625 hg19 1 wgEncodeUwRepliSeqImr90G1bPctSignalRep1 PctSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases IMR90 G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecG2PctSignalRep1 HUVEC G2 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW DS9852 hg19 1 wgEncodeUwRepliSeqHuvecG2PctSignalRep1 PctSignal umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HUVEC G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecS4PctSignalRep1 HUVEC S4 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW DS9856 hg19 1 wgEncodeUwRepliSeqHuvecS4PctSignalRep1 PctSignal umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HUVEC S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecS3PctSignalRep1 HUVEC S3 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW DS9855 hg19 1 wgEncodeUwRepliSeqHuvecS3PctSignalRep1 PctSignal umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HUVEC S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecS2PctSignalRep1 HUVEC S2 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW DS9854 hg19 1 wgEncodeUwRepliSeqHuvecS2PctSignalRep1 PctSignal umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HUVEC S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecS1PctSignalRep1 HUVEC S1 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW DS9853 hg19 1 wgEncodeUwRepliSeqHuvecS1PctSignalRep1 PctSignal umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HUVEC S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecG1bPctSignalRep1 HUVEC G1b 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW DS9851 hg19 1 wgEncodeUwRepliSeqHuvecG1bPctSignalRep1 PctSignal umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HUVEC G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2G2PctSignalRep1 HepG2 G2 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW DS19718 hg19 1 wgEncodeUwRepliSeqHepg2G2PctSignalRep1 PctSignal hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HepG2 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2S4PctSignalRep1 HepG2 S4 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW DS19722 hg19 1 wgEncodeUwRepliSeqHepg2S4PctSignalRep1 PctSignal hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HepG2 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2S3PctSignalRep1 HepG2 S3 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW DS19721 hg19 1 wgEncodeUwRepliSeqHepg2S3PctSignalRep1 PctSignal hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HepG2 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2S2PctSignalRep1 HepG2 S2 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW DS19720 hg19 1 wgEncodeUwRepliSeqHepg2S2PctSignalRep1 PctSignal hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HepG2 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2S1PctSignalRep1 HepG2 S1 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW DS19719 hg19 1 wgEncodeUwRepliSeqHepg2S1PctSignalRep1 PctSignal hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HepG2 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2G1bPctSignalRep1 HepG2 G1b 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW DS19717 hg19 1 wgEncodeUwRepliSeqHepg2G1bPctSignalRep1 PctSignal hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HepG2 G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3G2PctSignalRep1 HeLa-S3 G2 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW DS9942 hg19 1 wgEncodeUwRepliSeqHelas3G2PctSignalRep1 PctSignal cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HeLa-S3 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3S4PctSignalRep1 HeLa-S3 S4 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW DS9946 hg19 1 wgEncodeUwRepliSeqHelas3S4PctSignalRep1 PctSignal cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HeLa-S3 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3S3PctSignalRep1 HeLa-S3 S3 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW DS9945 hg19 1 wgEncodeUwRepliSeqHelas3S3PctSignalRep1 PctSignal cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HeLa-S3 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3S2PctSignalRep1 HeLa-S3 S2 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW DS9944 hg19 1 wgEncodeUwRepliSeqHelas3S2PctSignalRep1 PctSignal cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HeLa-S3 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3S1PctSignalRep1 HeLa-S3 S1 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW DS9943 hg19 1 wgEncodeUwRepliSeqHelas3S1PctSignalRep1 PctSignal cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HeLa-S3 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3G1bPctSignalRep1 HeLa-S3 G1b 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW DS9941 hg19 1 wgEncodeUwRepliSeqHelas3G1bPctSignalRep1 PctSignal cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases HeLa-S3 G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562G2PctSignalRep1 K562 G2 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW DS8838 hg19 1 wgEncodeUwRepliSeqK562G2PctSignalRep1 PctSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases K562 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562S4PctSignalRep1 K562 S4 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW DS8842 hg19 1 wgEncodeUwRepliSeqK562S4PctSignalRep1 PctSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases K562 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562S3PctSignalRep1 K562 S3 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW DS8841 hg19 1 wgEncodeUwRepliSeqK562S3PctSignalRep1 PctSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases K562 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562S2PctSignalRep1 K562 S2 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW DS8840 hg19 1 wgEncodeUwRepliSeqK562S2PctSignalRep1 PctSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases K562 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562S1PctSignalRep1 K562 S1 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW DS8839 hg19 1 wgEncodeUwRepliSeqK562S1PctSignalRep1 PctSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases K562 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562G1PctSignalRep1 K562 G1 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW DS8837 hg19 1 wgEncodeUwRepliSeqK562G1PctSignalRep1 PctSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases K562 G1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878G2PctSignalRep1 GM12878 G2 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW DS9807 hg19 1 wgEncodeUwRepliSeqGm12878G2PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12878 G2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878S4PctSignalRep1 GM12878 S4 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW DS9811 hg19 1 wgEncodeUwRepliSeqGm12878S4PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12878 S4-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878S3PctSignalRep1 GM12878 S3 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW DS9810 hg19 1 wgEncodeUwRepliSeqGm12878S3PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12878 S3-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878S2PctSignalRep1 GM12878 S2 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW DS9809 hg19 1 wgEncodeUwRepliSeqGm12878S2PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12878 S2-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878S1PctSignalRep1 GM12878 S1 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW DS9808 hg19 1 wgEncodeUwRepliSeqGm12878S1PctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12878 S1-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878G1bPctSignalRep1 GM12878 G1b 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW DS9806 hg19 1 wgEncodeUwRepliSeqGm12878G1bPctSignalRep1 PctSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Signal over an interval as a percentage of normalized tag densities over all phases GM12878 G1b-Phase Repli-seq Percentage-normalized Signal Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqViewPeaks Peaks Replication Timing by Repli-seq from ENCODE/University of Washington Regulation 
wgEncodeUwRepliSeqNhekPkRep1 NHEK Pk 1 NHEK RepliSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEH002249 2249 GSM923445 Stam UW NHEK-1 hg19 1 F wgEncodeUwRepliSeqNhekPkRep1 Peaks epidermal keratinocytes Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Regions of enriched signal in experiment NHEK Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12813PkRep1 GM12813 Pk 1 GM12813 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002240 2240 GSM923450 Stam UW GM12813-1 hg19 1 wgEncodeUwRepliSeqGm12813PkRep1 Peaks B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12813 Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12812PkRep1 GM12812 Pk 1 GM12812 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002239 2239 GSM923439 Stam UW GM12812-1 hg19 1 wgEncodeUwRepliSeqGm12812PkRep1 Peaks B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12812 Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12801PkRep1 GM12801 Pk 1 GM12801 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002238 2238 GSM923440 Stam UW GM12801-1 hg19 1 wgEncodeUwRepliSeqGm12801PkRep1 Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12801 Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm06990PkRep1 GM06990 Pk 1 GM06990 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002237 2237 GSM923443 Stam UW GM06990-1 hg19 1 wgEncodeUwRepliSeqGm06990PkRep1 Peaks B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjPkRep2 BJ Pk 2 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW BJ-2 hg19 2 wgEncodeUwRepliSeqBjPkRep2 Peaks skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ Repli-seq Peaks Rep 2 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBjPkRep1 BJ Pk 1 BJ RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002236 2236 GSM923444 Stam UW BJ-1 hg19 1 wgEncodeUwRepliSeqBjPkRep1 Peaks skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqBg02esPkRep1 BG02ES Pk 1 BG02ES RepliSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEH002250 2250 GSM923453 Stam UW BG02ES-1 hg19 1 wgEncodeUwRepliSeqBg02esPkRep1 Peaks embryonic stem cell (hESC), BG02, treatment: H9 conditioned medium Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BG02ES Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqSknshPkRep1 SK-N-SH Pk 1 SK-N-SH RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002384 2384 GSM923441 Stam UW SK-N-SH_RA-1 hg19 1 wgEncodeUwRepliSeqSknshPkRep1 Peaks neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqMcf7PkRep1 MCF-7 Pk 1 MCF-7 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002247 2247 GSM923442 Stam UW MCF-7-1 hg19 1 wgEncodeUwRepliSeqMcf7PkRep1 Peaks mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqImr90PkRep1 IMR90 Pk 1 IMR90 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002245 2245 GSM923447 Stam UW IMR90-1 hg19 1 wgEncodeUwRepliSeqImr90PkRep1 Peaks fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment IMR90 Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHuvecPkRep1 HUVEC Pk 1 HUVEC RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002242 2242 GSM923452 Stam UW HUVEC-1 hg19 1 wgEncodeUwRepliSeqHuvecPkRep1 Peaks umbilical vein endothelial cells Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHepg2PkRep1 HepG2 Pk 1 HepG2 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002244 2244 GSM923446 Stam UW HepG2-1 hg19 1 wgEncodeUwRepliSeqHepg2PkRep1 Peaks hepatocellular carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2-Phase Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqHelas3PkRep1 HeLa-S3 Pk 1 HeLa-S3 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002243 2243 GSM923449 Stam UW HeLa-S3-1 hg19 1 wgEncodeUwRepliSeqHelas3PkRep1 Peaks cervical carcinoma Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3-Phase Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqK562PkRep1 K562 Pk 1 K562 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 wgEncodeEH002246 2246 GSM923448 Stam UW K562-1 hg19 1 wgEncodeUwRepliSeqK562PkRep1 Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
wgEncodeUwRepliSeqGm12878PkRep1 GM12878 Pk 1 GM12878 RepliSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002241 2241 GSM923451 Stam UW GM12878-1 hg19 1 wgEncodeUwRepliSeqGm12878PkRep1 Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Assessment of DNA Replication Timing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 Repli-seq Peaks Rep 1 from ENCODE/UW Regulation 
vegaGeneComposite Vega Genes Vega Annotations Genes and Gene Predictions Description and Methods This track shows gene annotations from the Vertebrate Genome Annotation (Vega) database. Annotations are divided into two subtracks from the Vega Human Genome Annotation project: Vega Protein-Coding and Non-Coding Gene Annotations Vega Annotated Pseudogenes and Immunoglobulin Segments The following information is an excerpt from the Vertebrate Genome Annotation home page: &quot;The Vega database is designed to be a central repository for high-quality, frequently updated manual annotation of different vertebrate finished genome sequence. Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone-by-clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). The annotation is based on supporting evidence only.&quot; &quot;In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.&quot; Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. Transcript type (and other details) may be found by clicking on the transcript identifier which forms the outside link to the Vega transcript details page. Further information on the gene and transcript classification may be found here. Credits Thanks to Steve Trevanion at the Wellcome Trust Sanger Institute for providing the GTF and FASTA files for the Vega annotations. Vega acknowledgements and publications are listed here. 
vegaPseudoGene Vega Pseudogenes Vega Annotated Pseudogenes and Immunoglobulin Segments Genes and Gene Predictions Description and Methods This track shows gene annotations from the Vertebrate Genome Annotation (Vega) database. Annotations are divided into two subtracks from the Vega Human Genome Annotation project: Vega Protein-Coding and Non-Coding Gene Annotations Vega Annotated Pseudogenes and Immunoglobulin Segments The following information is an excerpt from the Vertebrate Genome Annotation home page: &quot;The Vega database is designed to be a central repository for high-quality, frequently updated manual annotation of different vertebrate finished genome sequence. Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone-by-clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). The annotation is based on supporting evidence only.&quot; &quot;In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.&quot; Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. Transcript type (and other details) may be found by clicking on the transcript identifier which forms the outside link to the Vega transcript details page. Further information on the gene and transcript classification may be found here. Credits Thanks to Steve Trevanion at the Wellcome Trust Sanger Institute for providing the GTF and FASTA files for the Vega annotations. Vega acknowledgements and publications are listed here. 
vegaGene Vega Protein Genes Vega Protein-Coding Annotations Genes and Gene Predictions Description and Methods This track shows gene annotations from the Vertebrate Genome Annotation (Vega) database. Annotations are divided into two subtracks from the Vega Human Genome Annotation project: Vega Protein-Coding and Non-Coding Gene Annotations Vega Annotated Pseudogenes and Immunoglobulin Segments The following information is an excerpt from the Vertebrate Genome Annotation home page: &quot;The Vega database is designed to be a central repository for high-quality, frequently updated manual annotation of different vertebrate finished genome sequence. Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone-by-clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). The annotation is based on supporting evidence only.&quot; &quot;In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.&quot; Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. Transcript type (and other details) may be found by clicking on the transcript identifier which forms the outside link to the Vega transcript details page. Further information on the gene and transcript classification may be found here. Credits Thanks to Steve Trevanion at the Wellcome Trust Sanger Institute for providing the GTF and FASTA files for the Vega annotations. Vega acknowledgements and publications are listed here. 
vistaEnhancersBb VISTA Enhancers VISTA Enhancers Regulation Description This track shows potential enhancers whose activity was experimentally validated in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. More information can be found on the VISTA Enhancer Browser page. Display Conventions and Configuration Items appearing in red (positive) indicate that a reproducible pattern was observed in the in vivo enhancer assay. Items appearing in blue (negative) indicate that NO reproducible pattern was observed in the in vivo enhancer assay. Note that this annotation refers only to the single developmental timepoint that was tested in this screen (e11.5) and does not exclude the possibility that this region is a reproducible enhancer active at earlier or later timepoints in development. Methods Excerpted from the Vista Enhancer Mouse Enhancer Screen Handbook and Methods page at the Lawrence Berkeley National Laboratory (LBNL) website: Enhancer Candidate Identification Most enhancer candidate sequences are identified by extreme evolutionary sequence conservation or by ChIP-seq. Detailed information related to enhancer identification by extreme evolutionary conservation can be found in the following publications: Pennacchio et al., Genomic strategies to identify mammalian regulatory sequences. Nature Rev Genet 2001 Nobrega et al., Nobrega et al., Scanning human gene deserts for long-range enhancers. Science 2003 Pennacchio et al., In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006 Visel et al., Enhancer identification through comparative genomics. Semin Cell Dev Biol. 2007 Visel et al., Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nature Genet 2008 Detailed information related to enhancer identification by ChIP-seq can be found in the following publications: Visel et al., ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009 Visel et al., Genomic views of distant-acting enhancers. Nature 2009 See the Transgenic Mouse Assay section for experimental procedures that were used to perform the transgenic assays: Mouse Enhancer Screen Handbook and Methods UCSC converted the Experimental Data for hg19 and mm9 into bigBed format using the bedToBigBed utility. The data for hg38 was lifted over from hg19. The data for mm10 and mm39 were lifted over from mm9. Data Access VISTA Enhancers data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser's REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. Credits Thanks to the Lawrence Berkeley National Laboratory for providing this data References Visel A, Minovitsky S, Dubchak I, Pennacchio LA. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92. PMID: 17130149; PMC: PMC1716724 
pubsBingBlat Web Sequences DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research Phenotype and Literature Description This track is powered by Bing! and Microsoft Research. UCSC collaborators at Microsoft Research (Bob Davidson, David Heckerman) implemented a DNA sequence detector and processed thirty days of web crawler updates, which covers roughly 40 billion webpages. The results were mapped with BLAT to the genome. Display Convention and Configuration The track indicates the location of sequences on web pages mapped to the genome, labelled with the web page URL. If the web page includes invisible meta data, then the first author and a year of publication is shown instead of the URL. All matches of one web page are grouped (&quot;chained&quot;) together. Web page titles are shown when you move the mouse cursor over the features. Thicker parts of the features (exons) represent matching sequences, connected by thin lines to matches from the same web page within 30 kbp. The subtrack "individual sequence matches" activates automatically when the user clicks a sequence match and follows the link "Show sequence matches individually" from the details page. Mouse-overs show flanking text around the sequence, and clicking features links to BLAT alignments. - --> Methods All file types (PDFs and various Microsoft Office formats) were converted to text. The results were processed to find groups of words that look like DNA/RNA sequences. These were then mapped with BLAT to the human genome using the same software as used in the Publication track. Credits DNA sequence detection by Bob Davidson at Microsoft Research. HTML parsing and sequence mapping by Maximilian Haeussler at UCSC. References Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM, Open Regulatory Annotation Consortium. Text-mining assisted regulatory annotation. Genome Biol. 2008;9(2):R31. PMID: 18271954; PMC: PMC2374703 Haeussler M, Gerner M, Bergman CM. Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics. 2011 Apr 1;27(7):980-6. PMID: 21325301; PMC: PMC3065681 Van Noorden R. Trouble at the text mine. Nature. 2012 Mar 7;483(7388):134-5. 
windowmaskerSdust WM + SDust Genomic Intervals Masked by WindowMasker + SDust Repeats Description This track depicts masked sequence as determined by WindowMasker. The WindowMasker tool is included in the NCBI C++ toolkit. The source code for the entire toolkit is available from the NCBI FTP site. Methods To create this track, WindowMasker was run with the following parameters: windowmasker -mk_counts true -input hg19.fa -output wm_counts windowmasker -ustat wm_counts -sdust true -input hg19.fa -output repeats.bed The repeats.bed (BED3) file was loaded into the &quot;windowmaskerSdust&quot; table for this track. References Morgulis A, Gertz EM, Sch&auml;ffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941 
pseudoYale60 Yale Pseudo60 Yale Pseudogenes based on Ensembl Release 60 Genes and Gene Predictions Description This track shows pseudogenes identified by the Yale Pseudogene Pipeline. Pseudogenes are defined in this analysis as genomic sequences that are similar to known genes with various inactivating disablements (e.g., premature stop codons or frameshifts) in their &quot;putative&quot; protein coding regions. Pseudogenes are flagged as either recently processed, recently duplicated, or of uncertain origin (either ancient fragments or resulting from a single-exon parent). The following color key is used: ColorMeaning &nbsp;Recently duplicated &nbsp;Ambiguous &nbsp;Recently processed Methods Briefly, the protein sequences of known human genes (as annotated by Ensembl Release 60) were used to search for similarities, not overlapping with known genes. It was determined whether the matching sequences were disabled copies of genes based on the occurrences of premature stop codons or frameshifts. The intron-exon structure of the functional gene was further used to infer whether a pseudogene was recently duplicated or processed. A duplicated pseudogene retains the intron-exon structure of its parent functional gene, whereas a processed pseudogene shows evidence that this structure has been spliced out. Small pseudogene sequences that cannot be confidently assigned to either the processed or duplicated category may be ancient fragments. Further details are in the references below. Credits These data were generated by the pseudogene annotation group in the Gerstein Lab at Yale University. References More information is available from Pseudogene.org. Zhang Z, Harrison PM, Liu Y, Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res. 2003 Dec;13(12):2541-58. PMID: 14656962; PMC: PMC403796 Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol. 2005 May 27;349(1):27-45. PMID: 15876366